commit
f0eba24f89
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@ -0,0 +1,31 @@ |
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cmake_minimum_required(VERSION 2.8) |
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project(GKlib C) |
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option(BUILD_SHARED_LIBS "Build shared libraries (.dll/.so) instead of static ones (.lib/.a)" OFF) |
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get_filename_component(abs "." ABSOLUTE) |
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set(GKLIB_PATH ${abs}) |
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unset(abs) |
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include(GKlibSystem.cmake) |
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include_directories(".") |
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if(MSVC) |
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include_directories("win32") |
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file(GLOB win32_sources RELATIVE "win32" "*.c") |
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else(MSVC) |
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set(win32_sources, "") |
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endif(MSVC) |
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add_library(GKlib ${GKlib_sources} ${win32_sources}) |
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if(UNIX) |
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target_link_libraries(GKlib m) |
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endif(UNIX) |
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include_directories("test") |
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add_subdirectory("test") |
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install(TARGETS GKlib |
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ARCHIVE DESTINATION lib/${LINSTALL_PATH} |
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LIBRARY DESTINATION lib/${LINSTALL_PATH}) |
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install(FILES ${GKlib_includes} DESTINATION include/${HINSTALL_PATH}) |
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@ -0,0 +1,85 @@ |
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/*
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* GKlib.h |
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*
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* George's library of most frequently used routines |
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* |
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* $Id: GKlib.h 14866 2013-08-03 16:40:04Z karypis $ |
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* |
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*/ |
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#ifndef _GKLIB_H_ |
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#define _GKLIB_H_ 1 |
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#define GKMSPACE |
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#if defined(_MSC_VER) |
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#define __MSC__ |
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#endif |
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#if defined(__ICC) |
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#define __ICC__ |
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#endif |
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#include "gk_arch.h" /*!< This should be here, prior to the includes */ |
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/*************************************************************************
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* Header file inclusion section |
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**************************************************************************/ |
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#include <stddef.h> |
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#include <stdlib.h> |
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#include <stdarg.h> |
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#include <stdio.h> |
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#include <memory.h> |
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#include <errno.h> |
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#include <ctype.h> |
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#include <math.h> |
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#include <float.h> |
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#include <time.h> |
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#include <string.h> |
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#include <limits.h> |
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#include <signal.h> |
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#include <setjmp.h> |
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#include <assert.h> |
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#include <sys/stat.h> |
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#if defined(__WITHPCRE__) |
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#include <pcreposix.h> |
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#else |
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#if defined(USE_GKREGEX) |
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#include "gkregex.h" |
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#else |
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#include <regex.h> |
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#endif /* defined(USE_GKREGEX) */ |
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#endif /* defined(__WITHPCRE__) */ |
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#if defined(__OPENMP__) |
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#include <omp.h> |
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#endif |
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#include <gk_types.h> |
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#include <gk_struct.h> |
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#include <gk_externs.h> |
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#include <gk_defs.h> |
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#include <gk_macros.h> |
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#include <gk_getopt.h> |
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#include <gk_mksort.h> |
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#include <gk_mkblas.h> |
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#include <gk_mkmemory.h> |
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#include <gk_mkpqueue.h> |
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#include <gk_mkpqueue2.h> |
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#include <gk_mkrandom.h> |
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#include <gk_mkutils.h> |
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#include <gk_proto.h> |
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#endif /* GKlib.h */ |
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@ -0,0 +1,152 @@ |
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# Helper modules. |
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include(CheckFunctionExists) |
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include(CheckIncludeFile) |
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# Setup options. |
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option(GDB "enable use of GDB" OFF) |
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option(ASSERT "turn asserts on" OFF) |
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option(ASSERT2 "additional assertions" OFF) |
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option(DEBUG "add debugging support" OFF) |
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option(GPROF "add gprof support" OFF) |
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option(VALGRIND "add valgrind support" OFF) |
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option(OPENMP "enable OpenMP support" OFF) |
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option(PCRE "enable PCRE support" OFF) |
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option(GKREGEX "enable GKREGEX support" OFF) |
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option(GKRAND "enable GKRAND support" OFF) |
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option(NO_X86 "enable NO_X86 support" OFF) |
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# Add compiler flags. |
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if(MSVC) |
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set(GKlib_COPTS "/Ox") |
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set(GKlib_COPTIONS "-DWIN32 -DMSC -D_CRT_SECURE_NO_DEPRECATE -DUSE_GKREGEX") |
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elseif(MINGW) |
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set(GKlib_COPTS "-DUSE_GKREGEX") |
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else() |
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set(GKlib_COPTIONS "-DLINUX -D_FILE_OFFSET_BITS=64") |
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endif(MSVC) |
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if(CYGWIN) |
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set(GKlib_COPTIONS "${GKlib_COPTIONS} -DCYGWIN") |
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endif(CYGWIN) |
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if(CMAKE_COMPILER_IS_GNUCC) |
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# GCC opts. |
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set(GKlib_COPTIONS "${GKlib_COPTIONS} -std=c99 -fno-strict-aliasing") |
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if(VALGRIND) |
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set(GKlib_COPTIONS "${GK_COPTIONS} -march=x86-64 -mtune=generic") |
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else() |
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# -march=native is not a valid flag on PPC: |
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if(CMAKE_SYSTEM_PROCESSOR MATCHES "power|ppc|powerpc|ppc64|powerpc64" OR (APPLE AND CMAKE_OSX_ARCHITECTURES MATCHES "ppc|ppc64")) |
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set(GKlib_COPTIONS "${GKlib_COPTIONS} -mtune=native") |
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else() |
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set(GKlib_COPTIONS "${GKlib_COPTIONS} -march=native") |
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endif() |
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endif(VALGRIND) |
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if(NOT MINGW) |
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set(GKlib_COPTIONS "${GKlib_COPTIONS} -fPIC") |
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endif(NOT MINGW) |
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# GCC warnings. |
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set(GKlib_COPTIONS "${GKlib_COPTIONS} -Werror -Wall -pedantic -Wno-unused-function -Wno-unused-but-set-variable -Wno-unused-variable -Wno-unknown-pragmas -Wno-unused-label") |
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elseif(${CMAKE_C_COMPILER_ID} MATCHES "Sun") |
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# Sun insists on -xc99. |
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set(GKlib_COPTIONS "${GKlib_COPTIONS} -xc99") |
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endif(CMAKE_COMPILER_IS_GNUCC) |
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# Intel compiler |
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if(${CMAKE_C_COMPILER_ID} MATCHES "Intel") |
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set(GKlib_COPTIONS "${GKlib_COPTIONS} -xHost -std=c99") |
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endif() |
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# Find OpenMP if it is requested. |
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if(OPENMP) |
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include(FindOpenMP) |
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if(OPENMP_FOUND) |
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set(GKlib_COPTIONS "${GKlib_COPTIONS} -D__OPENMP__ ${OpenMP_C_FLAGS}") |
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else() |
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message(WARNING "OpenMP was requested but support was not found") |
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endif(OPENMP_FOUND) |
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endif(OPENMP) |
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# Set the CPU type |
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if(NO_X86) |
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set(GKlib_COPTIONS "${GKlib_COPTIONS} -DNO_X86=${NO_X86}") |
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endif(NO_X86) |
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# Add various definitions. |
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if(GDB) |
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set(GKlib_COPTS "${GKlib_COPTS} -g") |
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set(GKlib_COPTIONS "${GKlib_COPTIONS} -Werror") |
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else() |
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set(GKlib_COPTS "-O3") |
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endif(GDB) |
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if(DEBUG) |
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set(GKlib_COPTS "-g") |
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set(GKlib_COPTIONS "${GKlib_COPTIONS} -DDEBUG") |
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endif(DEBUG) |
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if(GPROF) |
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set(GKlib_COPTS "-pg") |
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endif(GPROF) |
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if(NOT ASSERT) |
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set(GKlib_COPTIONS "${GKlib_COPTIONS} -DNDEBUG") |
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endif(NOT ASSERT) |
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if(NOT ASSERT2) |
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set(GKlib_COPTIONS "${GKlib_COPTIONS} -DNDEBUG2") |
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endif(NOT ASSERT2) |
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# Add various options |
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if(PCRE) |
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set(GKlib_COPTIONS "${GKlib_COPTIONS} -D__WITHPCRE__") |
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endif(PCRE) |
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if(GKREGEX) |
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set(GKlib_COPTIONS "${GKlib_COPTIONS} -DUSE_GKREGEX") |
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endif(GKREGEX) |
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if(GKRAND) |
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set(GKlib_COPTIONS "${GKlib_COPTIONS} -DUSE_GKRAND") |
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endif(GKRAND) |
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# Check for features. |
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check_include_file(execinfo.h HAVE_EXECINFO_H) |
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if(HAVE_EXECINFO_H) |
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set(GKlib_COPTIONS "${GKlib_COPTIONS} -DHAVE_EXECINFO_H") |
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endif(HAVE_EXECINFO_H) |
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check_function_exists(getline HAVE_GETLINE) |
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if(HAVE_GETLINE) |
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set(GKlib_COPTIONS "${GKlib_COPTIONS} -DHAVE_GETLINE") |
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endif(HAVE_GETLINE) |
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# Custom check for TLS. |
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if(MSVC) |
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set(GKlib_COPTIONS "${GKlib_COPTIONS} -D__thread=__declspec(thread)") |
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# This if checks if that value is cached or not. |
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if("${HAVE_THREADLOCALSTORAGE}" MATCHES "^${HAVE_THREADLOCALSTORAGE}$") |
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try_compile(HAVE_THREADLOCALSTORAGE |
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${CMAKE_BINARY_DIR} |
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${GKLIB_PATH}/conf/check_thread_storage.c) |
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if(HAVE_THREADLOCALSTORAGE) |
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message(STATUS "checking for thread-local storage - found") |
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else() |
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message(STATUS "checking for thread-local storage - not found") |
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endif() |
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endif() |
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if(NOT HAVE_THREADLOCALSTORAGE) |
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set(GKlib_COPTIONS "${GKlib_COPTIONS} -D__thread=") |
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endif() |
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endif() |
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# Finally set the official C flags. |
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set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${GKlib_COPTIONS} ${GKlib_COPTS}") |
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# Find GKlib sources. |
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file(GLOB GKlib_sources ${GKLIB_PATH}/*.c) |
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file(GLOB GKlib_includes ${GKLIB_PATH}/*.h) |
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@ -0,0 +1,18 @@ |
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Copyright & License Notice |
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--------------------------- |
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Copyright 1995-2018, Regents of the University of Minnesota |
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Licensed under the Apache License, Version 2.0 (the "License"); |
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you may not use this file except in compliance with the License. |
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You may obtain a copy of the License at |
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http://www.apache.org/licenses/LICENSE-2.0 |
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Unless required by applicable law or agreed to in writing, software |
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distributed under the License is distributed on an "AS IS" BASIS, |
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WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or |
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implied. See the License for the specific language governing |
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permissions and limitations under the License. |
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@ -0,0 +1,87 @@ |
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# Configuration options.
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cc = gcc
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prefix = ~/local
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openmp = not-set
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gdb = not-set
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assert = not-set
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assert2 = not-set
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debug = not-set
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gprof = not-set
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valgrind = not-set
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pcre = not-set
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gkregex = not-set
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gkrand = not-set
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# Basically proxies everything to the builddir cmake.
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cputype = $(shell uname -m | sed "s/\\ /_/g")
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systype = $(shell uname -s)
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BUILDDIR = build/$(systype)-$(cputype)
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# Process configuration options.
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CONFIG_FLAGS = -DCMAKE_VERBOSE_MAKEFILE=1
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ifneq ($(gdb), not-set) |
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CONFIG_FLAGS += -DGDB=$(gdb)
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endif |
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ifneq ($(assert), not-set) |
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CONFIG_FLAGS += -DASSERT=$(assert)
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endif |
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ifneq ($(assert2), not-set) |
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CONFIG_FLAGS += -DASSERT2=$(assert2)
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endif |
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ifneq ($(debug), not-set) |
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CONFIG_FLAGS += -DDEBUG=$(debug)
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endif |
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ifneq ($(gprof), not-set) |
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CONFIG_FLAGS += -DGPROF=$(gprof)
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endif |
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ifneq ($(valgrind), not-set) |
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CONFIG_FLAGS += -DVALGRIND=$(valgrind)
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endif |
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ifneq ($(openmp), not-set) |
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CONFIG_FLAGS += -DOPENMP=$(openmp)
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endif |
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ifneq ($(pcre), not-set) |
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CONFIG_FLAGS += -DPCRE=$(pcre)
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endif |
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ifneq ($(gkregex), not-set) |
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CONFIG_FLAGS += -DGKREGEX=$(pcre)
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endif |
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ifneq ($(gkrand), not-set) |
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CONFIG_FLAGS += -DGKRAND=$(pcre)
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endif |
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ifneq ($(prefix), not-set) |
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CONFIG_FLAGS += -DCMAKE_INSTALL_PREFIX=$(prefix)
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endif |
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ifneq ($(cc), not-set) |
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CONFIG_FLAGS += -DCMAKE_C_COMPILER=$(cc)
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|
endif |
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ifneq ($(cputype), x86_64) |
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CONFIG_FLAGS += -DNO_X86=$(cputype)
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endif |
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|
define run-config |
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mkdir -p $(BUILDDIR) |
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cd $(BUILDDIR) && cmake $(CURDIR) $(CONFIG_FLAGS) |
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endef |
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all clean install: $(BUILDDIR) |
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make -C $(BUILDDIR) $@
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uninstall: |
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xargs rm < $(BUILDDIR)/install_manifest.txt
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$(BUILDDIR): |
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$(run-config)
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config: distclean |
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$(run-config)
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distclean: |
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rm -rf $(BUILDDIR)
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remake: |
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find . -name CMakeLists.txt -exec touch {} ';'
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|
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.PHONY: config distclean all clean install uninstall remake |
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@ -0,0 +1,54 @@ |
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# GKlib |
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A library of various helper routines and frameworks used by many of the lab's software |
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|
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|
## Build requirements |
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- CMake 2.8, found at http://www.cmake.org/, as well as GNU make. |
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|
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|
Assuming that the above are available, two commands should suffice to |
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build the software: |
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``` |
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make config |
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make |
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``` |
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|
||||||
|
## Configuring the build |
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|
It is primarily configured by passing options to make config. For example: |
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``` |
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|
make config cc=icc |
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|
``` |
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|
|
||||||
|
would configure it to be built using icc. |
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|
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|
Configuration options are: |
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|
``` |
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|
cc=[compiler] - The C compiler to use [default: gcc] |
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|
prefix=[PATH] - Set the installation prefix [default: ~/local] |
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|
openmp=set - To build a version with OpenMP support |
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|
``` |
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|
|
||||||
|
|
||||||
|
## Building and installing |
||||||
|
To build and install, run the following |
||||||
|
``` |
||||||
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make |
||||||
|
make install |
||||||
|
``` |
||||||
|
|
||||||
|
By default, the library file, header file, and binaries will be installed in |
||||||
|
``` |
||||||
|
~/local/lib |
||||||
|
~/local/include |
||||||
|
~/local/bin |
||||||
|
``` |
||||||
|
|
||||||
|
## Other make commands |
||||||
|
make uninstall |
||||||
|
Removes all files installed by 'make install'. |
||||||
|
|
||||||
|
make clean |
||||||
|
Removes all object files but retains the configuration options. |
||||||
|
|
||||||
|
make distclean |
||||||
|
Performs clean and completely removes the build directory. |
||||||
|
|
||||||
|
|
||||||
@ -0,0 +1,12 @@ |
|||||||
|
#!/usr/bin/env bash |
||||||
|
|
||||||
|
if [ -z "$1" ] |
||||||
|
then |
||||||
|
printf "Usage: setup.sh install_directory [dependencies].\n" 1>&2 |
||||||
|
exit 1 |
||||||
|
fi |
||||||
|
|
||||||
|
cd $(dirname $0) |
||||||
|
libname=$(basename $(pwd)) |
||||||
|
make config shared=1 prefix="$1" |
||||||
|
make install |
||||||
@ -0,0 +1,95 @@ |
|||||||
|
/*!
|
||||||
|
\file b64.c |
||||||
|
\brief This file contains some simple 8bit-to-6bit encoding/deconding routines |
||||||
|
|
||||||
|
Most of these routines are outdated and should be converted using glibc's equivalent |
||||||
|
routines. |
||||||
|
|
||||||
|
\date Started 2/22/05 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: b64.c 10711 2011-08-31 22:23:04Z karypis $ \endverbatim |
||||||
|
|
||||||
|
\verbatim
|
||||||
|
$Copyright$
|
||||||
|
$License$ |
||||||
|
\endverbatim |
||||||
|
|
||||||
|
*/ |
||||||
|
|
||||||
|
|
||||||
|
#include "GKlib.h" |
||||||
|
|
||||||
|
#define B64OFFSET 48 /* This is the '0' number */ |
||||||
|
|
||||||
|
|
||||||
|
/******************************************************************************
|
||||||
|
* Encode 3 '8-bit' binary bytes as 4 '6-bit' characters |
||||||
|
*******************************************************************************/ |
||||||
|
void encodeblock(unsigned char *in, unsigned char *out) |
||||||
|
{ |
||||||
|
out[0] = (in[0] >> 2); |
||||||
|
out[1] = (((in[0] & 0x03) << 4) | (in[1] >> 4)); |
||||||
|
out[2] = (((in[1] & 0x0f) << 2) | (in[2] >> 6)); |
||||||
|
out[3] = (in[2] & 0x3f); |
||||||
|
|
||||||
|
out[0] += B64OFFSET; |
||||||
|
out[1] += B64OFFSET; |
||||||
|
out[2] += B64OFFSET; |
||||||
|
out[3] += B64OFFSET; |
||||||
|
|
||||||
|
// printf("%c %c %c %c %2x %2x %2x %2x %2x %2x %2x\n", out[0], out[1], out[2], out[3], out[0], out[1], out[2], out[3], in[0], in[1], in[2]);
|
||||||
|
} |
||||||
|
|
||||||
|
/******************************************************************************
|
||||||
|
* Decode 4 '6-bit' characters into 3 '8-bit' binary bytes |
||||||
|
*******************************************************************************/ |
||||||
|
void decodeblock(unsigned char *in, unsigned char *out) |
||||||
|
{
|
||||||
|
in[0] -= B64OFFSET; |
||||||
|
in[1] -= B64OFFSET; |
||||||
|
in[2] -= B64OFFSET; |
||||||
|
in[3] -= B64OFFSET; |
||||||
|
|
||||||
|
out[0] = (in[0] << 2 | in[1] >> 4); |
||||||
|
out[1] = (in[1] << 4 | in[2] >> 2); |
||||||
|
out[2] = (in[2] << 6 | in[3]); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/******************************************************************************
|
||||||
|
* This function encodes an input array of bytes into a base64 encoding. Memory |
||||||
|
* for the output array is assumed to have been allocated by the calling program |
||||||
|
* and be sufficiently large. The output string is NULL terminated. |
||||||
|
*******************************************************************************/ |
||||||
|
void GKEncodeBase64(int nbytes, unsigned char *inbuffer, unsigned char *outbuffer) |
||||||
|
{ |
||||||
|
int i, j; |
||||||
|
|
||||||
|
if (nbytes%3 != 0) |
||||||
|
gk_errexit(SIGERR, "GKEncodeBase64: Input buffer size should be a multiple of 3! (%d)\n", nbytes); |
||||||
|
|
||||||
|
for (j=0, i=0; i<nbytes; i+=3, j+=4)
|
||||||
|
encodeblock(inbuffer+i, outbuffer+j); |
||||||
|
|
||||||
|
//printf("%d %d\n", nbytes, j);
|
||||||
|
outbuffer[j] = '\0'; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/******************************************************************************
|
||||||
|
* This function decodes an input array of base64 characters into their actual |
||||||
|
* 8-bit codes. Memory * for the output array is assumed to have been allocated
|
||||||
|
* by the calling program and be sufficiently large. The padding is discarded. |
||||||
|
*******************************************************************************/ |
||||||
|
void GKDecodeBase64(int nbytes, unsigned char *inbuffer, unsigned char *outbuffer) |
||||||
|
{ |
||||||
|
int i, j; |
||||||
|
|
||||||
|
if (nbytes%4 != 0) |
||||||
|
gk_errexit(SIGERR, "GKDecodeBase64: Input buffer size should be a multiple of 4! (%d)\n", nbytes); |
||||||
|
|
||||||
|
for (j=0, i=0; i<nbytes; i+=4, j+=3)
|
||||||
|
decodeblock(inbuffer+i, outbuffer+j); |
||||||
|
} |
||||||
|
|
||||||
@ -0,0 +1,37 @@ |
|||||||
|
/*!
|
||||||
|
\file blas.c |
||||||
|
\brief This file contains GKlib's implementation of BLAS-like routines |
||||||
|
|
||||||
|
The BLAS routines that are currently implemented are mostly level-one. |
||||||
|
They follow a naming convention of the type gk_[type][name], where |
||||||
|
[type] is one of c, i, f, and d, based on C's four standard scalar |
||||||
|
datatypes of characters, integers, floats, and doubles. |
||||||
|
|
||||||
|
These routines are implemented using a generic macro template, |
||||||
|
which is used for code generation. |
||||||
|
|
||||||
|
\date Started 9/28/95 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: blas.c 14330 2013-05-18 12:15:15Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Use the templates to generate BLAS routines for the scalar data types */ |
||||||
|
/*************************************************************************/ |
||||||
|
GK_MKBLAS(gk_c, char, int) |
||||||
|
GK_MKBLAS(gk_i, int, int) |
||||||
|
GK_MKBLAS(gk_i32, int32_t, int32_t) |
||||||
|
GK_MKBLAS(gk_i64, int64_t, int64_t) |
||||||
|
GK_MKBLAS(gk_z, ssize_t, ssize_t) |
||||||
|
GK_MKBLAS(gk_zu, size_t, size_t) |
||||||
|
GK_MKBLAS(gk_f, float, float) |
||||||
|
GK_MKBLAS(gk_d, double, double) |
||||||
|
GK_MKBLAS(gk_idx, gk_idx_t, gk_idx_t) |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
@ -0,0 +1,126 @@ |
|||||||
|
/*!
|
||||||
|
\file
|
||||||
|
\brief Functions dealing with simulating cache behavior for performance |
||||||
|
modeling and analysis; |
||||||
|
|
||||||
|
\date Started 4/13/18 |
||||||
|
\author George |
||||||
|
\author Copyright 1997-2011, Regents of the University of Minnesota
|
||||||
|
\version $Id: cache.c 21991 2018-04-16 03:08:12Z karypis $ |
||||||
|
*/ |
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function creates a cache
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
gk_cache_t *gk_cacheCreate(uint32_t nway, uint32_t lnbits, size_t cnbits) |
||||||
|
{ |
||||||
|
gk_cache_t *cache; |
||||||
|
|
||||||
|
cache = (gk_cache_t *)gk_malloc(sizeof(gk_cache_t), "gk_cacheCreate: cache"); |
||||||
|
memset(cache, 0, sizeof(gk_cache_t)); |
||||||
|
|
||||||
|
cache->nway = nway; |
||||||
|
cache->lnbits = lnbits; |
||||||
|
cache->cnbits = cnbits; |
||||||
|
cache->csize = 1<<cnbits; |
||||||
|
cache->cmask = cache->csize-1; |
||||||
|
|
||||||
|
cache->latimes = gk_ui64smalloc(cache->csize*nway, 0, "gk_cacheCreate: latimes"); |
||||||
|
cache->clines = gk_zusmalloc(cache->csize*nway, 0, "gk_cacheCreate: clines"); |
||||||
|
|
||||||
|
return cache; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function resets a cache
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_cacheReset(gk_cache_t *cache) |
||||||
|
{ |
||||||
|
cache->nhits = 0; |
||||||
|
cache->nmisses = 0; |
||||||
|
|
||||||
|
gk_ui64set(cache->csize*cache->nway, 0, cache->latimes); |
||||||
|
gk_zuset(cache->csize*cache->nway, 0, cache->clines); |
||||||
|
|
||||||
|
return; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function destroys a cache.
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_cacheDestroy(gk_cache_t **r_cache) |
||||||
|
{ |
||||||
|
gk_cache_t *cache = *r_cache; |
||||||
|
|
||||||
|
if (cache == NULL) |
||||||
|
return; |
||||||
|
|
||||||
|
gk_free((void **)&cache->clines, &cache->latimes, &cache, LTERM); |
||||||
|
|
||||||
|
*r_cache = NULL; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function simulates a load(ptr) operation.
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
int gk_cacheLoad(gk_cache_t *cache, size_t addr) |
||||||
|
{ |
||||||
|
uint32_t i, nway=cache->nway; |
||||||
|
size_t lru=0; |
||||||
|
|
||||||
|
//printf("%16"PRIx64" ", (uint64_t)addr);
|
||||||
|
addr = addr>>(cache->lnbits); |
||||||
|
//printf("%16"PRIx64" %16"PRIx64" %16"PRIx64" ", (uint64_t)addr, (uint64_t)addr&(cache->cmask), (uint64_t)cache->cmask);
|
||||||
|
|
||||||
|
size_t *clines = cache->clines + (addr&(cache->cmask)); |
||||||
|
uint64_t *latimes = cache->latimes + (addr&(cache->cmask)); |
||||||
|
|
||||||
|
cache->clock++; |
||||||
|
for (i=0; i<nway; i++) { /* look for hits */ |
||||||
|
if (clines[i] == addr) {
|
||||||
|
cache->nhits++; |
||||||
|
latimes[i] = cache->clock; |
||||||
|
goto DONE; |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
for (i=0; i<nway; i++) { /* look for empty spots or the lru spot */ |
||||||
|
if (clines[i] == 0) { |
||||||
|
lru = i; |
||||||
|
break; |
||||||
|
} |
||||||
|
else if (latimes[i] < latimes[lru]) { |
||||||
|
lru = i; |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
/* initial fill or replace */ |
||||||
|
cache->nmisses++; |
||||||
|
clines[lru] = addr; |
||||||
|
latimes[lru] = cache->clock; |
||||||
|
|
||||||
|
DONE: |
||||||
|
//printf(" %"PRIu64" %"PRIu64"\n", cache->nhits, cache->clock);
|
||||||
|
return 1; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function returns the cache's hitrate
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
double gk_cacheGetHitRate(gk_cache_t *cache) |
||||||
|
{ |
||||||
|
return ((double)cache->nhits)/((double)(cache->clock+1)); |
||||||
|
} |
||||||
|
|
||||||
@ -0,0 +1,5 @@ |
|||||||
|
extern __thread int x; |
||||||
|
|
||||||
|
int main(int argc, char **argv) { |
||||||
|
return 0; |
||||||
|
} |
||||||
@ -0,0 +1,214 @@ |
|||||||
|
/*!
|
||||||
|
\file error.c |
||||||
|
\brief Various error-handling functions |
||||||
|
|
||||||
|
This file contains functions dealing with error reporting and termination |
||||||
|
|
||||||
|
\author George |
||||||
|
\date 1/1/2007 |
||||||
|
\version\verbatim $Id: error.c 10711 2011-08-31 22:23:04Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
|
||||||
|
#define _GK_ERROR_C_ /* this is needed to properly declare the gk_jub* variables |
||||||
|
as an extern function in GKlib.h */ |
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
|
||||||
|
/* These are the jmp_buf for the graceful exit in case of severe errors.
|
||||||
|
Multiple buffers are defined to allow for recursive invokation. */ |
||||||
|
#define MAX_JBUFS 128 |
||||||
|
__thread int gk_cur_jbufs=-1; |
||||||
|
__thread jmp_buf gk_jbufs[MAX_JBUFS]; |
||||||
|
__thread jmp_buf gk_jbuf; |
||||||
|
|
||||||
|
typedef void (*gksighandler_t)(int); |
||||||
|
|
||||||
|
/* These are the holders of the old singal handlers for the trapped signals */ |
||||||
|
static __thread gksighandler_t old_SIGMEM_handler; /* Custom signal */ |
||||||
|
static __thread gksighandler_t old_SIGERR_handler; /* Custom signal */ |
||||||
|
static __thread gksighandler_t old_SIGMEM_handlers[MAX_JBUFS]; /* Custom signal */ |
||||||
|
static __thread gksighandler_t old_SIGERR_handlers[MAX_JBUFS]; /* Custom signal */ |
||||||
|
|
||||||
|
/* The following is used to control if the gk_errexit() will actually abort or not.
|
||||||
|
There is always a single copy of this variable */ |
||||||
|
static int gk_exit_on_error = 1; |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function sets the gk_exit_on_error variable
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_set_exit_on_error(int value) |
||||||
|
{ |
||||||
|
gk_exit_on_error = value; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function prints an error message and exits
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
void errexit(char *f_str,...) |
||||||
|
{ |
||||||
|
va_list argp; |
||||||
|
|
||||||
|
va_start(argp, f_str); |
||||||
|
vfprintf(stderr, f_str, argp); |
||||||
|
va_end(argp); |
||||||
|
|
||||||
|
if (strlen(f_str) == 0 || f_str[strlen(f_str)-1] != '\n') |
||||||
|
fprintf(stderr,"\n"); |
||||||
|
fflush(stderr); |
||||||
|
|
||||||
|
if (gk_exit_on_error) |
||||||
|
exit(-2); |
||||||
|
|
||||||
|
/* abort(); */ |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function prints an error message and raises a signum signal
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_errexit(int signum, char *f_str,...) |
||||||
|
{ |
||||||
|
va_list argp; |
||||||
|
|
||||||
|
va_start(argp, f_str); |
||||||
|
vfprintf(stderr, f_str, argp); |
||||||
|
va_end(argp); |
||||||
|
|
||||||
|
fprintf(stderr,"\n"); |
||||||
|
fflush(stderr); |
||||||
|
|
||||||
|
if (gk_exit_on_error) |
||||||
|
raise(signum); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/***************************************************************************/ |
||||||
|
/*! This function sets a number of signal handlers and sets the return point
|
||||||
|
of a longjmp |
||||||
|
*/ |
||||||
|
/***************************************************************************/ |
||||||
|
int gk_sigtrap()
|
||||||
|
{ |
||||||
|
if (gk_cur_jbufs+1 >= MAX_JBUFS) |
||||||
|
return 0; |
||||||
|
|
||||||
|
gk_cur_jbufs++; |
||||||
|
|
||||||
|
old_SIGMEM_handlers[gk_cur_jbufs] = signal(SIGMEM, gk_sigthrow); |
||||||
|
old_SIGERR_handlers[gk_cur_jbufs] = signal(SIGERR, gk_sigthrow); |
||||||
|
|
||||||
|
return 1; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/***************************************************************************/ |
||||||
|
/*! This function sets the handlers for the signals to their default handlers
|
||||||
|
*/ |
||||||
|
/***************************************************************************/ |
||||||
|
int gk_siguntrap()
|
||||||
|
{ |
||||||
|
if (gk_cur_jbufs == -1) |
||||||
|
return 0; |
||||||
|
|
||||||
|
signal(SIGMEM, old_SIGMEM_handlers[gk_cur_jbufs]); |
||||||
|
signal(SIGERR, old_SIGERR_handlers[gk_cur_jbufs]); |
||||||
|
|
||||||
|
gk_cur_jbufs--; |
||||||
|
|
||||||
|
return 1; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function is the custome signal handler, which all it does is to
|
||||||
|
perform a longjump to the most recent saved environment
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_sigthrow(int signum) |
||||||
|
{ |
||||||
|
longjmp(gk_jbufs[gk_cur_jbufs], signum); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/***************************************************************************
|
||||||
|
* This function sets a number of signal handlers and sets the return point
|
||||||
|
* of a longjmp |
||||||
|
****************************************************************************/ |
||||||
|
void gk_SetSignalHandlers()
|
||||||
|
{ |
||||||
|
old_SIGMEM_handler = signal(SIGMEM, gk_NonLocalExit_Handler); |
||||||
|
old_SIGERR_handler = signal(SIGERR, gk_NonLocalExit_Handler); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/***************************************************************************
|
||||||
|
* This function sets the handlers for the signals to their default handlers |
||||||
|
****************************************************************************/ |
||||||
|
void gk_UnsetSignalHandlers()
|
||||||
|
{ |
||||||
|
signal(SIGMEM, old_SIGMEM_handler); |
||||||
|
signal(SIGERR, old_SIGERR_handler); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************
|
||||||
|
* This function is the handler for SIGUSR1 that implements the cleaning up
|
||||||
|
* process prior to a non-local exit. |
||||||
|
**************************************************************************/ |
||||||
|
void gk_NonLocalExit_Handler(int signum) |
||||||
|
{ |
||||||
|
longjmp(gk_jbuf, signum); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! \brief Thread-safe implementation of strerror() */ |
||||||
|
/**************************************************************************/ |
||||||
|
char *gk_strerror(int errnum) |
||||||
|
{ |
||||||
|
#if defined(WIN32) || defined(__MINGW32__) |
||||||
|
return strerror(errnum); |
||||||
|
#else |
||||||
|
#ifndef SUNOS |
||||||
|
static __thread char buf[1024]; |
||||||
|
|
||||||
|
strerror_r(errnum, buf, 1024); |
||||||
|
|
||||||
|
buf[1023] = '\0'; |
||||||
|
return buf; |
||||||
|
#else |
||||||
|
return strerror(errnum); |
||||||
|
#endif |
||||||
|
#endif |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************
|
||||||
|
* This function prints a backtrace of calling functions |
||||||
|
**************************************************************************/ |
||||||
|
void PrintBackTrace() |
||||||
|
{ |
||||||
|
#ifdef HAVE_EXECINFO_H |
||||||
|
void *array[10]; |
||||||
|
int i, size; |
||||||
|
char **strings; |
||||||
|
|
||||||
|
size = backtrace(array, 10); |
||||||
|
strings = backtrace_symbols(array, size); |
||||||
|
|
||||||
|
printf("Obtained %d stack frames.\n", size); |
||||||
|
for (i=0; i<size; i++) { |
||||||
|
printf("%s\n", strings[i]); |
||||||
|
} |
||||||
|
free(strings); |
||||||
|
#endif |
||||||
|
} |
||||||
@ -0,0 +1,132 @@ |
|||||||
|
/*!
|
||||||
|
\file evaluate.c |
||||||
|
\brief Various routines to evaluate classification performance |
||||||
|
|
||||||
|
\author George |
||||||
|
\date 9/23/2008 |
||||||
|
\version\verbatim $Id: evaluate.c 13328 2012-12-31 14:57:40Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
/**********************************************************************
|
||||||
|
* This function computes the max accuracy score of a ranked list, |
||||||
|
* given +1/-1 class list |
||||||
|
**********************************************************************/ |
||||||
|
float ComputeAccuracy(int n, gk_fkv_t *list) |
||||||
|
{ |
||||||
|
int i, P, N, TP, FN = 0; |
||||||
|
float bAccuracy = 0.0; |
||||||
|
float acc; |
||||||
|
|
||||||
|
for (P=0, i=0;i<n;i++) |
||||||
|
P += (list[i].val == 1? 1 : 0); |
||||||
|
N = n - P; |
||||||
|
|
||||||
|
TP = FN = 0; |
||||||
|
|
||||||
|
for(i=0; i<n; i++){ |
||||||
|
if (list[i].val == 1) |
||||||
|
TP++;
|
||||||
|
else |
||||||
|
FN++; |
||||||
|
|
||||||
|
acc = (TP + N - FN) * 100.0/ (P + N) ; |
||||||
|
if (acc > bAccuracy) |
||||||
|
bAccuracy = acc; |
||||||
|
} |
||||||
|
|
||||||
|
return bAccuracy; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*****************************************************************************
|
||||||
|
* This function computes the ROC score of a ranked list, given a +1/-1 class |
||||||
|
* list. |
||||||
|
******************************************************************************/ |
||||||
|
float ComputeROCn(int n, int maxN, gk_fkv_t *list) |
||||||
|
{ |
||||||
|
int i, P, TP, FP, TPprev, FPprev, AUC; |
||||||
|
float prev; |
||||||
|
|
||||||
|
FP = TP = FPprev = TPprev = AUC = 0; |
||||||
|
prev = list[0].key -1; |
||||||
|
|
||||||
|
for (P=0, i=0; i<n; i++) |
||||||
|
P += (list[i].val == 1 ? 1 : 0); |
||||||
|
|
||||||
|
for (i=0; i<n && FP < maxN; i++) { |
||||||
|
if (list[i].key != prev) { |
||||||
|
AUC += (TP+TPprev)*(FP-FPprev)/2; |
||||||
|
prev = list[i].key; |
||||||
|
FPprev = FP; |
||||||
|
TPprev = TP; |
||||||
|
} |
||||||
|
if (list[i].val == 1)
|
||||||
|
TP++; |
||||||
|
else { |
||||||
|
FP++; |
||||||
|
} |
||||||
|
} |
||||||
|
AUC += (TP+TPprev)*(FP-FPprev)/2; |
||||||
|
|
||||||
|
return (TP*FP > 0 ? (float)(1.0*AUC/(P*FP)) : 0.0); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*****************************************************************************
|
||||||
|
* This function computes the median rate of false positive for each positive |
||||||
|
* instance. |
||||||
|
******************************************************************************/ |
||||||
|
float ComputeMedianRFP(int n, gk_fkv_t *list) |
||||||
|
{ |
||||||
|
int i, P, N, TP, FP; |
||||||
|
|
||||||
|
P = N = 0; |
||||||
|
for (i=0; i<n; i++) { |
||||||
|
if (list[i].val == 1) |
||||||
|
P++; |
||||||
|
else |
||||||
|
N++; |
||||||
|
} |
||||||
|
|
||||||
|
FP = TP = 0; |
||||||
|
for (i=0; i<n && TP < (P+1)/2; i++) { |
||||||
|
if (list[i].val == 1)
|
||||||
|
TP++; |
||||||
|
else
|
||||||
|
FP++; |
||||||
|
} |
||||||
|
|
||||||
|
return 1.0*FP/N; |
||||||
|
} |
||||||
|
|
||||||
|
/*********************************************************
|
||||||
|
* Compute the mean |
||||||
|
********************************************************/ |
||||||
|
float ComputeMean (int n, float *values) |
||||||
|
{ |
||||||
|
int i; |
||||||
|
float mean = 0.0; |
||||||
|
|
||||||
|
for(i=0; i < n; i++) |
||||||
|
mean += values[i]; |
||||||
|
|
||||||
|
return 1.0 * mean/ n; |
||||||
|
} |
||||||
|
|
||||||
|
/********************************************************
|
||||||
|
* Compute the standard deviation |
||||||
|
********************************************************/ |
||||||
|
float ComputeStdDev(int n, float *values) |
||||||
|
{ |
||||||
|
int i; |
||||||
|
float mean = ComputeMean(n, values); |
||||||
|
float stdDev = 0; |
||||||
|
|
||||||
|
for(i=0;i<n;i++){ |
||||||
|
stdDev += (values[i] - mean)* (values[i] - mean); |
||||||
|
} |
||||||
|
|
||||||
|
return sqrt(1.0 * stdDev/n); |
||||||
|
} |
||||||
@ -0,0 +1,142 @@ |
|||||||
|
/*!
|
||||||
|
\file dfkvkselect.c |
||||||
|
\brief Sorts only the largest k values |
||||||
|
|
||||||
|
\date Started 7/14/00 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: fkvkselect.c 10711 2011-08-31 22:23:04Z karypis $\endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
/* Byte-wise swap two items of size SIZE. */ |
||||||
|
#define QSSWAP(a, b, stmp) do { stmp = (a); (a) = (b); (b) = stmp; } while (0) |
||||||
|
|
||||||
|
|
||||||
|
/******************************************************************************/ |
||||||
|
/*! This function puts the 'topk' largest values in the beginning of the array */ |
||||||
|
/*******************************************************************************/ |
||||||
|
int gk_dfkvkselect(size_t n, int topk, gk_fkv_t *cand) |
||||||
|
{ |
||||||
|
int i, j, lo, hi, mid; |
||||||
|
gk_fkv_t stmp; |
||||||
|
float pivot; |
||||||
|
|
||||||
|
if (n <= topk) |
||||||
|
return n; /* return if the array has fewer elements than we want */ |
||||||
|
|
||||||
|
for (lo=0, hi=n-1; lo < hi;) { |
||||||
|
mid = lo + ((hi-lo) >> 1); |
||||||
|
|
||||||
|
/* select the median */ |
||||||
|
if (cand[lo].key < cand[mid].key) |
||||||
|
mid = lo; |
||||||
|
if (cand[hi].key > cand[mid].key) |
||||||
|
mid = hi; |
||||||
|
else
|
||||||
|
goto jump_over; |
||||||
|
if (cand[lo].key < cand[mid].key) |
||||||
|
mid = lo; |
||||||
|
|
||||||
|
jump_over: |
||||||
|
QSSWAP(cand[mid], cand[hi], stmp); |
||||||
|
pivot = cand[hi].key; |
||||||
|
|
||||||
|
/* the partitioning algorithm */ |
||||||
|
for (i=lo-1, j=lo; j<hi; j++) { |
||||||
|
if (cand[j].key >= pivot) { |
||||||
|
i++; |
||||||
|
QSSWAP(cand[i], cand[j], stmp); |
||||||
|
} |
||||||
|
} |
||||||
|
i++; |
||||||
|
QSSWAP(cand[i], cand[hi], stmp); |
||||||
|
|
||||||
|
|
||||||
|
if (i > topk)
|
||||||
|
hi = i-1; |
||||||
|
else if (i < topk) |
||||||
|
lo = i+1; |
||||||
|
else |
||||||
|
break; |
||||||
|
} |
||||||
|
|
||||||
|
/*
|
||||||
|
if (cand[lo].key < cand[hi].key) |
||||||
|
printf("Hmm Error: %d %d %d %f %f\n", i, lo, hi, cand[lo].key, cand[hi].key); |
||||||
|
|
||||||
|
|
||||||
|
for (i=topk; i<n; i++) { |
||||||
|
for (j=0; j<topk; j++) |
||||||
|
if (cand[i].key > cand[j].key) |
||||||
|
printf("Hmm Error: %d %d %f %f %d %d\n", i, j, cand[i].key, cand[j].key, lo, hi); |
||||||
|
} |
||||||
|
*/ |
||||||
|
|
||||||
|
return topk; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/******************************************************************************/ |
||||||
|
/*! This function puts the 'topk' smallest values in the beginning of the array */ |
||||||
|
/*******************************************************************************/ |
||||||
|
int gk_ifkvkselect(size_t n, int topk, gk_fkv_t *cand) |
||||||
|
{ |
||||||
|
int i, j, lo, hi, mid; |
||||||
|
gk_fkv_t stmp; |
||||||
|
float pivot; |
||||||
|
|
||||||
|
if (n <= topk) |
||||||
|
return n; /* return if the array has fewer elements than we want */ |
||||||
|
|
||||||
|
for (lo=0, hi=n-1; lo < hi;) { |
||||||
|
mid = lo + ((hi-lo) >> 1); |
||||||
|
|
||||||
|
/* select the median */ |
||||||
|
if (cand[lo].key > cand[mid].key) |
||||||
|
mid = lo; |
||||||
|
if (cand[hi].key < cand[mid].key) |
||||||
|
mid = hi; |
||||||
|
else
|
||||||
|
goto jump_over; |
||||||
|
if (cand[lo].key > cand[mid].key) |
||||||
|
mid = lo; |
||||||
|
|
||||||
|
jump_over: |
||||||
|
QSSWAP(cand[mid], cand[hi], stmp); |
||||||
|
pivot = cand[hi].key; |
||||||
|
|
||||||
|
/* the partitioning algorithm */ |
||||||
|
for (i=lo-1, j=lo; j<hi; j++) { |
||||||
|
if (cand[j].key <= pivot) { |
||||||
|
i++; |
||||||
|
QSSWAP(cand[i], cand[j], stmp); |
||||||
|
} |
||||||
|
} |
||||||
|
i++; |
||||||
|
QSSWAP(cand[i], cand[hi], stmp); |
||||||
|
|
||||||
|
|
||||||
|
if (i > topk)
|
||||||
|
hi = i-1; |
||||||
|
else if (i < topk) |
||||||
|
lo = i+1; |
||||||
|
else |
||||||
|
break; |
||||||
|
} |
||||||
|
|
||||||
|
/*
|
||||||
|
if (cand[lo].key > cand[hi].key) |
||||||
|
printf("Hmm Error: %d %d %d %f %f\n", i, lo, hi, cand[lo].key, cand[hi].key); |
||||||
|
|
||||||
|
|
||||||
|
for (i=topk; i<n; i++) { |
||||||
|
for (j=0; j<topk; j++) |
||||||
|
if (cand[i].key < cand[j].key) |
||||||
|
printf("Hmm Error: %d %d %f %f %d %d\n", i, j, cand[i].key, cand[j].key, lo, hi); |
||||||
|
} |
||||||
|
*/ |
||||||
|
|
||||||
|
return topk; |
||||||
|
} |
||||||
@ -0,0 +1,225 @@ |
|||||||
|
/*!
|
||||||
|
\file fs.c |
||||||
|
\brief Various file-system functions. |
||||||
|
|
||||||
|
This file contains various functions that deal with interfacing with
|
||||||
|
the filesystem in a portable way. |
||||||
|
|
||||||
|
\date Started 4/10/95 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: fs.c 14332 2013-05-18 12:22:57Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************
|
||||||
|
* This function checks if a file exists |
||||||
|
**************************************************************************/ |
||||||
|
int gk_fexists(char *fname) |
||||||
|
{ |
||||||
|
struct stat status; |
||||||
|
|
||||||
|
if (stat(fname, &status) == -1) |
||||||
|
return 0; |
||||||
|
|
||||||
|
return S_ISREG(status.st_mode); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************
|
||||||
|
* This function checks if a directory exists |
||||||
|
**************************************************************************/ |
||||||
|
int gk_dexists(char *dirname) |
||||||
|
{ |
||||||
|
struct stat status; |
||||||
|
|
||||||
|
if (stat(dirname, &status) == -1) |
||||||
|
return 0; |
||||||
|
|
||||||
|
return S_ISDIR(status.st_mode); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! \brief Returns the size of the file in bytes
|
||||||
|
|
||||||
|
This function returns the size of a file as a 64 bit integer. If there
|
||||||
|
were any errors in stat'ing the file, -1 is returned. |
||||||
|
\note That due to the -1 return code, the maximum file size is limited to |
||||||
|
63 bits (which I guess is okay for now). |
||||||
|
*/ |
||||||
|
/**************************************************************************/ |
||||||
|
ssize_t gk_getfsize(char *filename) |
||||||
|
{ |
||||||
|
struct stat status; |
||||||
|
|
||||||
|
if (stat(filename, &status) == -1)
|
||||||
|
return -1; |
||||||
|
|
||||||
|
return (size_t)(status.st_size); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function gets some basic statistics about the file.
|
||||||
|
\param fname is the name of the file |
||||||
|
\param r_nlines is the number of lines in the file. If it is NULL, |
||||||
|
this information is not returned. |
||||||
|
\param r_ntokens is the number of tokens in the file. If it is NULL, |
||||||
|
this information is not returned. |
||||||
|
\param r_max_nlntokens is the maximum number of tokens in any line |
||||||
|
in the file. If it is NULL this information is not returned. |
||||||
|
\param r_nbytes is the number of bytes in the file. If it is NULL, |
||||||
|
this information is not returned. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_getfilestats(char *fname, size_t *r_nlines, size_t *r_ntokens,
|
||||||
|
size_t *r_max_nlntokens, size_t *r_nbytes) |
||||||
|
{ |
||||||
|
size_t nlines=0, ntokens=0, max_nlntokens=0, nbytes=0, oldntokens=0, nread; |
||||||
|
int intoken=0; |
||||||
|
char buffer[4097], *cptr; |
||||||
|
FILE *fpin; |
||||||
|
|
||||||
|
fpin = gk_fopen(fname, "r", "gk_GetFileStats"); |
||||||
|
|
||||||
|
while (!feof(fpin)) { |
||||||
|
nread = fread(buffer, sizeof(char), 4096, fpin); |
||||||
|
nbytes += nread; |
||||||
|
|
||||||
|
buffer[nread] = '\0'; /* There is space for this one */ |
||||||
|
for (cptr=buffer; *cptr!='\0'; cptr++) { |
||||||
|
if (*cptr == '\n') { |
||||||
|
nlines++; |
||||||
|
ntokens += intoken; |
||||||
|
intoken = 0; |
||||||
|
if (max_nlntokens < ntokens-oldntokens) |
||||||
|
max_nlntokens = ntokens-oldntokens; |
||||||
|
oldntokens = ntokens; |
||||||
|
} |
||||||
|
else if (*cptr == ' ' || *cptr == '\t') { |
||||||
|
ntokens += intoken; |
||||||
|
intoken = 0; |
||||||
|
} |
||||||
|
else { |
||||||
|
intoken = 1; |
||||||
|
} |
||||||
|
} |
||||||
|
} |
||||||
|
ntokens += intoken; |
||||||
|
if (max_nlntokens < ntokens-oldntokens) |
||||||
|
max_nlntokens = ntokens-oldntokens; |
||||||
|
|
||||||
|
gk_fclose(fpin); |
||||||
|
|
||||||
|
if (r_nlines != NULL) |
||||||
|
*r_nlines = nlines; |
||||||
|
if (r_ntokens != NULL) |
||||||
|
*r_ntokens = ntokens; |
||||||
|
if (r_max_nlntokens != NULL) |
||||||
|
*r_max_nlntokens = max_nlntokens; |
||||||
|
if (r_nbytes != NULL) |
||||||
|
*r_nbytes = nbytes; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************
|
||||||
|
* This function takes in a potentially full path specification of a file |
||||||
|
* and just returns a string containing just the basename of the file. |
||||||
|
* The basename is derived from the actual filename by stripping the last |
||||||
|
* .ext part. |
||||||
|
**************************************************************************/ |
||||||
|
char *gk_getbasename(char *path) |
||||||
|
{ |
||||||
|
char *startptr, *endptr; |
||||||
|
char *basename; |
||||||
|
|
||||||
|
if ((startptr = strrchr(path, '/')) == NULL)
|
||||||
|
startptr = path; |
||||||
|
else
|
||||||
|
startptr = startptr+1; |
||||||
|
|
||||||
|
basename = gk_strdup(startptr); |
||||||
|
|
||||||
|
if ((endptr = strrchr(basename, '.')) != NULL)
|
||||||
|
*endptr = '\0'; |
||||||
|
|
||||||
|
return basename; |
||||||
|
} |
||||||
|
|
||||||
|
/*************************************************************************
|
||||||
|
* This function takes in a potentially full path specification of a file |
||||||
|
* and just returns a string corresponding to its file extension. The |
||||||
|
* extension of a file is considered to be the string right after the
|
||||||
|
* last '.' character. |
||||||
|
**************************************************************************/ |
||||||
|
char *gk_getextname(char *path) |
||||||
|
{ |
||||||
|
char *startptr; |
||||||
|
|
||||||
|
if ((startptr = strrchr(path, '.')) == NULL)
|
||||||
|
return gk_strdup(path); |
||||||
|
else
|
||||||
|
return gk_strdup(startptr+1); |
||||||
|
} |
||||||
|
|
||||||
|
/*************************************************************************
|
||||||
|
* This function takes in a potentially full path specification of a file |
||||||
|
* and just returns a string containing just the filename. |
||||||
|
**************************************************************************/ |
||||||
|
char *gk_getfilename(char *path) |
||||||
|
{ |
||||||
|
char *startptr; |
||||||
|
|
||||||
|
if ((startptr = strrchr(path, '/')) == NULL)
|
||||||
|
return gk_strdup(path); |
||||||
|
else
|
||||||
|
return gk_strdup(startptr+1); |
||||||
|
} |
||||||
|
|
||||||
|
/*************************************************************************
|
||||||
|
* This function takes in a potentially full path specification of a file |
||||||
|
* and extracts the directory path component if it exists, otherwise it |
||||||
|
* returns "./" as the path. The memory for it is dynamically allocated. |
||||||
|
**************************************************************************/ |
||||||
|
char *getpathname(char *path) |
||||||
|
{ |
||||||
|
char *endptr, *tmp; |
||||||
|
|
||||||
|
if ((endptr = strrchr(path, '/')) == NULL) { |
||||||
|
return gk_strdup("."); |
||||||
|
} |
||||||
|
else { |
||||||
|
tmp = gk_strdup(path); |
||||||
|
*(strrchr(tmp, '/')) = '\0'; |
||||||
|
return tmp; |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************
|
||||||
|
* This function creates a path |
||||||
|
**************************************************************************/ |
||||||
|
int gk_mkpath(char *pathname) |
||||||
|
{ |
||||||
|
char tmp[2048]; |
||||||
|
|
||||||
|
sprintf(tmp, "mkdir -p %s", pathname); |
||||||
|
return system(tmp); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************
|
||||||
|
* This function deletes a directory tree and all of its contents |
||||||
|
**************************************************************************/ |
||||||
|
int gk_rmpath(char *pathname) |
||||||
|
{ |
||||||
|
char tmp[2048]; |
||||||
|
|
||||||
|
sprintf(tmp, "rm -r %s", pathname); |
||||||
|
return system(tmp); |
||||||
|
} |
||||||
@ -0,0 +1,855 @@ |
|||||||
|
/*************************************************************************/ |
||||||
|
/*! \file getopt.c
|
||||||
|
\brief Command line parsing
|
||||||
|
|
||||||
|
This file contains a implementation of GNU's Getopt facility. The purpose |
||||||
|
for including it here is to ensure portability across different unix- and |
||||||
|
windows-based systems. |
||||||
|
|
||||||
|
\warning
|
||||||
|
The implementation provided here uses the \c gk_ prefix for all variables |
||||||
|
used by the standard Getopt facility to communicate with the program. |
||||||
|
So, do read the documentation here. |
||||||
|
|
||||||
|
\verbatim |
||||||
|
Copyright (C) 1987,88,89,90,91,92,93,94,95,96,98,99,2000,2001 |
||||||
|
Free Software Foundation, Inc. This file is part of the GNU C Library. |
||||||
|
|
||||||
|
The GNU C Library is free software; you can redistribute it and/or |
||||||
|
modify it under the terms of the GNU Lesser General Public |
||||||
|
License as published by the Free Software Foundation; either |
||||||
|
version 2.1 of the License, or (at your option) any later version. |
||||||
|
|
||||||
|
The GNU C Library is distributed in the hope that it will be useful, |
||||||
|
but WITHOUT ANY WARRANTY; without even the implied warranty of |
||||||
|
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
||||||
|
Lesser General Public License for more details. |
||||||
|
|
||||||
|
You should have received a copy of the GNU Lesser General Public |
||||||
|
License along with the GNU C Library; if not, write to the Free |
||||||
|
Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA |
||||||
|
02111-1307 USA.
|
||||||
|
\endverbatim |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
|
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/* Local function prototypes */ |
||||||
|
/*************************************************************************/ |
||||||
|
static void exchange (char **); |
||||||
|
static char *gk_getopt_initialize (int, char **, char *); |
||||||
|
static int gk_getopt_internal(int argc, char **argv, char *optstring,
|
||||||
|
struct gk_option *longopts, int *longind, int long_only); |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! \brief For communication arguments to the caller.
|
||||||
|
|
||||||
|
This variable is set by getopt to point at the value of the option argument,
|
||||||
|
for those options that accept arguments. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
char *gk_optarg; |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! \brief Index in ARGV of the next element to be scanned.
|
||||||
|
|
||||||
|
This variable is set by getopt to the index of the next element of the argv
|
||||||
|
array to be processed. Once getopt has found all of the option arguments,
|
||||||
|
you can use this variable to determine where the remaining non-option arguments
|
||||||
|
begin.
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
int gk_optind = 1;
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! \brief Controls error reporting for unrecognized options.
|
||||||
|
|
||||||
|
If the value of this variable is nonzero, then getopt prints an error
|
||||||
|
message to the standard error stream if it encounters an unknown option
|
||||||
|
character or an option with a missing required argument. This is the default
|
||||||
|
behavior. If you set this variable to zero, getopt does not print any messages, |
||||||
|
but it still returns the character ? to indicate an error. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
int gk_opterr = 1; |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! \brief Stores unknown option characters
|
||||||
|
|
||||||
|
When getopt encounters an unknown option character or an option with a
|
||||||
|
missing required argument, it stores that option character in this
|
||||||
|
variable. You can use this for providing your own diagnostic messages. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
int gk_optopt = '?'; |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*
|
||||||
|
Records that the getopt facility has been initialized. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
int gk_getopt_initialized; |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*
|
||||||
|
The next char to be scanned in the option-element in which the last option
|
||||||
|
character we returned was found. This allows us to pick up the scan where
|
||||||
|
we left off. |
||||||
|
|
||||||
|
If this is zero, or a null string, it means resume the scan by advancing
|
||||||
|
to the next ARGV-element.
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
static char *nextchar; |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*
|
||||||
|
Value of POSIXLY_CORRECT environment variable.
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
static char *posixly_correct; |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*
|
||||||
|
Describe how to deal with options that follow non-option ARGV-elements. |
||||||
|
|
||||||
|
If the caller did not specify anything, the default is REQUIRE_ORDER if
|
||||||
|
the environment variable POSIXLY_CORRECT is defined, PERMUTE otherwise. |
||||||
|
|
||||||
|
REQUIRE_ORDER means don't recognize them as options; stop option processing
|
||||||
|
when the first non-option is seen. This is what Unix does. This mode of
|
||||||
|
operation is selected by either setting the environment variable
|
||||||
|
POSIXLY_CORRECT, or using `+' as the first character of the list of
|
||||||
|
option characters. |
||||||
|
|
||||||
|
PERMUTE is the default. We permute the contents of ARGV as we scan, so
|
||||||
|
that eventually all the non-options are at the end. This allows options |
||||||
|
to be given in any order, even with programs that were not written to |
||||||
|
expect this. |
||||||
|
|
||||||
|
RETURN_IN_ORDER is an option available to programs that were written |
||||||
|
to expect options and other ARGV-elements in any order and that care
|
||||||
|
about the ordering of the two. We describe each non-option ARGV-element |
||||||
|
as if it were the argument of an option with character code 1. |
||||||
|
Using `-' as the first character of the list of option characters |
||||||
|
selects this mode of operation. |
||||||
|
|
||||||
|
The special argument `--' forces an end of option-scanning regardless |
||||||
|
of the value of `ordering'. In the case of RETURN_IN_ORDER, only |
||||||
|
`--' can cause `getopt' to return -1 with `gk_optind' != ARGC.
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
static enum |
||||||
|
{ |
||||||
|
REQUIRE_ORDER, PERMUTE, RETURN_IN_ORDER |
||||||
|
} ordering; |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*
|
||||||
|
Describe the part of ARGV that contains non-options that have |
||||||
|
been skipped. `first_nonopt' is the index in ARGV of the first of them; |
||||||
|
`last_nonopt' is the index after the last of them.
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
static int first_nonopt; |
||||||
|
static int last_nonopt; |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*
|
||||||
|
Handle permutation of arguments.
|
||||||
|
|
||||||
|
Exchange two adjacent subsequences of ARGV.
|
||||||
|
One subsequence is elements [first_nonopt,last_nonopt) |
||||||
|
which contains all the non-options that have been skipped so far. |
||||||
|
The other is elements [last_nonopt,gk_optind), which contains all |
||||||
|
the options processed since those non-options were skipped. |
||||||
|
|
||||||
|
`first_nonopt' and `last_nonopt' are relocated so that they describe |
||||||
|
the new indices of the non-options in ARGV after they are moved.
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
static void exchange (char **argv) |
||||||
|
{ |
||||||
|
int bottom = first_nonopt; |
||||||
|
int middle = last_nonopt; |
||||||
|
int top = gk_optind; |
||||||
|
char *tem; |
||||||
|
|
||||||
|
/* Exchange the shorter segment with the far end of the longer segment.
|
||||||
|
That puts the shorter segment into the right place. |
||||||
|
It leaves the longer segment in the right place overall, |
||||||
|
but it consists of two parts that need to be swapped next. */ |
||||||
|
|
||||||
|
while (top > middle && middle > bottom) { |
||||||
|
if (top - middle > middle - bottom) { |
||||||
|
/* Bottom segment is the short one. */ |
||||||
|
int len = middle - bottom; |
||||||
|
register int i; |
||||||
|
|
||||||
|
/* Swap it with the top part of the top segment. */ |
||||||
|
for (i = 0; i < len; i++) { |
||||||
|
tem = argv[bottom + i]; |
||||||
|
argv[bottom + i] = argv[top - (middle - bottom) + i]; |
||||||
|
argv[top - (middle - bottom) + i] = tem; |
||||||
|
} |
||||||
|
/* Exclude the moved bottom segment from further swapping. */ |
||||||
|
top -= len; |
||||||
|
} |
||||||
|
else { |
||||||
|
/* Top segment is the short one. */ |
||||||
|
int len = top - middle; |
||||||
|
register int i; |
||||||
|
|
||||||
|
/* Swap it with the bottom part of the bottom segment. */ |
||||||
|
for (i = 0; i < len; i++) { |
||||||
|
tem = argv[bottom + i]; |
||||||
|
argv[bottom + i] = argv[middle + i]; |
||||||
|
argv[middle + i] = tem; |
||||||
|
} |
||||||
|
/* Exclude the moved top segment from further swapping. */ |
||||||
|
bottom += len; |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
/* Update records for the slots the non-options now occupy. */ |
||||||
|
|
||||||
|
first_nonopt += (gk_optind - last_nonopt); |
||||||
|
last_nonopt = gk_optind; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*
|
||||||
|
Initialize the internal data when the first call is made.
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
static char *gk_getopt_initialize (int argc, char **argv, char *optstring) |
||||||
|
{ |
||||||
|
/* Start processing options with ARGV-element 1 (since ARGV-element 0
|
||||||
|
is the program name); the sequence of previously skipped |
||||||
|
non-option ARGV-elements is empty. */ |
||||||
|
|
||||||
|
first_nonopt = last_nonopt = gk_optind; |
||||||
|
|
||||||
|
nextchar = NULL; |
||||||
|
|
||||||
|
posixly_correct = getenv("POSIXLY_CORRECT"); |
||||||
|
|
||||||
|
/* Determine how to handle the ordering of options and nonoptions. */ |
||||||
|
if (optstring[0] == '-') { |
||||||
|
ordering = RETURN_IN_ORDER; |
||||||
|
++optstring; |
||||||
|
} |
||||||
|
else if (optstring[0] == '+') { |
||||||
|
ordering = REQUIRE_ORDER; |
||||||
|
++optstring; |
||||||
|
} |
||||||
|
else if (posixly_correct != NULL) |
||||||
|
ordering = REQUIRE_ORDER; |
||||||
|
else |
||||||
|
ordering = PERMUTE; |
||||||
|
|
||||||
|
return optstring; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*
|
||||||
|
Scan elements of ARGV (whose length is ARGC) for option characters |
||||||
|
given in OPTSTRING. |
||||||
|
|
||||||
|
If an element of ARGV starts with '-', and is not exactly "-" or "--", |
||||||
|
then it is an option element. The characters of this element |
||||||
|
(aside from the initial '-') are option characters. If `getopt' |
||||||
|
is called repeatedly, it returns successively each of the option characters |
||||||
|
from each of the option elements. |
||||||
|
|
||||||
|
If `getopt' finds another option character, it returns that character, |
||||||
|
updating `gk_optind' and `nextchar' so that the next call to `getopt' can |
||||||
|
resume the scan with the following option character or ARGV-element. |
||||||
|
|
||||||
|
If there are no more option characters, `getopt' returns -1. |
||||||
|
Then `gk_optind' is the index in ARGV of the first ARGV-element |
||||||
|
that is not an option. (The ARGV-elements have been permuted |
||||||
|
so that those that are not options now come last.) |
||||||
|
|
||||||
|
OPTSTRING is a string containing the legitimate option characters. |
||||||
|
If an option character is seen that is not listed in OPTSTRING, |
||||||
|
return '?' after printing an error message. If you set `gk_opterr' to |
||||||
|
zero, the error message is suppressed but we still return '?'. |
||||||
|
|
||||||
|
If a char in OPTSTRING is followed by a colon, that means it wants an arg, |
||||||
|
so the following text in the same ARGV-element, or the text of the following |
||||||
|
ARGV-element, is returned in `gk_optarg'. Two colons mean an option that |
||||||
|
wants an optional arg; if there is text in the current ARGV-element, |
||||||
|
it is returned in `gk_optarg', otherwise `gk_optarg' is set to zero. |
||||||
|
|
||||||
|
If OPTSTRING starts with `-' or `+', it requests different methods of |
||||||
|
handling the non-option ARGV-elements. |
||||||
|
See the comments about RETURN_IN_ORDER and REQUIRE_ORDER, above. |
||||||
|
|
||||||
|
Long-named options begin with `--' instead of `-'. |
||||||
|
Their names may be abbreviated as long as the abbreviation is unique |
||||||
|
or is an exact match for some defined option. If they have an |
||||||
|
argument, it follows the option name in the same ARGV-element, separated |
||||||
|
from the option name by a `=', or else the in next ARGV-element. |
||||||
|
When `getopt' finds a long-named option, it returns 0 if that option's |
||||||
|
`flag' field is nonzero, the value of the option's `val' field |
||||||
|
if the `flag' field is zero. |
||||||
|
|
||||||
|
LONGOPTS is a vector of `struct gk_option' terminated by an |
||||||
|
element containing a name which is zero. |
||||||
|
|
||||||
|
LONGIND returns the index in LONGOPT of the long-named option found. |
||||||
|
It is only valid when a long-named option has been found by the most |
||||||
|
recent call. |
||||||
|
|
||||||
|
If LONG_ONLY is nonzero, '-' as well as '--' can introduce |
||||||
|
long-named options.
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
static int gk_getopt_internal(int argc, char **argv, char *optstring,
|
||||||
|
struct gk_option *longopts, int *longind, int long_only) |
||||||
|
{ |
||||||
|
int print_errors = gk_opterr; |
||||||
|
if (optstring[0] == ':') |
||||||
|
print_errors = 0; |
||||||
|
|
||||||
|
if (argc < 1) |
||||||
|
return -1; |
||||||
|
|
||||||
|
gk_optarg = NULL; |
||||||
|
|
||||||
|
if (gk_optind == 0 || !gk_getopt_initialized) { |
||||||
|
if (gk_optind == 0) |
||||||
|
gk_optind = 1; /* Don't scan ARGV[0], the program name. */ |
||||||
|
|
||||||
|
optstring = gk_getopt_initialize (argc, argv, optstring); |
||||||
|
gk_getopt_initialized = 1; |
||||||
|
} |
||||||
|
|
||||||
|
/* Test whether ARGV[gk_optind] points to a non-option argument.
|
||||||
|
Either it does not have option syntax, or there is an environment flag |
||||||
|
from the shell indicating it is not an option. The later information |
||||||
|
is only used when the used in the GNU libc. */ |
||||||
|
# define NONOPTION_P (argv[gk_optind][0] != '-' || argv[gk_optind][1] == '\0') |
||||||
|
|
||||||
|
if (nextchar == NULL || *nextchar == '\0') { |
||||||
|
/* Advance to the next ARGV-element. */ |
||||||
|
|
||||||
|
/* Give FIRST_NONOPT & LAST_NONOPT rational values if OPTIND has been
|
||||||
|
moved back by the user (who may also have changed the arguments). */ |
||||||
|
if (last_nonopt > gk_optind) |
||||||
|
last_nonopt = gk_optind; |
||||||
|
if (first_nonopt > gk_optind) |
||||||
|
first_nonopt = gk_optind; |
||||||
|
|
||||||
|
if (ordering == PERMUTE) { |
||||||
|
/* If we have just processed some options following some non-options,
|
||||||
|
exchange them so that the options come first. */ |
||||||
|
|
||||||
|
if (first_nonopt != last_nonopt && last_nonopt != gk_optind) |
||||||
|
exchange ((char **) argv); |
||||||
|
else if (last_nonopt != gk_optind) |
||||||
|
first_nonopt = gk_optind; |
||||||
|
|
||||||
|
/* Skip any additional non-options
|
||||||
|
and extend the range of non-options previously skipped. */ |
||||||
|
|
||||||
|
while (gk_optind < argc && NONOPTION_P) |
||||||
|
gk_optind++; |
||||||
|
|
||||||
|
last_nonopt = gk_optind; |
||||||
|
} |
||||||
|
|
||||||
|
/* The special ARGV-element `--' means premature end of options.
|
||||||
|
Skip it like a null option, |
||||||
|
then exchange with previous non-options as if it were an option, |
||||||
|
then skip everything else like a non-option. */ |
||||||
|
|
||||||
|
if (gk_optind != argc && !strcmp (argv[gk_optind], "--")) { |
||||||
|
gk_optind++; |
||||||
|
|
||||||
|
if (first_nonopt != last_nonopt && last_nonopt != gk_optind) |
||||||
|
exchange ((char **) argv); |
||||||
|
else if (first_nonopt == last_nonopt) |
||||||
|
first_nonopt = gk_optind; |
||||||
|
last_nonopt = argc; |
||||||
|
|
||||||
|
gk_optind = argc; |
||||||
|
} |
||||||
|
|
||||||
|
/* If we have done all the ARGV-elements, stop the scan
|
||||||
|
and back over any non-options that we skipped and permuted. */ |
||||||
|
|
||||||
|
if (gk_optind == argc) { |
||||||
|
/* Set the next-arg-index to point at the non-options
|
||||||
|
that we previously skipped, so the caller will digest them. */ |
||||||
|
if (first_nonopt != last_nonopt) |
||||||
|
gk_optind = first_nonopt; |
||||||
|
return -1; |
||||||
|
} |
||||||
|
|
||||||
|
/* If we have come to a non-option and did not permute it,
|
||||||
|
either stop the scan or describe it to the caller and pass it by. */ |
||||||
|
|
||||||
|
if (NONOPTION_P) { |
||||||
|
if (ordering == REQUIRE_ORDER) |
||||||
|
return -1; |
||||||
|
gk_optarg = argv[gk_optind++]; |
||||||
|
return 1; |
||||||
|
} |
||||||
|
|
||||||
|
/* We have found another option-ARGV-element.
|
||||||
|
Skip the initial punctuation. */ |
||||||
|
|
||||||
|
nextchar = (argv[gk_optind] + 1 + (longopts != NULL && argv[gk_optind][1] == '-')); |
||||||
|
} |
||||||
|
|
||||||
|
/* Decode the current option-ARGV-element. */ |
||||||
|
|
||||||
|
/* Check whether the ARGV-element is a long option.
|
||||||
|
|
||||||
|
If long_only and the ARGV-element has the form "-f", where f is |
||||||
|
a valid short option, don't consider it an abbreviated form of |
||||||
|
a long option that starts with f. Otherwise there would be no |
||||||
|
way to give the -f short option. |
||||||
|
|
||||||
|
On the other hand, if there's a long option "fubar" and |
||||||
|
the ARGV-element is "-fu", do consider that an abbreviation of |
||||||
|
the long option, just like "--fu", and not "-f" with arg "u". |
||||||
|
|
||||||
|
This distinction seems to be the most useful approach. */ |
||||||
|
|
||||||
|
if (longopts != NULL && (argv[gk_optind][1] == '-' || (long_only && (argv[gk_optind][2] || !strchr(optstring, argv[gk_optind][1]))))) { |
||||||
|
char *nameend; |
||||||
|
struct gk_option *p; |
||||||
|
struct gk_option *pfound = NULL; |
||||||
|
int exact = 0; |
||||||
|
int ambig = 0; |
||||||
|
int indfound = -1; |
||||||
|
int option_index; |
||||||
|
|
||||||
|
for (nameend = nextchar; *nameend && *nameend != '='; nameend++) |
||||||
|
/* Do nothing. */ ; |
||||||
|
|
||||||
|
/* Test all long options for either exact match or abbreviated matches. */ |
||||||
|
for (p = longopts, option_index = 0; p->name; p++, option_index++) { |
||||||
|
if (!strncmp (p->name, nextchar, nameend - nextchar)) { |
||||||
|
if ((unsigned int) (nameend - nextchar) == (unsigned int) strlen (p->name)) { |
||||||
|
/* Exact match found. */ |
||||||
|
pfound = p; |
||||||
|
indfound = option_index; |
||||||
|
exact = 1; |
||||||
|
break; |
||||||
|
} |
||||||
|
else if (pfound == NULL) { |
||||||
|
/* First nonexact match found. */ |
||||||
|
pfound = p; |
||||||
|
indfound = option_index; |
||||||
|
} |
||||||
|
else if (long_only || pfound->has_arg != p->has_arg || pfound->flag != p->flag || pfound->val != p->val) |
||||||
|
/* Second or later nonexact match found. */ |
||||||
|
ambig = 1; |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
if (ambig && !exact) { |
||||||
|
if (print_errors) |
||||||
|
fprintf(stderr, "%s: option `%s' is ambiguous\n", argv[0], argv[gk_optind]); |
||||||
|
|
||||||
|
nextchar += strlen (nextchar); |
||||||
|
gk_optind++; |
||||||
|
gk_optopt = 0; |
||||||
|
return '?'; |
||||||
|
} |
||||||
|
|
||||||
|
if (pfound != NULL) { |
||||||
|
option_index = indfound; |
||||||
|
gk_optind++; |
||||||
|
if (*nameend) { |
||||||
|
/* Don't test has_arg with >, because some C compilers don't allow it to be used on enums. */ |
||||||
|
if (pfound->has_arg) |
||||||
|
gk_optarg = nameend + 1; |
||||||
|
else { |
||||||
|
if (print_errors) { |
||||||
|
if (argv[gk_optind - 1][1] == '-') |
||||||
|
/* --option */ |
||||||
|
fprintf(stderr, "%s: option `--%s' doesn't allow an argument\n", argv[0], pfound->name); |
||||||
|
else |
||||||
|
/* +option or -option */ |
||||||
|
fprintf(stderr, "%s: option `%c%s' doesn't allow an argument\n", argv[0], argv[gk_optind - 1][0], pfound->name); |
||||||
|
} |
||||||
|
|
||||||
|
nextchar += strlen (nextchar); |
||||||
|
|
||||||
|
gk_optopt = pfound->val; |
||||||
|
return '?'; |
||||||
|
} |
||||||
|
} |
||||||
|
else if (pfound->has_arg == 1) { |
||||||
|
if (gk_optind < argc) |
||||||
|
gk_optarg = argv[gk_optind++]; |
||||||
|
else { |
||||||
|
if (print_errors) |
||||||
|
fprintf(stderr, "%s: option `%s' requires an argument\n", argv[0], argv[gk_optind - 1]); |
||||||
|
nextchar += strlen (nextchar); |
||||||
|
gk_optopt = pfound->val; |
||||||
|
return optstring[0] == ':' ? ':' : '?'; |
||||||
|
} |
||||||
|
} |
||||||
|
nextchar += strlen (nextchar); |
||||||
|
if (longind != NULL) |
||||||
|
*longind = option_index; |
||||||
|
if (pfound->flag) { |
||||||
|
*(pfound->flag) = pfound->val; |
||||||
|
return 0; |
||||||
|
} |
||||||
|
return pfound->val; |
||||||
|
} |
||||||
|
|
||||||
|
/* Can't find it as a long option. If this is not getopt_long_only,
|
||||||
|
or the option starts with '--' or is not a valid short |
||||||
|
option, then it's an error. Otherwise interpret it as a short option. */ |
||||||
|
if (!long_only || argv[gk_optind][1] == '-' || strchr(optstring, *nextchar) == NULL) { |
||||||
|
if (print_errors) { |
||||||
|
if (argv[gk_optind][1] == '-') |
||||||
|
/* --option */ |
||||||
|
fprintf(stderr, "%s: unrecognized option `--%s'\n", argv[0], nextchar); |
||||||
|
else |
||||||
|
/* +option or -option */ |
||||||
|
fprintf(stderr, "%s: unrecognized option `%c%s'\n", argv[0], argv[gk_optind][0], nextchar); |
||||||
|
} |
||||||
|
nextchar = (char *) ""; |
||||||
|
gk_optind++; |
||||||
|
gk_optopt = 0; |
||||||
|
return '?'; |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
/* Look at and handle the next short option-character. */ |
||||||
|
{ |
||||||
|
char c = *nextchar++; |
||||||
|
char *temp = strchr(optstring, c); |
||||||
|
|
||||||
|
/* Increment `gk_optind' when we start to process its last character. */ |
||||||
|
if (*nextchar == '\0') |
||||||
|
++gk_optind; |
||||||
|
|
||||||
|
if (temp == NULL || c == ':') { |
||||||
|
if (print_errors) { |
||||||
|
if (posixly_correct) |
||||||
|
/* 1003.2 specifies the format of this message. */ |
||||||
|
fprintf(stderr, "%s: illegal option -- %c\n", argv[0], c); |
||||||
|
else |
||||||
|
fprintf(stderr, "%s: invalid option -- %c\n", argv[0], c); |
||||||
|
} |
||||||
|
gk_optopt = c; |
||||||
|
return '?'; |
||||||
|
} |
||||||
|
|
||||||
|
/* Convenience. Treat POSIX -W foo same as long option --foo */ |
||||||
|
if (temp[0] == 'W' && temp[1] == ';') { |
||||||
|
char *nameend; |
||||||
|
struct gk_option *p; |
||||||
|
struct gk_option *pfound = NULL; |
||||||
|
int exact = 0; |
||||||
|
int ambig = 0; |
||||||
|
int indfound = 0; |
||||||
|
int option_index; |
||||||
|
|
||||||
|
/* This is an option that requires an argument. */ |
||||||
|
if (*nextchar != '\0') { |
||||||
|
gk_optarg = nextchar; |
||||||
|
/* If we end this ARGV-element by taking the rest as an arg,
|
||||||
|
we must advance to the next element now. */ |
||||||
|
gk_optind++; |
||||||
|
} |
||||||
|
else if (gk_optind == argc) { |
||||||
|
if (print_errors) { |
||||||
|
/* 1003.2 specifies the format of this message. */ |
||||||
|
fprintf(stderr, "%s: option requires an argument -- %c\n", argv[0], c); |
||||||
|
} |
||||||
|
gk_optopt = c; |
||||||
|
if (optstring[0] == ':') |
||||||
|
c = ':'; |
||||||
|
else |
||||||
|
c = '?'; |
||||||
|
return c; |
||||||
|
} |
||||||
|
else |
||||||
|
/* We already incremented `gk_optind' once; increment it again when taking next ARGV-elt as argument. */ |
||||||
|
gk_optarg = argv[gk_optind++]; |
||||||
|
|
||||||
|
/* gk_optarg is now the argument, see if it's in the table of longopts. */ |
||||||
|
|
||||||
|
for (nextchar = nameend = gk_optarg; *nameend && *nameend != '='; nameend++) |
||||||
|
/* Do nothing. */ ; |
||||||
|
|
||||||
|
/* Test all long options for either exact match or abbreviated matches. */ |
||||||
|
for (p = longopts, option_index = 0; p->name; p++, option_index++) { |
||||||
|
if (!strncmp (p->name, nextchar, nameend - nextchar)) { |
||||||
|
if ((unsigned int) (nameend - nextchar) == strlen (p->name)) { |
||||||
|
/* Exact match found. */ |
||||||
|
pfound = p; |
||||||
|
indfound = option_index; |
||||||
|
exact = 1; |
||||||
|
break; |
||||||
|
} |
||||||
|
else if (pfound == NULL) { |
||||||
|
/* First nonexact match found. */ |
||||||
|
pfound = p; |
||||||
|
indfound = option_index; |
||||||
|
} |
||||||
|
else |
||||||
|
/* Second or later nonexact match found. */ |
||||||
|
ambig = 1; |
||||||
|
} |
||||||
|
} |
||||||
|
if (ambig && !exact) { |
||||||
|
if (print_errors) |
||||||
|
fprintf(stderr, "%s: option `-W %s' is ambiguous\n", argv[0], argv[gk_optind]); |
||||||
|
nextchar += strlen (nextchar); |
||||||
|
gk_optind++; |
||||||
|
return '?'; |
||||||
|
} |
||||||
|
if (pfound != NULL) { |
||||||
|
option_index = indfound; |
||||||
|
if (*nameend) { |
||||||
|
/* Don't test has_arg with >, because some C compilers don't allow it to be used on enums. */ |
||||||
|
if (pfound->has_arg) |
||||||
|
gk_optarg = nameend + 1; |
||||||
|
else { |
||||||
|
if (print_errors) |
||||||
|
fprintf(stderr, "%s: option `-W %s' doesn't allow an argument\n", argv[0], pfound->name); |
||||||
|
|
||||||
|
nextchar += strlen (nextchar); |
||||||
|
return '?'; |
||||||
|
} |
||||||
|
} |
||||||
|
else if (pfound->has_arg == 1) { |
||||||
|
if (gk_optind < argc) |
||||||
|
gk_optarg = argv[gk_optind++]; |
||||||
|
else { |
||||||
|
if (print_errors) |
||||||
|
fprintf(stderr, "%s: option `%s' requires an argument\n", argv[0], argv[gk_optind - 1]); |
||||||
|
nextchar += strlen (nextchar); |
||||||
|
return optstring[0] == ':' ? ':' : '?'; |
||||||
|
} |
||||||
|
} |
||||||
|
nextchar += strlen (nextchar); |
||||||
|
if (longind != NULL) |
||||||
|
*longind = option_index; |
||||||
|
if (pfound->flag) { |
||||||
|
*(pfound->flag) = pfound->val; |
||||||
|
return 0; |
||||||
|
} |
||||||
|
return pfound->val; |
||||||
|
} |
||||||
|
nextchar = NULL; |
||||||
|
return 'W'; /* Let the application handle it. */ |
||||||
|
} |
||||||
|
|
||||||
|
if (temp[1] == ':') { |
||||||
|
if (temp[2] == ':') { |
||||||
|
/* This is an option that accepts an argument optionally. */ |
||||||
|
if (*nextchar != '\0') { |
||||||
|
gk_optarg = nextchar; |
||||||
|
gk_optind++; |
||||||
|
} |
||||||
|
else |
||||||
|
gk_optarg = NULL; |
||||||
|
nextchar = NULL; |
||||||
|
} |
||||||
|
else { |
||||||
|
/* This is an option that requires an argument. */ |
||||||
|
if (*nextchar != '\0') { |
||||||
|
gk_optarg = nextchar; |
||||||
|
/* If we end this ARGV-element by taking the rest as an arg, we must advance to the next element now. */ |
||||||
|
gk_optind++; |
||||||
|
} |
||||||
|
else if (gk_optind == argc) { |
||||||
|
if (print_errors) { |
||||||
|
/* 1003.2 specifies the format of this message. */ |
||||||
|
fprintf(stderr, "%s: option requires an argument -- %c\n", argv[0], c); |
||||||
|
} |
||||||
|
gk_optopt = c; |
||||||
|
if (optstring[0] == ':') |
||||||
|
c = ':'; |
||||||
|
else |
||||||
|
c = '?'; |
||||||
|
} |
||||||
|
else |
||||||
|
/* We already incremented `gk_optind' once; increment it again when taking next ARGV-elt as argument. */ |
||||||
|
gk_optarg = argv[gk_optind++]; |
||||||
|
nextchar = NULL; |
||||||
|
} |
||||||
|
} |
||||||
|
return c; |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! \brief Parse command-line arguments
|
||||||
|
|
||||||
|
The gk_getopt() function gets the next option argument from the argument
|
||||||
|
list specified by the \c argv and \c argc arguments. Normally these values
|
||||||
|
come directly from the arguments received by main(). |
||||||
|
|
||||||
|
\param argc is the number of command line arguments passed to main(). |
||||||
|
\param argv is an array of strings storing the above command line
|
||||||
|
arguments. |
||||||
|
\param options is a string that specifies the option characters that
|
||||||
|
are valid for this program. An option character in this string
|
||||||
|
can be followed by a colon (`:') to indicate that it takes a
|
||||||
|
required argument. If an option character is followed by two
|
||||||
|
colons (`::'), its argument is optional; this is a GNU extension. |
||||||
|
|
||||||
|
\return
|
||||||
|
It returns the option character for the next command line option. When no
|
||||||
|
more option arguments are available, it returns -1. There may still be
|
||||||
|
more non-option arguments; you must compare the external variable
|
||||||
|
#gk_optind against the \c argc parameter to check this. |
||||||
|
|
||||||
|
\return
|
||||||
|
If the option has an argument, gk_getopt() returns the argument by storing
|
||||||
|
it in the variable #gk_optarg. You don't ordinarily need to copy the
|
||||||
|
#gk_optarg string, since it is a pointer into the original \c argv array, |
||||||
|
not into a static area that might be overwritten. |
||||||
|
|
||||||
|
\return
|
||||||
|
If gk_getopt() finds an option character in \c argv that was not included
|
||||||
|
in options, or a missing option argument, it returns `?' and sets the
|
||||||
|
external variable #gk_optopt to the actual option character.
|
||||||
|
If the first character of options is a colon (`:'), then gk_getopt()
|
||||||
|
returns `:' instead of `?' to indicate a missing option argument.
|
||||||
|
In addition, if the external variable #gk_opterr is nonzero (which is
|
||||||
|
the default), gk_getopt() prints an error message. This variable is
|
||||||
|
set by gk_getopt() to point at the value of the option argument,
|
||||||
|
for those options that accept arguments. |
||||||
|
|
||||||
|
|
||||||
|
gk_getopt() has three ways to deal with options that follow non-options
|
||||||
|
\c argv elements. The special argument <tt>`--'</tt> forces in all cases
|
||||||
|
the end of option scanning. |
||||||
|
- The default is to permute the contents of \c argv while scanning it
|
||||||
|
so that eventually all the non-options are at the end. This allows
|
||||||
|
options to be given in any order, even with programs that were not
|
||||||
|
written to expect this. |
||||||
|
- If the options argument string begins with a hyphen (`-'), this is
|
||||||
|
treated specially. It permits arguments that are not options to be
|
||||||
|
returned as if they were associated with option character `\\1'. |
||||||
|
- POSIX demands the following behavior: The first non-option stops
|
||||||
|
option processing. This mode is selected by either setting the
|
||||||
|
environment variable POSIXLY_CORRECT or beginning the options |
||||||
|
argument string with a plus sign (`+').
|
||||||
|
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
int gk_getopt(int argc, char **argv, char *options) |
||||||
|
{ |
||||||
|
return gk_getopt_internal(argc, argv, options, NULL, NULL, 0); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! \brief Parse command-line arguments with long options
|
||||||
|
|
||||||
|
This function accepts GNU-style long options as well as single-character
|
||||||
|
options.
|
||||||
|
|
||||||
|
\param argc is the number of command line arguments passed to main(). |
||||||
|
\param argv is an array of strings storing the above command line
|
||||||
|
arguments. |
||||||
|
\param options describes the short options to accept, just as it does
|
||||||
|
in gk_getopt().
|
||||||
|
\param long_options describes the long options to accept. See the
|
||||||
|
defintion of ::gk_option for more information. |
||||||
|
\param opt_index this is a returned variable. For any long option,
|
||||||
|
gk_getopt_long() tells you the index in the array \c long_options
|
||||||
|
of the options definition, by storing it into <tt>*opt_index</tt>.
|
||||||
|
You can get the name of the option with <tt>longopts[*opt_index].name</tt>.
|
||||||
|
So you can distinguish among long options either by the values
|
||||||
|
in their val fields or by their indices. You can also distinguish
|
||||||
|
in this way among long options that set flags. |
||||||
|
|
||||||
|
|
||||||
|
\return |
||||||
|
When gk_getopt_long() encounters a short option, it does the same thing
|
||||||
|
that gk_getopt() would do: it returns the character code for the option,
|
||||||
|
and stores the options argument (if it has one) in #gk_optarg. |
||||||
|
|
||||||
|
\return |
||||||
|
When gk_getopt_long() encounters a long option, it takes actions based
|
||||||
|
on the flag and val fields of the definition of that option. |
||||||
|
|
||||||
|
\return |
||||||
|
If flag is a null pointer, then gk_getopt_long() returns the contents
|
||||||
|
of val to indicate which option it found. You should arrange distinct
|
||||||
|
values in the val field for options with different meanings, so you
|
||||||
|
can decode these values after gk_getopt_long() returns. If the long
|
||||||
|
option is equivalent to a short option, you can use the short option's
|
||||||
|
character code in val. |
||||||
|
|
||||||
|
\return |
||||||
|
If flag is not a null pointer, that means this option should just set
|
||||||
|
a flag in the program. The flag is a variable of type int that you
|
||||||
|
define. Put the address of the flag in the flag field. Put in the
|
||||||
|
val field the value you would like this option to store in the flag.
|
||||||
|
In this case, gk_getopt_long() returns 0. |
||||||
|
|
||||||
|
\return |
||||||
|
When a long option has an argument, gk_getopt_long() puts the argument
|
||||||
|
value in the variable #gk_optarg before returning. When the option has
|
||||||
|
no argument, the value in #gk_optarg is a null pointer. This is |
||||||
|
how you can tell whether an optional argument was supplied. |
||||||
|
|
||||||
|
\return |
||||||
|
When gk_getopt_long() has no more options to handle, it returns -1,
|
||||||
|
and leaves in the variable #gk_optind the index in argv of the next
|
||||||
|
remaining argument.
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
int gk_getopt_long( int argc, char **argv, char *options,
|
||||||
|
struct gk_option *long_options, int *opt_index) |
||||||
|
{ |
||||||
|
return gk_getopt_internal (argc, argv, options, long_options, opt_index, 0); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! \brief Parse command-line arguments with only long options
|
||||||
|
|
||||||
|
Like gk_getopt_long(), but '-' as well as '--' can indicate a long option. |
||||||
|
If an option that starts with '-' (not '--') doesn't match a long option, |
||||||
|
but does match a short option, it is parsed as a short option instead.
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
int gk_getopt_long_only(int argc, char **argv, char *options,
|
||||||
|
struct gk_option *long_options, int *opt_index) |
||||||
|
{ |
||||||
|
return gk_getopt_internal(argc, argv, options, long_options, opt_index, 1); |
||||||
|
} |
||||||
|
|
||||||
@ -0,0 +1,70 @@ |
|||||||
|
/*!
|
||||||
|
\file gk_arch.h |
||||||
|
\brief This file contains various architecture-specific declerations |
||||||
|
|
||||||
|
\date Started 3/27/2007 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: gk_arch.h 21637 2018-01-03 22:37:24Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
#ifndef _GK_ARCH_H_ |
||||||
|
#define _GK_ARCH_H_ |
||||||
|
|
||||||
|
/*************************************************************************
|
||||||
|
* Architecture-specific differences in header files |
||||||
|
**************************************************************************/ |
||||||
|
#ifdef LINUX |
||||||
|
#if !defined(__USE_XOPEN) |
||||||
|
#define __USE_XOPEN |
||||||
|
#endif |
||||||
|
#if !defined(_XOPEN_SOURCE) |
||||||
|
#define _XOPEN_SOURCE 600 |
||||||
|
#endif |
||||||
|
#if !defined(__USE_XOPEN2K) |
||||||
|
#define __USE_XOPEN2K |
||||||
|
#endif |
||||||
|
#endif |
||||||
|
|
||||||
|
|
||||||
|
#ifdef HAVE_EXECINFO_H |
||||||
|
#include <execinfo.h> |
||||||
|
#endif |
||||||
|
|
||||||
|
|
||||||
|
#ifdef __MSC__ |
||||||
|
#include "gk_ms_stdint.h" |
||||||
|
#include "gk_ms_inttypes.h" |
||||||
|
#include "gk_ms_stat.h" |
||||||
|
#include "win32/adapt.h" |
||||||
|
#else |
||||||
|
#ifndef SUNOS |
||||||
|
#include <stdint.h> |
||||||
|
#endif |
||||||
|
#include <inttypes.h> |
||||||
|
#include <sys/types.h> |
||||||
|
#ifndef __MINGW32__ |
||||||
|
#include <sys/resource.h> |
||||||
|
#endif |
||||||
|
#include <sys/time.h> |
||||||
|
#include <unistd.h> |
||||||
|
#endif |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************
|
||||||
|
* Architecture-specific modifications |
||||||
|
**************************************************************************/ |
||||||
|
#ifdef WIN32 |
||||||
|
typedef ptrdiff_t ssize_t; |
||||||
|
#endif |
||||||
|
|
||||||
|
|
||||||
|
#ifdef SUNOS |
||||||
|
#define PTRDIFF_MAX INT64_MAX |
||||||
|
#endif |
||||||
|
|
||||||
|
/* MSC does not have INFINITY defined */ |
||||||
|
#ifndef INFINITY |
||||||
|
#define INFINITY FLT_MAX |
||||||
|
#endif |
||||||
|
|
||||||
|
#endif |
||||||
@ -0,0 +1,87 @@ |
|||||||
|
/*!
|
||||||
|
\file gk_defs.h |
||||||
|
\brief This file contains various constants definitions |
||||||
|
|
||||||
|
\date Started 3/27/2007 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: gk_defs.h 22039 2018-05-26 16:34:48Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
#ifndef _GK_DEFS_H_ |
||||||
|
#define _GK_DEFS_H_ |
||||||
|
|
||||||
|
|
||||||
|
#define LTERM (void **) 0 /* List terminator for GKfree() */ |
||||||
|
|
||||||
|
/* mopt_t types */ |
||||||
|
#define GK_MOPT_MARK 1 |
||||||
|
#define GK_MOPT_CORE 2 |
||||||
|
#define GK_MOPT_HEAP 3 |
||||||
|
|
||||||
|
#define HTABLE_EMPTY -1 |
||||||
|
#define HTABLE_DELETED -2 |
||||||
|
#define HTABLE_FIRST 1 |
||||||
|
#define HTABLE_NEXT 2 |
||||||
|
|
||||||
|
/* pdb corruption bit switches */ |
||||||
|
#define CRP_ALTLOCS 1 |
||||||
|
#define CRP_MISSINGCA 2 |
||||||
|
#define CRP_MISSINGBB 4 |
||||||
|
#define CRP_MULTICHAIN 8 |
||||||
|
#define CRP_MULTICA 16 |
||||||
|
#define CRP_MULTIBB 32 |
||||||
|
|
||||||
|
#define MAXLINELEN 300000 |
||||||
|
|
||||||
|
/* GKlib signals to standard signal mapping */ |
||||||
|
#define SIGMEM SIGABRT |
||||||
|
#define SIGERR SIGTERM |
||||||
|
|
||||||
|
|
||||||
|
/* CSR-related defines */ |
||||||
|
#define GK_CSR_ROW 1 |
||||||
|
#define GK_CSR_COL 2 |
||||||
|
#define GK_CSR_ROWCOL 3 |
||||||
|
|
||||||
|
#define GK_CSR_MAXTF 1 |
||||||
|
#define GK_CSR_SQRT 2 |
||||||
|
#define GK_CSR_POW25 3 |
||||||
|
#define GK_CSR_POW65 4 |
||||||
|
#define GK_CSR_POW75 5 |
||||||
|
#define GK_CSR_POW85 6 |
||||||
|
#define GK_CSR_LOG 7 |
||||||
|
#define GK_CSR_IDF 8 |
||||||
|
#define GK_CSR_IDF2 9 |
||||||
|
#define GK_CSR_MAXTF2 10 |
||||||
|
|
||||||
|
#define GK_CSR_DOTP 1 |
||||||
|
#define GK_CSR_COS 2 |
||||||
|
#define GK_CSR_JAC 3 |
||||||
|
#define GK_CSR_MIN 4 |
||||||
|
#define GK_CSR_AMIN 5 |
||||||
|
|
||||||
|
#define GK_CSR_FMT_AUTO 2 |
||||||
|
#define GK_CSR_FMT_CLUTO 1 |
||||||
|
#define GK_CSR_FMT_CSR 2 |
||||||
|
#define GK_CSR_FMT_METIS 3 |
||||||
|
#define GK_CSR_FMT_BINROW 4 |
||||||
|
#define GK_CSR_FMT_BINCOL 5 |
||||||
|
#define GK_CSR_FMT_IJV 6 |
||||||
|
#define GK_CSR_FMT_BIJV 7 |
||||||
|
|
||||||
|
#define GK_CSR_SYM_SUM 1 |
||||||
|
#define GK_CSR_SYM_MIN 2 |
||||||
|
#define GK_CSR_SYM_MAX 3 |
||||||
|
#define GK_CSR_SYM_AVG 4 |
||||||
|
|
||||||
|
|
||||||
|
#define GK_GRAPH_FMT_METIS 1 |
||||||
|
#define GK_GRAPH_FMT_IJV 2 |
||||||
|
#define GK_GRAPH_FMT_HIJV 3 |
||||||
|
|
||||||
|
#define GK_GRAPH_SYM_SUM 1 |
||||||
|
#define GK_GRAPH_SYM_MIN 2 |
||||||
|
#define GK_GRAPH_SYM_MAX 3 |
||||||
|
#define GK_GRAPH_SYM_AVG 4 |
||||||
|
|
||||||
|
#endif |
||||||
@ -0,0 +1,25 @@ |
|||||||
|
/*!
|
||||||
|
\file gk_externs.h |
||||||
|
\brief This file contains definitions of external variables created by GKlib |
||||||
|
|
||||||
|
\date Started 3/27/2007 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: gk_externs.h 10711 2011-08-31 22:23:04Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
#ifndef _GK_EXTERNS_H_ |
||||||
|
#define _GK_EXTERNS_H_ |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************
|
||||||
|
* Extern variable definition. Hopefully, the __thread makes them thread-safe. |
||||||
|
**************************************************************************/ |
||||||
|
#ifndef _GK_ERROR_C_ |
||||||
|
/* declared in error.c */ |
||||||
|
extern __thread int gk_cur_jbufs; |
||||||
|
extern __thread jmp_buf gk_jbufs[]; |
||||||
|
extern __thread jmp_buf gk_jbuf; |
||||||
|
|
||||||
|
#endif |
||||||
|
|
||||||
|
#endif |
||||||
@ -0,0 +1,64 @@ |
|||||||
|
/*!
|
||||||
|
\file gk_getopt.h |
||||||
|
\brief This file contains GNU's externs/structs/prototypes |
||||||
|
|
||||||
|
\date Started 3/27/2007 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: gk_getopt.h 10711 2011-08-31 22:23:04Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
#ifndef _GK_GETOPT_H_ |
||||||
|
#define _GK_GETOPT_H_ |
||||||
|
|
||||||
|
|
||||||
|
/* Externals from getopt.c */ |
||||||
|
extern char *gk_optarg; |
||||||
|
extern int gk_optind; |
||||||
|
extern int gk_opterr; |
||||||
|
extern int gk_optopt; |
||||||
|
|
||||||
|
|
||||||
|
/*! \brief The structure that stores the information about the command-line options
|
||||||
|
|
||||||
|
This structure describes a single long option name for the sake of
|
||||||
|
gk_getopt_long(). The argument <tt>long_options</tt> must be an array
|
||||||
|
of these structures, one for each long option. Terminate the array with
|
||||||
|
an element containing all zeros. |
||||||
|
*/ |
||||||
|
struct gk_option { |
||||||
|
char *name; /*!< This field is the name of the option. */ |
||||||
|
int has_arg; /*!< This field says whether the option takes an argument.
|
||||||
|
It is an integer, and there are three legitimate values:
|
||||||
|
no_argument, required_argument and optional_argument.
|
||||||
|
*/ |
||||||
|
int *flag; /*!< See the discussion on ::gk_option#val */ |
||||||
|
int val; /*!< These fields control how to report or act on the option
|
||||||
|
when it occurs.
|
||||||
|
|
||||||
|
If flag is a null pointer, then the val is a value which
|
||||||
|
identifies this option. Often these values are chosen
|
||||||
|
to uniquely identify particular long options. |
||||||
|
|
||||||
|
If flag is not a null pointer, it should be the address
|
||||||
|
of an int variable which is the flag for this option.
|
||||||
|
The value in val is the value to store in the flag to
|
||||||
|
indicate that the option was seen. */ |
||||||
|
}; |
||||||
|
|
||||||
|
/* Names for the values of the `has_arg' field of `struct gk_option'. */ |
||||||
|
#define no_argument 0 |
||||||
|
#define required_argument 1 |
||||||
|
#define optional_argument 2 |
||||||
|
|
||||||
|
|
||||||
|
/* Function prototypes */ |
||||||
|
extern int gk_getopt(int argc, char **argv, char *shortopts); |
||||||
|
extern int gk_getopt_long(int argc, char **argv, char *shortopts, |
||||||
|
struct gk_option *longopts, int *longind); |
||||||
|
extern int gk_getopt_long_only (int argc, char **argv, |
||||||
|
char *shortopts, struct gk_option *longopts, int *longind); |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
#endif |
||||||
|
|
||||||
@ -0,0 +1,169 @@ |
|||||||
|
/*!
|
||||||
|
\file gk_macros.h |
||||||
|
\brief This file contains various macros |
||||||
|
|
||||||
|
\date Started 3/27/2007 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: gk_macros.h 15048 2013-08-31 19:38:14Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
#ifndef _GK_MACROS_H_ |
||||||
|
#define _GK_MACROS_H_ |
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* Usefull commands
|
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
#define gk_max(a, b) ((a) >= (b) ? (a) : (b)) |
||||||
|
#define gk_min(a, b) ((a) >= (b) ? (b) : (a)) |
||||||
|
#define gk_max3(a, b, c) ((a) >= (b) && (a) >= (c) ? (a) : ((b) >= (a) && (b) >= (c) ? (b) : (c))) |
||||||
|
#define gk_SWAP(a, b, tmp) do {(tmp) = (a); (a) = (b); (b) = (tmp);} while(0) |
||||||
|
#define INC_DEC(a, b, val) do {(a) += (val); (b) -= (val);} while(0) |
||||||
|
#define sign(a, b) ((a >= 0 ? b : -b)) |
||||||
|
|
||||||
|
#define ONEOVERRANDMAX (1.0/(RAND_MAX+1.0)) |
||||||
|
#define RandomInRange(u) ((int) (ONEOVERRANDMAX*(u)*rand())) |
||||||
|
#define RandomInRange_r(s, u) ((int) (ONEOVERRANDMAX*(u)*rand_r(s))) |
||||||
|
|
||||||
|
#define gk_abs(x) ((x) >= 0 ? (x) : -(x)) |
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* Timing macros |
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
#define gk_clearcputimer(tmr) (tmr = 0.0) |
||||||
|
#define gk_startcputimer(tmr) (tmr -= gk_CPUSeconds()) |
||||||
|
#define gk_stopcputimer(tmr) (tmr += gk_CPUSeconds()) |
||||||
|
#define gk_getcputimer(tmr) (tmr) |
||||||
|
|
||||||
|
#define gk_clearwctimer(tmr) (tmr = 0.0) |
||||||
|
#define gk_startwctimer(tmr) (tmr -= gk_WClockSeconds()) |
||||||
|
#define gk_stopwctimer(tmr) (tmr += gk_WClockSeconds()) |
||||||
|
#define gk_getwctimer(tmr) (tmr) |
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* dbglvl handling macros |
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
#define IFSET(a, flag, cmd) if ((a)&(flag)) (cmd); |
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* gracefull library exit macro |
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
#define GKSETJMP() (setjmp(gk_return_to_entry)) |
||||||
|
#define gk_sigcatch() (setjmp(gk_jbufs[gk_cur_jbufs])) |
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* Debuging memory leaks |
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
#ifdef DMALLOC |
||||||
|
# define MALLOC_CHECK(ptr) \ |
||||||
|
if (malloc_verify((ptr)) == DMALLOC_VERIFY_ERROR) { \
|
||||||
|
printf("***MALLOC_CHECK failed on line %d of file %s: " #ptr "\n", \
|
||||||
|
__LINE__, __FILE__); \
|
||||||
|
abort(); \
|
||||||
|
} |
||||||
|
#else |
||||||
|
# define MALLOC_CHECK(ptr) ; |
||||||
|
#endif |
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* CSR conversion macros |
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
#define MAKECSR(i, n, a) \ |
||||||
|
do { \
|
||||||
|
for (i=1; i<n; i++) a[i] += a[i-1]; \
|
||||||
|
for (i=n; i>0; i--) a[i] = a[i-1]; \
|
||||||
|
a[0] = 0; \
|
||||||
|
} while(0)
|
||||||
|
|
||||||
|
#define SHIFTCSR(i, n, a) \ |
||||||
|
do { \
|
||||||
|
for (i=n; i>0; i--) a[i] = a[i-1]; \
|
||||||
|
a[0] = 0; \
|
||||||
|
} while(0)
|
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* ASSERTS that cannot be turned off! |
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
#define GKASSERT(expr) \ |
||||||
|
if (!(expr)) { \
|
||||||
|
printf("***ASSERTION failed on line %d of file %s: " #expr "\n", \
|
||||||
|
__LINE__, __FILE__); \
|
||||||
|
abort(); \
|
||||||
|
} |
||||||
|
|
||||||
|
#define GKASSERTP(expr,msg) \ |
||||||
|
if (!(expr)) { \
|
||||||
|
printf("***ASSERTION failed on line %d of file %s: " #expr "\n", \
|
||||||
|
__LINE__, __FILE__); \
|
||||||
|
printf msg ; \
|
||||||
|
printf("\n"); \
|
||||||
|
abort(); \
|
||||||
|
} |
||||||
|
|
||||||
|
#define GKCUASSERT(expr) \ |
||||||
|
if (!(expr)) { \
|
||||||
|
printf("***ASSERTION failed on line %d of file %s: " #expr "\n", \
|
||||||
|
__LINE__, __FILE__); \
|
||||||
|
} |
||||||
|
|
||||||
|
#define GKWARN(expr) \ |
||||||
|
if (!(expr)) { \
|
||||||
|
printf("***ASSERTION failed on line %d of file %s: " #expr "\n", \
|
||||||
|
__LINE__, __FILE__); \
|
||||||
|
} |
||||||
|
|
||||||
|
#define GKCUASSERTP(expr,msg) \ |
||||||
|
if (!(expr)) { \
|
||||||
|
printf("***ASSERTION failed on line %d of file %s: " #expr "\n", \
|
||||||
|
__LINE__, __FILE__); \
|
||||||
|
printf msg ; \
|
||||||
|
printf("\n"); \
|
||||||
|
} |
||||||
|
|
||||||
|
#define GKWARNP(expr,msg) \ |
||||||
|
if (!(expr)) { \
|
||||||
|
printf("***ASSERTION failed on line %d of file %s: " #expr "\n", \
|
||||||
|
__LINE__, __FILE__); \
|
||||||
|
printf msg ; \
|
||||||
|
printf("\n"); \
|
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* Program Assertions |
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
#ifndef NDEBUG |
||||||
|
# define ASSERT(expr) \ |
||||||
|
if (!(expr)) { \
|
||||||
|
printf("***ASSERTION failed on line %d of file %s: " #expr "\n", \
|
||||||
|
__LINE__, __FILE__); \
|
||||||
|
assert(expr); \
|
||||||
|
} |
||||||
|
|
||||||
|
# define ASSERTP(expr,msg) \ |
||||||
|
if (!(expr)) { \
|
||||||
|
printf("***ASSERTION failed on line %d of file %s: " #expr "\n", \
|
||||||
|
__LINE__, __FILE__); \
|
||||||
|
printf msg ; \
|
||||||
|
printf("\n"); \
|
||||||
|
assert(expr); \
|
||||||
|
} |
||||||
|
#else |
||||||
|
# define ASSERT(expr) ; |
||||||
|
# define ASSERTP(expr,msg) ; |
||||||
|
#endif |
||||||
|
|
||||||
|
#ifndef NDEBUG2 |
||||||
|
# define ASSERT2 ASSERT |
||||||
|
# define ASSERTP2 ASSERTP |
||||||
|
#else |
||||||
|
# define ASSERT2(expr) ; |
||||||
|
# define ASSERTP2(expr,msg) ; |
||||||
|
#endif |
||||||
|
|
||||||
|
|
||||||
|
#endif |
||||||
@ -0,0 +1,203 @@ |
|||||||
|
/*!
|
||||||
|
\file gk_mkblas.h |
||||||
|
\brief Templates for BLAS-like routines |
||||||
|
|
||||||
|
\date Started 3/28/07 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: gk_mkblas.h 16304 2014-02-25 14:27:19Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
#ifndef _GK_MKBLAS_H_ |
||||||
|
#define _GK_MKBLAS_H_ |
||||||
|
|
||||||
|
|
||||||
|
#define GK_MKBLAS(PRFX, TYPE, OUTTYPE) \ |
||||||
|
/*************************************************************************/\
|
||||||
|
/*! The macro for gk_?incset()-class of routines */\
|
||||||
|
/*************************************************************************/\
|
||||||
|
TYPE *PRFX ## incset(size_t n, TYPE baseval, TYPE *x)\
|
||||||
|
{\
|
||||||
|
size_t i;\
|
||||||
|
\
|
||||||
|
for (i=0; i<n; i++)\
|
||||||
|
x[i] = baseval+i;\
|
||||||
|
\
|
||||||
|
return x;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! The macro for gk_?max()-class of routines */\
|
||||||
|
/*************************************************************************/\
|
||||||
|
TYPE PRFX ## max(size_t n, TYPE *x, size_t incx)\
|
||||||
|
{\
|
||||||
|
size_t i;\
|
||||||
|
TYPE max;\
|
||||||
|
\
|
||||||
|
if (n <= 0) return (TYPE) 0;\
|
||||||
|
\
|
||||||
|
for (max=(*x), x+=incx, i=1; i<n; i++, x+=incx)\
|
||||||
|
max = ((*x) > max ? (*x) : max);\
|
||||||
|
\
|
||||||
|
return max;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! The macro for gk_?min()-class of routines */\
|
||||||
|
/*************************************************************************/\
|
||||||
|
TYPE PRFX ## min(size_t n, TYPE *x, size_t incx)\
|
||||||
|
{\
|
||||||
|
size_t i;\
|
||||||
|
TYPE min;\
|
||||||
|
\
|
||||||
|
if (n <= 0) return (TYPE) 0;\
|
||||||
|
\
|
||||||
|
for (min=(*x), x+=incx, i=1; i<n; i++, x+=incx)\
|
||||||
|
min = ((*x) < min ? (*x) : min);\
|
||||||
|
\
|
||||||
|
return min;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! The macro for gk_?argmax()-class of routines */\
|
||||||
|
/*************************************************************************/\
|
||||||
|
size_t PRFX ## argmax(size_t n, TYPE *x, size_t incx)\
|
||||||
|
{\
|
||||||
|
size_t i, j, max=0;\
|
||||||
|
\
|
||||||
|
for (i=1, j=incx; i<n; i++, j+=incx)\
|
||||||
|
max = (x[j] > x[max] ? j : max);\
|
||||||
|
\
|
||||||
|
return (size_t)(max/incx);\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! The macro for gk_?argmin()-class of routines */\
|
||||||
|
/*************************************************************************/\
|
||||||
|
size_t PRFX ## argmin(size_t n, TYPE *x, size_t incx)\
|
||||||
|
{\
|
||||||
|
size_t i, j, min=0;\
|
||||||
|
\
|
||||||
|
for (i=1, j=incx; i<n; i++, j+=incx)\
|
||||||
|
min = (x[j] < x[min] ? j : min);\
|
||||||
|
\
|
||||||
|
return (size_t)(min/incx);\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! The macro for gk_?argmax_n()-class of routines */\
|
||||||
|
/*************************************************************************/\
|
||||||
|
size_t PRFX ## argmax_n(size_t n, TYPE *x, size_t incx, size_t k)\
|
||||||
|
{\
|
||||||
|
size_t i, j, max_n;\
|
||||||
|
PRFX ## kv_t *cand;\
|
||||||
|
\
|
||||||
|
cand = PRFX ## kvmalloc(n, "GK_ARGMAX_N: cand");\
|
||||||
|
\
|
||||||
|
for (i=0, j=0; i<n; i++, j+=incx) {\
|
||||||
|
cand[i].val = i;\
|
||||||
|
cand[i].key = x[j];\
|
||||||
|
}\
|
||||||
|
PRFX ## kvsortd(n, cand);\
|
||||||
|
\
|
||||||
|
max_n = cand[k-1].val;\
|
||||||
|
\
|
||||||
|
gk_free((void *)&cand, LTERM);\
|
||||||
|
\
|
||||||
|
return max_n;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! The macro for gk_?sum()-class of routines */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
OUTTYPE PRFX ## sum(size_t n, TYPE *x, size_t incx)\
|
||||||
|
{\
|
||||||
|
size_t i;\
|
||||||
|
OUTTYPE sum = 0;\
|
||||||
|
\
|
||||||
|
for (i=0; i<n; i++, x+=incx)\
|
||||||
|
sum += (*x);\
|
||||||
|
\
|
||||||
|
return sum;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! The macro for gk_?scale()-class of routines */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
TYPE *PRFX ## scale(size_t n, TYPE alpha, TYPE *x, size_t incx)\
|
||||||
|
{\
|
||||||
|
size_t i;\
|
||||||
|
\
|
||||||
|
for (i=0; i<n; i++, x+=incx)\
|
||||||
|
(*x) *= alpha;\
|
||||||
|
\
|
||||||
|
return x;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! The macro for gk_?norm2()-class of routines */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
OUTTYPE PRFX ## norm2(size_t n, TYPE *x, size_t incx)\
|
||||||
|
{\
|
||||||
|
size_t i;\
|
||||||
|
OUTTYPE partial = 0;\
|
||||||
|
\
|
||||||
|
for (i=0; i<n; i++, x+=incx)\
|
||||||
|
partial += (*x) * (*x);\
|
||||||
|
\
|
||||||
|
return (partial > 0 ? (OUTTYPE)sqrt((double)partial) : (OUTTYPE)0);\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! The macro for gk_?dot()-class of routines */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
OUTTYPE PRFX ## dot(size_t n, TYPE *x, size_t incx, TYPE *y, size_t incy)\
|
||||||
|
{\
|
||||||
|
size_t i;\
|
||||||
|
OUTTYPE partial = 0.0;\
|
||||||
|
\
|
||||||
|
for (i=0; i<n; i++, x+=incx, y+=incy)\
|
||||||
|
partial += (*x) * (*y);\
|
||||||
|
\
|
||||||
|
return partial;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! The macro for gk_?axpy()-class of routines */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
TYPE *PRFX ## axpy(size_t n, TYPE alpha, TYPE *x, size_t incx, TYPE *y, size_t incy)\
|
||||||
|
{\
|
||||||
|
size_t i;\
|
||||||
|
TYPE *y_in = y;\
|
||||||
|
\
|
||||||
|
for (i=0; i<n; i++, x+=incx, y+=incy)\
|
||||||
|
*y += alpha*(*x);\
|
||||||
|
\
|
||||||
|
return y_in;\
|
||||||
|
}\
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
#define GK_MKBLAS_PROTO(PRFX, TYPE, OUTTYPE) \ |
||||||
|
TYPE *PRFX ## incset(size_t n, TYPE baseval, TYPE *x);\
|
||||||
|
TYPE PRFX ## max(size_t n, TYPE *x, size_t incx);\
|
||||||
|
TYPE PRFX ## min(size_t n, TYPE *x, size_t incx);\
|
||||||
|
size_t PRFX ## argmax(size_t n, TYPE *x, size_t incx);\
|
||||||
|
size_t PRFX ## argmin(size_t n, TYPE *x, size_t incx);\
|
||||||
|
size_t PRFX ## argmax_n(size_t n, TYPE *x, size_t incx, size_t k);\
|
||||||
|
OUTTYPE PRFX ## sum(size_t n, TYPE *x, size_t incx);\
|
||||||
|
TYPE *PRFX ## scale(size_t n, TYPE alpha, TYPE *x, size_t incx);\
|
||||||
|
OUTTYPE PRFX ## norm2(size_t n, TYPE *x, size_t incx);\
|
||||||
|
OUTTYPE PRFX ## dot(size_t n, TYPE *x, size_t incx, TYPE *y, size_t incy);\
|
||||||
|
TYPE *PRFX ## axpy(size_t n, TYPE alpha, TYPE *x, size_t incx, TYPE *y, size_t incy);\
|
||||||
|
|
||||||
|
|
||||||
|
#endif |
||||||
@ -0,0 +1,142 @@ |
|||||||
|
/*!
|
||||||
|
\file gk_mkmemory.h |
||||||
|
\brief Templates for memory allocation routines |
||||||
|
|
||||||
|
\date Started 3/29/07 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: gk_mkmemory.h 10711 2011-08-31 22:23:04Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
#ifndef _GK_MKMEMORY_H_ |
||||||
|
#define _GK_MKMEMORY_H_ |
||||||
|
|
||||||
|
|
||||||
|
#define GK_MKALLOC(PRFX, TYPE)\ |
||||||
|
/*************************************************************************/\
|
||||||
|
/*! The macro for gk_?malloc()-class of routines */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
TYPE *PRFX ## malloc(size_t n, char *msg)\
|
||||||
|
{\
|
||||||
|
return (TYPE *)gk_malloc(sizeof(TYPE)*n, msg);\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! The macro for gk_?realloc()-class of routines */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
TYPE *PRFX ## realloc(TYPE *ptr, size_t n, char *msg)\
|
||||||
|
{\
|
||||||
|
return (TYPE *)gk_realloc((void *)ptr, sizeof(TYPE)*n, msg);\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! The macro for gk_?smalloc()-class of routines */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
TYPE *PRFX ## smalloc(size_t n, TYPE ival, char *msg)\
|
||||||
|
{\
|
||||||
|
TYPE *ptr;\
|
||||||
|
\
|
||||||
|
ptr = (TYPE *)gk_malloc(sizeof(TYPE)*n, msg);\
|
||||||
|
if (ptr == NULL) \
|
||||||
|
return NULL; \
|
||||||
|
\
|
||||||
|
return PRFX ## set(n, ival, ptr); \
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! The macro for gk_?set()-class of routines */\
|
||||||
|
/*************************************************************************/\
|
||||||
|
TYPE *PRFX ## set(size_t n, TYPE val, TYPE *x)\
|
||||||
|
{\
|
||||||
|
size_t i;\
|
||||||
|
\
|
||||||
|
for (i=0; i<n; i++)\
|
||||||
|
x[i] = val;\
|
||||||
|
\
|
||||||
|
return x;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! The macro for gk_?set()-class of routines */\
|
||||||
|
/*************************************************************************/\
|
||||||
|
TYPE *PRFX ## copy(size_t n, TYPE *a, TYPE *b)\
|
||||||
|
{\
|
||||||
|
return (TYPE *)memmove((void *)b, (void *)a, sizeof(TYPE)*n);\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! The macro for gk_?AllocMatrix()-class of routines */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
TYPE **PRFX ## AllocMatrix(size_t ndim1, size_t ndim2, TYPE value, char *errmsg)\
|
||||||
|
{\
|
||||||
|
gk_idx_t i, j;\
|
||||||
|
TYPE **matrix;\
|
||||||
|
\
|
||||||
|
matrix = (TYPE **)gk_malloc(ndim1*sizeof(TYPE *), errmsg);\
|
||||||
|
if (matrix == NULL) \
|
||||||
|
return NULL;\
|
||||||
|
\
|
||||||
|
for (i=0; i<ndim1; i++) { \
|
||||||
|
matrix[i] = PRFX ## smalloc(ndim2, value, errmsg);\
|
||||||
|
if (matrix[i] == NULL) { \
|
||||||
|
for (j=0; j<i; j++) \
|
||||||
|
gk_free((void **)&matrix[j], LTERM); \
|
||||||
|
return NULL; \
|
||||||
|
} \
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
return matrix;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! The macro for gk_?AllocMatrix()-class of routines */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
void PRFX ## FreeMatrix(TYPE ***r_matrix, size_t ndim1, size_t ndim2)\
|
||||||
|
{\
|
||||||
|
gk_idx_t i;\
|
||||||
|
TYPE **matrix;\
|
||||||
|
\
|
||||||
|
if (*r_matrix == NULL) \
|
||||||
|
return; \
|
||||||
|
\
|
||||||
|
matrix = *r_matrix;\
|
||||||
|
\
|
||||||
|
for (i=0; i<ndim1; i++) \
|
||||||
|
gk_free((void **)&(matrix[i]), LTERM);\
|
||||||
|
\
|
||||||
|
gk_free((void **)r_matrix, LTERM);\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! The macro for gk_?SetMatrix()-class of routines */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
void PRFX ## SetMatrix(TYPE **matrix, size_t ndim1, size_t ndim2, TYPE value)\
|
||||||
|
{\
|
||||||
|
gk_idx_t i, j;\
|
||||||
|
\
|
||||||
|
for (i=0; i<ndim1; i++) {\
|
||||||
|
for (j=0; j<ndim2; j++)\
|
||||||
|
matrix[i][j] = value;\
|
||||||
|
}\
|
||||||
|
}\
|
||||||
|
|
||||||
|
|
||||||
|
#define GK_MKALLOC_PROTO(PRFX, TYPE)\ |
||||||
|
TYPE *PRFX ## malloc(size_t n, char *msg);\
|
||||||
|
TYPE *PRFX ## realloc(TYPE *ptr, size_t n, char *msg);\
|
||||||
|
TYPE *PRFX ## smalloc(size_t n, TYPE ival, char *msg);\
|
||||||
|
TYPE *PRFX ## set(size_t n, TYPE val, TYPE *x);\
|
||||||
|
TYPE *PRFX ## copy(size_t n, TYPE *a, TYPE *b);\
|
||||||
|
TYPE **PRFX ## AllocMatrix(size_t ndim1, size_t ndim2, TYPE value, char *errmsg);\
|
||||||
|
void PRFX ## FreeMatrix(TYPE ***r_matrix, size_t ndim1, size_t ndim2);\
|
||||||
|
void PRFX ## SetMatrix(TYPE **matrix, size_t ndim1, size_t ndim2, TYPE value);\
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
#endif |
||||||
@ -0,0 +1,440 @@ |
|||||||
|
/*!
|
||||||
|
\file gk_mkpqueue.h |
||||||
|
\brief Templates for priority queues |
||||||
|
|
||||||
|
\date Started 4/09/07 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: gk_mkpqueue.h 21742 2018-01-26 16:59:15Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
|
||||||
|
#ifndef _GK_MKPQUEUE_H |
||||||
|
#define _GK_MKPQUEUE_H |
||||||
|
|
||||||
|
|
||||||
|
#define GK_MKPQUEUE(FPRFX, PQT, KVT, KT, VT, KVMALLOC, KMAX, KEY_LT)\ |
||||||
|
/*************************************************************************/\
|
||||||
|
/*! This function creates and initializes a priority queue */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
PQT *FPRFX ## Create(size_t maxnodes)\
|
||||||
|
{\
|
||||||
|
PQT *queue; \
|
||||||
|
\
|
||||||
|
queue = (PQT *)gk_malloc(sizeof(PQT), "gk_pqCreate: queue");\
|
||||||
|
FPRFX ## Init(queue, maxnodes);\
|
||||||
|
\
|
||||||
|
return queue;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! This function initializes the data structures of the priority queue */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
void FPRFX ## Init(PQT *queue, size_t maxnodes)\
|
||||||
|
{\
|
||||||
|
queue->nnodes = 0;\
|
||||||
|
queue->maxnodes = maxnodes;\
|
||||||
|
\
|
||||||
|
queue->heap = KVMALLOC(maxnodes, "gk_PQInit: heap");\
|
||||||
|
queue->locator = gk_idxsmalloc(maxnodes, -1, "gk_PQInit: locator");\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! This function resets the priority queue */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
void FPRFX ## Reset(PQT *queue)\
|
||||||
|
{\
|
||||||
|
ssize_t i;\
|
||||||
|
ssize_t *locator=queue->locator;\
|
||||||
|
KVT *heap=queue->heap;\
|
||||||
|
\
|
||||||
|
for (i=queue->nnodes-1; i>=0; i--)\
|
||||||
|
locator[heap[i].val] = -1;\
|
||||||
|
queue->nnodes = 0;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! This function frees the internal datastructures of the priority queue */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
void FPRFX ## Free(PQT *queue)\
|
||||||
|
{\
|
||||||
|
if (queue == NULL) return;\
|
||||||
|
gk_free((void **)&queue->heap, &queue->locator, LTERM);\
|
||||||
|
queue->maxnodes = 0;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! This function frees the internal datastructures of the priority queue \
|
||||||
|
and the queue itself */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
void FPRFX ## Destroy(PQT *queue)\
|
||||||
|
{\
|
||||||
|
if (queue == NULL) return;\
|
||||||
|
FPRFX ## Free(queue);\
|
||||||
|
gk_free((void **)&queue, LTERM);\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! This function returns the length of the queue */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
size_t FPRFX ## Length(PQT *queue)\
|
||||||
|
{\
|
||||||
|
return queue->nnodes;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! This function adds an item in the priority queue */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
int FPRFX ## Insert(PQT *queue, VT node, KT key)\
|
||||||
|
{\
|
||||||
|
ssize_t i, j;\
|
||||||
|
ssize_t *locator=queue->locator;\
|
||||||
|
KVT *heap=queue->heap;\
|
||||||
|
\
|
||||||
|
ASSERT2(FPRFX ## CheckHeap(queue));\
|
||||||
|
\
|
||||||
|
ASSERT(locator[node] == -1);\
|
||||||
|
\
|
||||||
|
i = queue->nnodes++;\
|
||||||
|
while (i > 0) {\
|
||||||
|
j = (i-1)>>1;\
|
||||||
|
if (KEY_LT(key, heap[j].key)) {\
|
||||||
|
heap[i] = heap[j];\
|
||||||
|
locator[heap[i].val] = i;\
|
||||||
|
i = j;\
|
||||||
|
}\
|
||||||
|
else\
|
||||||
|
break;\
|
||||||
|
}\
|
||||||
|
ASSERT(i >= 0);\
|
||||||
|
heap[i].key = key;\
|
||||||
|
heap[i].val = node;\
|
||||||
|
locator[node] = i;\
|
||||||
|
\
|
||||||
|
ASSERT2(FPRFX ## CheckHeap(queue));\
|
||||||
|
\
|
||||||
|
return 0;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! This function deletes an item from the priority queue */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
int FPRFX ## Delete(PQT *queue, VT node)\
|
||||||
|
{\
|
||||||
|
ssize_t i, j;\
|
||||||
|
size_t nnodes;\
|
||||||
|
KT newkey, oldkey;\
|
||||||
|
ssize_t *locator=queue->locator;\
|
||||||
|
KVT *heap=queue->heap;\
|
||||||
|
\
|
||||||
|
ASSERT(locator[node] != -1);\
|
||||||
|
ASSERT(heap[locator[node]].val == node);\
|
||||||
|
\
|
||||||
|
ASSERT2(FPRFX ## CheckHeap(queue));\
|
||||||
|
\
|
||||||
|
i = locator[node];\
|
||||||
|
locator[node] = -1;\
|
||||||
|
\
|
||||||
|
if (--queue->nnodes > 0 && heap[queue->nnodes].val != node) {\
|
||||||
|
node = heap[queue->nnodes].val;\
|
||||||
|
newkey = heap[queue->nnodes].key;\
|
||||||
|
oldkey = heap[i].key;\
|
||||||
|
\
|
||||||
|
if (KEY_LT(newkey, oldkey)) { /* Filter-up */\
|
||||||
|
while (i > 0) {\
|
||||||
|
j = (i-1)>>1;\
|
||||||
|
if (KEY_LT(newkey, heap[j].key)) {\
|
||||||
|
heap[i] = heap[j];\
|
||||||
|
locator[heap[i].val] = i;\
|
||||||
|
i = j;\
|
||||||
|
}\
|
||||||
|
else\
|
||||||
|
break;\
|
||||||
|
}\
|
||||||
|
}\
|
||||||
|
else { /* Filter down */\
|
||||||
|
nnodes = queue->nnodes;\
|
||||||
|
while ((j=(i<<1)+1) < nnodes) {\
|
||||||
|
if (KEY_LT(heap[j].key, newkey)) {\
|
||||||
|
if (j+1 < nnodes && KEY_LT(heap[j+1].key, heap[j].key))\
|
||||||
|
j++;\
|
||||||
|
heap[i] = heap[j];\
|
||||||
|
locator[heap[i].val] = i;\
|
||||||
|
i = j;\
|
||||||
|
}\
|
||||||
|
else if (j+1 < nnodes && KEY_LT(heap[j+1].key, newkey)) {\
|
||||||
|
j++;\
|
||||||
|
heap[i] = heap[j];\
|
||||||
|
locator[heap[i].val] = i;\
|
||||||
|
i = j;\
|
||||||
|
}\
|
||||||
|
else\
|
||||||
|
break;\
|
||||||
|
}\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
heap[i].key = newkey;\
|
||||||
|
heap[i].val = node;\
|
||||||
|
locator[node] = i;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
ASSERT2(FPRFX ## CheckHeap(queue));\
|
||||||
|
\
|
||||||
|
return 0;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! This function updates the key values associated for a particular item */ \
|
||||||
|
/**************************************************************************/\
|
||||||
|
void FPRFX ## Update(PQT *queue, VT node, KT newkey)\
|
||||||
|
{\
|
||||||
|
ssize_t i, j;\
|
||||||
|
size_t nnodes;\
|
||||||
|
KT oldkey;\
|
||||||
|
ssize_t *locator=queue->locator;\
|
||||||
|
KVT *heap=queue->heap;\
|
||||||
|
\
|
||||||
|
oldkey = heap[locator[node]].key;\
|
||||||
|
if (!KEY_LT(newkey, oldkey) && !KEY_LT(oldkey, newkey)) return;\
|
||||||
|
\
|
||||||
|
ASSERT(locator[node] != -1);\
|
||||||
|
ASSERT(heap[locator[node]].val == node);\
|
||||||
|
ASSERT2(FPRFX ## CheckHeap(queue));\
|
||||||
|
\
|
||||||
|
i = locator[node];\
|
||||||
|
\
|
||||||
|
if (KEY_LT(newkey, oldkey)) { /* Filter-up */\
|
||||||
|
while (i > 0) {\
|
||||||
|
j = (i-1)>>1;\
|
||||||
|
if (KEY_LT(newkey, heap[j].key)) {\
|
||||||
|
heap[i] = heap[j];\
|
||||||
|
locator[heap[i].val] = i;\
|
||||||
|
i = j;\
|
||||||
|
}\
|
||||||
|
else\
|
||||||
|
break;\
|
||||||
|
}\
|
||||||
|
}\
|
||||||
|
else { /* Filter down */\
|
||||||
|
nnodes = queue->nnodes;\
|
||||||
|
while ((j=(i<<1)+1) < nnodes) {\
|
||||||
|
if (KEY_LT(heap[j].key, newkey)) {\
|
||||||
|
if (j+1 < nnodes && KEY_LT(heap[j+1].key, heap[j].key))\
|
||||||
|
j++;\
|
||||||
|
heap[i] = heap[j];\
|
||||||
|
locator[heap[i].val] = i;\
|
||||||
|
i = j;\
|
||||||
|
}\
|
||||||
|
else if (j+1 < nnodes && KEY_LT(heap[j+1].key, newkey)) {\
|
||||||
|
j++;\
|
||||||
|
heap[i] = heap[j];\
|
||||||
|
locator[heap[i].val] = i;\
|
||||||
|
i = j;\
|
||||||
|
}\
|
||||||
|
else\
|
||||||
|
break;\
|
||||||
|
}\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
heap[i].key = newkey;\
|
||||||
|
heap[i].val = node;\
|
||||||
|
locator[node] = i;\
|
||||||
|
\
|
||||||
|
ASSERT2(FPRFX ## CheckHeap(queue));\
|
||||||
|
\
|
||||||
|
return;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! This function returns the item at the top of the queue and removes\
|
||||||
|
it from the priority queue */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
VT FPRFX ## GetTop(PQT *queue)\
|
||||||
|
{\
|
||||||
|
ssize_t i, j;\
|
||||||
|
ssize_t *locator;\
|
||||||
|
KVT *heap;\
|
||||||
|
VT vtx, node;\
|
||||||
|
KT key;\
|
||||||
|
\
|
||||||
|
ASSERT2(FPRFX ## CheckHeap(queue));\
|
||||||
|
\
|
||||||
|
if (queue->nnodes == 0)\
|
||||||
|
return -1;\
|
||||||
|
\
|
||||||
|
queue->nnodes--;\
|
||||||
|
\
|
||||||
|
heap = queue->heap;\
|
||||||
|
locator = queue->locator;\
|
||||||
|
\
|
||||||
|
vtx = heap[0].val;\
|
||||||
|
locator[vtx] = -1;\
|
||||||
|
\
|
||||||
|
if ((i = queue->nnodes) > 0) {\
|
||||||
|
key = heap[i].key;\
|
||||||
|
node = heap[i].val;\
|
||||||
|
i = 0;\
|
||||||
|
while ((j=2*i+1) < queue->nnodes) {\
|
||||||
|
if (KEY_LT(heap[j].key, key)) {\
|
||||||
|
if (j+1 < queue->nnodes && KEY_LT(heap[j+1].key, heap[j].key))\
|
||||||
|
j = j+1;\
|
||||||
|
heap[i] = heap[j];\
|
||||||
|
locator[heap[i].val] = i;\
|
||||||
|
i = j;\
|
||||||
|
}\
|
||||||
|
else if (j+1 < queue->nnodes && KEY_LT(heap[j+1].key, key)) {\
|
||||||
|
j = j+1;\
|
||||||
|
heap[i] = heap[j];\
|
||||||
|
locator[heap[i].val] = i;\
|
||||||
|
i = j;\
|
||||||
|
}\
|
||||||
|
else\
|
||||||
|
break;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
heap[i].key = key;\
|
||||||
|
heap[i].val = node;\
|
||||||
|
locator[node] = i;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
ASSERT2(FPRFX ## CheckHeap(queue));\
|
||||||
|
return vtx;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! This function returns the item at the top of the queue. The item is not\
|
||||||
|
deleted from the queue. */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
VT FPRFX ## SeeTopVal(PQT *queue)\
|
||||||
|
{\
|
||||||
|
return (queue->nnodes == 0 ? -1 : queue->heap[0].val);\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! This function returns the key of the top item. The item is not\
|
||||||
|
deleted from the queue. */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
KT FPRFX ## SeeTopKey(PQT *queue)\
|
||||||
|
{\
|
||||||
|
return (queue->nnodes == 0 ? KMAX : queue->heap[0].key);\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! This function returns the key of a specific item */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
KT FPRFX ## SeeKey(PQT *queue, VT node)\
|
||||||
|
{\
|
||||||
|
ssize_t *locator;\
|
||||||
|
KVT *heap;\
|
||||||
|
\
|
||||||
|
heap = queue->heap;\
|
||||||
|
locator = queue->locator;\
|
||||||
|
\
|
||||||
|
return heap[locator[node]].key;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! This function returns the first item in a breadth-first traversal of\
|
||||||
|
the heap whose key is less than maxwgt. This function is here due to\
|
||||||
|
hMETIS and is not general!*/\
|
||||||
|
/**************************************************************************/\
|
||||||
|
/*\
|
||||||
|
VT FPRFX ## SeeConstraintTop(PQT *queue, KT maxwgt, KT *wgts)\
|
||||||
|
{\
|
||||||
|
ssize_t i;\
|
||||||
|
\
|
||||||
|
if (queue->nnodes == 0)\
|
||||||
|
return -1;\
|
||||||
|
\
|
||||||
|
if (maxwgt <= 1000)\
|
||||||
|
return FPRFX ## SeeTopVal(queue);\
|
||||||
|
\
|
||||||
|
for (i=0; i<queue->nnodes; i++) {\
|
||||||
|
if (queue->heap[i].key > 0) {\
|
||||||
|
if (wgts[queue->heap[i].val] <= maxwgt)\
|
||||||
|
return queue->heap[i].val;\
|
||||||
|
}\
|
||||||
|
else {\
|
||||||
|
if (queue->heap[i/2].key <= 0)\
|
||||||
|
break;\
|
||||||
|
}\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
return queue->heap[0].val;\
|
||||||
|
\
|
||||||
|
}\
|
||||||
|
*/\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! This functions checks the consistency of the heap */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
int FPRFX ## CheckHeap(PQT *queue)\
|
||||||
|
{\
|
||||||
|
ssize_t i, j;\
|
||||||
|
size_t nnodes;\
|
||||||
|
ssize_t *locator;\
|
||||||
|
KVT *heap;\
|
||||||
|
\
|
||||||
|
heap = queue->heap;\
|
||||||
|
locator = queue->locator;\
|
||||||
|
nnodes = queue->nnodes;\
|
||||||
|
\
|
||||||
|
if (nnodes == 0)\
|
||||||
|
return 1;\
|
||||||
|
\
|
||||||
|
ASSERT(locator[heap[0].val] == 0);\
|
||||||
|
for (i=1; i<nnodes; i++) {\
|
||||||
|
ASSERT(locator[heap[i].val] == i);\
|
||||||
|
ASSERT(!KEY_LT(heap[i].key, heap[(i-1)/2].key));\
|
||||||
|
}\
|
||||||
|
for (i=1; i<nnodes; i++)\
|
||||||
|
ASSERT(!KEY_LT(heap[i].key, heap[0].key));\
|
||||||
|
\
|
||||||
|
for (j=i=0; i<queue->maxnodes; i++) {\
|
||||||
|
if (locator[i] != -1)\
|
||||||
|
j++;\
|
||||||
|
}\
|
||||||
|
ASSERTP(j == nnodes, ("%jd %jd\n", (intmax_t)j, (intmax_t)nnodes));\
|
||||||
|
\
|
||||||
|
return 1;\
|
||||||
|
}\
|
||||||
|
|
||||||
|
|
||||||
|
#define GK_MKPQUEUE_PROTO(FPRFX, PQT, KT, VT)\ |
||||||
|
PQT * FPRFX ## Create(size_t maxnodes);\
|
||||||
|
void FPRFX ## Init(PQT *queue, size_t maxnodes);\
|
||||||
|
void FPRFX ## Reset(PQT *queue);\
|
||||||
|
void FPRFX ## Free(PQT *queue);\
|
||||||
|
void FPRFX ## Destroy(PQT *queue);\
|
||||||
|
size_t FPRFX ## Length(PQT *queue);\
|
||||||
|
int FPRFX ## Insert(PQT *queue, VT node, KT key);\
|
||||||
|
int FPRFX ## Delete(PQT *queue, VT node);\
|
||||||
|
void FPRFX ## Update(PQT *queue, VT node, KT newkey);\
|
||||||
|
VT FPRFX ## GetTop(PQT *queue);\
|
||||||
|
VT FPRFX ## SeeTopVal(PQT *queue);\
|
||||||
|
KT FPRFX ## SeeTopKey(PQT *queue);\
|
||||||
|
KT FPRFX ## SeeKey(PQT *queue, VT node);\
|
||||||
|
VT FPRFX ## SeeConstraintTop(PQT *queue, KT maxwgt, KT *wgts);\
|
||||||
|
int FPRFX ## CheckHeap(PQT *queue);\
|
||||||
|
|
||||||
|
|
||||||
|
/* This is how these macros are used
|
||||||
|
GK_MKPQUEUE(gk_dkvPQ, gk_dkvPQ_t, double, gk_idx_t, gk_dkvmalloc, DBL_MAX) |
||||||
|
GK_MKPQUEUE_PROTO(gk_dkvPQ, gk_dkvPQ_t, double, gk_idx_t) |
||||||
|
*/ |
||||||
|
|
||||||
|
|
||||||
|
#endif |
||||||
@ -0,0 +1,215 @@ |
|||||||
|
/*!
|
||||||
|
\file gk_mkpqueue2.h |
||||||
|
\brief Templates for priority queues that do not utilize locators and as such |
||||||
|
they can use different types of values. |
||||||
|
|
||||||
|
\date Started 4/09/07 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: gk_mkpqueue2.h 13005 2012-10-23 22:34:36Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
|
||||||
|
#ifndef _GK_MKPQUEUE2_H |
||||||
|
#define _GK_MKPQUEUE2_H |
||||||
|
|
||||||
|
|
||||||
|
#define GK_MKPQUEUE2(FPRFX, PQT, KT, VT, KMALLOC, VMALLOC, KMAX, KEY_LT)\ |
||||||
|
/*************************************************************************/\
|
||||||
|
/*! This function creates and initializes a priority queue */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
PQT *FPRFX ## Create2(ssize_t maxnodes)\
|
||||||
|
{\
|
||||||
|
PQT *queue; \
|
||||||
|
\
|
||||||
|
if ((queue = (PQT *)gk_malloc(sizeof(PQT), "gk_pqCreate2: queue")) != NULL) {\
|
||||||
|
memset(queue, 0, sizeof(PQT));\
|
||||||
|
queue->nnodes = 0;\
|
||||||
|
queue->maxnodes = maxnodes;\
|
||||||
|
queue->keys = KMALLOC(maxnodes, "gk_pqCreate2: keys");\
|
||||||
|
queue->vals = VMALLOC(maxnodes, "gk_pqCreate2: vals");\
|
||||||
|
\
|
||||||
|
if (queue->keys == NULL || queue->vals == NULL)\
|
||||||
|
gk_free((void **)&queue->keys, &queue->vals, &queue, LTERM);\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
return queue;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! This function resets the priority queue */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
void FPRFX ## Reset2(PQT *queue)\
|
||||||
|
{\
|
||||||
|
queue->nnodes = 0;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! This function frees the internal datastructures of the priority queue */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
void FPRFX ## Destroy2(PQT **r_queue)\
|
||||||
|
{\
|
||||||
|
PQT *queue = *r_queue; \
|
||||||
|
if (queue == NULL) return;\
|
||||||
|
gk_free((void **)&queue->keys, &queue->vals, &queue, LTERM);\
|
||||||
|
*r_queue = NULL;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! This function returns the length of the queue */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
size_t FPRFX ## Length2(PQT *queue)\
|
||||||
|
{\
|
||||||
|
return queue->nnodes;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! This function adds an item in the priority queue. */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
int FPRFX ## Insert2(PQT *queue, VT val, KT key)\
|
||||||
|
{\
|
||||||
|
ssize_t i, j;\
|
||||||
|
KT *keys=queue->keys;\
|
||||||
|
VT *vals=queue->vals;\
|
||||||
|
\
|
||||||
|
ASSERT2(FPRFX ## CheckHeap2(queue));\
|
||||||
|
\
|
||||||
|
if (queue->nnodes == queue->maxnodes) \
|
||||||
|
return 0;\
|
||||||
|
\
|
||||||
|
ASSERT2(FPRFX ## CheckHeap2(queue));\
|
||||||
|
\
|
||||||
|
i = queue->nnodes++;\
|
||||||
|
while (i > 0) {\
|
||||||
|
j = (i-1)>>1;\
|
||||||
|
if (KEY_LT(key, keys[j])) {\
|
||||||
|
keys[i] = keys[j];\
|
||||||
|
vals[i] = vals[j];\
|
||||||
|
i = j;\
|
||||||
|
}\
|
||||||
|
else\
|
||||||
|
break;\
|
||||||
|
}\
|
||||||
|
ASSERT(i >= 0);\
|
||||||
|
keys[i] = key;\
|
||||||
|
vals[i] = val;\
|
||||||
|
\
|
||||||
|
ASSERT2(FPRFX ## CheckHeap2(queue));\
|
||||||
|
\
|
||||||
|
return 1;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! This function returns the item at the top of the queue and removes\
|
||||||
|
it from the priority queue */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
int FPRFX ## GetTop2(PQT *queue, VT *r_val)\
|
||||||
|
{\
|
||||||
|
ssize_t i, j;\
|
||||||
|
KT key, *keys=queue->keys;\
|
||||||
|
VT val, *vals=queue->vals;\
|
||||||
|
\
|
||||||
|
ASSERT2(FPRFX ## CheckHeap2(queue));\
|
||||||
|
\
|
||||||
|
if (queue->nnodes == 0)\
|
||||||
|
return 0;\
|
||||||
|
\
|
||||||
|
queue->nnodes--;\
|
||||||
|
\
|
||||||
|
*r_val = vals[0];\
|
||||||
|
\
|
||||||
|
if ((i = queue->nnodes) > 0) {\
|
||||||
|
key = keys[i];\
|
||||||
|
val = vals[i];\
|
||||||
|
i = 0;\
|
||||||
|
while ((j=2*i+1) < queue->nnodes) {\
|
||||||
|
if (KEY_LT(keys[j], key)) {\
|
||||||
|
if (j+1 < queue->nnodes && KEY_LT(keys[j+1], keys[j]))\
|
||||||
|
j = j+1;\
|
||||||
|
keys[i] = keys[j];\
|
||||||
|
vals[i] = vals[j];\
|
||||||
|
i = j;\
|
||||||
|
}\
|
||||||
|
else if (j+1 < queue->nnodes && KEY_LT(keys[j+1], key)) {\
|
||||||
|
j = j+1;\
|
||||||
|
keys[i] = keys[j];\
|
||||||
|
vals[i] = vals[j];\
|
||||||
|
i = j;\
|
||||||
|
}\
|
||||||
|
else\
|
||||||
|
break;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
keys[i] = key;\
|
||||||
|
vals[i] = val;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
ASSERT2(FPRFX ## CheckHeap2(queue));\
|
||||||
|
\
|
||||||
|
return 1;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! This function returns the item at the top of the queue. The item is not\
|
||||||
|
deleted from the queue. */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
int FPRFX ## SeeTopVal2(PQT *queue, VT *r_val)\
|
||||||
|
{\
|
||||||
|
if (queue->nnodes == 0) \
|
||||||
|
return 0;\
|
||||||
|
\
|
||||||
|
*r_val = queue->vals[0];\
|
||||||
|
\
|
||||||
|
return 1;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! This function returns the key of the top item. The item is not\
|
||||||
|
deleted from the queue. */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
KT FPRFX ## SeeTopKey2(PQT *queue)\
|
||||||
|
{\
|
||||||
|
return (queue->nnodes == 0 ? KMAX : queue->keys[0]);\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! This functions checks the consistency of the heap */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
int FPRFX ## CheckHeap2(PQT *queue)\
|
||||||
|
{\
|
||||||
|
ssize_t i;\
|
||||||
|
KT *keys=queue->keys;\
|
||||||
|
\
|
||||||
|
if (queue->nnodes == 0)\
|
||||||
|
return 1;\
|
||||||
|
\
|
||||||
|
for (i=1; i<queue->nnodes; i++) {\
|
||||||
|
ASSERT(!KEY_LT(keys[i], keys[(i-1)/2]));\
|
||||||
|
}\
|
||||||
|
for (i=1; i<queue->nnodes; i++)\
|
||||||
|
ASSERT(!KEY_LT(keys[i], keys[0]));\
|
||||||
|
\
|
||||||
|
return 1;\
|
||||||
|
}\
|
||||||
|
|
||||||
|
|
||||||
|
#define GK_MKPQUEUE2_PROTO(FPRFX, PQT, KT, VT)\ |
||||||
|
PQT * FPRFX ## Create2(ssize_t maxnodes);\
|
||||||
|
void FPRFX ## Reset2(PQT *queue);\
|
||||||
|
void FPRFX ## Destroy2(PQT **r_queue);\
|
||||||
|
size_t FPRFX ## Length2(PQT *queue);\
|
||||||
|
int FPRFX ## Insert2(PQT *queue, VT node, KT key);\
|
||||||
|
int FPRFX ## GetTop2(PQT *queue, VT *r_val);\
|
||||||
|
int FPRFX ## SeeTopVal2(PQT *queue, VT *r_val);\
|
||||||
|
KT FPRFX ## SeeTopKey2(PQT *queue);\
|
||||||
|
int FPRFX ## CheckHeap2(PQT *queue);\
|
||||||
|
|
||||||
|
|
||||||
|
#endif |
||||||
@ -0,0 +1,123 @@ |
|||||||
|
/*!
|
||||||
|
\file
|
||||||
|
\brief Templates for portable random number generation |
||||||
|
|
||||||
|
\date Started 5/17/07 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: gk_mkrandom.h 10711 2011-08-31 22:23:04Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
|
||||||
|
#ifndef _GK_MKRANDOM_H |
||||||
|
#define _GK_MKRANDOM_H |
||||||
|
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! The generator for the rand() related routines. \
|
||||||
|
\params RNGT the datatype that defines the range of values over which\
|
||||||
|
random numbers will be generated\
|
||||||
|
\params VALT the datatype that defines the contents of the array to \
|
||||||
|
be permuted by randArrayPermute() \
|
||||||
|
\params FPRFX the function prefix \
|
||||||
|
*/\
|
||||||
|
/**************************************************************************/\
|
||||||
|
#define GK_MKRANDOM(FPRFX, RNGT, VALT)\ |
||||||
|
/*************************************************************************/\
|
||||||
|
/*! Initializes the generator */ \
|
||||||
|
/**************************************************************************/\
|
||||||
|
void FPRFX ## srand(RNGT seed) \
|
||||||
|
{\
|
||||||
|
gk_randinit((uint64_t) seed);\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! Returns a random number */ \
|
||||||
|
/**************************************************************************/\
|
||||||
|
RNGT FPRFX ## rand() \
|
||||||
|
{\
|
||||||
|
if (sizeof(RNGT) <= sizeof(int32_t)) \
|
||||||
|
return (RNGT)gk_randint32(); \
|
||||||
|
else \
|
||||||
|
return (RNGT)gk_randint64(); \
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! Returns a random number between [0, max) */ \
|
||||||
|
/**************************************************************************/\
|
||||||
|
RNGT FPRFX ## randInRange(RNGT max) \
|
||||||
|
{\
|
||||||
|
return (RNGT)((FPRFX ## rand())%max); \
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! Randomly permutes the elements of an array p[]. \
|
||||||
|
flag == 1, p[i] = i prior to permutation, \
|
||||||
|
flag == 0, p[] is not initialized. */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
void FPRFX ## randArrayPermute(RNGT n, VALT *p, RNGT nshuffles, int flag)\
|
||||||
|
{\
|
||||||
|
RNGT i, u, v;\
|
||||||
|
VALT tmp;\
|
||||||
|
\
|
||||||
|
if (flag == 1) {\
|
||||||
|
for (i=0; i<n; i++)\
|
||||||
|
p[i] = (VALT)i;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
if (n < 10) {\
|
||||||
|
for (i=0; i<n; i++) {\
|
||||||
|
v = FPRFX ## randInRange(n);\
|
||||||
|
u = FPRFX ## randInRange(n);\
|
||||||
|
gk_SWAP(p[v], p[u], tmp);\
|
||||||
|
}\
|
||||||
|
}\
|
||||||
|
else {\
|
||||||
|
for (i=0; i<nshuffles; i++) {\
|
||||||
|
v = FPRFX ## randInRange(n-3);\
|
||||||
|
u = FPRFX ## randInRange(n-3);\
|
||||||
|
/*gk_SWAP(p[v+0], p[u+0], tmp);*/\
|
||||||
|
/*gk_SWAP(p[v+1], p[u+1], tmp);*/\
|
||||||
|
/*gk_SWAP(p[v+2], p[u+2], tmp);*/\
|
||||||
|
/*gk_SWAP(p[v+3], p[u+3], tmp);*/\
|
||||||
|
gk_SWAP(p[v+0], p[u+2], tmp);\
|
||||||
|
gk_SWAP(p[v+1], p[u+3], tmp);\
|
||||||
|
gk_SWAP(p[v+2], p[u+0], tmp);\
|
||||||
|
gk_SWAP(p[v+3], p[u+1], tmp);\
|
||||||
|
}\
|
||||||
|
}\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
\
|
||||||
|
/*************************************************************************/\
|
||||||
|
/*! Randomly permutes the elements of an array p[]. \
|
||||||
|
flag == 1, p[i] = i prior to permutation, \
|
||||||
|
flag == 0, p[] is not initialized. */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
void FPRFX ## randArrayPermuteFine(RNGT n, VALT *p, int flag)\
|
||||||
|
{\
|
||||||
|
RNGT i, v;\
|
||||||
|
VALT tmp;\
|
||||||
|
\
|
||||||
|
if (flag == 1) {\
|
||||||
|
for (i=0; i<n; i++)\
|
||||||
|
p[i] = (VALT)i;\
|
||||||
|
}\
|
||||||
|
\
|
||||||
|
for (i=0; i<n; i++) {\
|
||||||
|
v = FPRFX ## randInRange(n);\
|
||||||
|
gk_SWAP(p[i], p[v], tmp);\
|
||||||
|
}\
|
||||||
|
}\
|
||||||
|
|
||||||
|
|
||||||
|
#define GK_MKRANDOM_PROTO(FPRFX, RNGT, VALT)\ |
||||||
|
void FPRFX ## srand(RNGT seed); \
|
||||||
|
RNGT FPRFX ## rand(); \
|
||||||
|
RNGT FPRFX ## randInRange(RNGT max); \
|
||||||
|
void FPRFX ## randArrayPermute(RNGT n, VALT *p, RNGT nshuffles, int flag);\
|
||||||
|
void FPRFX ## randArrayPermuteFine(RNGT n, VALT *p, int flag);\
|
||||||
|
|
||||||
|
|
||||||
|
#endif |
||||||
@ -0,0 +1,271 @@ |
|||||||
|
/*!
|
||||||
|
\file gk_mksort.h |
||||||
|
\brief Templates for the qsort routine |
||||||
|
|
||||||
|
\date Started 3/28/07 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: gk_mksort.h 21051 2017-05-25 04:36:14Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
|
||||||
|
#ifndef _GK_MKSORT_H_ |
||||||
|
#define _GK_MKSORT_H_ |
||||||
|
|
||||||
|
/* Adopted from GNU glibc by Mjt.
|
||||||
|
* See stdlib/qsort.c in glibc */ |
||||||
|
|
||||||
|
/* Copyright (C) 1991, 1992, 1996, 1997, 1999 Free Software Foundation, Inc.
|
||||||
|
This file is part of the GNU C Library. |
||||||
|
Written by Douglas C. Schmidt (schmidt@ics.uci.edu). |
||||||
|
|
||||||
|
The GNU C Library is free software; you can redistribute it and/or |
||||||
|
modify it under the terms of the GNU Lesser General Public |
||||||
|
License as published by the Free Software Foundation; either |
||||||
|
version 2.1 of the License, or (at your option) any later version. |
||||||
|
|
||||||
|
The GNU C Library is distributed in the hope that it will be useful, |
||||||
|
but WITHOUT ANY WARRANTY; without even the implied warranty of |
||||||
|
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
||||||
|
Lesser General Public License for more details. |
||||||
|
|
||||||
|
You should have received a copy of the GNU Lesser General Public |
||||||
|
License along with the GNU C Library; if not, write to the Free |
||||||
|
Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA |
||||||
|
02111-1307 USA. */ |
||||||
|
|
||||||
|
/* in-line qsort implementation. Differs from traditional qsort() routine
|
||||||
|
* in that it is a macro, not a function, and instead of passing an address |
||||||
|
* of a comparision routine to the function, it is possible to inline |
||||||
|
* comparision routine, thus speed up sorting alot. |
||||||
|
* |
||||||
|
* Usage: |
||||||
|
* #include "iqsort.h" |
||||||
|
* #define islt(a,b) (strcmp((*a),(*b))<0) |
||||||
|
* char *arr[]; |
||||||
|
* int n; |
||||||
|
* GKQSORT(char*, arr, n, islt); |
||||||
|
* |
||||||
|
* The "prototype" and 4 arguments are: |
||||||
|
* GKQSORT(TYPE,BASE,NELT,ISLT) |
||||||
|
* 1) type of each element, TYPE, |
||||||
|
* 2) address of the beginning of the array, of type TYPE*, |
||||||
|
* 3) number of elements in the array, and |
||||||
|
* 4) comparision routine. |
||||||
|
* Array pointer and number of elements are referenced only once. |
||||||
|
* This is similar to a call |
||||||
|
* qsort(BASE,NELT,sizeof(TYPE),ISLT) |
||||||
|
* with the difference in last parameter. |
||||||
|
* Note the islt macro/routine (it receives pointers to two elements): |
||||||
|
* the only condition of interest is whenever one element is less than |
||||||
|
* another, no other conditions (greather than, equal to etc) are tested. |
||||||
|
* So, for example, to define integer sort, use: |
||||||
|
* #define islt(a,b) ((*a)<(*b)) |
||||||
|
* GKQSORT(int, arr, n, islt) |
||||||
|
* |
||||||
|
* The macro could be used to implement a sorting function (see examples |
||||||
|
* below), or to implement the sorting algorithm inline. That is, either |
||||||
|
* create a sorting function and use it whenever you want to sort something, |
||||||
|
* or use GKQSORT() macro directly instead a call to such routine. Note that |
||||||
|
* the macro expands to quite some code (compiled size of int qsort on x86 |
||||||
|
* is about 700..800 bytes). |
||||||
|
* |
||||||
|
* Using this macro directly it isn't possible to implement traditional |
||||||
|
* qsort() routine, because the macro assumes sizeof(element) == sizeof(TYPE), |
||||||
|
* while qsort() allows element size to be different. |
||||||
|
* |
||||||
|
* Several ready-to-use examples: |
||||||
|
* |
||||||
|
* Sorting array of integers: |
||||||
|
* void int_qsort(int *arr, unsigned n) { |
||||||
|
* #define int_lt(a,b) ((*a)<(*b)) |
||||||
|
* GKQSORT(int, arr, n, int_lt); |
||||||
|
* } |
||||||
|
* |
||||||
|
* Sorting array of string pointers: |
||||||
|
* void str_qsort(char *arr[], unsigned n) { |
||||||
|
* #define str_lt(a,b) (strcmp((*a),(*b)) < 0) |
||||||
|
* GKQSORT(char*, arr, n, str_lt); |
||||||
|
* } |
||||||
|
* |
||||||
|
* Sorting array of structures: |
||||||
|
* |
||||||
|
* struct elt { |
||||||
|
* int key; |
||||||
|
* ... |
||||||
|
* }; |
||||||
|
* void elt_qsort(struct elt *arr, unsigned n) { |
||||||
|
* #define elt_lt(a,b) ((a)->key < (b)->key) |
||||||
|
* GKQSORT(struct elt, arr, n, elt_lt); |
||||||
|
* } |
||||||
|
* |
||||||
|
* And so on. |
||||||
|
*/ |
||||||
|
|
||||||
|
/* Swap two items pointed to by A and B using temporary buffer t. */ |
||||||
|
#define _GKQSORT_SWAP(a, b, t) ((void)((t = *a), (*a = *b), (*b = t))) |
||||||
|
|
||||||
|
/* Discontinue quicksort algorithm when partition gets below this size. */ |
||||||
|
#define _GKQSORT_MAX_THRESH 8 |
||||||
|
|
||||||
|
/* The next 4 #defines implement a very fast in-line stack abstraction. */ |
||||||
|
#define _GKQSORT_STACK_SIZE (8 * sizeof(size_t)) |
||||||
|
#define _GKQSORT_PUSH(top, low, high) (((top->_lo = (low)), (top->_hi = (high)), ++top)) |
||||||
|
#define _GKQSORT_POP(low, high, top) ((--top, (low = top->_lo), (high = top->_hi))) |
||||||
|
#define _GKQSORT_STACK_NOT_EMPTY (_stack < _top) |
||||||
|
|
||||||
|
|
||||||
|
/* The main code starts here... */ |
||||||
|
#define GK_MKQSORT(GKQSORT_TYPE,GKQSORT_BASE,GKQSORT_NELT,GKQSORT_LT) \ |
||||||
|
{ \
|
||||||
|
GKQSORT_TYPE *const _base = (GKQSORT_BASE); \
|
||||||
|
const size_t _elems = (GKQSORT_NELT); \
|
||||||
|
GKQSORT_TYPE _hold; \
|
||||||
|
\
|
||||||
|
if (_elems < 1) \
|
||||||
|
return; \
|
||||||
|
\
|
||||||
|
/* Don't declare two variables of type GKQSORT_TYPE in a single \
|
||||||
|
* statement: eg `TYPE a, b;', in case if TYPE is a pointer, \
|
||||||
|
* expands to `type* a, b;' wich isn't what we want. \
|
||||||
|
*/ \
|
||||||
|
\
|
||||||
|
if (_elems > _GKQSORT_MAX_THRESH) { \
|
||||||
|
GKQSORT_TYPE *_lo = _base; \
|
||||||
|
GKQSORT_TYPE *_hi = _lo + _elems - 1; \
|
||||||
|
struct { \
|
||||||
|
GKQSORT_TYPE *_hi; GKQSORT_TYPE *_lo; \
|
||||||
|
} _stack[_GKQSORT_STACK_SIZE], *_top = _stack + 1; \
|
||||||
|
\
|
||||||
|
while (_GKQSORT_STACK_NOT_EMPTY) { \
|
||||||
|
GKQSORT_TYPE *_left_ptr; GKQSORT_TYPE *_right_ptr; \
|
||||||
|
\
|
||||||
|
/* Select median value from among LO, MID, and HI. Rearrange \
|
||||||
|
LO and HI so the three values are sorted. This lowers the \
|
||||||
|
probability of picking a pathological pivot value and \
|
||||||
|
skips a comparison for both the LEFT_PTR and RIGHT_PTR in \
|
||||||
|
the while loops. */ \
|
||||||
|
\
|
||||||
|
GKQSORT_TYPE *_mid = _lo + ((_hi - _lo) >> 1); \
|
||||||
|
\
|
||||||
|
if (GKQSORT_LT (_mid, _lo)) \
|
||||||
|
_GKQSORT_SWAP (_mid, _lo, _hold); \
|
||||||
|
if (GKQSORT_LT (_hi, _mid)) \
|
||||||
|
_GKQSORT_SWAP (_mid, _hi, _hold); \
|
||||||
|
else \
|
||||||
|
goto _jump_over; \
|
||||||
|
if (GKQSORT_LT (_mid, _lo)) \
|
||||||
|
_GKQSORT_SWAP (_mid, _lo, _hold); \
|
||||||
|
_jump_over:; \
|
||||||
|
\
|
||||||
|
_left_ptr = _lo + 1; \
|
||||||
|
_right_ptr = _hi - 1; \
|
||||||
|
\
|
||||||
|
/* Here's the famous ``collapse the walls'' section of quicksort. \
|
||||||
|
Gotta like those tight inner loops! They are the main reason \
|
||||||
|
that this algorithm runs much faster than others. */ \
|
||||||
|
do { \
|
||||||
|
while (GKQSORT_LT (_left_ptr, _mid)) \
|
||||||
|
++_left_ptr; \
|
||||||
|
\
|
||||||
|
while (GKQSORT_LT (_mid, _right_ptr)) \
|
||||||
|
--_right_ptr; \
|
||||||
|
\
|
||||||
|
if (_left_ptr < _right_ptr) { \
|
||||||
|
_GKQSORT_SWAP (_left_ptr, _right_ptr, _hold); \
|
||||||
|
if (_mid == _left_ptr) \
|
||||||
|
_mid = _right_ptr; \
|
||||||
|
else if (_mid == _right_ptr) \
|
||||||
|
_mid = _left_ptr; \
|
||||||
|
++_left_ptr; \
|
||||||
|
--_right_ptr; \
|
||||||
|
} \
|
||||||
|
else if (_left_ptr == _right_ptr) { \
|
||||||
|
++_left_ptr; \
|
||||||
|
--_right_ptr; \
|
||||||
|
break; \
|
||||||
|
} \
|
||||||
|
} while (_left_ptr <= _right_ptr); \
|
||||||
|
\
|
||||||
|
/* Set up pointers for next iteration. First determine whether \
|
||||||
|
left and right partitions are below the threshold size. If so, \
|
||||||
|
ignore one or both. Otherwise, push the larger partition's \
|
||||||
|
bounds on the stack and continue sorting the smaller one. */ \
|
||||||
|
\
|
||||||
|
if (_right_ptr - _lo <= _GKQSORT_MAX_THRESH) { \
|
||||||
|
if (_hi - _left_ptr <= _GKQSORT_MAX_THRESH) \
|
||||||
|
/* Ignore both small partitions. */ \
|
||||||
|
_GKQSORT_POP (_lo, _hi, _top); \
|
||||||
|
else \
|
||||||
|
/* Ignore small left partition. */ \
|
||||||
|
_lo = _left_ptr; \
|
||||||
|
} \
|
||||||
|
else if (_hi - _left_ptr <= _GKQSORT_MAX_THRESH) \
|
||||||
|
/* Ignore small right partition. */ \
|
||||||
|
_hi = _right_ptr; \
|
||||||
|
else if (_right_ptr - _lo > _hi - _left_ptr) { \
|
||||||
|
/* Push larger left partition indices. */ \
|
||||||
|
_GKQSORT_PUSH (_top, _lo, _right_ptr); \
|
||||||
|
_lo = _left_ptr; \
|
||||||
|
} \
|
||||||
|
else { \
|
||||||
|
/* Push larger right partition indices. */ \
|
||||||
|
_GKQSORT_PUSH (_top, _left_ptr, _hi); \
|
||||||
|
_hi = _right_ptr; \
|
||||||
|
} \
|
||||||
|
} \
|
||||||
|
} \
|
||||||
|
\
|
||||||
|
/* Once the BASE array is partially sorted by quicksort the rest \
|
||||||
|
is completely sorted using insertion sort, since this is efficient \
|
||||||
|
for partitions below MAX_THRESH size. BASE points to the \
|
||||||
|
beginning of the array to sort, and END_PTR points at the very \
|
||||||
|
last element in the array (*not* one beyond it!). */ \
|
||||||
|
\
|
||||||
|
{ \
|
||||||
|
GKQSORT_TYPE *const _end_ptr = _base + _elems - 1; \
|
||||||
|
GKQSORT_TYPE *_tmp_ptr = _base; \
|
||||||
|
register GKQSORT_TYPE *_run_ptr; \
|
||||||
|
GKQSORT_TYPE *_thresh; \
|
||||||
|
\
|
||||||
|
_thresh = _base + _GKQSORT_MAX_THRESH; \
|
||||||
|
if (_thresh > _end_ptr) \
|
||||||
|
_thresh = _end_ptr; \
|
||||||
|
\
|
||||||
|
/* Find smallest element in first threshold and place it at the \
|
||||||
|
array's beginning. This is the smallest array element, \
|
||||||
|
and the operation speeds up insertion sort's inner loop. */ \
|
||||||
|
\
|
||||||
|
for (_run_ptr = _tmp_ptr + 1; _run_ptr <= _thresh; ++_run_ptr) \
|
||||||
|
if (GKQSORT_LT (_run_ptr, _tmp_ptr)) \
|
||||||
|
_tmp_ptr = _run_ptr; \
|
||||||
|
\
|
||||||
|
if (_tmp_ptr != _base) \
|
||||||
|
_GKQSORT_SWAP (_tmp_ptr, _base, _hold); \
|
||||||
|
\
|
||||||
|
/* Insertion sort, running from left-hand-side \
|
||||||
|
* up to right-hand-side. */ \
|
||||||
|
\
|
||||||
|
_run_ptr = _base + 1; \
|
||||||
|
while (++_run_ptr <= _end_ptr) { \
|
||||||
|
_tmp_ptr = _run_ptr - 1; \
|
||||||
|
while (GKQSORT_LT (_run_ptr, _tmp_ptr)) \
|
||||||
|
--_tmp_ptr; \
|
||||||
|
\
|
||||||
|
++_tmp_ptr; \
|
||||||
|
if (_tmp_ptr != _run_ptr) { \
|
||||||
|
GKQSORT_TYPE *_trav = _run_ptr + 1; \
|
||||||
|
while (--_trav >= _run_ptr) { \
|
||||||
|
GKQSORT_TYPE *_hi; GKQSORT_TYPE *_lo; \
|
||||||
|
_hold = *_trav; \
|
||||||
|
\
|
||||||
|
for (_hi = _lo = _trav; --_lo >= _tmp_ptr; _hi = _lo) \
|
||||||
|
*_hi = *_lo; \
|
||||||
|
*_hi = _hold; \
|
||||||
|
} \
|
||||||
|
} \
|
||||||
|
} \
|
||||||
|
} \
|
||||||
|
\
|
||||||
|
} |
||||||
|
|
||||||
|
#endif |
||||||
@ -0,0 +1,40 @@ |
|||||||
|
/*!
|
||||||
|
\file
|
||||||
|
\brief Templates for various utility routines |
||||||
|
|
||||||
|
\date Started 5/28/07 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: gk_mkutils.h 10711 2011-08-31 22:23:04Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
#ifndef _GK_MKUTILS_H_ |
||||||
|
#define _GK_MKUTILS_H_ |
||||||
|
|
||||||
|
|
||||||
|
#define GK_MKARRAY2CSR(PRFX, TYPE)\ |
||||||
|
/*************************************************************************/\
|
||||||
|
/*! The macro for gk_?array2csr() routine */\
|
||||||
|
/**************************************************************************/\
|
||||||
|
void PRFX ## array2csr(TYPE n, TYPE range, TYPE *array, TYPE *ptr, TYPE *ind)\
|
||||||
|
{\
|
||||||
|
TYPE i;\
|
||||||
|
\
|
||||||
|
for (i=0; i<=range; i++)\
|
||||||
|
ptr[i] = 0;\
|
||||||
|
\
|
||||||
|
for (i=0; i<n; i++)\
|
||||||
|
ptr[array[i]]++;\
|
||||||
|
\
|
||||||
|
/* Compute the ptr, ind structure */\
|
||||||
|
MAKECSR(i, range, ptr);\
|
||||||
|
for (i=0; i<n; i++)\
|
||||||
|
ind[ptr[array[i]]++] = i;\
|
||||||
|
SHIFTCSR(i, range, ptr);\
|
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
#define GK_MKARRAY2CSR_PROTO(PRFX, TYPE)\ |
||||||
|
void PRFX ## array2csr(TYPE n, TYPE range, TYPE *array, TYPE *ptr, TYPE *ind);\
|
||||||
|
|
||||||
|
|
||||||
|
#endif |
||||||
@ -0,0 +1,301 @@ |
|||||||
|
// ISO C9x compliant inttypes.h for Microsoft Visual Studio
|
||||||
|
// Based on ISO/IEC 9899:TC2 Committee draft (May 6, 2005) WG14/N1124
|
||||||
|
//
|
||||||
|
// Copyright (c) 2006 Alexander Chemeris
|
||||||
|
//
|
||||||
|
// Redistribution and use in source and binary forms, with or without
|
||||||
|
// modification, are permitted provided that the following conditions are met:
|
||||||
|
//
|
||||||
|
// 1. Redistributions of source code must retain the above copyright notice,
|
||||||
|
// this list of conditions and the following disclaimer.
|
||||||
|
//
|
||||||
|
// 2. Redistributions in binary form must reproduce the above copyright
|
||||||
|
// notice, this list of conditions and the following disclaimer in the
|
||||||
|
// documentation and/or other materials provided with the distribution.
|
||||||
|
//
|
||||||
|
// 3. The name of the author may be used to endorse or promote products
|
||||||
|
// derived from this software without specific prior written permission.
|
||||||
|
//
|
||||||
|
// THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR IMPLIED
|
||||||
|
// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
|
||||||
|
// MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
|
||||||
|
// EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
|
||||||
|
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
|
||||||
|
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
|
||||||
|
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
|
||||||
|
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
|
||||||
|
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
|
||||||
|
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
||||||
|
//
|
||||||
|
///////////////////////////////////////////////////////////////////////////////
|
||||||
|
|
||||||
|
#ifndef _MSC_VER // [
|
||||||
|
#error "Use this header only with Microsoft Visual C++ compilers!" |
||||||
|
#endif // _MSC_VER ]
|
||||||
|
|
||||||
|
#ifndef _MSC_INTTYPES_H_ // [
|
||||||
|
#define _MSC_INTTYPES_H_ |
||||||
|
|
||||||
|
#if _MSC_VER > 1000 |
||||||
|
#pragma once |
||||||
|
#endif |
||||||
|
|
||||||
|
#include "gk_ms_stdint.h" |
||||||
|
|
||||||
|
// 7.8 Format conversion of integer types
|
||||||
|
|
||||||
|
typedef struct { |
||||||
|
intmax_t quot; |
||||||
|
intmax_t rem; |
||||||
|
} imaxdiv_t; |
||||||
|
|
||||||
|
// 7.8.1 Macros for format specifiers
|
||||||
|
|
||||||
|
// The fprintf macros for signed integers are:
|
||||||
|
#define PRId8 "d" |
||||||
|
#define PRIi8 "i" |
||||||
|
#define PRIdLEAST8 "d" |
||||||
|
#define PRIiLEAST8 "i" |
||||||
|
#define PRIdFAST8 "d" |
||||||
|
#define PRIiFAST8 "i" |
||||||
|
|
||||||
|
#define PRId16 "hd" |
||||||
|
#define PRIi16 "hi" |
||||||
|
#define PRIdLEAST16 "hd" |
||||||
|
#define PRIiLEAST16 "hi" |
||||||
|
#define PRIdFAST16 "hd" |
||||||
|
#define PRIiFAST16 "hi" |
||||||
|
|
||||||
|
#define PRId32 "I32d" |
||||||
|
#define PRIi32 "I32i" |
||||||
|
#define PRIdLEAST32 "I32d" |
||||||
|
#define PRIiLEAST32 "I32i" |
||||||
|
#define PRIdFAST32 "I32d" |
||||||
|
#define PRIiFAST32 "I32i" |
||||||
|
|
||||||
|
#define PRId64 "I64d" |
||||||
|
#define PRIi64 "I64i" |
||||||
|
#define PRIdLEAST64 "I64d" |
||||||
|
#define PRIiLEAST64 "I64i" |
||||||
|
#define PRIdFAST64 "I64d" |
||||||
|
#define PRIiFAST64 "I64i" |
||||||
|
|
||||||
|
#define PRIdMAX "I64d" |
||||||
|
#define PRIiMAX "I64i" |
||||||
|
|
||||||
|
#define PRIdPTR "Id" |
||||||
|
#define PRIiPTR "Ii" |
||||||
|
|
||||||
|
// The fprintf macros for unsigned integers are:
|
||||||
|
#define PRIo8 "o" |
||||||
|
#define PRIu8 "u" |
||||||
|
#define PRIx8 "x" |
||||||
|
#define PRIX8 "X" |
||||||
|
#define PRIoLEAST8 "o" |
||||||
|
#define PRIuLEAST8 "u" |
||||||
|
#define PRIxLEAST8 "x" |
||||||
|
#define PRIXLEAST8 "X" |
||||||
|
#define PRIoFAST8 "o" |
||||||
|
#define PRIuFAST8 "u" |
||||||
|
#define PRIxFAST8 "x" |
||||||
|
#define PRIXFAST8 "X" |
||||||
|
|
||||||
|
#define PRIo16 "ho" |
||||||
|
#define PRIu16 "hu" |
||||||
|
#define PRIx16 "hx" |
||||||
|
#define PRIX16 "hX" |
||||||
|
#define PRIoLEAST16 "ho" |
||||||
|
#define PRIuLEAST16 "hu" |
||||||
|
#define PRIxLEAST16 "hx" |
||||||
|
#define PRIXLEAST16 "hX" |
||||||
|
#define PRIoFAST16 "ho" |
||||||
|
#define PRIuFAST16 "hu" |
||||||
|
#define PRIxFAST16 "hx" |
||||||
|
#define PRIXFAST16 "hX" |
||||||
|
|
||||||
|
#define PRIo32 "I32o" |
||||||
|
#define PRIu32 "I32u" |
||||||
|
#define PRIx32 "I32x" |
||||||
|
#define PRIX32 "I32X" |
||||||
|
#define PRIoLEAST32 "I32o" |
||||||
|
#define PRIuLEAST32 "I32u" |
||||||
|
#define PRIxLEAST32 "I32x" |
||||||
|
#define PRIXLEAST32 "I32X" |
||||||
|
#define PRIoFAST32 "I32o" |
||||||
|
#define PRIuFAST32 "I32u" |
||||||
|
#define PRIxFAST32 "I32x" |
||||||
|
#define PRIXFAST32 "I32X" |
||||||
|
|
||||||
|
#define PRIo64 "I64o" |
||||||
|
#define PRIu64 "I64u" |
||||||
|
#define PRIx64 "I64x" |
||||||
|
#define PRIX64 "I64X" |
||||||
|
#define PRIoLEAST64 "I64o" |
||||||
|
#define PRIuLEAST64 "I64u" |
||||||
|
#define PRIxLEAST64 "I64x" |
||||||
|
#define PRIXLEAST64 "I64X" |
||||||
|
#define PRIoFAST64 "I64o" |
||||||
|
#define PRIuFAST64 "I64u" |
||||||
|
#define PRIxFAST64 "I64x" |
||||||
|
#define PRIXFAST64 "I64X" |
||||||
|
|
||||||
|
#define PRIoMAX "I64o" |
||||||
|
#define PRIuMAX "I64u" |
||||||
|
#define PRIxMAX "I64x" |
||||||
|
#define PRIXMAX "I64X" |
||||||
|
|
||||||
|
#define PRIoPTR "Io" |
||||||
|
#define PRIuPTR "Iu" |
||||||
|
#define PRIxPTR "Ix" |
||||||
|
#define PRIXPTR "IX" |
||||||
|
|
||||||
|
// The fscanf macros for signed integers are:
|
||||||
|
#define SCNd8 "d" |
||||||
|
#define SCNi8 "i" |
||||||
|
#define SCNdLEAST8 "d" |
||||||
|
#define SCNiLEAST8 "i" |
||||||
|
#define SCNdFAST8 "d" |
||||||
|
#define SCNiFAST8 "i" |
||||||
|
|
||||||
|
#define SCNd16 "hd" |
||||||
|
#define SCNi16 "hi" |
||||||
|
#define SCNdLEAST16 "hd" |
||||||
|
#define SCNiLEAST16 "hi" |
||||||
|
#define SCNdFAST16 "hd" |
||||||
|
#define SCNiFAST16 "hi" |
||||||
|
|
||||||
|
#define SCNd32 "ld" |
||||||
|
#define SCNi32 "li" |
||||||
|
#define SCNdLEAST32 "ld" |
||||||
|
#define SCNiLEAST32 "li" |
||||||
|
#define SCNdFAST32 "ld" |
||||||
|
#define SCNiFAST32 "li" |
||||||
|
|
||||||
|
#define SCNd64 "I64d" |
||||||
|
#define SCNi64 "I64i" |
||||||
|
#define SCNdLEAST64 "I64d" |
||||||
|
#define SCNiLEAST64 "I64i" |
||||||
|
#define SCNdFAST64 "I64d" |
||||||
|
#define SCNiFAST64 "I64i" |
||||||
|
|
||||||
|
#define SCNdMAX "I64d" |
||||||
|
#define SCNiMAX "I64i" |
||||||
|
|
||||||
|
#ifdef _WIN64 // [
|
||||||
|
# define SCNdPTR "I64d" |
||||||
|
# define SCNiPTR "I64i" |
||||||
|
#else // _WIN64 ][
|
||||||
|
# define SCNdPTR "ld" |
||||||
|
# define SCNiPTR "li" |
||||||
|
#endif // _WIN64 ]
|
||||||
|
|
||||||
|
// The fscanf macros for unsigned integers are:
|
||||||
|
#define SCNo8 "o" |
||||||
|
#define SCNu8 "u" |
||||||
|
#define SCNx8 "x" |
||||||
|
#define SCNX8 "X" |
||||||
|
#define SCNoLEAST8 "o" |
||||||
|
#define SCNuLEAST8 "u" |
||||||
|
#define SCNxLEAST8 "x" |
||||||
|
#define SCNXLEAST8 "X" |
||||||
|
#define SCNoFAST8 "o" |
||||||
|
#define SCNuFAST8 "u" |
||||||
|
#define SCNxFAST8 "x" |
||||||
|
#define SCNXFAST8 "X" |
||||||
|
|
||||||
|
#define SCNo16 "ho" |
||||||
|
#define SCNu16 "hu" |
||||||
|
#define SCNx16 "hx" |
||||||
|
#define SCNX16 "hX" |
||||||
|
#define SCNoLEAST16 "ho" |
||||||
|
#define SCNuLEAST16 "hu" |
||||||
|
#define SCNxLEAST16 "hx" |
||||||
|
#define SCNXLEAST16 "hX" |
||||||
|
#define SCNoFAST16 "ho" |
||||||
|
#define SCNuFAST16 "hu" |
||||||
|
#define SCNxFAST16 "hx" |
||||||
|
#define SCNXFAST16 "hX" |
||||||
|
|
||||||
|
#define SCNo32 "lo" |
||||||
|
#define SCNu32 "lu" |
||||||
|
#define SCNx32 "lx" |
||||||
|
#define SCNX32 "lX" |
||||||
|
#define SCNoLEAST32 "lo" |
||||||
|
#define SCNuLEAST32 "lu" |
||||||
|
#define SCNxLEAST32 "lx" |
||||||
|
#define SCNXLEAST32 "lX" |
||||||
|
#define SCNoFAST32 "lo" |
||||||
|
#define SCNuFAST32 "lu" |
||||||
|
#define SCNxFAST32 "lx" |
||||||
|
#define SCNXFAST32 "lX" |
||||||
|
|
||||||
|
#define SCNo64 "I64o" |
||||||
|
#define SCNu64 "I64u" |
||||||
|
#define SCNx64 "I64x" |
||||||
|
#define SCNX64 "I64X" |
||||||
|
#define SCNoLEAST64 "I64o" |
||||||
|
#define SCNuLEAST64 "I64u" |
||||||
|
#define SCNxLEAST64 "I64x" |
||||||
|
#define SCNXLEAST64 "I64X" |
||||||
|
#define SCNoFAST64 "I64o" |
||||||
|
#define SCNuFAST64 "I64u" |
||||||
|
#define SCNxFAST64 "I64x" |
||||||
|
#define SCNXFAST64 "I64X" |
||||||
|
|
||||||
|
#define SCNoMAX "I64o" |
||||||
|
#define SCNuMAX "I64u" |
||||||
|
#define SCNxMAX "I64x" |
||||||
|
#define SCNXMAX "I64X" |
||||||
|
|
||||||
|
#ifdef _WIN64 // [
|
||||||
|
# define SCNoPTR "I64o" |
||||||
|
# define SCNuPTR "I64u" |
||||||
|
# define SCNxPTR "I64x" |
||||||
|
# define SCNXPTR "I64X" |
||||||
|
#else // _WIN64 ][
|
||||||
|
# define SCNoPTR "lo" |
||||||
|
# define SCNuPTR "lu" |
||||||
|
# define SCNxPTR "lx" |
||||||
|
# define SCNXPTR "lX" |
||||||
|
#endif // _WIN64 ]
|
||||||
|
|
||||||
|
// 7.8.2 Functions for greatest-width integer types
|
||||||
|
|
||||||
|
// 7.8.2.1 The imaxabs function
|
||||||
|
#define imaxabs _abs64 |
||||||
|
|
||||||
|
// 7.8.2.2 The imaxdiv function
|
||||||
|
|
||||||
|
// This is modified version of div() function from Microsoft's div.c found
|
||||||
|
// in %MSVC.NET%\crt\src\div.c
|
||||||
|
#ifdef STATIC_IMAXDIV // [
|
||||||
|
static |
||||||
|
#else // STATIC_IMAXDIV ][
|
||||||
|
_inline |
||||||
|
#endif // STATIC_IMAXDIV ]
|
||||||
|
imaxdiv_t __cdecl imaxdiv(intmax_t numer, intmax_t denom) |
||||||
|
{ |
||||||
|
imaxdiv_t result; |
||||||
|
|
||||||
|
result.quot = numer / denom; |
||||||
|
result.rem = numer % denom; |
||||||
|
|
||||||
|
if (numer < 0 && result.rem > 0) { |
||||||
|
// did division wrong; must fix up
|
||||||
|
++result.quot; |
||||||
|
result.rem -= denom; |
||||||
|
} |
||||||
|
|
||||||
|
return result; |
||||||
|
} |
||||||
|
|
||||||
|
// 7.8.2.3 The strtoimax and strtoumax functions
|
||||||
|
#define strtoimax _strtoi64 |
||||||
|
#define strtoumax _strtoui64 |
||||||
|
|
||||||
|
// 7.8.2.4 The wcstoimax and wcstoumax functions
|
||||||
|
#define wcstoimax _wcstoi64 |
||||||
|
#define wcstoumax _wcstoui64 |
||||||
|
|
||||||
|
|
||||||
|
#endif // _MSC_INTTYPES_H_ ]
|
||||||
@ -0,0 +1,22 @@ |
|||||||
|
#ifndef _MSC_VER // [
|
||||||
|
#error "Use this header only with Microsoft Visual C++ compilers!" |
||||||
|
#endif // _MSC_VER ]
|
||||||
|
|
||||||
|
#ifndef _MS_STAT_H_ |
||||||
|
#define _MS_STAT_H_ |
||||||
|
|
||||||
|
#if _MSC_VER > 1000 |
||||||
|
#pragma once |
||||||
|
#endif |
||||||
|
|
||||||
|
#include <sys/stat.h> |
||||||
|
/* Test macros for file types. */ |
||||||
|
|
||||||
|
#define __S_ISTYPE(mode, mask) (((mode) & S_IFMT) == (mask)) |
||||||
|
|
||||||
|
#define S_ISDIR(mode) __S_ISTYPE((mode), S_IFDIR) |
||||||
|
#define S_ISCHR(mode) __S_ISTYPE((mode), S_IFCHR) |
||||||
|
#define S_ISBLK(mode) __S_ISTYPE((mode), S_IFBLK) |
||||||
|
#define S_ISREG(mode) __S_ISTYPE((mode), S_IFREG) |
||||||
|
|
||||||
|
#endif |
||||||
@ -0,0 +1,222 @@ |
|||||||
|
// ISO C9x compliant stdint.h for Microsoft Visual Studio
|
||||||
|
// Based on ISO/IEC 9899:TC2 Committee draft (May 6, 2005) WG14/N1124
|
||||||
|
//
|
||||||
|
// Copyright (c) 2006 Alexander Chemeris
|
||||||
|
//
|
||||||
|
// Redistribution and use in source and binary forms, with or without
|
||||||
|
// modification, are permitted provided that the following conditions are met:
|
||||||
|
//
|
||||||
|
// 1. Redistributions of source code must retain the above copyright notice,
|
||||||
|
// this list of conditions and the following disclaimer.
|
||||||
|
//
|
||||||
|
// 2. Redistributions in binary form must reproduce the above copyright
|
||||||
|
// notice, this list of conditions and the following disclaimer in the
|
||||||
|
// documentation and/or other materials provided with the distribution.
|
||||||
|
//
|
||||||
|
// 3. The name of the author may be used to endorse or promote products
|
||||||
|
// derived from this software without specific prior written permission.
|
||||||
|
//
|
||||||
|
// THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR IMPLIED
|
||||||
|
// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
|
||||||
|
// MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
|
||||||
|
// EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
|
||||||
|
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
|
||||||
|
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
|
||||||
|
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
|
||||||
|
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
|
||||||
|
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
|
||||||
|
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
||||||
|
//
|
||||||
|
///////////////////////////////////////////////////////////////////////////////
|
||||||
|
|
||||||
|
#ifndef _MSC_VER // [
|
||||||
|
#error "Use this header only with Microsoft Visual C++ compilers!" |
||||||
|
#endif // _MSC_VER ]
|
||||||
|
|
||||||
|
#ifndef _MSC_STDINT_H_ // [
|
||||||
|
#define _MSC_STDINT_H_ |
||||||
|
|
||||||
|
#if _MSC_VER > 1000 |
||||||
|
#pragma once |
||||||
|
#endif |
||||||
|
|
||||||
|
#include <limits.h> |
||||||
|
|
||||||
|
// For Visual Studio 6 in C++ mode wrap <wchar.h> include with 'extern "C++" {}'
|
||||||
|
// or compiler give many errors like this:
|
||||||
|
// error C2733: second C linkage of overloaded function 'wmemchr' not allowed
|
||||||
|
#if (_MSC_VER < 1300) && defined(__cplusplus) |
||||||
|
extern "C++" { |
||||||
|
#endif |
||||||
|
# include <wchar.h> |
||||||
|
#if (_MSC_VER < 1300) && defined(__cplusplus) |
||||||
|
} |
||||||
|
#endif |
||||||
|
|
||||||
|
// 7.18.1 Integer types
|
||||||
|
|
||||||
|
// 7.18.1.1 Exact-width integer types
|
||||||
|
typedef __int8 int8_t; |
||||||
|
typedef __int16 int16_t; |
||||||
|
typedef __int32 int32_t; |
||||||
|
typedef __int64 int64_t; |
||||||
|
typedef unsigned __int8 uint8_t; |
||||||
|
typedef unsigned __int16 uint16_t; |
||||||
|
typedef unsigned __int32 uint32_t; |
||||||
|
typedef unsigned __int64 uint64_t; |
||||||
|
|
||||||
|
// 7.18.1.2 Minimum-width integer types
|
||||||
|
typedef int8_t int_least8_t; |
||||||
|
typedef int16_t int_least16_t; |
||||||
|
typedef int32_t int_least32_t; |
||||||
|
typedef int64_t int_least64_t; |
||||||
|
typedef uint8_t uint_least8_t; |
||||||
|
typedef uint16_t uint_least16_t; |
||||||
|
typedef uint32_t uint_least32_t; |
||||||
|
typedef uint64_t uint_least64_t; |
||||||
|
|
||||||
|
// 7.18.1.3 Fastest minimum-width integer types
|
||||||
|
typedef int8_t int_fast8_t; |
||||||
|
typedef int16_t int_fast16_t; |
||||||
|
typedef int32_t int_fast32_t; |
||||||
|
typedef int64_t int_fast64_t; |
||||||
|
typedef uint8_t uint_fast8_t; |
||||||
|
typedef uint16_t uint_fast16_t; |
||||||
|
typedef uint32_t uint_fast32_t; |
||||||
|
typedef uint64_t uint_fast64_t; |
||||||
|
|
||||||
|
// 7.18.1.4 Integer types capable of holding object pointers
|
||||||
|
#ifdef _WIN64 // [
|
||||||
|
typedef __int64 intptr_t; |
||||||
|
typedef unsigned __int64 uintptr_t; |
||||||
|
#else // _WIN64 ][
|
||||||
|
typedef int intptr_t; |
||||||
|
typedef unsigned int uintptr_t; |
||||||
|
#endif // _WIN64 ]
|
||||||
|
|
||||||
|
// 7.18.1.5 Greatest-width integer types
|
||||||
|
typedef int64_t intmax_t; |
||||||
|
typedef uint64_t uintmax_t; |
||||||
|
|
||||||
|
|
||||||
|
// 7.18.2 Limits of specified-width integer types
|
||||||
|
|
||||||
|
#if !defined(__cplusplus) || defined(__STDC_LIMIT_MACROS) // [ See footnote 220 at page 257 and footnote 221 at page 259
|
||||||
|
|
||||||
|
// 7.18.2.1 Limits of exact-width integer types
|
||||||
|
#define INT8_MIN ((int8_t)_I8_MIN) |
||||||
|
#define INT8_MAX _I8_MAX |
||||||
|
#define INT16_MIN ((int16_t)_I16_MIN) |
||||||
|
#define INT16_MAX _I16_MAX |
||||||
|
#define INT32_MIN ((int32_t)_I32_MIN) |
||||||
|
#define INT32_MAX _I32_MAX |
||||||
|
#define INT64_MIN ((int64_t)_I64_MIN) |
||||||
|
#define INT64_MAX _I64_MAX |
||||||
|
#define UINT8_MAX _UI8_MAX |
||||||
|
#define UINT16_MAX _UI16_MAX |
||||||
|
#define UINT32_MAX _UI32_MAX |
||||||
|
#define UINT64_MAX _UI64_MAX |
||||||
|
|
||||||
|
// 7.18.2.2 Limits of minimum-width integer types
|
||||||
|
#define INT_LEAST8_MIN INT8_MIN |
||||||
|
#define INT_LEAST8_MAX INT8_MAX |
||||||
|
#define INT_LEAST16_MIN INT16_MIN |
||||||
|
#define INT_LEAST16_MAX INT16_MAX |
||||||
|
#define INT_LEAST32_MIN INT32_MIN |
||||||
|
#define INT_LEAST32_MAX INT32_MAX |
||||||
|
#define INT_LEAST64_MIN INT64_MIN |
||||||
|
#define INT_LEAST64_MAX INT64_MAX |
||||||
|
#define UINT_LEAST8_MAX UINT8_MAX |
||||||
|
#define UINT_LEAST16_MAX UINT16_MAX |
||||||
|
#define UINT_LEAST32_MAX UINT32_MAX |
||||||
|
#define UINT_LEAST64_MAX UINT64_MAX |
||||||
|
|
||||||
|
// 7.18.2.3 Limits of fastest minimum-width integer types
|
||||||
|
#define INT_FAST8_MIN INT8_MIN |
||||||
|
#define INT_FAST8_MAX INT8_MAX |
||||||
|
#define INT_FAST16_MIN INT16_MIN |
||||||
|
#define INT_FAST16_MAX INT16_MAX |
||||||
|
#define INT_FAST32_MIN INT32_MIN |
||||||
|
#define INT_FAST32_MAX INT32_MAX |
||||||
|
#define INT_FAST64_MIN INT64_MIN |
||||||
|
#define INT_FAST64_MAX INT64_MAX |
||||||
|
#define UINT_FAST8_MAX UINT8_MAX |
||||||
|
#define UINT_FAST16_MAX UINT16_MAX |
||||||
|
#define UINT_FAST32_MAX UINT32_MAX |
||||||
|
#define UINT_FAST64_MAX UINT64_MAX |
||||||
|
|
||||||
|
// 7.18.2.4 Limits of integer types capable of holding object pointers
|
||||||
|
#ifdef _WIN64 // [
|
||||||
|
# define INTPTR_MIN INT64_MIN |
||||||
|
# define INTPTR_MAX INT64_MAX |
||||||
|
# define UINTPTR_MAX UINT64_MAX |
||||||
|
#else // _WIN64 ][
|
||||||
|
# define INTPTR_MIN INT32_MIN |
||||||
|
# define INTPTR_MAX INT32_MAX |
||||||
|
# define UINTPTR_MAX UINT32_MAX |
||||||
|
#endif // _WIN64 ]
|
||||||
|
|
||||||
|
// 7.18.2.5 Limits of greatest-width integer types
|
||||||
|
#define INTMAX_MIN INT64_MIN |
||||||
|
#define INTMAX_MAX INT64_MAX |
||||||
|
#define UINTMAX_MAX UINT64_MAX |
||||||
|
|
||||||
|
// 7.18.3 Limits of other integer types
|
||||||
|
|
||||||
|
#ifdef _WIN64 // [
|
||||||
|
# define PTRDIFF_MIN _I64_MIN |
||||||
|
# define PTRDIFF_MAX _I64_MAX |
||||||
|
#else // _WIN64 ][
|
||||||
|
# define PTRDIFF_MIN _I32_MIN |
||||||
|
# define PTRDIFF_MAX _I32_MAX |
||||||
|
#endif // _WIN64 ]
|
||||||
|
|
||||||
|
#define SIG_ATOMIC_MIN INT_MIN |
||||||
|
#define SIG_ATOMIC_MAX INT_MAX |
||||||
|
|
||||||
|
#ifndef SIZE_MAX // [
|
||||||
|
# ifdef _WIN64 // [
|
||||||
|
# define SIZE_MAX _UI64_MAX |
||||||
|
# else // _WIN64 ][
|
||||||
|
# define SIZE_MAX _UI32_MAX |
||||||
|
# endif // _WIN64 ]
|
||||||
|
#endif // SIZE_MAX ]
|
||||||
|
|
||||||
|
// WCHAR_MIN and WCHAR_MAX are also defined in <wchar.h>
|
||||||
|
#ifndef WCHAR_MIN // [
|
||||||
|
# define WCHAR_MIN 0 |
||||||
|
#endif // WCHAR_MIN ]
|
||||||
|
#ifndef WCHAR_MAX // [
|
||||||
|
# define WCHAR_MAX _UI16_MAX |
||||||
|
#endif // WCHAR_MAX ]
|
||||||
|
|
||||||
|
#define WINT_MIN 0 |
||||||
|
#define WINT_MAX _UI16_MAX |
||||||
|
|
||||||
|
#endif // __STDC_LIMIT_MACROS ]
|
||||||
|
|
||||||
|
|
||||||
|
// 7.18.4 Limits of other integer types
|
||||||
|
|
||||||
|
#if !defined(__cplusplus) || defined(__STDC_CONSTANT_MACROS) // [ See footnote 224 at page 260
|
||||||
|
|
||||||
|
// 7.18.4.1 Macros for minimum-width integer constants
|
||||||
|
|
||||||
|
#define INT8_C(val) val##i8 |
||||||
|
#define INT16_C(val) val##i16 |
||||||
|
#define INT32_C(val) val##i32 |
||||||
|
#define INT64_C(val) val##i64 |
||||||
|
|
||||||
|
#define UINT8_C(val) val##ui8 |
||||||
|
#define UINT16_C(val) val##ui16 |
||||||
|
#define UINT32_C(val) val##ui32 |
||||||
|
#define UINT64_C(val) val##ui64 |
||||||
|
|
||||||
|
// 7.18.4.2 Macros for greatest-width integer constants
|
||||||
|
#define INTMAX_C INT64_C |
||||||
|
#define UINTMAX_C UINT64_C |
||||||
|
|
||||||
|
#endif // __STDC_CONSTANT_MACROS ]
|
||||||
|
|
||||||
|
|
||||||
|
#endif // _MSC_STDINT_H_ ]
|
||||||
@ -0,0 +1,426 @@ |
|||||||
|
/*!
|
||||||
|
\file gk_proto.h |
||||||
|
\brief This file contains function prototypes |
||||||
|
|
||||||
|
\date Started 3/27/2007 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: gk_proto.h 22010 2018-05-14 20:20:26Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
#ifndef _GK_PROTO_H_ |
||||||
|
#define _GK_PROTO_H_ |
||||||
|
|
||||||
|
#ifdef __cplusplus |
||||||
|
extern "C" { |
||||||
|
#endif |
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* blas.c
|
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
GK_MKBLAS_PROTO(gk_c, char, int) |
||||||
|
GK_MKBLAS_PROTO(gk_i, int, int) |
||||||
|
GK_MKBLAS_PROTO(gk_i8, int8_t, int8_t) |
||||||
|
GK_MKBLAS_PROTO(gk_i16, int16_t, int16_t) |
||||||
|
GK_MKBLAS_PROTO(gk_i32, int32_t, int32_t) |
||||||
|
GK_MKBLAS_PROTO(gk_i64, int64_t, int64_t) |
||||||
|
GK_MKBLAS_PROTO(gk_z, ssize_t, ssize_t) |
||||||
|
GK_MKBLAS_PROTO(gk_zu, size_t, size_t) |
||||||
|
GK_MKBLAS_PROTO(gk_f, float, float) |
||||||
|
GK_MKBLAS_PROTO(gk_d, double, double) |
||||||
|
GK_MKBLAS_PROTO(gk_idx, gk_idx_t, gk_idx_t) |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* io.c |
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
FILE *gk_fopen(char *, char *, const char *); |
||||||
|
void gk_fclose(FILE *); |
||||||
|
ssize_t gk_read(int fd, void *vbuf, size_t count); |
||||||
|
ssize_t gk_write(int fd, void *vbuf, size_t count); |
||||||
|
ssize_t gk_getline(char **lineptr, size_t *n, FILE *stream); |
||||||
|
char **gk_readfile(char *fname, size_t *r_nlines); |
||||||
|
int32_t *gk_i32readfile(char *fname, size_t *r_nlines); |
||||||
|
int64_t *gk_i64readfile(char *fname, size_t *r_nlines); |
||||||
|
ssize_t *gk_zreadfile(char *fname, size_t *r_nlines); |
||||||
|
char *gk_creadfilebin(char *fname, size_t *r_nelmnts); |
||||||
|
size_t gk_cwritefilebin(char *fname, size_t n, char *a); |
||||||
|
int32_t *gk_i32readfilebin(char *fname, size_t *r_nelmnts); |
||||||
|
size_t gk_i32writefilebin(char *fname, size_t n, int32_t *a); |
||||||
|
int64_t *gk_i64readfilebin(char *fname, size_t *r_nelmnts); |
||||||
|
size_t gk_i64writefilebin(char *fname, size_t n, int64_t *a); |
||||||
|
ssize_t *gk_zreadfilebin(char *fname, size_t *r_nelmnts); |
||||||
|
size_t gk_zwritefilebin(char *fname, size_t n, ssize_t *a); |
||||||
|
float *gk_freadfilebin(char *fname, size_t *r_nelmnts); |
||||||
|
size_t gk_fwritefilebin(char *fname, size_t n, float *a); |
||||||
|
double *gk_dreadfilebin(char *fname, size_t *r_nelmnts); |
||||||
|
size_t gk_dwritefilebin(char *fname, size_t n, double *a); |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* fs.c |
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
int gk_fexists(char *); |
||||||
|
int gk_dexists(char *); |
||||||
|
ssize_t gk_getfsize(char *); |
||||||
|
void gk_getfilestats(char *fname, size_t *r_nlines, size_t *r_ntokens,
|
||||||
|
size_t *r_max_nlntokens, size_t *r_nbytes); |
||||||
|
char *gk_getbasename(char *path); |
||||||
|
char *gk_getextname(char *path); |
||||||
|
char *gk_getfilename(char *path); |
||||||
|
char *gk_getpathname(char *path); |
||||||
|
int gk_mkpath(char *); |
||||||
|
int gk_rmpath(char *); |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* memory.c |
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
GK_MKALLOC_PROTO(gk_c, char) |
||||||
|
GK_MKALLOC_PROTO(gk_i, int) |
||||||
|
GK_MKALLOC_PROTO(gk_i8, int8_t) |
||||||
|
GK_MKALLOC_PROTO(gk_i16, int16_t) |
||||||
|
GK_MKALLOC_PROTO(gk_i32, int32_t) |
||||||
|
GK_MKALLOC_PROTO(gk_i64, int64_t) |
||||||
|
GK_MKALLOC_PROTO(gk_ui8, uint8_t) |
||||||
|
GK_MKALLOC_PROTO(gk_ui16, uint16_t) |
||||||
|
GK_MKALLOC_PROTO(gk_ui32, uint32_t) |
||||||
|
GK_MKALLOC_PROTO(gk_ui64, uint64_t) |
||||||
|
GK_MKALLOC_PROTO(gk_z, ssize_t) |
||||||
|
GK_MKALLOC_PROTO(gk_zu, size_t) |
||||||
|
GK_MKALLOC_PROTO(gk_f, float) |
||||||
|
GK_MKALLOC_PROTO(gk_d, double) |
||||||
|
GK_MKALLOC_PROTO(gk_idx, gk_idx_t) |
||||||
|
|
||||||
|
GK_MKALLOC_PROTO(gk_ckv, gk_ckv_t) |
||||||
|
GK_MKALLOC_PROTO(gk_ikv, gk_ikv_t) |
||||||
|
GK_MKALLOC_PROTO(gk_i8kv, gk_i8kv_t) |
||||||
|
GK_MKALLOC_PROTO(gk_i16kv, gk_i16kv_t) |
||||||
|
GK_MKALLOC_PROTO(gk_i32kv, gk_i32kv_t) |
||||||
|
GK_MKALLOC_PROTO(gk_i64kv, gk_i64kv_t) |
||||||
|
GK_MKALLOC_PROTO(gk_zkv, gk_zkv_t) |
||||||
|
GK_MKALLOC_PROTO(gk_zukv, gk_zukv_t) |
||||||
|
GK_MKALLOC_PROTO(gk_fkv, gk_fkv_t) |
||||||
|
GK_MKALLOC_PROTO(gk_dkv, gk_dkv_t) |
||||||
|
GK_MKALLOC_PROTO(gk_skv, gk_skv_t) |
||||||
|
GK_MKALLOC_PROTO(gk_idxkv, gk_idxkv_t) |
||||||
|
|
||||||
|
void gk_AllocMatrix(void ***, size_t, size_t , size_t); |
||||||
|
void gk_FreeMatrix(void ***, size_t, size_t); |
||||||
|
int gk_malloc_init(); |
||||||
|
void gk_malloc_cleanup(int showstats); |
||||||
|
void *gk_malloc(size_t nbytes, char *msg); |
||||||
|
void *gk_realloc(void *oldptr, size_t nbytes, char *msg); |
||||||
|
void gk_free(void **ptr1,...); |
||||||
|
size_t gk_GetCurMemoryUsed(); |
||||||
|
size_t gk_GetMaxMemoryUsed(); |
||||||
|
void gk_GetVMInfo(size_t *vmsize, size_t *vmrss); |
||||||
|
size_t gk_GetProcVmPeak(); |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* seq.c |
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
gk_seq_t *gk_seq_ReadGKMODPSSM(char *file_name); |
||||||
|
gk_i2cc2i_t *gk_i2cc2i_create_common(char *alphabet); |
||||||
|
void gk_seq_init(gk_seq_t *seq); |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* error.c |
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
void gk_set_exit_on_error(int value); |
||||||
|
void errexit(char *,...); |
||||||
|
void gk_errexit(int signum, char *,...); |
||||||
|
int gk_sigtrap(); |
||||||
|
int gk_siguntrap(); |
||||||
|
void gk_sigthrow(int signum); |
||||||
|
void gk_SetSignalHandlers(); |
||||||
|
void gk_UnsetSignalHandlers(); |
||||||
|
void gk_NonLocalExit_Handler(int signum); |
||||||
|
char *gk_strerror(int errnum); |
||||||
|
void PrintBackTrace(); |
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* util.c |
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
void gk_RandomPermute(size_t, int *, int); |
||||||
|
void gk_array2csr(size_t n, size_t range, int *array, int *ptr, int *ind); |
||||||
|
int gk_log2(int); |
||||||
|
int gk_ispow2(int); |
||||||
|
float gk_flog2(float); |
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* time.c |
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
gk_wclock_t gk_WClockSeconds(void); |
||||||
|
double gk_CPUSeconds(void); |
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* string.c |
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
char *gk_strchr_replace(char *str, char *fromlist, char *tolist); |
||||||
|
int gk_strstr_replace(char *str, char *pattern, char *replacement, char *options, char **new_str); |
||||||
|
char *gk_strtprune(char *, char *); |
||||||
|
char *gk_strhprune(char *, char *); |
||||||
|
char *gk_strtoupper(char *);
|
||||||
|
char *gk_strtolower(char *);
|
||||||
|
char *gk_strdup(char *orgstr); |
||||||
|
int gk_strcasecmp(char *s1, char *s2); |
||||||
|
int gk_strrcmp(char *s1, char *s2); |
||||||
|
char *gk_time2str(time_t time); |
||||||
|
time_t gk_str2time(char *str); |
||||||
|
int gk_GetStringID(gk_StringMap_t *strmap, char *key); |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* sort.c
|
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
void gk_csorti(size_t, char *); |
||||||
|
void gk_csortd(size_t, char *); |
||||||
|
void gk_isorti(size_t, int *); |
||||||
|
void gk_isortd(size_t, int *); |
||||||
|
void gk_i32sorti(size_t, int32_t *); |
||||||
|
void gk_i32sortd(size_t, int32_t *); |
||||||
|
void gk_i64sorti(size_t, int64_t *); |
||||||
|
void gk_i64sortd(size_t, int64_t *); |
||||||
|
void gk_ui32sorti(size_t, uint32_t *); |
||||||
|
void gk_ui32sortd(size_t, uint32_t *); |
||||||
|
void gk_ui64sorti(size_t, uint64_t *); |
||||||
|
void gk_ui64sortd(size_t, uint64_t *); |
||||||
|
void gk_fsorti(size_t, float *); |
||||||
|
void gk_fsortd(size_t, float *); |
||||||
|
void gk_dsorti(size_t, double *); |
||||||
|
void gk_dsortd(size_t, double *); |
||||||
|
void gk_idxsorti(size_t, gk_idx_t *); |
||||||
|
void gk_idxsortd(size_t, gk_idx_t *); |
||||||
|
void gk_ckvsorti(size_t, gk_ckv_t *); |
||||||
|
void gk_ckvsortd(size_t, gk_ckv_t *); |
||||||
|
void gk_ikvsorti(size_t, gk_ikv_t *); |
||||||
|
void gk_ikvsortd(size_t, gk_ikv_t *); |
||||||
|
void gk_i32kvsorti(size_t, gk_i32kv_t *); |
||||||
|
void gk_i32kvsortd(size_t, gk_i32kv_t *); |
||||||
|
void gk_i64kvsorti(size_t, gk_i64kv_t *); |
||||||
|
void gk_i64kvsortd(size_t, gk_i64kv_t *); |
||||||
|
void gk_zkvsorti(size_t, gk_zkv_t *); |
||||||
|
void gk_zkvsortd(size_t, gk_zkv_t *); |
||||||
|
void gk_zukvsorti(size_t, gk_zukv_t *); |
||||||
|
void gk_zukvsortd(size_t, gk_zukv_t *); |
||||||
|
void gk_fkvsorti(size_t, gk_fkv_t *); |
||||||
|
void gk_fkvsortd(size_t, gk_fkv_t *); |
||||||
|
void gk_dkvsorti(size_t, gk_dkv_t *); |
||||||
|
void gk_dkvsortd(size_t, gk_dkv_t *); |
||||||
|
void gk_skvsorti(size_t, gk_skv_t *); |
||||||
|
void gk_skvsortd(size_t, gk_skv_t *); |
||||||
|
void gk_idxkvsorti(size_t, gk_idxkv_t *); |
||||||
|
void gk_idxkvsortd(size_t, gk_idxkv_t *); |
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* Selection routines |
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
int gk_dfkvkselect(size_t, int, gk_fkv_t *); |
||||||
|
int gk_ifkvkselect(size_t, int, gk_fkv_t *); |
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* Priority queue
|
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
GK_MKPQUEUE_PROTO(gk_ipq, gk_ipq_t, int, gk_idx_t) |
||||||
|
GK_MKPQUEUE_PROTO(gk_i32pq, gk_i32pq_t, int32_t, gk_idx_t) |
||||||
|
GK_MKPQUEUE_PROTO(gk_i64pq, gk_i64pq_t, int64_t, gk_idx_t) |
||||||
|
GK_MKPQUEUE_PROTO(gk_fpq, gk_fpq_t, float, gk_idx_t) |
||||||
|
GK_MKPQUEUE_PROTO(gk_dpq, gk_dpq_t, double, gk_idx_t) |
||||||
|
GK_MKPQUEUE_PROTO(gk_idxpq, gk_idxpq_t, gk_idx_t, gk_idx_t) |
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* HTable routines |
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
gk_HTable_t *HTable_Create(int nelements); |
||||||
|
void HTable_Reset(gk_HTable_t *htable); |
||||||
|
void HTable_Resize(gk_HTable_t *htable, int nelements); |
||||||
|
void HTable_Insert(gk_HTable_t *htable, int key, int val); |
||||||
|
void HTable_Delete(gk_HTable_t *htable, int key); |
||||||
|
int HTable_Search(gk_HTable_t *htable, int key); |
||||||
|
int HTable_GetNext(gk_HTable_t *htable, int key, int *val, int type); |
||||||
|
int HTable_SearchAndDelete(gk_HTable_t *htable, int key); |
||||||
|
void HTable_Destroy(gk_HTable_t *htable); |
||||||
|
int HTable_HFunction(int nelements, int key); |
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* Tokenizer routines |
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
void gk_strtokenize(char *line, char *delim, gk_Tokens_t *tokens); |
||||||
|
void gk_freetokenslist(gk_Tokens_t *tokens); |
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* Encoder/Decoder |
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
void encodeblock(unsigned char *in, unsigned char *out); |
||||||
|
void decodeblock(unsigned char *in, unsigned char *out); |
||||||
|
void GKEncodeBase64(int nbytes, unsigned char *inbuffer, unsigned char *outbuffer); |
||||||
|
void GKDecodeBase64(int nbytes, unsigned char *inbuffer, unsigned char *outbuffer); |
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* random.c |
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
GK_MKRANDOM_PROTO(gk_c, size_t, char) |
||||||
|
GK_MKRANDOM_PROTO(gk_i, size_t, int) |
||||||
|
GK_MKRANDOM_PROTO(gk_i32, size_t, int32_t) |
||||||
|
GK_MKRANDOM_PROTO(gk_f, size_t, float) |
||||||
|
GK_MKRANDOM_PROTO(gk_d, size_t, double) |
||||||
|
GK_MKRANDOM_PROTO(gk_idx, size_t, gk_idx_t) |
||||||
|
GK_MKRANDOM_PROTO(gk_z, size_t, ssize_t) |
||||||
|
GK_MKRANDOM_PROTO(gk_zu, size_t, size_t) |
||||||
|
void gk_randinit(uint64_t); |
||||||
|
uint64_t gk_randint64(void); |
||||||
|
uint32_t gk_randint32(void); |
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* OpenMP fake functions |
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
#if !defined(__OPENMP__) |
||||||
|
void omp_set_num_threads(int num_threads); |
||||||
|
int omp_get_num_threads(void); |
||||||
|
int omp_get_max_threads(void); |
||||||
|
int omp_get_thread_num(void); |
||||||
|
int omp_get_num_procs(void); |
||||||
|
int omp_in_parallel(void); |
||||||
|
void omp_set_dynamic(int num_threads); |
||||||
|
int omp_get_dynamic(void); |
||||||
|
void omp_set_nested(int nested); |
||||||
|
int omp_get_nested(void); |
||||||
|
#endif /* __OPENMP__ */ |
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* CSR-related functions |
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
gk_csr_t *gk_csr_Create(); |
||||||
|
void gk_csr_Init(gk_csr_t *mat); |
||||||
|
void gk_csr_Free(gk_csr_t **mat); |
||||||
|
void gk_csr_FreeContents(gk_csr_t *mat); |
||||||
|
gk_csr_t *gk_csr_Dup(gk_csr_t *mat); |
||||||
|
gk_csr_t *gk_csr_ExtractSubmatrix(gk_csr_t *mat, int rstart, int nrows); |
||||||
|
gk_csr_t *gk_csr_ExtractRows(gk_csr_t *mat, int nrows, int *rind); |
||||||
|
gk_csr_t *gk_csr_ExtractPartition(gk_csr_t *mat, int *part, int pid); |
||||||
|
gk_csr_t **gk_csr_Split(gk_csr_t *mat, int *color); |
||||||
|
int gk_csr_DetermineFormat(char *filename, int format); |
||||||
|
gk_csr_t *gk_csr_Read(char *filename, int format, int readvals, int numbering); |
||||||
|
void gk_csr_Write(gk_csr_t *mat, char *filename, int format, int writevals, int numbering); |
||||||
|
gk_csr_t *gk_csr_Prune(gk_csr_t *mat, int what, int minf, int maxf); |
||||||
|
gk_csr_t *gk_csr_LowFilter(gk_csr_t *mat, int what, int norm, float fraction); |
||||||
|
gk_csr_t *gk_csr_TopKPlusFilter(gk_csr_t *mat, int what, int topk, float keepval); |
||||||
|
gk_csr_t *gk_csr_ZScoreFilter(gk_csr_t *mat, int what, float zscore); |
||||||
|
void gk_csr_CompactColumns(gk_csr_t *mat); |
||||||
|
void gk_csr_SortIndices(gk_csr_t *mat, int what); |
||||||
|
void gk_csr_CreateIndex(gk_csr_t *mat, int what); |
||||||
|
void gk_csr_Normalize(gk_csr_t *mat, int what, int norm); |
||||||
|
void gk_csr_Scale(gk_csr_t *mat, int type); |
||||||
|
void gk_csr_ComputeSums(gk_csr_t *mat, int what); |
||||||
|
void gk_csr_ComputeNorms(gk_csr_t *mat, int what); |
||||||
|
void gk_csr_ComputeSquaredNorms(gk_csr_t *mat, int what); |
||||||
|
gk_csr_t *gk_csr_Shuffle(gk_csr_t *mat, int what, int summetric); |
||||||
|
gk_csr_t *gk_csr_Transpose(gk_csr_t *mat); |
||||||
|
float gk_csr_ComputeSimilarity(gk_csr_t *mat, int i1, int i2, int what, int simtype); |
||||||
|
float gk_csr_ComputePairSimilarity(gk_csr_t *mat_a, gk_csr_t *mat_b, int i1, int i2, int what, int simtype); |
||||||
|
int gk_csr_GetSimilarRows(gk_csr_t *mat, int nqterms, int *qind, float *qval, |
||||||
|
int simtype, int nsim, float minsim, gk_fkv_t *hits, int *_imarker, |
||||||
|
gk_fkv_t *i_cand); |
||||||
|
int gk_csr_FindConnectedComponents(gk_csr_t *mat, int32_t *cptr, int32_t *cind, |
||||||
|
int32_t *cids); |
||||||
|
gk_csr_t *gk_csr_MakeSymmetric(gk_csr_t *mat, int op); |
||||||
|
gk_csr_t *gk_csr_ReorderSymmetric(gk_csr_t *mat, int32_t *perm, int32_t *iperm); |
||||||
|
void gk_csr_ComputeBFSOrderingSymmetric(gk_csr_t *mat, int maxdegree, int v,
|
||||||
|
int32_t **r_perm, int32_t **r_iperm); |
||||||
|
void gk_csr_ComputeBestFOrderingSymmetric(gk_csr_t *mat, int v, int type, |
||||||
|
int32_t **r_perm, int32_t **r_iperm); |
||||||
|
|
||||||
|
|
||||||
|
/* itemsets.c */ |
||||||
|
void gk_find_frequent_itemsets(int ntrans, ssize_t *tranptr, int *tranind, |
||||||
|
int minfreq, int maxfreq, int minlen, int maxlen, |
||||||
|
void (*process_itemset)(void *stateptr, int nitems, int *itemind, |
||||||
|
int ntrans, int *tranind), |
||||||
|
void *stateptr); |
||||||
|
|
||||||
|
|
||||||
|
/* evaluate.c */ |
||||||
|
float ComputeAccuracy(int n, gk_fkv_t *list); |
||||||
|
float ComputeROCn(int n, int maxN, gk_fkv_t *list); |
||||||
|
float ComputeMedianRFP(int n, gk_fkv_t *list); |
||||||
|
float ComputeMean (int n, float *values); |
||||||
|
float ComputeStdDev(int n, float *values); |
||||||
|
|
||||||
|
|
||||||
|
/* mcore.c */ |
||||||
|
gk_mcore_t *gk_mcoreCreate(size_t coresize); |
||||||
|
gk_mcore_t *gk_gkmcoreCreate(); |
||||||
|
void gk_mcoreDestroy(gk_mcore_t **r_mcore, int showstats); |
||||||
|
void gk_gkmcoreDestroy(gk_mcore_t **r_mcore, int showstats); |
||||||
|
void *gk_mcoreMalloc(gk_mcore_t *mcore, size_t nbytes); |
||||||
|
void gk_mcorePush(gk_mcore_t *mcore); |
||||||
|
void gk_gkmcorePush(gk_mcore_t *mcore); |
||||||
|
void gk_mcorePop(gk_mcore_t *mcore); |
||||||
|
void gk_gkmcorePop(gk_mcore_t *mcore); |
||||||
|
void gk_mcoreAdd(gk_mcore_t *mcore, int type, size_t nbytes, void *ptr); |
||||||
|
void gk_gkmcoreAdd(gk_mcore_t *mcore, int type, size_t nbytes, void *ptr); |
||||||
|
void gk_mcoreDel(gk_mcore_t *mcore, void *ptr); |
||||||
|
void gk_gkmcoreDel(gk_mcore_t *mcore, void *ptr); |
||||||
|
|
||||||
|
/* rw.c */ |
||||||
|
int gk_rw_PageRank(gk_csr_t *mat, float lamda, float eps, int max_niter, float *pr); |
||||||
|
|
||||||
|
|
||||||
|
/* graph.c */ |
||||||
|
gk_graph_t *gk_graph_Create(); |
||||||
|
void gk_graph_Init(gk_graph_t *graph); |
||||||
|
void gk_graph_Free(gk_graph_t **graph); |
||||||
|
void gk_graph_FreeContents(gk_graph_t *graph); |
||||||
|
gk_graph_t *gk_graph_Read(char *filename, int format, int hasvals,
|
||||||
|
int numbering, int isfewgts, int isfvwgts, int isfvsizes); |
||||||
|
void gk_graph_Write(gk_graph_t *graph, char *filename, int format, int numbering); |
||||||
|
gk_graph_t *gk_graph_Dup(gk_graph_t *graph); |
||||||
|
gk_graph_t *gk_graph_Transpose(gk_graph_t *graph); |
||||||
|
gk_graph_t *gk_graph_ExtractSubgraph(gk_graph_t *graph, int vstart, int nvtxs); |
||||||
|
gk_graph_t *gk_graph_Reorder(gk_graph_t *graph, int32_t *perm, int32_t *iperm); |
||||||
|
int gk_graph_FindComponents(gk_graph_t *graph, int32_t *cptr, int32_t *cind); |
||||||
|
void gk_graph_ComputeBFSOrdering(gk_graph_t *graph, int v, int32_t **r_perm,
|
||||||
|
int32_t **r_iperm); |
||||||
|
void gk_graph_ComputeBestFOrdering0(gk_graph_t *graph, int v, int type, |
||||||
|
int32_t **r_perm, int32_t **r_iperm); |
||||||
|
void gk_graph_ComputeBestFOrdering(gk_graph_t *graph, int v, int type, |
||||||
|
int32_t **r_perm, int32_t **r_iperm); |
||||||
|
void gk_graph_SingleSourceShortestPaths(gk_graph_t *graph, int v, void **r_sps); |
||||||
|
void gk_graph_SortAdjacencies(gk_graph_t *graph); |
||||||
|
gk_graph_t *gk_graph_MakeSymmetric(gk_graph_t *graph, int op); |
||||||
|
|
||||||
|
|
||||||
|
/* cache.c */ |
||||||
|
gk_cache_t *gk_cacheCreate(uint32_t nway, uint32_t lnbits, size_t cnbits); |
||||||
|
void gk_cacheReset(gk_cache_t *cache); |
||||||
|
void gk_cacheDestroy(gk_cache_t **r_cache); |
||||||
|
int gk_cacheLoad(gk_cache_t *cache, size_t addr); |
||||||
|
double gk_cacheGetHitRate(gk_cache_t *cache); |
||||||
|
|
||||||
|
|
||||||
|
#ifdef __cplusplus |
||||||
|
} |
||||||
|
#endif |
||||||
|
|
||||||
|
|
||||||
|
#endif |
||||||
|
|
||||||
@ -0,0 +1,296 @@ |
|||||||
|
/*!
|
||||||
|
\file gk_struct.h |
||||||
|
\brief This file contains various datastructures used/provided by GKlib |
||||||
|
|
||||||
|
\date Started 3/27/2007 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: gk_struct.h 21988 2018-04-16 00:11:19Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
#ifndef _GK_STRUCT_H_ |
||||||
|
#define _GK_STRUCT_H_ |
||||||
|
|
||||||
|
|
||||||
|
/********************************************************************/ |
||||||
|
/*! Generator for gk_??KeyVal_t data structure */ |
||||||
|
/********************************************************************/ |
||||||
|
#define GK_MKKEYVALUE_T(NAME, KEYTYPE, VALTYPE) \ |
||||||
|
typedef struct {\
|
||||||
|
KEYTYPE key;\
|
||||||
|
VALTYPE val;\
|
||||||
|
} NAME;\
|
||||||
|
|
||||||
|
/* The actual KeyVal data structures */ |
||||||
|
GK_MKKEYVALUE_T(gk_ckv_t, char, ssize_t) |
||||||
|
GK_MKKEYVALUE_T(gk_ikv_t, int, ssize_t) |
||||||
|
GK_MKKEYVALUE_T(gk_i8kv_t, int8_t, ssize_t) |
||||||
|
GK_MKKEYVALUE_T(gk_i16kv_t, int16_t, ssize_t) |
||||||
|
GK_MKKEYVALUE_T(gk_i32kv_t, int32_t, ssize_t) |
||||||
|
GK_MKKEYVALUE_T(gk_i64kv_t, int64_t, ssize_t) |
||||||
|
GK_MKKEYVALUE_T(gk_zkv_t, ssize_t, ssize_t) |
||||||
|
GK_MKKEYVALUE_T(gk_zukv_t, size_t, ssize_t) |
||||||
|
GK_MKKEYVALUE_T(gk_fkv_t, float, ssize_t) |
||||||
|
GK_MKKEYVALUE_T(gk_dkv_t, double, ssize_t) |
||||||
|
GK_MKKEYVALUE_T(gk_skv_t, char *, ssize_t) |
||||||
|
GK_MKKEYVALUE_T(gk_idxkv_t, gk_idx_t, gk_idx_t) |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/********************************************************************/ |
||||||
|
/*! Generator for gk_?pq_t data structure */ |
||||||
|
/********************************************************************/ |
||||||
|
#define GK_MKPQUEUE_T(NAME, KVTYPE)\ |
||||||
|
typedef struct {\
|
||||||
|
size_t nnodes;\
|
||||||
|
size_t maxnodes;\
|
||||||
|
\
|
||||||
|
/* Heap version of the data structure */ \
|
||||||
|
KVTYPE *heap;\
|
||||||
|
ssize_t *locator;\
|
||||||
|
} NAME;\
|
||||||
|
|
||||||
|
GK_MKPQUEUE_T(gk_ipq_t, gk_ikv_t) |
||||||
|
GK_MKPQUEUE_T(gk_i32pq_t, gk_i32kv_t) |
||||||
|
GK_MKPQUEUE_T(gk_i64pq_t, gk_i64kv_t) |
||||||
|
GK_MKPQUEUE_T(gk_fpq_t, gk_fkv_t) |
||||||
|
GK_MKPQUEUE_T(gk_dpq_t, gk_dkv_t) |
||||||
|
GK_MKPQUEUE_T(gk_idxpq_t, gk_idxkv_t) |
||||||
|
|
||||||
|
|
||||||
|
#define GK_MKPQUEUE2_T(NAME, KTYPE, VTYPE)\ |
||||||
|
typedef struct {\
|
||||||
|
ssize_t nnodes;\
|
||||||
|
ssize_t maxnodes;\
|
||||||
|
\
|
||||||
|
/* Heap version of the data structure */ \
|
||||||
|
KTYPE *keys;\
|
||||||
|
VTYPE *vals;\
|
||||||
|
} NAME;\
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* The following data structure stores a sparse CSR format |
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
typedef struct gk_csr_t { |
||||||
|
int32_t nrows, ncols; |
||||||
|
ssize_t *rowptr, *colptr; |
||||||
|
int32_t *rowind, *colind; |
||||||
|
int32_t *rowids, *colids; |
||||||
|
int32_t *rlabels, *clabels; |
||||||
|
int32_t *rmap, *cmap; |
||||||
|
float *rowval, *colval; |
||||||
|
float *rnorms, *cnorms; |
||||||
|
float *rsums, *csums; |
||||||
|
float *rsizes, *csizes; |
||||||
|
float *rvols, *cvols; |
||||||
|
float *rwgts, *cwgts; |
||||||
|
} gk_csr_t; |
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* The following data structure stores a sparse graph
|
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
typedef struct gk_graph_t { |
||||||
|
int32_t nvtxs; /*!< The number of vertices in the graph */ |
||||||
|
ssize_t *xadj; /*!< The ptr-structure of the adjncy list */ |
||||||
|
int32_t *adjncy; /*!< The adjacency list of the graph */ |
||||||
|
int32_t *iadjwgt; /*!< The integer edge weights */ |
||||||
|
float *fadjwgt; /*!< The floating point edge weights */ |
||||||
|
int32_t *ivwgts; /*!< The integer vertex weights */ |
||||||
|
float *fvwgts; /*!< The floating point vertex weights */ |
||||||
|
int32_t *ivsizes; /*!< The integer vertex sizes */ |
||||||
|
float *fvsizes; /*!< The floating point vertex sizes */ |
||||||
|
int32_t *vlabels; /*!< The labels of the vertices */ |
||||||
|
} gk_graph_t; |
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* The following data structure stores stores a string as a
|
||||||
|
* pair of its allocated buffer and the buffer itself. |
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
typedef struct gk_str_t { |
||||||
|
size_t len; |
||||||
|
char *buf; |
||||||
|
} gk_str_t; |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------
|
||||||
|
* The following data structure implements a string-2-int mapping |
||||||
|
* table used for parsing command-line options |
||||||
|
*-------------------------------------------------------------*/ |
||||||
|
typedef struct gk_StringMap_t { |
||||||
|
char *name; |
||||||
|
int id; |
||||||
|
} gk_StringMap_t; |
||||||
|
|
||||||
|
|
||||||
|
/*------------------------------------------------------------
|
||||||
|
* This structure implements a simple hash table |
||||||
|
*------------------------------------------------------------*/ |
||||||
|
typedef struct gk_HTable_t { |
||||||
|
int nelements; /* The overall size of the hash-table */ |
||||||
|
int htsize; /* The current size of the hash-table */ |
||||||
|
gk_ikv_t *harray; /* The actual hash-table */ |
||||||
|
} gk_HTable_t; |
||||||
|
|
||||||
|
|
||||||
|
/*------------------------------------------------------------
|
||||||
|
* This structure implements a gk_Tokens_t list returned by the |
||||||
|
* string tokenizer |
||||||
|
*------------------------------------------------------------*/ |
||||||
|
typedef struct gk_Tokens_t { |
||||||
|
int ntoks; /* The number of tokens in the input string */ |
||||||
|
char *strbuf; /* The memory that stores all the entries */ |
||||||
|
char **list; /* Pointers to the strbuf for each element */ |
||||||
|
} gk_Tokens_t; |
||||||
|
|
||||||
|
|
||||||
|
/*------------------------------------------------------------
|
||||||
|
* This structure implements storage for an atom in a pdb file |
||||||
|
*------------------------------------------------------------*/ |
||||||
|
typedef struct atom { |
||||||
|
int serial; |
||||||
|
char *name; |
||||||
|
char altLoc; |
||||||
|
char *resname; |
||||||
|
char chainid;
|
||||||
|
int rserial; |
||||||
|
char icode; |
||||||
|
char element; |
||||||
|
double x; |
||||||
|
double y; |
||||||
|
double z; |
||||||
|
double opcy; |
||||||
|
double tmpt; |
||||||
|
} atom; |
||||||
|
|
||||||
|
|
||||||
|
/*------------------------------------------------------------
|
||||||
|
* This structure implements storage for a center of mass for |
||||||
|
* a single residue. |
||||||
|
*------------------------------------------------------------*/ |
||||||
|
typedef struct center_of_mass { |
||||||
|
char name; |
||||||
|
double x; |
||||||
|
double y; |
||||||
|
double z; |
||||||
|
} center_of_mass; |
||||||
|
|
||||||
|
|
||||||
|
/*------------------------------------------------------------
|
||||||
|
* This structure implements storage for a pdb protein
|
||||||
|
*------------------------------------------------------------*/ |
||||||
|
typedef struct pdbf { |
||||||
|
int natoms; /* Number of atoms */ |
||||||
|
int nresidues; /* Number of residues based on coordinates */ |
||||||
|
int ncas; |
||||||
|
int nbbs; |
||||||
|
int corruption; |
||||||
|
char *resSeq; /* Residue sequence based on coordinates */ |
||||||
|
char **threeresSeq; /* three-letter residue sequence */ |
||||||
|
atom *atoms; |
||||||
|
atom **bbs; |
||||||
|
atom **cas; |
||||||
|
center_of_mass *cm; |
||||||
|
} pdbf; |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************
|
||||||
|
* Localization Structures for converting characters to integers |
||||||
|
**************************************************************/ |
||||||
|
typedef struct gk_i2cc2i_t { |
||||||
|
int n; |
||||||
|
char *i2c; |
||||||
|
int *c2i; |
||||||
|
} gk_i2cc2i_t; |
||||||
|
|
||||||
|
|
||||||
|
/*******************************************************************
|
||||||
|
*This structure implements storage of a protein sequence |
||||||
|
* *****************************************************************/ |
||||||
|
typedef struct gk_seq_t { |
||||||
|
|
||||||
|
int len; /*Number of Residues */ |
||||||
|
int *sequence; /* Stores the sequence*/ |
||||||
|
|
||||||
|
|
||||||
|
int **pssm; /* Stores the pssm matrix */ |
||||||
|
int **psfm; /* Stores the psfm matrix */ |
||||||
|
char *name; /* Stores the name of the sequence */ |
||||||
|
|
||||||
|
int nsymbols; |
||||||
|
|
||||||
|
|
||||||
|
} gk_seq_t; |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! The following data structure stores information about a memory
|
||||||
|
allocation operation that can either be served from gk_mcore_t or by |
||||||
|
a gk_malloc if not sufficient workspace memory is available. */ |
||||||
|
/*************************************************************************/ |
||||||
|
typedef struct gk_mop_t { |
||||||
|
int type; |
||||||
|
ssize_t nbytes; |
||||||
|
void *ptr; |
||||||
|
} gk_mop_t; |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! The following structure defines the mcore for GKlib's customized
|
||||||
|
memory allocations. */ |
||||||
|
/*************************************************************************/ |
||||||
|
typedef struct gk_mcore_t { |
||||||
|
/* Workspace information */ |
||||||
|
size_t coresize; /*!< The amount of core memory that has been allocated */ |
||||||
|
size_t corecpos; /*!< Index of the first free location in core */ |
||||||
|
void *core; /*!< Pointer to the core itself */ |
||||||
|
|
||||||
|
/* These are for implementing a stack-based allocation scheme using both
|
||||||
|
core and also dynamically allocated memory */ |
||||||
|
size_t nmops; /*!< The number of maop_t entries that have been allocated */ |
||||||
|
size_t cmop; /*!< Index of the first free location in maops */ |
||||||
|
gk_mop_t *mops; /*!< The array recording the maop_t operations */ |
||||||
|
|
||||||
|
/* These are for keeping various statistics for wspacemalloc */ |
||||||
|
size_t num_callocs; /*!< The number of core mallocs */ |
||||||
|
size_t num_hallocs; /*!< The number of heap mallocs */ |
||||||
|
size_t size_callocs; /*!< The total # of bytes in core mallocs */ |
||||||
|
size_t size_hallocs; /*!< The total # of bytes in heap mallocs */ |
||||||
|
size_t cur_callocs; /*!< The current # of bytes in core mallocs */ |
||||||
|
size_t cur_hallocs; /*!< The current # of bytes in heap mallocs */ |
||||||
|
size_t max_callocs; /*!< The maximum # of bytes in core mallocs at any given time */ |
||||||
|
size_t max_hallocs; /*!< The maximum # of bytes in heap mallocs at any given time */ |
||||||
|
|
||||||
|
} gk_mcore_t; |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! The following structure is used for cache simulation for performance
|
||||||
|
modeling and analysis. */ |
||||||
|
/*************************************************************************/ |
||||||
|
typedef struct gk_cache_t { |
||||||
|
/*! The total cache is nway*(2^(cnbits+lnbits)) bytes */ |
||||||
|
uint32_t nway; /*!< the associativity of the cache */ |
||||||
|
uint32_t lnbits; /*!< the number of address bits indexing the cache line */ |
||||||
|
uint32_t cnbits; /*!< the number of address bits indexing the cache */ |
||||||
|
size_t csize; /*!< 2^cnbits */ |
||||||
|
size_t cmask; /*!< csize-1 */ |
||||||
|
|
||||||
|
uint64_t clock; /*!< a clock in terms of accesses */ |
||||||
|
|
||||||
|
uint64_t *latimes; /*!< a cacheline-level last access time */ |
||||||
|
size_t *clines; /*!< the cache in terms of cachelines */ |
||||||
|
|
||||||
|
uint64_t nhits; /*!< counts the number of hits */ |
||||||
|
uint64_t nmisses; /*!< counts the number of misses */ |
||||||
|
} gk_cache_t; |
||||||
|
|
||||||
|
|
||||||
|
#endif |
||||||
@ -0,0 +1,38 @@ |
|||||||
|
/*!
|
||||||
|
\file gk_types.h |
||||||
|
\brief This file contains basic scalar datatype used in GKlib |
||||||
|
|
||||||
|
\date Started 3/27/2007 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: gk_types.h 10711 2011-08-31 22:23:04Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
#ifndef _GK_TYPES_H_ |
||||||
|
#define _GK_TYPES_H_ |
||||||
|
|
||||||
|
/*************************************************************************
|
||||||
|
* Basic data type definitions. These definitions allow GKlib to separate |
||||||
|
* the following elemental types: |
||||||
|
* - loop iterator variables, which are set to size_t |
||||||
|
* - signed and unsigned int variables that can be set to any # of bits |
||||||
|
* - signed and unsigned long variables that can be set to any # of bits |
||||||
|
* - real variables, which can be set to single or double precision. |
||||||
|
**************************************************************************/ |
||||||
|
/*typedef ptrdiff_t gk_idx_t; */ /* index variable */ |
||||||
|
typedef ssize_t gk_idx_t; /* index variable */ |
||||||
|
typedef int32_t gk_int_t; /* integer values */ |
||||||
|
typedef uint32_t gk_uint_t; /* unsigned integer values */ |
||||||
|
typedef int64_t gk_long_t; /* long integer values */ |
||||||
|
typedef uint64_t gk_ulong_t; /* unsigned long integer values */ |
||||||
|
typedef float gk_real_t; /* real type */ |
||||||
|
typedef double gk_dreal_t; /* double precission real type */ |
||||||
|
typedef double gk_wclock_t; /* wall-clock time */ |
||||||
|
|
||||||
|
/*#define GK_IDX_MAX PTRDIFF_MAX*/ |
||||||
|
#define GK_IDX_MAX ((SIZE_MAX>>1)-2) |
||||||
|
|
||||||
|
#define PRIGKIDX "zd" |
||||||
|
#define SCNGKIDX "zd" |
||||||
|
|
||||||
|
|
||||||
|
#endif |
||||||
@ -0,0 +1,107 @@ |
|||||||
|
/*!
|
||||||
|
\file util.c |
||||||
|
\brief Various utility routines |
||||||
|
|
||||||
|
\date Started 4/12/2007 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: gk_util.c 16223 2014-02-15 21:34:09Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************
|
||||||
|
* This file randomly permutes the contents of an array. |
||||||
|
* flag == 0, don't initialize perm |
||||||
|
* flag == 1, set p[i] = i
|
||||||
|
**************************************************************************/ |
||||||
|
void gk_RandomPermute(size_t n, int *p, int flag) |
||||||
|
{ |
||||||
|
size_t i, u, v; |
||||||
|
int tmp; |
||||||
|
|
||||||
|
if (flag == 1) { |
||||||
|
for (i=0; i<n; i++) |
||||||
|
p[i] = i; |
||||||
|
} |
||||||
|
|
||||||
|
for (i=0; i<n/2; i++) { |
||||||
|
v = RandomInRange(n); |
||||||
|
u = RandomInRange(n); |
||||||
|
gk_SWAP(p[v], p[u], tmp); |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/************************************************************************/ |
||||||
|
/*!
|
||||||
|
\brief Converts an element-based set membership into a CSR-format set-based |
||||||
|
membership. |
||||||
|
|
||||||
|
For example, it takes an array such as part[] that stores where each
|
||||||
|
element belongs to and returns a pair of arrays (pptr[], pind[]) that
|
||||||
|
store in CSF format the list of elements belonging in each partition. |
||||||
|
|
||||||
|
\param n
|
||||||
|
the number of elements in the array (e.g., # of vertices) |
||||||
|
\param range
|
||||||
|
the cardinality of the set (e.g., # of partitions) |
||||||
|
\param array |
||||||
|
the array that stores the per-element set membership |
||||||
|
\param ptr |
||||||
|
the array that will store the starting indices in ind for |
||||||
|
the elements of each set. This is filled by the routine and |
||||||
|
its size should be at least range+1. |
||||||
|
\param ind |
||||||
|
the array that stores consecutively which elements belong to |
||||||
|
each set. The size of this array should be n. |
||||||
|
*/ |
||||||
|
/************************************************************************/ |
||||||
|
void gk_array2csr(size_t n, size_t range, int *array, int *ptr, int *ind) |
||||||
|
{ |
||||||
|
size_t i; |
||||||
|
|
||||||
|
gk_iset(range+1, 0, ptr); |
||||||
|
|
||||||
|
for (i=0; i<n; i++)
|
||||||
|
ptr[array[i]]++; |
||||||
|
|
||||||
|
/* Compute the ptr, ind structure */ |
||||||
|
MAKECSR(i, range, ptr); |
||||||
|
for (i=0; i<n; i++) |
||||||
|
ind[ptr[array[i]]++] = i; |
||||||
|
SHIFTCSR(i, range, ptr); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************
|
||||||
|
* This function returns the log2(x) |
||||||
|
**************************************************************************/ |
||||||
|
int gk_log2(int a) |
||||||
|
{ |
||||||
|
size_t i; |
||||||
|
|
||||||
|
for (i=1; a > 1; i++, a = a>>1); |
||||||
|
return i-1; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************
|
||||||
|
* This function checks if the argument is a power of 2 |
||||||
|
**************************************************************************/ |
||||||
|
int gk_ispow2(int a) |
||||||
|
{ |
||||||
|
return (a == (1<<gk_log2(a))); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************
|
||||||
|
* This function returns the log2(x) |
||||||
|
**************************************************************************/ |
||||||
|
float gk_flog2(float a) |
||||||
|
{ |
||||||
|
return log(a)/log(2.0); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
@ -0,0 +1,247 @@ |
|||||||
|
/*
|
||||||
|
* Copyright 2004, Regents of the University of Minnesota |
||||||
|
* |
||||||
|
* This file contains routines for manipulating a direct-access hash table |
||||||
|
* |
||||||
|
* Started 3/22/04 |
||||||
|
* George |
||||||
|
* |
||||||
|
*/ |
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
/******************************************************************************
|
||||||
|
* This function creates the hash-table |
||||||
|
*******************************************************************************/ |
||||||
|
gk_HTable_t *HTable_Create(int nelements) |
||||||
|
{ |
||||||
|
gk_HTable_t *htable; |
||||||
|
|
||||||
|
htable = gk_malloc(sizeof(gk_HTable_t), "HTable_Create: htable"); |
||||||
|
htable->harray = gk_ikvmalloc(nelements, "HTable_Create: harray"); |
||||||
|
htable->nelements = nelements; |
||||||
|
|
||||||
|
HTable_Reset(htable); |
||||||
|
|
||||||
|
return htable; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/******************************************************************************
|
||||||
|
* This function resets the data-structures associated with the hash-table |
||||||
|
*******************************************************************************/ |
||||||
|
void HTable_Reset(gk_HTable_t *htable) |
||||||
|
{ |
||||||
|
int i; |
||||||
|
|
||||||
|
for (i=0; i<htable->nelements; i++) |
||||||
|
htable->harray[i].key = HTABLE_EMPTY; |
||||||
|
htable->htsize = 0; |
||||||
|
|
||||||
|
} |
||||||
|
|
||||||
|
/******************************************************************************
|
||||||
|
* This function resizes the hash-table |
||||||
|
*******************************************************************************/ |
||||||
|
void HTable_Resize(gk_HTable_t *htable, int nelements) |
||||||
|
{ |
||||||
|
int i, old_nelements; |
||||||
|
gk_ikv_t *old_harray; |
||||||
|
|
||||||
|
old_nelements = htable->nelements; |
||||||
|
old_harray = htable->harray; |
||||||
|
|
||||||
|
/* prepare larger hash */ |
||||||
|
htable->nelements = nelements; |
||||||
|
htable->htsize = 0; |
||||||
|
htable->harray = gk_ikvmalloc(nelements, "HTable_Resize: harray"); |
||||||
|
for (i=0; i<nelements; i++) |
||||||
|
htable->harray[i].key = HTABLE_EMPTY; |
||||||
|
|
||||||
|
/* reassign the values */ |
||||||
|
for (i=0; i<old_nelements; i++) |
||||||
|
if (old_harray[i].key != HTABLE_EMPTY) |
||||||
|
HTable_Insert(htable, old_harray[i].key, old_harray[i].val); |
||||||
|
|
||||||
|
/* remove old harray */ |
||||||
|
gk_free((void **)&old_harray, LTERM); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/******************************************************************************
|
||||||
|
* This function inserts a key-value pair in the array |
||||||
|
*******************************************************************************/ |
||||||
|
void HTable_Insert(gk_HTable_t *htable, int key, int val) |
||||||
|
{ |
||||||
|
int i, first; |
||||||
|
|
||||||
|
if (htable->htsize > htable->nelements/2) |
||||||
|
HTable_Resize(htable, 2*htable->nelements); |
||||||
|
|
||||||
|
first = HTable_HFunction(htable->nelements, key); |
||||||
|
|
||||||
|
for (i=first; i<htable->nelements; i++) { |
||||||
|
if (htable->harray[i].key == HTABLE_EMPTY || htable->harray[i].key == HTABLE_DELETED) { |
||||||
|
htable->harray[i].key = key; |
||||||
|
htable->harray[i].val = val; |
||||||
|
htable->htsize++; |
||||||
|
return; |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
for (i=0; i<first; i++) { |
||||||
|
if (htable->harray[i].key == HTABLE_EMPTY || htable->harray[i].key == HTABLE_DELETED) { |
||||||
|
htable->harray[i].key = key; |
||||||
|
htable->harray[i].val = val; |
||||||
|
htable->htsize++; |
||||||
|
return; |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/******************************************************************************
|
||||||
|
* This function deletes key from the htable |
||||||
|
*******************************************************************************/ |
||||||
|
void HTable_Delete(gk_HTable_t *htable, int key) |
||||||
|
{ |
||||||
|
int i, first; |
||||||
|
|
||||||
|
first = HTable_HFunction(htable->nelements, key); |
||||||
|
|
||||||
|
for (i=first; i<htable->nelements; i++) { |
||||||
|
if (htable->harray[i].key == key) { |
||||||
|
htable->harray[i].key = HTABLE_DELETED; |
||||||
|
htable->htsize--; |
||||||
|
return; |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
for (i=0; i<first; i++) { |
||||||
|
if (htable->harray[i].key == key) { |
||||||
|
htable->harray[i].key = HTABLE_DELETED; |
||||||
|
htable->htsize--; |
||||||
|
return; |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/******************************************************************************
|
||||||
|
* This function returns the data associated with the key in the hastable |
||||||
|
*******************************************************************************/ |
||||||
|
int HTable_Search(gk_HTable_t *htable, int key) |
||||||
|
{ |
||||||
|
int i, first; |
||||||
|
|
||||||
|
first = HTable_HFunction(htable->nelements, key); |
||||||
|
|
||||||
|
for (i=first; i<htable->nelements; i++) { |
||||||
|
if (htable->harray[i].key == key)
|
||||||
|
return htable->harray[i].val; |
||||||
|
else if (htable->harray[i].key == HTABLE_EMPTY) |
||||||
|
return -1; |
||||||
|
} |
||||||
|
|
||||||
|
for (i=0; i<first; i++) { |
||||||
|
if (htable->harray[i].key == key)
|
||||||
|
return htable->harray[i].val; |
||||||
|
else if (htable->harray[i].key == HTABLE_EMPTY) |
||||||
|
return -1; |
||||||
|
} |
||||||
|
|
||||||
|
return -1; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/******************************************************************************
|
||||||
|
* This function returns the next key/val |
||||||
|
*******************************************************************************/ |
||||||
|
int HTable_GetNext(gk_HTable_t *htable, int key, int *r_val, int type) |
||||||
|
{ |
||||||
|
int i; |
||||||
|
static int first, last; |
||||||
|
|
||||||
|
if (type == HTABLE_FIRST) |
||||||
|
first = last = HTable_HFunction(htable->nelements, key); |
||||||
|
|
||||||
|
if (first > last) { |
||||||
|
for (i=first; i<htable->nelements; i++) { |
||||||
|
if (htable->harray[i].key == key) { |
||||||
|
*r_val = htable->harray[i].val; |
||||||
|
first = i+1; |
||||||
|
return 1; |
||||||
|
} |
||||||
|
else if (htable->harray[i].key == HTABLE_EMPTY) |
||||||
|
return -1; |
||||||
|
} |
||||||
|
first = 0; |
||||||
|
} |
||||||
|
|
||||||
|
for (i=first; i<last; i++) { |
||||||
|
if (htable->harray[i].key == key) { |
||||||
|
*r_val = htable->harray[i].val; |
||||||
|
first = i+1; |
||||||
|
return 1; |
||||||
|
} |
||||||
|
else if (htable->harray[i].key == HTABLE_EMPTY) |
||||||
|
return -1; |
||||||
|
} |
||||||
|
|
||||||
|
return -1; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/******************************************************************************
|
||||||
|
* This function returns the data associated with the key in the hastable |
||||||
|
*******************************************************************************/ |
||||||
|
int HTable_SearchAndDelete(gk_HTable_t *htable, int key) |
||||||
|
{ |
||||||
|
int i, first; |
||||||
|
|
||||||
|
first = HTable_HFunction(htable->nelements, key); |
||||||
|
|
||||||
|
for (i=first; i<htable->nelements; i++) { |
||||||
|
if (htable->harray[i].key == key) { |
||||||
|
htable->harray[i].key = HTABLE_DELETED; |
||||||
|
htable->htsize--; |
||||||
|
return htable->harray[i].val; |
||||||
|
} |
||||||
|
else if (htable->harray[i].key == HTABLE_EMPTY) |
||||||
|
gk_errexit(SIGERR, "HTable_SearchAndDelete: Failed to find the key!\n"); |
||||||
|
} |
||||||
|
|
||||||
|
for (i=0; i<first; i++) { |
||||||
|
if (htable->harray[i].key == key) { |
||||||
|
htable->harray[i].key = HTABLE_DELETED; |
||||||
|
htable->htsize--; |
||||||
|
return htable->harray[i].val; |
||||||
|
} |
||||||
|
else if (htable->harray[i].key == HTABLE_EMPTY) |
||||||
|
gk_errexit(SIGERR, "HTable_SearchAndDelete: Failed to find the key!\n"); |
||||||
|
} |
||||||
|
|
||||||
|
return -1; |
||||||
|
|
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/******************************************************************************
|
||||||
|
* This function destroys the data structures associated with the hash-table |
||||||
|
*******************************************************************************/ |
||||||
|
void HTable_Destroy(gk_HTable_t *htable) |
||||||
|
{ |
||||||
|
gk_free((void **)&htable->harray, &htable, LTERM); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/******************************************************************************
|
||||||
|
* This is the hash-function. Based on multiplication |
||||||
|
*******************************************************************************/ |
||||||
|
int HTable_HFunction(int nelements, int key) |
||||||
|
{ |
||||||
|
return (int)(key%nelements); |
||||||
|
} |
||||||
@ -0,0 +1,681 @@ |
|||||||
|
/*!
|
||||||
|
\file io.c |
||||||
|
\brief Various file I/O functions. |
||||||
|
|
||||||
|
This file contains various functions that perform I/O. |
||||||
|
|
||||||
|
\date Started 4/10/95 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: io.c 18951 2015-08-08 20:10:46Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
#ifdef HAVE_GETLINE |
||||||
|
/* Get getline to be defined. */ |
||||||
|
#define _GNU_SOURCE |
||||||
|
#include <stdio.h> |
||||||
|
#undef _GNU_SOURCE |
||||||
|
#endif |
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
/*************************************************************************
|
||||||
|
* This function opens a file |
||||||
|
**************************************************************************/ |
||||||
|
FILE *gk_fopen(char *fname, char *mode, const char *msg) |
||||||
|
{ |
||||||
|
FILE *fp; |
||||||
|
char errmsg[8192]; |
||||||
|
|
||||||
|
fp = fopen(fname, mode); |
||||||
|
if (fp != NULL) |
||||||
|
return fp; |
||||||
|
|
||||||
|
sprintf(errmsg,"file: %s, mode: %s, [%s]", fname, mode, msg); |
||||||
|
perror(errmsg); |
||||||
|
errexit("Failed on gk_fopen()\n"); |
||||||
|
|
||||||
|
return NULL; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************
|
||||||
|
* This function closes a file |
||||||
|
**************************************************************************/ |
||||||
|
void gk_fclose(FILE *fp) |
||||||
|
{ |
||||||
|
fclose(fp); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function is a wrapper around the read() function that ensures
|
||||||
|
that all data is been read, by issuing multiple read requests. |
||||||
|
The only time when not 'count' items are read is when the EOF has been |
||||||
|
reached. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
ssize_t gk_read(int fd, void *vbuf, size_t count) |
||||||
|
{ |
||||||
|
char *buf = (char *)vbuf; |
||||||
|
ssize_t rsize, tsize=count; |
||||||
|
|
||||||
|
do { |
||||||
|
if ((rsize = read(fd, buf, tsize)) == -1) |
||||||
|
return -1; |
||||||
|
buf += rsize; |
||||||
|
tsize -= rsize; |
||||||
|
} while (tsize > 0 && rsize > 0); |
||||||
|
|
||||||
|
return count-tsize; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function is a wrapper around the write() function that ensures
|
||||||
|
that all data is been written, by issueing multiple write requests. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
ssize_t gk_write(int fd, void *vbuf, size_t count) |
||||||
|
{ |
||||||
|
char *buf = (char *)vbuf; |
||||||
|
ssize_t size, tsize=count; |
||||||
|
|
||||||
|
do { |
||||||
|
if ((size = write(fd, buf, tsize)) == -1) |
||||||
|
return -1; |
||||||
|
buf += size; |
||||||
|
tsize -= size; |
||||||
|
} while (tsize > 0); |
||||||
|
|
||||||
|
return count; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function is the GKlib implementation of glibc's getline()
|
||||||
|
function. |
||||||
|
\returns -1 if the EOF has been reached, otherwise it returns the
|
||||||
|
number of bytes read. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
ssize_t gk_getline(char **lineptr, size_t *n, FILE *stream) |
||||||
|
{ |
||||||
|
#ifdef HAVE_GETLINE |
||||||
|
return getline(lineptr, n, stream); |
||||||
|
#else |
||||||
|
size_t i; |
||||||
|
int ch; |
||||||
|
|
||||||
|
if (feof(stream)) |
||||||
|
return -1;
|
||||||
|
|
||||||
|
/* Initial memory allocation if *lineptr is NULL */ |
||||||
|
if (*lineptr == NULL || *n == 0) { |
||||||
|
*n = 1024; |
||||||
|
*lineptr = gk_malloc((*n)*sizeof(char), "gk_getline: lineptr"); |
||||||
|
} |
||||||
|
|
||||||
|
/* get into the main loop */ |
||||||
|
i = 0; |
||||||
|
while ((ch = getc(stream)) != EOF) { |
||||||
|
(*lineptr)[i++] = (char)ch; |
||||||
|
|
||||||
|
/* reallocate memory if reached at the end of the buffer. The +1 is for '\0' */ |
||||||
|
if (i+1 == *n) {
|
||||||
|
*n = 2*(*n); |
||||||
|
*lineptr = gk_realloc(*lineptr, (*n)*sizeof(char), "gk_getline: lineptr"); |
||||||
|
} |
||||||
|
|
||||||
|
if (ch == '\n') |
||||||
|
break; |
||||||
|
} |
||||||
|
(*lineptr)[i] = '\0'; |
||||||
|
|
||||||
|
return (i == 0 ? -1 : i); |
||||||
|
#endif |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function reads the contents of a text file and returns it in the
|
||||||
|
form of an array of strings. |
||||||
|
\param fname is the name of the file |
||||||
|
\param r_nlines is the number of lines in the file. If it is NULL, |
||||||
|
this information is not returned. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
char **gk_readfile(char *fname, size_t *r_nlines) |
||||||
|
{ |
||||||
|
size_t lnlen, nlines=0; |
||||||
|
char *line=NULL, **lines=NULL; |
||||||
|
FILE *fpin; |
||||||
|
|
||||||
|
gk_getfilestats(fname, &nlines, NULL, NULL, NULL); |
||||||
|
if (nlines > 0) { |
||||||
|
lines = (char **)gk_malloc(nlines*sizeof(char *), "gk_readfile: lines"); |
||||||
|
|
||||||
|
fpin = gk_fopen(fname, "r", "gk_readfile"); |
||||||
|
nlines = 0; |
||||||
|
while (gk_getline(&line, &lnlen, fpin) != -1) { |
||||||
|
gk_strtprune(line, "\n\r"); |
||||||
|
lines[nlines++] = gk_strdup(line); |
||||||
|
} |
||||||
|
gk_fclose(fpin); |
||||||
|
} |
||||||
|
|
||||||
|
gk_free((void **)&line, LTERM); |
||||||
|
|
||||||
|
if (r_nlines != NULL) |
||||||
|
*r_nlines = nlines; |
||||||
|
|
||||||
|
return lines; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function reads the contents of a file and returns it in the
|
||||||
|
form of an array of int32_t. |
||||||
|
\param fname is the name of the file |
||||||
|
\param r_nlines is the number of lines in the file. If it is NULL, |
||||||
|
this information is not returned. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
int32_t *gk_i32readfile(char *fname, size_t *r_nlines) |
||||||
|
{ |
||||||
|
size_t lnlen, nlines=0; |
||||||
|
char *line=NULL; |
||||||
|
int32_t *array=NULL; |
||||||
|
FILE *fpin; |
||||||
|
|
||||||
|
gk_getfilestats(fname, &nlines, NULL, NULL, NULL); |
||||||
|
if (nlines > 0) { |
||||||
|
array = gk_i32malloc(nlines, "gk_i32readfile: array"); |
||||||
|
|
||||||
|
fpin = gk_fopen(fname, "r", "gk_readfile"); |
||||||
|
nlines = 0; |
||||||
|
|
||||||
|
while (gk_getline(&line, &lnlen, fpin) != -1) { |
||||||
|
sscanf(line, "%"SCNd32, &array[nlines++]); |
||||||
|
} |
||||||
|
|
||||||
|
gk_fclose(fpin); |
||||||
|
} |
||||||
|
|
||||||
|
gk_free((void **)&line, LTERM); |
||||||
|
|
||||||
|
if (r_nlines != NULL) |
||||||
|
*r_nlines = nlines; |
||||||
|
|
||||||
|
return array; |
||||||
|
} |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function reads the contents of a file and returns it in the
|
||||||
|
form of an array of int64_t. |
||||||
|
\param fname is the name of the file |
||||||
|
\param r_nlines is the number of lines in the file. If it is NULL, |
||||||
|
this information is not returned. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
int64_t *gk_i64readfile(char *fname, size_t *r_nlines) |
||||||
|
{ |
||||||
|
size_t lnlen, nlines=0; |
||||||
|
char *line=NULL; |
||||||
|
int64_t *array=NULL; |
||||||
|
FILE *fpin; |
||||||
|
|
||||||
|
gk_getfilestats(fname, &nlines, NULL, NULL, NULL); |
||||||
|
if (nlines > 0) { |
||||||
|
array = gk_i64malloc(nlines, "gk_i64readfile: array"); |
||||||
|
|
||||||
|
fpin = gk_fopen(fname, "r", "gk_readfile"); |
||||||
|
nlines = 0; |
||||||
|
|
||||||
|
while (gk_getline(&line, &lnlen, fpin) != -1) { |
||||||
|
sscanf(line, "%"SCNd64, &array[nlines++]); |
||||||
|
} |
||||||
|
|
||||||
|
gk_fclose(fpin); |
||||||
|
} |
||||||
|
|
||||||
|
gk_free((void **)&line, LTERM); |
||||||
|
|
||||||
|
if (r_nlines != NULL) |
||||||
|
*r_nlines = nlines; |
||||||
|
|
||||||
|
return array; |
||||||
|
} |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function reads the contents of a file and returns it in the
|
||||||
|
form of an array of ssize_t. |
||||||
|
\param fname is the name of the file |
||||||
|
\param r_nlines is the number of lines in the file. If it is NULL, |
||||||
|
this information is not returned. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
ssize_t *gk_zreadfile(char *fname, size_t *r_nlines) |
||||||
|
{ |
||||||
|
size_t lnlen, nlines=0; |
||||||
|
char *line=NULL; |
||||||
|
ssize_t *array=NULL; |
||||||
|
FILE *fpin; |
||||||
|
|
||||||
|
gk_getfilestats(fname, &nlines, NULL, NULL, NULL); |
||||||
|
if (nlines > 0) { |
||||||
|
array = gk_zmalloc(nlines, "gk_zreadfile: array"); |
||||||
|
|
||||||
|
fpin = gk_fopen(fname, "r", "gk_readfile"); |
||||||
|
nlines = 0; |
||||||
|
|
||||||
|
while (gk_getline(&line, &lnlen, fpin) != -1) { |
||||||
|
sscanf(line, "%zd", &array[nlines++]); |
||||||
|
} |
||||||
|
|
||||||
|
gk_fclose(fpin); |
||||||
|
} |
||||||
|
|
||||||
|
gk_free((void **)&line, LTERM); |
||||||
|
|
||||||
|
if (r_nlines != NULL) |
||||||
|
*r_nlines = nlines; |
||||||
|
|
||||||
|
return array; |
||||||
|
} |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function reads the contents of a binary file and returns it in the
|
||||||
|
form of an array of char. |
||||||
|
\param fname is the name of the file |
||||||
|
\param r_nlines is the number of lines in the file. If it is NULL, |
||||||
|
this information is not returned. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
char *gk_creadfilebin(char *fname, size_t *r_nelmnts) |
||||||
|
{ |
||||||
|
size_t nelmnts; |
||||||
|
ssize_t fsize; |
||||||
|
char *array=NULL; |
||||||
|
FILE *fpin; |
||||||
|
|
||||||
|
*r_nelmnts = 0; |
||||||
|
|
||||||
|
fsize = gk_getfsize(fname); |
||||||
|
|
||||||
|
if (fsize == -1) { |
||||||
|
gk_errexit(SIGERR, "Failed to fstat(%s).\n", fname); |
||||||
|
return NULL; |
||||||
|
} |
||||||
|
|
||||||
|
nelmnts = fsize; |
||||||
|
array = gk_cmalloc(nelmnts, "gk_creadfilebin: array"); |
||||||
|
|
||||||
|
fpin = gk_fopen(fname, "rb", "gk_creadfilebin"); |
||||||
|
if (fread(array, sizeof(char), nelmnts, fpin) != nelmnts) { |
||||||
|
gk_errexit(SIGERR, "Failed to read the number of words requested. %zu\n", nelmnts); |
||||||
|
gk_free((void **)&array, LTERM); |
||||||
|
return NULL; |
||||||
|
} |
||||||
|
gk_fclose(fpin); |
||||||
|
|
||||||
|
*r_nelmnts = nelmnts; |
||||||
|
|
||||||
|
return array; |
||||||
|
} |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function writes the contents of an array into a binary file.
|
||||||
|
\param fname is the name of the file |
||||||
|
\param n the number of elements in the array. |
||||||
|
\param a the array to be written out. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
size_t gk_cwritefilebin(char *fname, size_t n, char *a) |
||||||
|
{ |
||||||
|
size_t fsize; |
||||||
|
FILE *fp; |
||||||
|
|
||||||
|
fp = gk_fopen(fname, "wb", "gk_writefilebin"); |
||||||
|
|
||||||
|
fsize = fwrite(a, sizeof(char), n, fp); |
||||||
|
|
||||||
|
gk_fclose(fp); |
||||||
|
|
||||||
|
return fsize; |
||||||
|
} |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function reads the contents of a binary file and returns it in the
|
||||||
|
form of an array of int32_t. |
||||||
|
\param fname is the name of the file |
||||||
|
\param r_nlines is the number of lines in the file. If it is NULL, |
||||||
|
this information is not returned. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
int32_t *gk_i32readfilebin(char *fname, size_t *r_nelmnts) |
||||||
|
{ |
||||||
|
size_t nelmnts; |
||||||
|
ssize_t fsize; |
||||||
|
int32_t *array=NULL; |
||||||
|
FILE *fpin; |
||||||
|
|
||||||
|
*r_nelmnts = 0; |
||||||
|
|
||||||
|
fsize = gk_getfsize(fname); |
||||||
|
|
||||||
|
if (fsize == -1) { |
||||||
|
gk_errexit(SIGERR, "Failed to fstat(%s).\n", fname); |
||||||
|
return NULL; |
||||||
|
} |
||||||
|
|
||||||
|
if (fsize%sizeof(int32_t) != 0) { |
||||||
|
gk_errexit(SIGERR, "The size [%zd] of the file [%s] is not in multiples of sizeof(int32_t).\n", fsize, fname); |
||||||
|
return NULL; |
||||||
|
} |
||||||
|
|
||||||
|
nelmnts = fsize/sizeof(int32_t); |
||||||
|
array = gk_i32malloc(nelmnts, "gk_i32readfilebin: array"); |
||||||
|
|
||||||
|
fpin = gk_fopen(fname, "rb", "gk_i32readfilebin"); |
||||||
|
|
||||||
|
if (fread(array, sizeof(int32_t), nelmnts, fpin) != nelmnts) { |
||||||
|
gk_errexit(SIGERR, "Failed to read the number of words requested. %zd\n", nelmnts); |
||||||
|
gk_free((void **)&array, LTERM); |
||||||
|
return NULL; |
||||||
|
} |
||||||
|
gk_fclose(fpin); |
||||||
|
|
||||||
|
*r_nelmnts = nelmnts; |
||||||
|
|
||||||
|
return array; |
||||||
|
} |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function writes the contents of an array into a binary file.
|
||||||
|
\param fname is the name of the file |
||||||
|
\param n the number of elements in the array. |
||||||
|
\param a the array to be written out. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
size_t gk_i32writefilebin(char *fname, size_t n, int32_t *a) |
||||||
|
{ |
||||||
|
size_t fsize; |
||||||
|
FILE *fp; |
||||||
|
|
||||||
|
fp = gk_fopen(fname, "wb", "gk_writefilebin"); |
||||||
|
|
||||||
|
fsize = fwrite(a, sizeof(int32_t), n, fp); |
||||||
|
|
||||||
|
gk_fclose(fp); |
||||||
|
|
||||||
|
return fsize; |
||||||
|
} |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function reads the contents of a binary file and returns it in the
|
||||||
|
form of an array of int64_t. |
||||||
|
\param fname is the name of the file |
||||||
|
\param r_nlines is the number of lines in the file. If it is NULL, |
||||||
|
this information is not returned. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
int64_t *gk_i64readfilebin(char *fname, size_t *r_nelmnts) |
||||||
|
{ |
||||||
|
size_t nelmnts; |
||||||
|
ssize_t fsize; |
||||||
|
int64_t *array=NULL; |
||||||
|
FILE *fpin; |
||||||
|
|
||||||
|
*r_nelmnts = 0; |
||||||
|
|
||||||
|
fsize = gk_getfsize(fname); |
||||||
|
|
||||||
|
if (fsize == -1) { |
||||||
|
gk_errexit(SIGERR, "Failed to fstat(%s).\n", fname); |
||||||
|
return NULL; |
||||||
|
} |
||||||
|
|
||||||
|
if (fsize%sizeof(int64_t) != 0) { |
||||||
|
gk_errexit(SIGERR, "The size of the file is not in multiples of sizeof(int64_t).\n"); |
||||||
|
return NULL; |
||||||
|
} |
||||||
|
|
||||||
|
nelmnts = fsize/sizeof(int64_t); |
||||||
|
array = gk_i64malloc(nelmnts, "gk_i64readfilebin: array"); |
||||||
|
|
||||||
|
fpin = gk_fopen(fname, "rb", "gk_i64readfilebin"); |
||||||
|
|
||||||
|
if (fread(array, sizeof(int64_t), nelmnts, fpin) != nelmnts) { |
||||||
|
gk_errexit(SIGERR, "Failed to read the number of words requested. %zd\n", nelmnts); |
||||||
|
gk_free((void **)&array, LTERM); |
||||||
|
return NULL; |
||||||
|
} |
||||||
|
gk_fclose(fpin); |
||||||
|
|
||||||
|
*r_nelmnts = nelmnts; |
||||||
|
|
||||||
|
return array; |
||||||
|
} |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function writes the contents of an array into a binary file.
|
||||||
|
\param fname is the name of the file |
||||||
|
\param n the number of elements in the array. |
||||||
|
\param a the array to be written out. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
size_t gk_i64writefilebin(char *fname, size_t n, int64_t *a) |
||||||
|
{ |
||||||
|
size_t fsize; |
||||||
|
FILE *fp; |
||||||
|
|
||||||
|
fp = gk_fopen(fname, "wb", "gk_writefilebin"); |
||||||
|
|
||||||
|
fsize = fwrite(a, sizeof(int64_t), n, fp); |
||||||
|
|
||||||
|
gk_fclose(fp); |
||||||
|
|
||||||
|
return fsize; |
||||||
|
} |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function reads the contents of a binary file and returns it in the
|
||||||
|
form of an array of ssize_t. |
||||||
|
\param fname is the name of the file |
||||||
|
\param r_nlines is the number of lines in the file. If it is NULL, |
||||||
|
this information is not returned. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
ssize_t *gk_zreadfilebin(char *fname, size_t *r_nelmnts) |
||||||
|
{ |
||||||
|
size_t nelmnts; |
||||||
|
ssize_t fsize; |
||||||
|
ssize_t *array=NULL; |
||||||
|
FILE *fpin; |
||||||
|
|
||||||
|
*r_nelmnts = 0; |
||||||
|
|
||||||
|
fsize = gk_getfsize(fname); |
||||||
|
|
||||||
|
if (fsize == -1) { |
||||||
|
gk_errexit(SIGERR, "Failed to fstat(%s).\n", fname); |
||||||
|
return NULL; |
||||||
|
} |
||||||
|
|
||||||
|
if (fsize%sizeof(ssize_t) != 0) { |
||||||
|
gk_errexit(SIGERR, "The size of the file is not in multiples of sizeof(ssize_t).\n"); |
||||||
|
return NULL; |
||||||
|
} |
||||||
|
|
||||||
|
nelmnts = fsize/sizeof(ssize_t); |
||||||
|
array = gk_zmalloc(nelmnts, "gk_zreadfilebin: array"); |
||||||
|
|
||||||
|
fpin = gk_fopen(fname, "rb", "gk_zreadfilebin"); |
||||||
|
|
||||||
|
if (fread(array, sizeof(ssize_t), nelmnts, fpin) != nelmnts) { |
||||||
|
gk_errexit(SIGERR, "Failed to read the number of words requested. %zd\n", nelmnts); |
||||||
|
gk_free((void **)&array, LTERM); |
||||||
|
return NULL; |
||||||
|
} |
||||||
|
gk_fclose(fpin); |
||||||
|
|
||||||
|
*r_nelmnts = nelmnts; |
||||||
|
|
||||||
|
return array; |
||||||
|
} |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function writes the contents of an array into a binary file.
|
||||||
|
\param fname is the name of the file |
||||||
|
\param n the number of elements in the array. |
||||||
|
\param a the array to be written out. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
size_t gk_zwritefilebin(char *fname, size_t n, ssize_t *a) |
||||||
|
{ |
||||||
|
size_t fsize; |
||||||
|
FILE *fp; |
||||||
|
|
||||||
|
fp = gk_fopen(fname, "wb", "gk_writefilebin"); |
||||||
|
|
||||||
|
fsize = fwrite(a, sizeof(ssize_t), n, fp); |
||||||
|
|
||||||
|
gk_fclose(fp); |
||||||
|
|
||||||
|
return fsize; |
||||||
|
} |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function reads the contents of a binary file and returns it in the
|
||||||
|
form of an array of float. |
||||||
|
\param fname is the name of the file |
||||||
|
\param r_nlines is the number of lines in the file. If it is NULL, |
||||||
|
this information is not returned. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
float *gk_freadfilebin(char *fname, size_t *r_nelmnts) |
||||||
|
{ |
||||||
|
size_t nelmnts; |
||||||
|
ssize_t fsize; |
||||||
|
float *array=NULL; |
||||||
|
FILE *fpin; |
||||||
|
|
||||||
|
*r_nelmnts = 0; |
||||||
|
|
||||||
|
fsize = gk_getfsize(fname); |
||||||
|
|
||||||
|
if (fsize == -1) { |
||||||
|
gk_errexit(SIGERR, "Failed to fstat(%s).\n", fname); |
||||||
|
return NULL; |
||||||
|
} |
||||||
|
|
||||||
|
if (fsize%sizeof(float) != 0) { |
||||||
|
gk_errexit(SIGERR, "The size of the file is not in multiples of sizeof(float).\n"); |
||||||
|
return NULL; |
||||||
|
} |
||||||
|
|
||||||
|
nelmnts = fsize/sizeof(float); |
||||||
|
array = gk_fmalloc(nelmnts, "gk_freadfilebin: array"); |
||||||
|
|
||||||
|
fpin = gk_fopen(fname, "rb", "gk_freadfilebin"); |
||||||
|
|
||||||
|
if (fread(array, sizeof(float), nelmnts, fpin) != nelmnts) { |
||||||
|
gk_errexit(SIGERR, "Failed to read the number of words requested. %zd\n", nelmnts); |
||||||
|
gk_free((void **)&array, LTERM); |
||||||
|
return NULL; |
||||||
|
} |
||||||
|
gk_fclose(fpin); |
||||||
|
|
||||||
|
*r_nelmnts = nelmnts; |
||||||
|
|
||||||
|
return array; |
||||||
|
} |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function writes the contents of an array into a binary file.
|
||||||
|
\param fname is the name of the file |
||||||
|
\param n the number of elements in the array. |
||||||
|
\param a the array to be written out. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
size_t gk_fwritefilebin(char *fname, size_t n, float *a) |
||||||
|
{ |
||||||
|
size_t fsize; |
||||||
|
FILE *fp; |
||||||
|
|
||||||
|
fp = gk_fopen(fname, "wb", "gk_fwritefilebin"); |
||||||
|
|
||||||
|
fsize = fwrite(a, sizeof(float), n, fp); |
||||||
|
|
||||||
|
gk_fclose(fp); |
||||||
|
|
||||||
|
return fsize; |
||||||
|
} |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function reads the contents of a binary file and returns it in the
|
||||||
|
form of an array of double. |
||||||
|
\param fname is the name of the file |
||||||
|
\param r_nlines is the number of lines in the file. If it is NULL, |
||||||
|
this information is not returned. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
double *gk_dreadfilebin(char *fname, size_t *r_nelmnts) |
||||||
|
{ |
||||||
|
size_t nelmnts; |
||||||
|
ssize_t fsize; |
||||||
|
double *array=NULL; |
||||||
|
FILE *fpin; |
||||||
|
|
||||||
|
*r_nelmnts = 0; |
||||||
|
|
||||||
|
fsize = gk_getfsize(fname); |
||||||
|
|
||||||
|
if (fsize == -1) { |
||||||
|
gk_errexit(SIGERR, "Failed to fstat(%s).\n", fname); |
||||||
|
return NULL; |
||||||
|
} |
||||||
|
|
||||||
|
if (fsize%sizeof(double) != 0) { |
||||||
|
gk_errexit(SIGERR, "The size of the file is not in multiples of sizeof(double).\n"); |
||||||
|
return NULL; |
||||||
|
} |
||||||
|
|
||||||
|
nelmnts = fsize/sizeof(double); |
||||||
|
array = gk_dmalloc(nelmnts, "gk_dreadfilebin: array"); |
||||||
|
|
||||||
|
fpin = gk_fopen(fname, "rb", "gk_dreadfilebin"); |
||||||
|
|
||||||
|
if (fread(array, sizeof(double), nelmnts, fpin) != nelmnts) { |
||||||
|
gk_errexit(SIGERR, "Failed to read the number of words requested. %zd\n", nelmnts); |
||||||
|
gk_free((void **)&array, LTERM); |
||||||
|
return NULL; |
||||||
|
} |
||||||
|
gk_fclose(fpin); |
||||||
|
|
||||||
|
*r_nelmnts = nelmnts; |
||||||
|
|
||||||
|
return array; |
||||||
|
} |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function writes the contents of an array into a binary file.
|
||||||
|
\param fname is the name of the file |
||||||
|
\param n the number of elements in the array. |
||||||
|
\param a the array to be written out. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
size_t gk_dwritefilebin(char *fname, size_t n, double *a) |
||||||
|
{ |
||||||
|
size_t fsize; |
||||||
|
FILE *fp; |
||||||
|
|
||||||
|
fp = gk_fopen(fname, "wb", "gk_writefilebin"); |
||||||
|
|
||||||
|
fsize = fwrite(a, sizeof(double), n, fp); |
||||||
|
|
||||||
|
gk_fclose(fp); |
||||||
|
|
||||||
|
return fsize; |
||||||
|
} |
||||||
|
|
||||||
@ -0,0 +1,210 @@ |
|||||||
|
/*!
|
||||||
|
* \file |
||||||
|
* \brief Frequent/Closed itemset discovery routines
|
||||||
|
* |
||||||
|
* This file contains the code for finding frequent/closed itemests. These routines |
||||||
|
* are implemented using a call-back mechanism to deal with the discovered itemsets. |
||||||
|
* |
||||||
|
* \date 6/13/2008 |
||||||
|
* \author George Karypis |
||||||
|
* \version\verbatim $Id: itemsets.c 19240 2015-10-22 12:41:19Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
/*-------------------------------------------------------------*/ |
||||||
|
/*! Data structures for use within this module */ |
||||||
|
/*-------------------------------------------------------------*/ |
||||||
|
typedef struct { |
||||||
|
int minfreq; /* the minimum frequency of a pattern */ |
||||||
|
int maxfreq; /* the maximum frequency of a pattern */ |
||||||
|
int minlen; /* the minimum length of the requested pattern */ |
||||||
|
int maxlen; /* the maximum length of the requested pattern */ |
||||||
|
int tnitems; /* the initial range of the item space */ |
||||||
|
|
||||||
|
/* the call-back function */ |
||||||
|
void (*callback)(void *stateptr, int nitems, int *itemids, int ntrans, int *transids);
|
||||||
|
void *stateptr; /* the user-supplied pointer to pass to the callback */ |
||||||
|
|
||||||
|
/* workspace variables */ |
||||||
|
int *rmarker; |
||||||
|
gk_ikv_t *cand; |
||||||
|
} isparams_t; |
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------*/ |
||||||
|
/*! Prototypes for this module */ |
||||||
|
/*-------------------------------------------------------------*/ |
||||||
|
void itemsets_find_frequent_itemsets(isparams_t *params, gk_csr_t *mat,
|
||||||
|
int preflen, int *prefix); |
||||||
|
gk_csr_t *itemsets_project_matrix(isparams_t *param, gk_csr_t *mat, int cid); |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! The entry point of the frequent itemset discovery code */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_find_frequent_itemsets(int ntrans, ssize_t *tranptr, int *tranind,
|
||||||
|
int minfreq, int maxfreq, int minlen, int maxlen,
|
||||||
|
void (*process_itemset)(void *stateptr, int nitems, int *itemids,
|
||||||
|
int ntrans, int *transids), |
||||||
|
void *stateptr) |
||||||
|
{ |
||||||
|
ssize_t i; |
||||||
|
gk_csr_t *mat, *pmat; |
||||||
|
isparams_t params; |
||||||
|
int *pattern; |
||||||
|
|
||||||
|
/* Create the matrix */ |
||||||
|
mat = gk_csr_Create(); |
||||||
|
mat->nrows = ntrans; |
||||||
|
mat->ncols = tranind[gk_iargmax(tranptr[ntrans], tranind, 1)]+1; |
||||||
|
mat->rowptr = gk_zcopy(ntrans+1, tranptr, gk_zmalloc(ntrans+1, "gk_find_frequent_itemsets: mat.rowptr")); |
||||||
|
mat->rowind = gk_icopy(tranptr[ntrans], tranind, gk_imalloc(tranptr[ntrans], "gk_find_frequent_itemsets: mat.rowind")); |
||||||
|
mat->colids = gk_iincset(mat->ncols, 0, gk_imalloc(mat->ncols, "gk_find_frequent_itemsets: mat.colids")); |
||||||
|
|
||||||
|
/* Setup the parameters */ |
||||||
|
params.minfreq = minfreq; |
||||||
|
params.maxfreq = (maxfreq == -1 ? mat->nrows : maxfreq); |
||||||
|
params.minlen = minlen; |
||||||
|
params.maxlen = (maxlen == -1 ? mat->ncols : maxlen); |
||||||
|
params.tnitems = mat->ncols; |
||||||
|
params.callback = process_itemset; |
||||||
|
params.stateptr = stateptr; |
||||||
|
params.rmarker = gk_ismalloc(mat->nrows, 0, "gk_find_frequent_itemsets: rmarker"); |
||||||
|
params.cand = gk_ikvmalloc(mat->ncols, "gk_find_frequent_itemsets: cand"); |
||||||
|
|
||||||
|
/* Perform the initial projection */ |
||||||
|
gk_csr_CreateIndex(mat, GK_CSR_COL); |
||||||
|
pmat = itemsets_project_matrix(¶ms, mat, -1); |
||||||
|
gk_csr_Free(&mat); |
||||||
|
|
||||||
|
pattern = gk_imalloc(pmat->ncols, "gk_find_frequent_itemsets: pattern"); |
||||||
|
itemsets_find_frequent_itemsets(¶ms, pmat, 0, pattern);
|
||||||
|
|
||||||
|
gk_csr_Free(&pmat); |
||||||
|
gk_free((void **)&pattern, ¶ms.rmarker, ¶ms.cand, LTERM); |
||||||
|
|
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! The recursive routine for DFS-based frequent pattern discovery */ |
||||||
|
/*************************************************************************/ |
||||||
|
void itemsets_find_frequent_itemsets(isparams_t *params, gk_csr_t *mat,
|
||||||
|
int preflen, int *prefix) |
||||||
|
{ |
||||||
|
ssize_t i; |
||||||
|
gk_csr_t *cmat; |
||||||
|
|
||||||
|
/* Project each frequent column */ |
||||||
|
for (i=0; i<mat->ncols; i++) { |
||||||
|
prefix[preflen] = mat->colids[i]; |
||||||
|
|
||||||
|
if (preflen+1 >= params->minlen) |
||||||
|
(*params->callback)(params->stateptr, preflen+1, prefix,
|
||||||
|
mat->colptr[i+1]-mat->colptr[i], mat->colind+mat->colptr[i]); |
||||||
|
|
||||||
|
if (preflen+1 < params->maxlen) { |
||||||
|
cmat = itemsets_project_matrix(params, mat, i); |
||||||
|
itemsets_find_frequent_itemsets(params, cmat, preflen+1, prefix); |
||||||
|
gk_csr_Free(&cmat); |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/******************************************************************************/ |
||||||
|
/*! This function projects a matrix w.r.t. to a particular column.
|
||||||
|
It performs the following steps: |
||||||
|
- Determines the length of each column that is remaining. |
||||||
|
- Sorts the columns in increasing length. |
||||||
|
- Creates a column-based version of the matrix with the proper |
||||||
|
column ordering. |
||||||
|
*/ |
||||||
|
/*******************************************************************************/ |
||||||
|
gk_csr_t *itemsets_project_matrix(isparams_t *params, gk_csr_t *mat, int cid) |
||||||
|
{ |
||||||
|
ssize_t i, j, k, ii, pnnz; |
||||||
|
int nrows, ncols, pnrows, pncols; |
||||||
|
ssize_t *colptr, *pcolptr; |
||||||
|
int *colind, *colids, *pcolind, *pcolids, *rmarker; |
||||||
|
gk_csr_t *pmat; |
||||||
|
gk_ikv_t *cand; |
||||||
|
|
||||||
|
nrows = mat->nrows; |
||||||
|
ncols = mat->ncols; |
||||||
|
colptr = mat->colptr; |
||||||
|
colind = mat->colind; |
||||||
|
colids = mat->colids; |
||||||
|
|
||||||
|
rmarker = params->rmarker; |
||||||
|
cand = params->cand; |
||||||
|
|
||||||
|
|
||||||
|
/* Allocate space for the projected matrix based on what you know thus far */ |
||||||
|
pmat = gk_csr_Create(); |
||||||
|
pmat->nrows = pnrows = (cid == -1 ? nrows : colptr[cid+1]-colptr[cid]); |
||||||
|
|
||||||
|
|
||||||
|
/* Mark the rows that will be kept and determine the prowids */ |
||||||
|
if (cid == -1) { /* Initial projection */ |
||||||
|
gk_iset(nrows, 1, rmarker); |
||||||
|
} |
||||||
|
else { /* The other projections */ |
||||||
|
for (i=colptr[cid]; i<colptr[cid+1]; i++)
|
||||||
|
rmarker[colind[i]] = 1; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/* Determine the length of each column that will be left in the projected matrix */ |
||||||
|
for (pncols=0, pnnz=0, i=cid+1; i<ncols; i++) { |
||||||
|
for (k=0, j=colptr[i]; j<colptr[i+1]; j++) { |
||||||
|
k += rmarker[colind[j]]; |
||||||
|
} |
||||||
|
if (k >= params->minfreq && k <= params->maxfreq) { |
||||||
|
cand[pncols].val = i; |
||||||
|
cand[pncols++].key = k; |
||||||
|
pnnz += k; |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
/* Sort the columns in increasing order */ |
||||||
|
gk_ikvsorti(pncols, cand); |
||||||
|
|
||||||
|
|
||||||
|
/* Allocate space for the remaining fields of the projected matrix */ |
||||||
|
pmat->ncols = pncols; |
||||||
|
pmat->colids = pcolids = gk_imalloc(pncols, "itemsets_project_matrix: pcolids"); |
||||||
|
pmat->colptr = pcolptr = gk_zmalloc(pncols+1, "itemsets_project_matrix: pcolptr"); |
||||||
|
pmat->colind = pcolind = gk_imalloc(pnnz, "itemsets_project_matrix: pcolind"); |
||||||
|
|
||||||
|
|
||||||
|
/* Populate the projected matrix */ |
||||||
|
pcolptr[0] = 0; |
||||||
|
for (pnnz=0, ii=0; ii<pncols; ii++) { |
||||||
|
i = cand[ii].val; |
||||||
|
for (j=colptr[i]; j<colptr[i+1]; j++) { |
||||||
|
if (rmarker[colind[j]])
|
||||||
|
pcolind[pnnz++] = colind[j]; |
||||||
|
} |
||||||
|
|
||||||
|
pcolids[ii] = colids[i]; |
||||||
|
pcolptr[ii+1] = pnnz; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/* Reset the rmarker array */ |
||||||
|
if (cid == -1) { /* Initial projection */ |
||||||
|
gk_iset(nrows, 0, rmarker); |
||||||
|
} |
||||||
|
else { /* The other projections */ |
||||||
|
for (i=colptr[cid]; i<colptr[cid+1]; i++)
|
||||||
|
rmarker[colind[i]] = 0; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
return pmat; |
||||||
|
} |
||||||
@ -0,0 +1,393 @@ |
|||||||
|
/*!
|
||||||
|
\file
|
||||||
|
\brief Functions dealing with creating and allocating mcores |
||||||
|
|
||||||
|
\date Started 5/30/11 |
||||||
|
\author George |
||||||
|
\author Copyright 1997-2011, Regents of the University of Minnesota
|
||||||
|
\version $Id: mcore.c 13953 2013-03-30 16:20:07Z karypis $ |
||||||
|
*/ |
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function creates an mcore
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
gk_mcore_t *gk_mcoreCreate(size_t coresize) |
||||||
|
{ |
||||||
|
gk_mcore_t *mcore; |
||||||
|
|
||||||
|
mcore = (gk_mcore_t *)gk_malloc(sizeof(gk_mcore_t), "gk_mcoreCreate: mcore"); |
||||||
|
memset(mcore, 0, sizeof(gk_mcore_t)); |
||||||
|
|
||||||
|
mcore->coresize = coresize; |
||||||
|
mcore->corecpos = 0; |
||||||
|
|
||||||
|
mcore->core = (coresize == 0 ? NULL : gk_malloc(mcore->coresize, "gk_mcoreCreate: core")); |
||||||
|
|
||||||
|
/* allocate the memory for keeping track of malloc ops */ |
||||||
|
mcore->nmops = 2048; |
||||||
|
mcore->cmop = 0; |
||||||
|
mcore->mops = (gk_mop_t *)gk_malloc(mcore->nmops*sizeof(gk_mop_t), "gk_mcoreCreate: mcore->mops"); |
||||||
|
|
||||||
|
return mcore; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function creates an mcore. This version is used for gkmcore.
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
gk_mcore_t *gk_gkmcoreCreate() |
||||||
|
{ |
||||||
|
gk_mcore_t *mcore; |
||||||
|
|
||||||
|
if ((mcore = (gk_mcore_t *)malloc(sizeof(gk_mcore_t))) == NULL) |
||||||
|
return NULL; |
||||||
|
memset(mcore, 0, sizeof(gk_mcore_t)); |
||||||
|
|
||||||
|
/* allocate the memory for keeping track of malloc ops */ |
||||||
|
mcore->nmops = 2048; |
||||||
|
mcore->cmop = 0; |
||||||
|
if ((mcore->mops = (gk_mop_t *)malloc(mcore->nmops*sizeof(gk_mop_t))) == NULL) { |
||||||
|
free(mcore); |
||||||
|
return NULL; |
||||||
|
} |
||||||
|
|
||||||
|
return mcore; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function destroys an mcore.
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_mcoreDestroy(gk_mcore_t **r_mcore, int showstats) |
||||||
|
{ |
||||||
|
gk_mcore_t *mcore = *r_mcore; |
||||||
|
|
||||||
|
if (mcore == NULL) |
||||||
|
return; |
||||||
|
|
||||||
|
if (showstats) |
||||||
|
printf("\n gk_mcore statistics\n"
|
||||||
|
" coresize: %12zu nmops: %12zu cmop: %6zu\n" |
||||||
|
" num_callocs: %12zu num_hallocs: %12zu\n" |
||||||
|
" size_callocs: %12zu size_hallocs: %12zu\n" |
||||||
|
" cur_callocs: %12zu cur_hallocs: %12zu\n" |
||||||
|
" max_callocs: %12zu max_hallocs: %12zu\n", |
||||||
|
mcore->coresize, mcore->nmops, mcore->cmop, |
||||||
|
mcore->num_callocs, mcore->num_hallocs, |
||||||
|
mcore->size_callocs, mcore->size_hallocs, |
||||||
|
mcore->cur_callocs, mcore->cur_hallocs, |
||||||
|
mcore->max_callocs, mcore->max_hallocs); |
||||||
|
|
||||||
|
if (mcore->cur_callocs != 0 || mcore->cur_hallocs != 0 || mcore->cmop != 0) { |
||||||
|
printf("***Warning: mcore memory was not fully freed when destroyed.\n" |
||||||
|
" cur_callocs: %6zu cur_hallocs: %6zu cmop: %6zu\n", |
||||||
|
mcore->cur_callocs, mcore->cur_hallocs, mcore->cmop); |
||||||
|
} |
||||||
|
|
||||||
|
gk_free((void **)&mcore->core, &mcore->mops, &mcore, LTERM); |
||||||
|
|
||||||
|
*r_mcore = NULL; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function destroys an mcore. This version is for gkmcore.
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_gkmcoreDestroy(gk_mcore_t **r_mcore, int showstats) |
||||||
|
{ |
||||||
|
gk_mcore_t *mcore = *r_mcore; |
||||||
|
|
||||||
|
if (mcore == NULL) |
||||||
|
return; |
||||||
|
|
||||||
|
if (showstats) |
||||||
|
printf("\n gk_mcore statistics\n"
|
||||||
|
" nmops: %12zu cmop: %6zu\n" |
||||||
|
" num_hallocs: %12zu\n" |
||||||
|
" size_hallocs: %12zu\n" |
||||||
|
" cur_hallocs: %12zu\n" |
||||||
|
" max_hallocs: %12zu\n", |
||||||
|
mcore->nmops, mcore->cmop, |
||||||
|
mcore->num_hallocs, |
||||||
|
mcore->size_hallocs, |
||||||
|
mcore->cur_hallocs, |
||||||
|
mcore->max_hallocs); |
||||||
|
|
||||||
|
if (mcore->cur_hallocs != 0 || mcore->cmop != 0) { |
||||||
|
printf("***Warning: mcore memory was not fully freed when destroyed.\n" |
||||||
|
" cur_hallocs: %6zu cmop: %6zu\n", |
||||||
|
mcore->cur_hallocs, mcore->cmop); |
||||||
|
} |
||||||
|
|
||||||
|
free(mcore->mops); |
||||||
|
free(mcore); |
||||||
|
|
||||||
|
*r_mcore = NULL; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function allocate space from the core/heap
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
void *gk_mcoreMalloc(gk_mcore_t *mcore, size_t nbytes) |
||||||
|
{ |
||||||
|
void *ptr; |
||||||
|
|
||||||
|
/* pad to make pointers 8-byte aligned */ |
||||||
|
nbytes += (nbytes%8 == 0 ? 0 : 8 - nbytes%8); |
||||||
|
|
||||||
|
if (mcore->corecpos + nbytes < mcore->coresize) { |
||||||
|
/* service this request from the core */ |
||||||
|
ptr = ((char *)mcore->core)+mcore->corecpos; |
||||||
|
mcore->corecpos += nbytes; |
||||||
|
|
||||||
|
gk_mcoreAdd(mcore, GK_MOPT_CORE, nbytes, ptr); |
||||||
|
} |
||||||
|
else { |
||||||
|
/* service this request from the heap */ |
||||||
|
ptr = gk_malloc(nbytes, "gk_mcoremalloc: ptr"); |
||||||
|
|
||||||
|
gk_mcoreAdd(mcore, GK_MOPT_HEAP, nbytes, ptr); |
||||||
|
} |
||||||
|
|
||||||
|
/*
|
||||||
|
printf("MCMALLOC: %zu %d %8zu\n", mcore->cmop-1,
|
||||||
|
mcore->mops[mcore->cmop-1].type, mcore->mops[mcore->cmop-1].nbytes); |
||||||
|
*/ |
||||||
|
|
||||||
|
return ptr; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function sets a marker in the stack of malloc ops to be used
|
||||||
|
subsequently for freeing purposes
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_mcorePush(gk_mcore_t *mcore) |
||||||
|
{ |
||||||
|
gk_mcoreAdd(mcore, GK_MOPT_MARK, 0, NULL); |
||||||
|
/* printf("MCPPUSH: %zu\n", mcore->cmop-1); */ |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function sets a marker in the stack of malloc ops to be used
|
||||||
|
subsequently for freeing purposes. This is the gkmcore version. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_gkmcorePush(gk_mcore_t *mcore) |
||||||
|
{ |
||||||
|
gk_gkmcoreAdd(mcore, GK_MOPT_MARK, 0, NULL); |
||||||
|
/* printf("MCPPUSH: %zu\n", mcore->cmop-1); */ |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function frees all mops since the last push
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_mcorePop(gk_mcore_t *mcore) |
||||||
|
{ |
||||||
|
while (mcore->cmop > 0) { |
||||||
|
mcore->cmop--; |
||||||
|
switch (mcore->mops[mcore->cmop].type) { |
||||||
|
case GK_MOPT_MARK: /* push marker */ |
||||||
|
goto DONE; |
||||||
|
break;
|
||||||
|
|
||||||
|
case GK_MOPT_CORE: /* core free */ |
||||||
|
if (mcore->corecpos < mcore->mops[mcore->cmop].nbytes) |
||||||
|
errexit("Internal Error: wspace's core is about to be over-freed [%zu, %zu, %zd]\n", |
||||||
|
mcore->coresize, mcore->corecpos, mcore->mops[mcore->cmop].nbytes); |
||||||
|
|
||||||
|
mcore->corecpos -= mcore->mops[mcore->cmop].nbytes; |
||||||
|
mcore->cur_callocs -= mcore->mops[mcore->cmop].nbytes; |
||||||
|
break; |
||||||
|
|
||||||
|
case GK_MOPT_HEAP: /* heap free */ |
||||||
|
gk_free((void **)&mcore->mops[mcore->cmop].ptr, LTERM); |
||||||
|
mcore->cur_hallocs -= mcore->mops[mcore->cmop].nbytes; |
||||||
|
break; |
||||||
|
|
||||||
|
default: |
||||||
|
gk_errexit(SIGMEM, "Unknown mop type of %d\n", mcore->mops[mcore->cmop].type); |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
DONE: |
||||||
|
; |
||||||
|
/*printf("MCPPOP: %zu\n", mcore->cmop); */ |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function frees all mops since the last push. This version is
|
||||||
|
for poping the gkmcore and it uses free instead of gk_free. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_gkmcorePop(gk_mcore_t *mcore) |
||||||
|
{ |
||||||
|
while (mcore->cmop > 0) { |
||||||
|
mcore->cmop--; |
||||||
|
switch (mcore->mops[mcore->cmop].type) { |
||||||
|
case GK_MOPT_MARK: /* push marker */ |
||||||
|
goto DONE; |
||||||
|
break;
|
||||||
|
|
||||||
|
case GK_MOPT_HEAP: /* heap free */ |
||||||
|
free(mcore->mops[mcore->cmop].ptr); |
||||||
|
mcore->cur_hallocs -= mcore->mops[mcore->cmop].nbytes; |
||||||
|
break; |
||||||
|
|
||||||
|
default: |
||||||
|
gk_errexit(SIGMEM, "Unknown mop type of %d\n", mcore->mops[mcore->cmop].type); |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
DONE: |
||||||
|
; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Adds a memory allocation at the end of the list.
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_mcoreAdd(gk_mcore_t *mcore, int type, size_t nbytes, void *ptr) |
||||||
|
{ |
||||||
|
if (mcore->cmop == mcore->nmops) { |
||||||
|
mcore->nmops *= 2; |
||||||
|
mcore->mops = realloc(mcore->mops, mcore->nmops*sizeof(gk_mop_t)); |
||||||
|
if (mcore->mops == NULL)
|
||||||
|
gk_errexit(SIGMEM, "***Memory allocation for gkmcore failed.\n"); |
||||||
|
} |
||||||
|
|
||||||
|
mcore->mops[mcore->cmop].type = type; |
||||||
|
mcore->mops[mcore->cmop].nbytes = nbytes; |
||||||
|
mcore->mops[mcore->cmop].ptr = ptr; |
||||||
|
mcore->cmop++; |
||||||
|
|
||||||
|
switch (type) { |
||||||
|
case GK_MOPT_MARK: |
||||||
|
break; |
||||||
|
|
||||||
|
case GK_MOPT_CORE: |
||||||
|
mcore->num_callocs++; |
||||||
|
mcore->size_callocs += nbytes; |
||||||
|
mcore->cur_callocs += nbytes; |
||||||
|
if (mcore->max_callocs < mcore->cur_callocs) |
||||||
|
mcore->max_callocs = mcore->cur_callocs; |
||||||
|
break; |
||||||
|
|
||||||
|
case GK_MOPT_HEAP: |
||||||
|
mcore->num_hallocs++; |
||||||
|
mcore->size_hallocs += nbytes; |
||||||
|
mcore->cur_hallocs += nbytes; |
||||||
|
if (mcore->max_hallocs < mcore->cur_hallocs) |
||||||
|
mcore->max_hallocs = mcore->cur_hallocs; |
||||||
|
break; |
||||||
|
default: |
||||||
|
gk_errexit(SIGMEM, "Incorrect mcore type operation.\n"); |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Adds a memory allocation at the end of the list. This is the gkmcore
|
||||||
|
version. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_gkmcoreAdd(gk_mcore_t *mcore, int type, size_t nbytes, void *ptr) |
||||||
|
{ |
||||||
|
if (mcore->cmop == mcore->nmops) { |
||||||
|
mcore->nmops *= 2; |
||||||
|
mcore->mops = realloc(mcore->mops, mcore->nmops*sizeof(gk_mop_t)); |
||||||
|
if (mcore->mops == NULL)
|
||||||
|
gk_errexit(SIGMEM, "***Memory allocation for gkmcore failed.\n"); |
||||||
|
} |
||||||
|
|
||||||
|
mcore->mops[mcore->cmop].type = type; |
||||||
|
mcore->mops[mcore->cmop].nbytes = nbytes; |
||||||
|
mcore->mops[mcore->cmop].ptr = ptr; |
||||||
|
mcore->cmop++; |
||||||
|
|
||||||
|
switch (type) { |
||||||
|
case GK_MOPT_MARK: |
||||||
|
break; |
||||||
|
|
||||||
|
case GK_MOPT_HEAP: |
||||||
|
mcore->num_hallocs++; |
||||||
|
mcore->size_hallocs += nbytes; |
||||||
|
mcore->cur_hallocs += nbytes; |
||||||
|
if (mcore->max_hallocs < mcore->cur_hallocs) |
||||||
|
mcore->max_hallocs = mcore->cur_hallocs; |
||||||
|
break; |
||||||
|
default: |
||||||
|
gk_errexit(SIGMEM, "Incorrect mcore type operation.\n"); |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function deletes the mop associated with the supplied pointer.
|
||||||
|
The mop has to be a heap allocation, otherwise it fails violently. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_mcoreDel(gk_mcore_t *mcore, void *ptr) |
||||||
|
{ |
||||||
|
int i; |
||||||
|
|
||||||
|
for (i=mcore->cmop-1; i>=0; i--) { |
||||||
|
if (mcore->mops[i].type == GK_MOPT_MARK) |
||||||
|
gk_errexit(SIGMEM, "Could not find pointer %p in mcore\n", ptr); |
||||||
|
|
||||||
|
if (mcore->mops[i].ptr == ptr) { |
||||||
|
if (mcore->mops[i].type != GK_MOPT_HEAP) |
||||||
|
gk_errexit(SIGMEM, "Trying to delete a non-HEAP mop.\n"); |
||||||
|
|
||||||
|
mcore->cur_hallocs -= mcore->mops[i].nbytes; |
||||||
|
mcore->mops[i] = mcore->mops[--mcore->cmop]; |
||||||
|
return; |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
gk_errexit(SIGMEM, "mcoreDel should never have been here!\n"); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function deletes the mop associated with the supplied pointer.
|
||||||
|
The mop has to be a heap allocation, otherwise it fails violently. |
||||||
|
This is the gkmcore version. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_gkmcoreDel(gk_mcore_t *mcore, void *ptr) |
||||||
|
{ |
||||||
|
int i; |
||||||
|
|
||||||
|
for (i=mcore->cmop-1; i>=0; i--) { |
||||||
|
if (mcore->mops[i].type == GK_MOPT_MARK) |
||||||
|
gk_errexit(SIGMEM, "Could not find pointer %p in mcore\n", ptr); |
||||||
|
|
||||||
|
if (mcore->mops[i].ptr == ptr) { |
||||||
|
if (mcore->mops[i].type != GK_MOPT_HEAP) |
||||||
|
gk_errexit(SIGMEM, "Trying to delete a non-HEAP mop.\n"); |
||||||
|
|
||||||
|
mcore->cur_hallocs -= mcore->mops[i].nbytes; |
||||||
|
mcore->mops[i] = mcore->mops[--mcore->cmop]; |
||||||
|
return; |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
gk_errexit(SIGMEM, "gkmcoreDel should never have been here!\n"); |
||||||
|
} |
||||||
|
|
||||||
@ -0,0 +1,307 @@ |
|||||||
|
/*!
|
||||||
|
\file memory.c |
||||||
|
\brief This file contains various allocation routines
|
||||||
|
|
||||||
|
The allocation routines included are for 1D and 2D arrays of the
|
||||||
|
most datatypes that GKlib support. Many of these routines are
|
||||||
|
defined with the help of the macros in gk_memory.h. These macros
|
||||||
|
can be used to define other memory allocation routines. |
||||||
|
|
||||||
|
\date Started 4/3/2007 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: memory.c 21050 2017-05-25 03:53:58Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
/* This is for the global mcore that tracks all heap allocations */ |
||||||
|
static __thread gk_mcore_t *gkmcore = NULL; |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Define the set of memory allocation routines for each data type */ |
||||||
|
/**************************************************************************/ |
||||||
|
GK_MKALLOC(gk_c, char) |
||||||
|
GK_MKALLOC(gk_i, int) |
||||||
|
GK_MKALLOC(gk_i8, int8_t) |
||||||
|
GK_MKALLOC(gk_i16, int16_t) |
||||||
|
GK_MKALLOC(gk_i32, int32_t) |
||||||
|
GK_MKALLOC(gk_i64, int64_t) |
||||||
|
GK_MKALLOC(gk_ui8, uint8_t) |
||||||
|
GK_MKALLOC(gk_ui16, uint16_t) |
||||||
|
GK_MKALLOC(gk_ui32, uint32_t) |
||||||
|
GK_MKALLOC(gk_ui64, uint64_t) |
||||||
|
GK_MKALLOC(gk_z, ssize_t) |
||||||
|
GK_MKALLOC(gk_zu, size_t) |
||||||
|
GK_MKALLOC(gk_f, float) |
||||||
|
GK_MKALLOC(gk_d, double) |
||||||
|
GK_MKALLOC(gk_idx, gk_idx_t) |
||||||
|
|
||||||
|
GK_MKALLOC(gk_ckv, gk_ckv_t) |
||||||
|
GK_MKALLOC(gk_ikv, gk_ikv_t) |
||||||
|
GK_MKALLOC(gk_i8kv, gk_i8kv_t) |
||||||
|
GK_MKALLOC(gk_i16kv, gk_i16kv_t) |
||||||
|
GK_MKALLOC(gk_i32kv, gk_i32kv_t) |
||||||
|
GK_MKALLOC(gk_i64kv, gk_i64kv_t) |
||||||
|
GK_MKALLOC(gk_zkv, gk_zkv_t) |
||||||
|
GK_MKALLOC(gk_zukv, gk_zukv_t) |
||||||
|
GK_MKALLOC(gk_fkv, gk_fkv_t) |
||||||
|
GK_MKALLOC(gk_dkv, gk_dkv_t) |
||||||
|
GK_MKALLOC(gk_skv, gk_skv_t) |
||||||
|
GK_MKALLOC(gk_idxkv, gk_idxkv_t) |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function allocates a two-dimensional matrix.
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_AllocMatrix(void ***r_matrix, size_t elmlen, size_t ndim1, size_t ndim2) |
||||||
|
{ |
||||||
|
size_t i, j; |
||||||
|
void **matrix; |
||||||
|
|
||||||
|
*r_matrix = NULL; |
||||||
|
|
||||||
|
if ((matrix = (void **)gk_malloc(ndim1*sizeof(void *), "gk_AllocMatrix: matrix")) == NULL) |
||||||
|
return; |
||||||
|
|
||||||
|
for (i=0; i<ndim1; i++) { |
||||||
|
if ((matrix[i] = (void *)gk_malloc(ndim2*elmlen, "gk_AllocMatrix: matrix[i]")) == NULL) { |
||||||
|
for (j=0; j<i; j++)
|
||||||
|
gk_free((void **)&matrix[j], LTERM); |
||||||
|
return; |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
*r_matrix = matrix; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function frees a two-dimensional matrix.
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_FreeMatrix(void ***r_matrix, size_t ndim1, size_t ndim2) |
||||||
|
{ |
||||||
|
size_t i; |
||||||
|
void **matrix; |
||||||
|
|
||||||
|
if ((matrix = *r_matrix) == NULL) |
||||||
|
return; |
||||||
|
|
||||||
|
for (i=0; i<ndim1; i++)
|
||||||
|
gk_free((void **)&matrix[i], LTERM); |
||||||
|
|
||||||
|
gk_free((void **)r_matrix, LTERM);
|
||||||
|
|
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function initializes tracking of heap allocations.
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
int gk_malloc_init() |
||||||
|
{ |
||||||
|
if (gkmcore == NULL) |
||||||
|
gkmcore = gk_gkmcoreCreate(); |
||||||
|
|
||||||
|
if (gkmcore == NULL) |
||||||
|
return 0; |
||||||
|
|
||||||
|
gk_gkmcorePush(gkmcore); |
||||||
|
|
||||||
|
return 1; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function frees the memory that has been allocated since the
|
||||||
|
last call to gk_malloc_init(). |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_malloc_cleanup(int showstats) |
||||||
|
{ |
||||||
|
if (gkmcore != NULL) { |
||||||
|
gk_gkmcorePop(gkmcore); |
||||||
|
if (gkmcore->cmop == 0) { |
||||||
|
gk_gkmcoreDestroy(&gkmcore, showstats); |
||||||
|
gkmcore = NULL; |
||||||
|
} |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function is my wrapper around malloc that provides the following
|
||||||
|
enhancements over malloc: |
||||||
|
* It always allocates one byte of memory, even if 0 bytes are requested. |
||||||
|
This is to ensure that checks of returned values do not lead to NULL |
||||||
|
due to 0 bytes requested. |
||||||
|
* It zeros-out the memory that is allocated. This is for a quick init |
||||||
|
of the underlying datastructures. |
||||||
|
*/ |
||||||
|
/**************************************************************************/ |
||||||
|
void *gk_malloc(size_t nbytes, char *msg) |
||||||
|
{ |
||||||
|
void *ptr=NULL; |
||||||
|
|
||||||
|
if (nbytes == 0) |
||||||
|
nbytes++; /* Force mallocs to actually allocate some memory */ |
||||||
|
|
||||||
|
ptr = (void *)malloc(nbytes); |
||||||
|
|
||||||
|
if (ptr == NULL) { |
||||||
|
fprintf(stderr, " Current memory used: %10zu bytes\n", gk_GetCurMemoryUsed()); |
||||||
|
fprintf(stderr, " Maximum memory used: %10zu bytes\n", gk_GetMaxMemoryUsed()); |
||||||
|
gk_errexit(SIGMEM, "***Memory allocation failed for %s. Requested size: %zu bytes",
|
||||||
|
msg, nbytes); |
||||||
|
return NULL; |
||||||
|
} |
||||||
|
|
||||||
|
/* add this memory allocation */ |
||||||
|
if (gkmcore != NULL) gk_gkmcoreAdd(gkmcore, GK_MOPT_HEAP, nbytes, ptr); |
||||||
|
|
||||||
|
return ptr; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************
|
||||||
|
* This function is my wrapper around realloc |
||||||
|
**************************************************************************/ |
||||||
|
void *gk_realloc(void *oldptr, size_t nbytes, char *msg) |
||||||
|
{ |
||||||
|
void *ptr=NULL; |
||||||
|
|
||||||
|
if (nbytes == 0) |
||||||
|
nbytes++; /* Force mallocs to actually allocate some memory */ |
||||||
|
|
||||||
|
/* remove this memory de-allocation */ |
||||||
|
if (gkmcore != NULL && oldptr != NULL) gk_gkmcoreDel(gkmcore, oldptr); |
||||||
|
|
||||||
|
ptr = (void *)realloc(oldptr, nbytes); |
||||||
|
|
||||||
|
if (ptr == NULL) { |
||||||
|
fprintf(stderr, " Maximum memory used: %10zu bytes\n", gk_GetMaxMemoryUsed()); |
||||||
|
fprintf(stderr, " Current memory used: %10zu bytes\n", gk_GetCurMemoryUsed()); |
||||||
|
gk_errexit(SIGMEM, "***Memory realloc failed for %s. " "Requested size: %zu bytes",
|
||||||
|
msg, nbytes); |
||||||
|
return NULL; |
||||||
|
} |
||||||
|
|
||||||
|
/* add this memory allocation */ |
||||||
|
if (gkmcore != NULL) gk_gkmcoreAdd(gkmcore, GK_MOPT_HEAP, nbytes, ptr); |
||||||
|
|
||||||
|
return ptr; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************
|
||||||
|
* This function is my wrapper around free, allows multiple pointers
|
||||||
|
**************************************************************************/ |
||||||
|
void gk_free(void **ptr1,...) |
||||||
|
{ |
||||||
|
va_list plist; |
||||||
|
void **ptr; |
||||||
|
|
||||||
|
if (*ptr1 != NULL) { |
||||||
|
free(*ptr1); |
||||||
|
|
||||||
|
/* remove this memory de-allocation */ |
||||||
|
if (gkmcore != NULL)
|
||||||
|
gk_gkmcoreDel(gkmcore, *ptr1); |
||||||
|
} |
||||||
|
*ptr1 = NULL; |
||||||
|
|
||||||
|
va_start(plist, ptr1); |
||||||
|
while ((ptr = va_arg(plist, void **)) != LTERM) { |
||||||
|
if (*ptr != NULL) { |
||||||
|
free(*ptr); |
||||||
|
|
||||||
|
/* remove this memory de-allocation */ |
||||||
|
if (gkmcore != NULL)
|
||||||
|
gk_gkmcoreDel(gkmcore, *ptr); |
||||||
|
} |
||||||
|
*ptr = NULL; |
||||||
|
} |
||||||
|
va_end(plist); |
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************
|
||||||
|
* This function returns the current ammount of dynamically allocated |
||||||
|
* memory that is used by the system |
||||||
|
**************************************************************************/ |
||||||
|
size_t gk_GetCurMemoryUsed() |
||||||
|
{ |
||||||
|
if (gkmcore == NULL) |
||||||
|
return 0; |
||||||
|
else |
||||||
|
return gkmcore->cur_hallocs; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************
|
||||||
|
* This function returns the maximum ammount of dynamically allocated
|
||||||
|
* memory that was used by the system |
||||||
|
**************************************************************************/ |
||||||
|
size_t gk_GetMaxMemoryUsed() |
||||||
|
{ |
||||||
|
if (gkmcore == NULL) |
||||||
|
return 0; |
||||||
|
else |
||||||
|
return gkmcore->max_hallocs; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function returns the VmSize and VmRSS of the calling process. */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_GetVMInfo(size_t *vmsize, size_t *vmrss) |
||||||
|
{ |
||||||
|
FILE *fp; |
||||||
|
char fname[1024]; |
||||||
|
|
||||||
|
sprintf(fname, "/proc/%d/statm", getpid()); |
||||||
|
fp = gk_fopen(fname, "r", "proc/pid/statm"); |
||||||
|
if (fscanf(fp, "%zu %zu", vmsize, vmrss) != 2) |
||||||
|
errexit("Failed to read to values from %s\n", fname); |
||||||
|
gk_fclose(fp); |
||||||
|
|
||||||
|
/*
|
||||||
|
*vmsize *= sysconf(_SC_PAGESIZE); |
||||||
|
*vmrss *= sysconf(_SC_PAGESIZE); |
||||||
|
*/ |
||||||
|
|
||||||
|
return; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function returns the peak virtual memory of the calling process
|
||||||
|
by reading the VmPeak field in /proc/self/status . */ |
||||||
|
/*************************************************************************/ |
||||||
|
size_t gk_GetProcVmPeak() |
||||||
|
{ |
||||||
|
FILE *fp; |
||||||
|
char line[128]; |
||||||
|
size_t vmpeak=0; |
||||||
|
|
||||||
|
if (gk_fexists("/proc/self/status")) { |
||||||
|
fp = gk_fopen("/proc/self/status", "r", "proc/self/status"); |
||||||
|
while (fgets(line, 128, fp) != NULL) { |
||||||
|
if (strncmp(line, "VmPeak:", 7) == 0) { |
||||||
|
vmpeak = atoll(line+8)*1024; |
||||||
|
break; |
||||||
|
} |
||||||
|
} |
||||||
|
gk_fclose(fp); |
||||||
|
} |
||||||
|
|
||||||
|
return vmpeak; |
||||||
|
} |
||||||
@ -0,0 +1,25 @@ |
|||||||
|
/*!
|
||||||
|
\file pqueue.c |
||||||
|
\brief This file implements various max-priority queues. |
||||||
|
|
||||||
|
The priority queues are generated using the GK_MKPQUEUE macro. |
||||||
|
|
||||||
|
\date Started 3/27/2007 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: pqueue.c 10711 2011-08-31 22:23:04Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Create the various max priority queues */ |
||||||
|
/*************************************************************************/ |
||||||
|
#define key_gt(a, b) ((a) > (b)) |
||||||
|
GK_MKPQUEUE(gk_ipq, gk_ipq_t, gk_ikv_t, int, gk_idx_t, gk_ikvmalloc, INT_MAX, key_gt) |
||||||
|
GK_MKPQUEUE(gk_i32pq, gk_i32pq_t, gk_i32kv_t, int32_t, gk_idx_t, gk_i32kvmalloc, INT32_MAX, key_gt) |
||||||
|
GK_MKPQUEUE(gk_i64pq, gk_i64pq_t, gk_i64kv_t, int64_t, gk_idx_t, gk_i64kvmalloc, INT64_MAX, key_gt) |
||||||
|
GK_MKPQUEUE(gk_fpq, gk_fpq_t, gk_fkv_t, float, gk_idx_t, gk_fkvmalloc, FLT_MAX, key_gt) |
||||||
|
GK_MKPQUEUE(gk_dpq, gk_dpq_t, gk_dkv_t, double, gk_idx_t, gk_dkvmalloc, DBL_MAX, key_gt) |
||||||
|
GK_MKPQUEUE(gk_idxpq, gk_idxpq_t, gk_idxkv_t, gk_idx_t, gk_idx_t, gk_idxkvmalloc, GK_IDX_MAX, key_gt) |
||||||
|
#undef key_gt |
||||||
@ -0,0 +1,136 @@ |
|||||||
|
/*!
|
||||||
|
\file
|
||||||
|
\brief Various routines for providing portable 32 and 64 bit random number |
||||||
|
generators. |
||||||
|
|
||||||
|
\date Started 5/17/2007 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: random.c 18796 2015-06-02 11:39:45Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Create the various random number functions */ |
||||||
|
/*************************************************************************/ |
||||||
|
GK_MKRANDOM(gk_c, size_t, char) |
||||||
|
GK_MKRANDOM(gk_i, size_t, int) |
||||||
|
GK_MKRANDOM(gk_i32, size_t, int32_t) |
||||||
|
GK_MKRANDOM(gk_f, size_t, float) |
||||||
|
GK_MKRANDOM(gk_d, size_t, double) |
||||||
|
GK_MKRANDOM(gk_idx, size_t, gk_idx_t) |
||||||
|
GK_MKRANDOM(gk_z, size_t, ssize_t) |
||||||
|
GK_MKRANDOM(gk_zu, size_t, size_t) |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! GKlib's built in random number generator for portability across
|
||||||
|
different architectures */ |
||||||
|
/*************************************************************************/ |
||||||
|
#ifdef USE_GKRAND |
||||||
|
/*
|
||||||
|
A C-program for MT19937-64 (2004/9/29 version). |
||||||
|
Coded by Takuji Nishimura and Makoto Matsumoto. |
||||||
|
|
||||||
|
This is a 64-bit version of Mersenne Twister pseudorandom number |
||||||
|
generator. |
||||||
|
|
||||||
|
Before using, initialize the state by using init_genrand64(seed)
|
||||||
|
or init_by_array64(init_key, key_length). |
||||||
|
|
||||||
|
Copyright (C) 2004, Makoto Matsumoto and Takuji Nishimura, |
||||||
|
All rights reserved.
|
||||||
|
|
||||||
|
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS |
||||||
|
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT |
||||||
|
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR |
||||||
|
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR |
||||||
|
CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, |
||||||
|
EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, |
||||||
|
PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR |
||||||
|
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF |
||||||
|
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING |
||||||
|
NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS |
||||||
|
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
||||||
|
*/ |
||||||
|
|
||||||
|
#define NN 312 |
||||||
|
#define MM 156 |
||||||
|
#define MATRIX_A 0xB5026F5AA96619E9ULL |
||||||
|
#define UM 0xFFFFFFFF80000000ULL /* Most significant 33 bits */ |
||||||
|
#define LM 0x7FFFFFFFULL /* Least significant 31 bits */ |
||||||
|
|
||||||
|
|
||||||
|
/* The array for the state vector */ |
||||||
|
static uint64_t mt[NN];
|
||||||
|
/* mti==NN+1 means mt[NN] is not initialized */ |
||||||
|
static int mti=NN+1;
|
||||||
|
#endif /* USE_GKRAND */ |
||||||
|
|
||||||
|
/* initializes mt[NN] with a seed */ |
||||||
|
void gk_randinit(uint64_t seed) |
||||||
|
{ |
||||||
|
#ifdef USE_GKRAND |
||||||
|
mt[0] = seed; |
||||||
|
for (mti=1; mti<NN; mti++)
|
||||||
|
mt[mti] = (6364136223846793005ULL * (mt[mti-1] ^ (mt[mti-1] >> 62)) + mti); |
||||||
|
#else |
||||||
|
srand((unsigned int) seed); |
||||||
|
#endif |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/* generates a random number on [0, 2^64-1]-interval */ |
||||||
|
uint64_t gk_randint64(void) |
||||||
|
{ |
||||||
|
#ifdef USE_GKRAND |
||||||
|
int i; |
||||||
|
unsigned long long x; |
||||||
|
static uint64_t mag01[2]={0ULL, MATRIX_A}; |
||||||
|
|
||||||
|
if (mti >= NN) { /* generate NN words at one time */ |
||||||
|
/* if init_genrand64() has not been called, */ |
||||||
|
/* a default initial seed is used */ |
||||||
|
if (mti == NN+1)
|
||||||
|
gk_randinit(5489ULL);
|
||||||
|
|
||||||
|
for (i=0; i<NN-MM; i++) { |
||||||
|
x = (mt[i]&UM)|(mt[i+1]&LM); |
||||||
|
mt[i] = mt[i+MM] ^ (x>>1) ^ mag01[(int)(x&1ULL)]; |
||||||
|
} |
||||||
|
for (; i<NN-1; i++) { |
||||||
|
x = (mt[i]&UM)|(mt[i+1]&LM); |
||||||
|
mt[i] = mt[i+(MM-NN)] ^ (x>>1) ^ mag01[(int)(x&1ULL)]; |
||||||
|
} |
||||||
|
x = (mt[NN-1]&UM)|(mt[0]&LM); |
||||||
|
mt[NN-1] = mt[MM-1] ^ (x>>1) ^ mag01[(int)(x&1ULL)]; |
||||||
|
|
||||||
|
mti = 0; |
||||||
|
} |
||||||
|
|
||||||
|
x = mt[mti++]; |
||||||
|
|
||||||
|
x ^= (x >> 29) & 0x5555555555555555ULL; |
||||||
|
x ^= (x << 17) & 0x71D67FFFEDA60000ULL; |
||||||
|
x ^= (x << 37) & 0xFFF7EEE000000000ULL; |
||||||
|
x ^= (x >> 43); |
||||||
|
|
||||||
|
return x & 0x7FFFFFFFFFFFFFFF; |
||||||
|
#else |
||||||
|
return (uint64_t)(((uint64_t) rand()) << 32 | ((uint64_t) rand())); |
||||||
|
#endif |
||||||
|
} |
||||||
|
|
||||||
|
/* generates a random number on [0, 2^32-1]-interval */ |
||||||
|
uint32_t gk_randint32(void) |
||||||
|
{ |
||||||
|
#ifdef USE_GKRAND |
||||||
|
return (uint32_t)(gk_randint64() & 0x7FFFFFFF); |
||||||
|
#else |
||||||
|
return (uint32_t)rand(); |
||||||
|
#endif |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
@ -0,0 +1,103 @@ |
|||||||
|
/*!
|
||||||
|
* \file
|
||||||
|
* |
||||||
|
* \brief Various routines that perform random-walk based operations |
||||||
|
on graphs stored as gk_csr_t matrices. |
||||||
|
* |
||||||
|
* \author George Karypis |
||||||
|
* \version\verbatim $Id: rw.c 11078 2011-11-12 00:20:44Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Computes the (personalized) page-rank of the vertices in a graph.
|
||||||
|
|
||||||
|
\param mat is the matrix storing the graph. |
||||||
|
\param lamda is the restart probability. |
||||||
|
\param eps is the error tolerance for convergance. |
||||||
|
\param max_niter is the maximum number of allowed iterations. |
||||||
|
\param pr on entry stores the restart distribution of the vertices.
|
||||||
|
This allows for the computation of personalized page-rank scores
|
||||||
|
by appropriately setting that parameter.
|
||||||
|
On return, pr stores the computed page ranks. |
||||||
|
|
||||||
|
\returns the number of iterations that were performed. |
||||||
|
*/ |
||||||
|
/**************************************************************************/ |
||||||
|
int gk_rw_PageRank(gk_csr_t *mat, float lamda, float eps, int max_niter, float *pr) |
||||||
|
{ |
||||||
|
ssize_t i, j, k, iter, nrows; |
||||||
|
double *rscale, *prold, *prnew, *prtmp; |
||||||
|
double fromsinks, error; |
||||||
|
ssize_t *rowptr; |
||||||
|
int *rowind; |
||||||
|
float *rowval; |
||||||
|
|
||||||
|
nrows = mat->nrows; |
||||||
|
rowptr = mat->rowptr; |
||||||
|
rowind = mat->rowind; |
||||||
|
rowval = mat->rowval; |
||||||
|
|
||||||
|
prold = gk_dsmalloc(nrows, 0, "gk_rw_PageRank: prnew"); |
||||||
|
prnew = gk_dsmalloc(nrows, 0, "gk_rw_PageRank: prold"); |
||||||
|
rscale = gk_dsmalloc(nrows, 0, "gk_rw_PageRank: rscale"); |
||||||
|
|
||||||
|
/* compute the scaling factors to get adjacency weights into transition
|
||||||
|
probabilities */ |
||||||
|
for (i=0; i<nrows; i++) { |
||||||
|
for (j=rowptr[i]; j<rowptr[i+1]; j++) |
||||||
|
rscale[i] += rowval[j]; |
||||||
|
if (rscale[i] > 0) |
||||||
|
rscale[i] = 1.0/rscale[i]; |
||||||
|
} |
||||||
|
|
||||||
|
/* the restart distribution is the initial pr scores */ |
||||||
|
for (i=0; i<nrows; i++) |
||||||
|
prnew[i] = pr[i]; |
||||||
|
|
||||||
|
/* get into the PR iteration */ |
||||||
|
for (iter=0; iter<max_niter; iter++) { |
||||||
|
gk_SWAP(prnew, prold, prtmp); |
||||||
|
gk_dset(nrows, 0.0, prnew); |
||||||
|
|
||||||
|
/* determine the total current PR score of the sinks so that you
|
||||||
|
can distribute them to all nodes according to the restart
|
||||||
|
distribution. */ |
||||||
|
for (fromsinks=0.0, i=0; i<nrows; i++) { |
||||||
|
if (rscale[i] == 0)
|
||||||
|
fromsinks += prold[i]; |
||||||
|
} |
||||||
|
|
||||||
|
/* push random-walk scores to the outlinks */ |
||||||
|
for (i=0; i<nrows; i++) { |
||||||
|
for (j=rowptr[i]; j<rowptr[i+1]; j++) |
||||||
|
prnew[rowind[j]] += prold[i]*rscale[i]*rowval[j]; |
||||||
|
} |
||||||
|
|
||||||
|
/* apply the restart conditions */ |
||||||
|
for (i=0; i<nrows; i++) { |
||||||
|
prnew[i] = lamda*(fromsinks*pr[i]+prnew[i]) + (1.0-lamda)*pr[i]; |
||||||
|
} |
||||||
|
|
||||||
|
/* compute the error */ |
||||||
|
for (error=0.0, i=0; i<nrows; i++)
|
||||||
|
error = (fabs(prnew[i]-prold[i]) > error ? fabs(prnew[i]-prold[i]) : error); |
||||||
|
|
||||||
|
//printf("nrm1: %le maxfabserr: %le\n", gk_dsum(nrows, prnew, 1), error);
|
||||||
|
|
||||||
|
if (error < eps) |
||||||
|
break; |
||||||
|
} |
||||||
|
|
||||||
|
/* store the computed pr scores into pr for output */ |
||||||
|
for (i=0; i<nrows; i++) |
||||||
|
pr[i] = prnew[i]; |
||||||
|
|
||||||
|
gk_free((void **)&prnew, &prold, &rscale, LTERM); |
||||||
|
|
||||||
|
return (int)(iter+1); |
||||||
|
|
||||||
|
} |
||||||
|
|
||||||
@ -0,0 +1,53 @@ |
|||||||
|
#!/usr/bin/perl -w |
||||||
|
|
||||||
|
die "Usage $0 <gfile> <ncopies>\n" unless @ARGV == 2; |
||||||
|
|
||||||
|
$filein = shift(@ARGV); |
||||||
|
$ncopies = shift(@ARGV); |
||||||
|
|
||||||
|
open(FPIN, "<$filein") or die "Could not open $filein. $!\n"; |
||||||
|
|
||||||
|
$_ = <FPIN>; |
||||||
|
chomp($_); |
||||||
|
($nvtxs, $nedges) = split(' ', $_); |
||||||
|
|
||||||
|
#print "nvtxs: $nvtxs, nedges: $nedges\n"; |
||||||
|
|
||||||
|
$u = 1; |
||||||
|
while (<FPIN>) { |
||||||
|
chomp($_); |
||||||
|
@edges = split(' ', $_); |
||||||
|
|
||||||
|
# put the within layer edges |
||||||
|
foreach $v (@edges) { |
||||||
|
next if $v < $u; |
||||||
|
for ($i=0; $i<$ncopies; $i++) { |
||||||
|
printf("%d %d\n", $i*$nvtxs+$u-1, $i*$nvtxs+$v-1); |
||||||
|
printf("%d %d\n", $i*$nvtxs+$v-1, $i*$nvtxs+$u-1); |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
# put the vertex across layer edges |
||||||
|
for ($i=0; $i<$ncopies-1; $i++) { |
||||||
|
printf("%d %d\n", $i*$nvtxs+$u-1, ($i+1)*$nvtxs+$u-1); |
||||||
|
printf("%d %d\n", ($i+1)*$nvtxs+$u-1, $i*$nvtxs+$u-1); |
||||||
|
} |
||||||
|
|
||||||
|
# put the adjacent across layer edges |
||||||
|
for ($i=0; $i<$ncopies-1; $i++) { |
||||||
|
$j=0; |
||||||
|
foreach $v (@edges) { |
||||||
|
$j++; |
||||||
|
next if (($j+$i)%2 == 0); |
||||||
|
printf("%d %d\n", $i*$nvtxs+$u-1, ($i+1)*$nvtxs+$v-1); |
||||||
|
printf("%d %d\n", ($i+1)*$nvtxs+$v-1, $i*$nvtxs+$u-1); |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
goto DONE; |
||||||
|
|
||||||
|
DONE: |
||||||
|
$u++; |
||||||
|
} |
||||||
|
|
||||||
|
close(FPIN); |
||||||
@ -0,0 +1,174 @@ |
|||||||
|
/*
|
||||||
|
* |
||||||
|
* Sequence handler library by Huzefa Rangwala |
||||||
|
* Date : 03.01.2007 |
||||||
|
* |
||||||
|
* |
||||||
|
* |
||||||
|
*/ |
||||||
|
|
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*********************************************************/ |
||||||
|
/* ! \brief Initializes the <tt>gk_seq_t</tt> variable
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
\param A pointer to gk_seq_t itself |
||||||
|
\returns null |
||||||
|
*/ |
||||||
|
/***********************************************************************/ |
||||||
|
|
||||||
|
void gk_seq_init(gk_seq_t *seq) |
||||||
|
{ |
||||||
|
|
||||||
|
seq->len = 0; |
||||||
|
seq->sequence = NULL; |
||||||
|
|
||||||
|
seq->pssm = NULL; |
||||||
|
seq->psfm = NULL; |
||||||
|
|
||||||
|
seq->name = NULL; |
||||||
|
|
||||||
|
} |
||||||
|
|
||||||
|
/***********************************************************************/ |
||||||
|
/*! \brief This function creates the localizations for the various sequences
|
||||||
|
|
||||||
|
\param string i.e amino acids, nucleotides, sequences |
||||||
|
\returns gk_i2cc2i_t variable |
||||||
|
*/ |
||||||
|
/*********************************************************************/ |
||||||
|
|
||||||
|
gk_i2cc2i_t *gk_i2cc2i_create_common(char *alphabet) |
||||||
|
{ |
||||||
|
|
||||||
|
|
||||||
|
int nsymbols; |
||||||
|
gk_idx_t i; |
||||||
|
gk_i2cc2i_t *t; |
||||||
|
|
||||||
|
nsymbols = strlen(alphabet); |
||||||
|
t = gk_malloc(sizeof(gk_i2cc2i_t),"gk_i2c_create_common"); |
||||||
|
t->n = nsymbols; |
||||||
|
t->i2c = gk_cmalloc(256, "gk_i2c_create_common"); |
||||||
|
t->c2i = gk_imalloc(256, "gk_i2c_create_common"); |
||||||
|
|
||||||
|
|
||||||
|
gk_cset(256, -1, t->i2c); |
||||||
|
gk_iset(256, -1, t->c2i); |
||||||
|
|
||||||
|
for(i=0;i<nsymbols;i++){ |
||||||
|
t->i2c[i] = alphabet[i]; |
||||||
|
t->c2i[(int)alphabet[i]] = i; |
||||||
|
} |
||||||
|
|
||||||
|
return t; |
||||||
|
|
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*********************************************************************/ |
||||||
|
/*! \brief This function reads a pssm in the format of gkmod pssm
|
||||||
|
|
||||||
|
\param file_name is the name of the pssm file |
||||||
|
\returns gk_seq_t |
||||||
|
*/ |
||||||
|
/********************************************************************/ |
||||||
|
gk_seq_t *gk_seq_ReadGKMODPSSM(char *filename) |
||||||
|
{ |
||||||
|
gk_seq_t *seq; |
||||||
|
gk_idx_t i, j, ii; |
||||||
|
size_t ntokens, nbytes, len; |
||||||
|
FILE *fpin; |
||||||
|
|
||||||
|
|
||||||
|
gk_Tokens_t tokens; |
||||||
|
static char *AAORDER = "ARNDCQEGHILKMFPSTWYVBZX*"; |
||||||
|
static int PSSMWIDTH = 20; |
||||||
|
char *header, line[MAXLINELEN]; |
||||||
|
gk_i2cc2i_t *converter; |
||||||
|
|
||||||
|
header = gk_cmalloc(PSSMWIDTH, "gk_seq_ReadGKMODPSSM: header"); |
||||||
|
|
||||||
|
converter = gk_i2cc2i_create_common(AAORDER); |
||||||
|
|
||||||
|
gk_getfilestats(filename, &len, &ntokens, NULL, &nbytes); |
||||||
|
len --; |
||||||
|
|
||||||
|
seq = gk_malloc(sizeof(gk_seq_t),"gk_seq_ReadGKMODPSSM"); |
||||||
|
gk_seq_init(seq); |
||||||
|
|
||||||
|
seq->len = len; |
||||||
|
seq->sequence = gk_imalloc(len, "gk_seq_ReadGKMODPSSM"); |
||||||
|
seq->pssm = gk_iAllocMatrix(len, PSSMWIDTH, 0, "gk_seq_ReadGKMODPSSM"); |
||||||
|
seq->psfm = gk_iAllocMatrix(len, PSSMWIDTH, 0, "gk_seq_ReadGKMODPSSM"); |
||||||
|
|
||||||
|
seq->nsymbols = PSSMWIDTH; |
||||||
|
seq->name = gk_getbasename(filename); |
||||||
|
|
||||||
|
fpin = gk_fopen(filename,"r","gk_seq_ReadGKMODPSSM"); |
||||||
|
|
||||||
|
|
||||||
|
/* Read the header line */ |
||||||
|
if (fgets(line, MAXLINELEN-1, fpin) == NULL) |
||||||
|
errexit("Unexpected end of file: %s\n", filename); |
||||||
|
gk_strtoupper(line); |
||||||
|
gk_strtokenize(line, " \t\n", &tokens); |
||||||
|
|
||||||
|
for (i=0; i<PSSMWIDTH; i++) |
||||||
|
header[i] = tokens.list[i][0]; |
||||||
|
|
||||||
|
gk_freetokenslist(&tokens); |
||||||
|
|
||||||
|
|
||||||
|
/* Read the rest of the lines */ |
||||||
|
for (i=0, ii=0; ii<len; ii++) { |
||||||
|
if (fgets(line, MAXLINELEN-1, fpin) == NULL) |
||||||
|
errexit("Unexpected end of file: %s\n", filename); |
||||||
|
gk_strtoupper(line); |
||||||
|
gk_strtokenize(line, " \t\n", &tokens); |
||||||
|
|
||||||
|
seq->sequence[i] = converter->c2i[(int)tokens.list[1][0]]; |
||||||
|
|
||||||
|
for (j=0; j<PSSMWIDTH; j++) { |
||||||
|
seq->pssm[i][converter->c2i[(int)header[j]]] = atoi(tokens.list[2+j]); |
||||||
|
seq->psfm[i][converter->c2i[(int)header[j]]] = atoi(tokens.list[2+PSSMWIDTH+j]); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
gk_freetokenslist(&tokens); |
||||||
|
i++; |
||||||
|
} |
||||||
|
|
||||||
|
seq->len = i; /* Reset the length if certain characters were skipped */ |
||||||
|
|
||||||
|
gk_free((void **)&header, LTERM); |
||||||
|
gk_fclose(fpin); |
||||||
|
|
||||||
|
return seq; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/**************************************************************************/ |
||||||
|
/*! \brief This function frees the memory allocated to the seq structure.
|
||||||
|
|
||||||
|
\param gk_seq_t |
||||||
|
\returns nothing |
||||||
|
*/ |
||||||
|
/**************************************************************************/ |
||||||
|
void gk_seq_free(gk_seq_t *seq) |
||||||
|
{ |
||||||
|
gk_iFreeMatrix(&seq->pssm, seq->len, seq->nsymbols); |
||||||
|
gk_iFreeMatrix(&seq->psfm, seq->len, seq->nsymbols); |
||||||
|
gk_free((void **)&seq->name, &seq->sequence, LTERM); |
||||||
|
//gk_free((void **)&seq, LTERM);
|
||||||
|
gk_free((void **) &seq, LTERM); |
||||||
|
|
||||||
|
} |
||||||
@ -0,0 +1,437 @@ |
|||||||
|
/*!
|
||||||
|
\file sort.c |
||||||
|
\brief This file contains GKlib's various sorting routines |
||||||
|
|
||||||
|
These routines are implemented using the GKSORT macro that is defined |
||||||
|
in gk_qsort.h and is based on GNU's GLIBC qsort() implementation. |
||||||
|
|
||||||
|
Additional sorting routines can be created using the same way that |
||||||
|
these routines where defined. |
||||||
|
|
||||||
|
\date Started 4/4/07 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: sort.c 21050 2017-05-25 03:53:58Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of chars in increasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_csorti(size_t n, char *base) |
||||||
|
{ |
||||||
|
#define char_lt(a, b) ((*a) < (*b)) |
||||||
|
GK_MKQSORT(char, base, n, char_lt); |
||||||
|
#undef char_lt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of chars in decreasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_csortd(size_t n, char *base) |
||||||
|
{ |
||||||
|
#define char_gt(a, b) ((*a) > (*b)) |
||||||
|
GK_MKQSORT(char, base, n, char_gt); |
||||||
|
#undef char_gt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of integers in increasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_isorti(size_t n, int *base) |
||||||
|
{ |
||||||
|
#define int_lt(a, b) ((*a) < (*b)) |
||||||
|
GK_MKQSORT(int, base, n, int_lt); |
||||||
|
#undef int_lt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of integers in decreasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_isortd(size_t n, int *base) |
||||||
|
{ |
||||||
|
#define int_gt(a, b) ((*a) > (*b)) |
||||||
|
GK_MKQSORT(int, base, n, int_gt); |
||||||
|
#undef int_gt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of integers in increasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_i32sorti(size_t n, int32_t *base) |
||||||
|
{ |
||||||
|
#define int_lt(a, b) ((*a) < (*b)) |
||||||
|
GK_MKQSORT(int32_t, base, n, int_lt); |
||||||
|
#undef int_lt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of integers in decreasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_i32sortd(size_t n, int32_t *base) |
||||||
|
{ |
||||||
|
#define int_gt(a, b) ((*a) > (*b)) |
||||||
|
GK_MKQSORT(int32_t, base, n, int_gt); |
||||||
|
#undef int_gt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of integers in increasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_i64sorti(size_t n, int64_t *base) |
||||||
|
{ |
||||||
|
#define int_lt(a, b) ((*a) < (*b)) |
||||||
|
GK_MKQSORT(int64_t, base, n, int_lt); |
||||||
|
#undef int_lt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of integers in increasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_ui32sorti(size_t n, uint32_t *base) |
||||||
|
{ |
||||||
|
#define int_lt(a, b) ((*a) < (*b)) |
||||||
|
GK_MKQSORT(uint32_t, base, n, int_lt); |
||||||
|
#undef int_lt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of integers in decreasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_ui32sortd(size_t n, uint32_t *base) |
||||||
|
{ |
||||||
|
#define int_gt(a, b) ((*a) > (*b)) |
||||||
|
GK_MKQSORT(uint32_t, base, n, int_gt); |
||||||
|
#undef int_gt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of integers in increasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_ui64sorti(size_t n, uint64_t *base) |
||||||
|
{ |
||||||
|
#define int_lt(a, b) ((*a) < (*b)) |
||||||
|
GK_MKQSORT(uint64_t, base, n, int_lt); |
||||||
|
#undef int_lt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of integers in decreasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_ui64sortd(size_t n, uint64_t *base) |
||||||
|
{ |
||||||
|
#define int_gt(a, b) ((*a) > (*b)) |
||||||
|
GK_MKQSORT(uint64_t, base, n, int_gt); |
||||||
|
#undef int_gt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of integers in decreasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_i64sortd(size_t n, int64_t *base) |
||||||
|
{ |
||||||
|
#define int_gt(a, b) ((*a) > (*b)) |
||||||
|
GK_MKQSORT(int64_t, base, n, int_gt); |
||||||
|
#undef int_gt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of floats in increasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_fsorti(size_t n, float *base) |
||||||
|
{ |
||||||
|
#define float_lt(a, b) ((*a) < (*b)) |
||||||
|
GK_MKQSORT(float, base, n, float_lt); |
||||||
|
#undef float_lt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of floats in decreasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_fsortd(size_t n, float *base) |
||||||
|
{ |
||||||
|
#define float_gt(a, b) ((*a) > (*b)) |
||||||
|
GK_MKQSORT(float, base, n, float_gt); |
||||||
|
#undef float_gt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of doubles in increasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_dsorti(size_t n, double *base) |
||||||
|
{ |
||||||
|
#define double_lt(a, b) ((*a) < (*b)) |
||||||
|
GK_MKQSORT(double, base, n, double_lt); |
||||||
|
#undef double_lt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of doubles in decreasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_dsortd(size_t n, double *base) |
||||||
|
{ |
||||||
|
#define double_gt(a, b) ((*a) > (*b)) |
||||||
|
GK_MKQSORT(double, base, n, double_gt); |
||||||
|
#undef double_gt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of gk_idx_t in increasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_idxsorti(size_t n, gk_idx_t *base) |
||||||
|
{ |
||||||
|
#define idx_lt(a, b) ((*a) < (*b)) |
||||||
|
GK_MKQSORT(gk_idx_t, base, n, idx_lt); |
||||||
|
#undef idx_lt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of gk_idx_t in decreasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_idxsortd(size_t n, gk_idx_t *base) |
||||||
|
{ |
||||||
|
#define idx_gt(a, b) ((*a) > (*b)) |
||||||
|
GK_MKQSORT(gk_idx_t, base, n, idx_gt); |
||||||
|
#undef idx_gt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of gk_ckv_t in increasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_ckvsorti(size_t n, gk_ckv_t *base) |
||||||
|
{ |
||||||
|
#define ckey_lt(a, b) ((a)->key < (b)->key) |
||||||
|
GK_MKQSORT(gk_ckv_t, base, n, ckey_lt); |
||||||
|
#undef ckey_lt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of gk_ckv_t in decreasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_ckvsortd(size_t n, gk_ckv_t *base) |
||||||
|
{ |
||||||
|
#define ckey_gt(a, b) ((a)->key > (b)->key) |
||||||
|
GK_MKQSORT(gk_ckv_t, base, n, ckey_gt); |
||||||
|
#undef ckey_gt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of gk_ikv_t in increasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_ikvsorti(size_t n, gk_ikv_t *base) |
||||||
|
{ |
||||||
|
#define ikey_lt(a, b) ((a)->key < (b)->key) |
||||||
|
GK_MKQSORT(gk_ikv_t, base, n, ikey_lt); |
||||||
|
#undef ikey_lt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of gk_ikv_t in decreasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_ikvsortd(size_t n, gk_ikv_t *base) |
||||||
|
{ |
||||||
|
#define ikey_gt(a, b) ((a)->key > (b)->key) |
||||||
|
GK_MKQSORT(gk_ikv_t, base, n, ikey_gt); |
||||||
|
#undef ikey_gt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of gk_i32kv_t in increasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_i32kvsorti(size_t n, gk_i32kv_t *base) |
||||||
|
{ |
||||||
|
#define ikey_lt(a, b) ((a)->key < (b)->key) |
||||||
|
GK_MKQSORT(gk_i32kv_t, base, n, ikey_lt); |
||||||
|
#undef ikey_lt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of gk_i32kv_t in decreasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_i32kvsortd(size_t n, gk_i32kv_t *base) |
||||||
|
{ |
||||||
|
#define ikey_gt(a, b) ((a)->key > (b)->key) |
||||||
|
GK_MKQSORT(gk_i32kv_t, base, n, ikey_gt); |
||||||
|
#undef ikey_gt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of gk_i64kv_t in increasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_i64kvsorti(size_t n, gk_i64kv_t *base) |
||||||
|
{ |
||||||
|
#define ikey_lt(a, b) ((a)->key < (b)->key) |
||||||
|
GK_MKQSORT(gk_i64kv_t, base, n, ikey_lt); |
||||||
|
#undef ikey_lt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of gk_i64kv_t in decreasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_i64kvsortd(size_t n, gk_i64kv_t *base) |
||||||
|
{ |
||||||
|
#define ikey_gt(a, b) ((a)->key > (b)->key) |
||||||
|
GK_MKQSORT(gk_i64kv_t, base, n, ikey_gt); |
||||||
|
#undef ikey_gt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of gk_zkv_t in increasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_zkvsorti(size_t n, gk_zkv_t *base) |
||||||
|
{ |
||||||
|
#define zkey_lt(a, b) ((a)->key < (b)->key) |
||||||
|
GK_MKQSORT(gk_zkv_t, base, n, zkey_lt); |
||||||
|
#undef zkey_lt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of gk_zkv_t in decreasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_zkvsortd(size_t n, gk_zkv_t *base) |
||||||
|
{ |
||||||
|
#define zkey_gt(a, b) ((a)->key > (b)->key) |
||||||
|
GK_MKQSORT(gk_zkv_t, base, n, zkey_gt); |
||||||
|
#undef zkey_gt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of gk_zukv_t in increasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_zukvsorti(size_t n, gk_zukv_t *base) |
||||||
|
{ |
||||||
|
#define zukey_lt(a, b) ((a)->key < (b)->key) |
||||||
|
GK_MKQSORT(gk_zukv_t, base, n, zukey_lt); |
||||||
|
#undef zukey_lt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of gk_zukv_t in decreasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_zukvsortd(size_t n, gk_zukv_t *base) |
||||||
|
{ |
||||||
|
#define zukey_gt(a, b) ((a)->key > (b)->key) |
||||||
|
GK_MKQSORT(gk_zukv_t, base, n, zukey_gt); |
||||||
|
#undef zukey_gt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of gk_fkv_t in increasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_fkvsorti(size_t n, gk_fkv_t *base) |
||||||
|
{ |
||||||
|
#define fkey_lt(a, b) ((a)->key < (b)->key) |
||||||
|
GK_MKQSORT(gk_fkv_t, base, n, fkey_lt); |
||||||
|
#undef fkey_lt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of gk_fkv_t in decreasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_fkvsortd(size_t n, gk_fkv_t *base) |
||||||
|
{ |
||||||
|
#define fkey_gt(a, b) ((a)->key > (b)->key) |
||||||
|
GK_MKQSORT(gk_fkv_t, base, n, fkey_gt); |
||||||
|
#undef fkey_gt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of gk_dkv_t in increasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_dkvsorti(size_t n, gk_dkv_t *base) |
||||||
|
{ |
||||||
|
#define dkey_lt(a, b) ((a)->key < (b)->key) |
||||||
|
GK_MKQSORT(gk_dkv_t, base, n, dkey_lt); |
||||||
|
#undef dkey_lt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of gk_fkv_t in decreasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_dkvsortd(size_t n, gk_dkv_t *base) |
||||||
|
{ |
||||||
|
#define dkey_gt(a, b) ((a)->key > (b)->key) |
||||||
|
GK_MKQSORT(gk_dkv_t, base, n, dkey_gt); |
||||||
|
#undef dkey_gt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of gk_skv_t in increasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_skvsorti(size_t n, gk_skv_t *base) |
||||||
|
{ |
||||||
|
#define skey_lt(a, b) (strcmp((a)->key, (b)->key) < 0) |
||||||
|
GK_MKQSORT(gk_skv_t, base, n, skey_lt); |
||||||
|
#undef skey_lt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of gk_skv_t in decreasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_skvsortd(size_t n, gk_skv_t *base) |
||||||
|
{ |
||||||
|
#define skey_gt(a, b) (strcmp((a)->key, (b)->key) > 0) |
||||||
|
GK_MKQSORT(gk_skv_t, base, n, skey_gt); |
||||||
|
#undef skey_gt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of gk_idxkv_t in increasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_idxkvsorti(size_t n, gk_idxkv_t *base) |
||||||
|
{ |
||||||
|
#define idxkey_lt(a, b) ((a)->key < (b)->key) |
||||||
|
GK_MKQSORT(gk_idxkv_t, base, n, idxkey_lt); |
||||||
|
#undef idxkey_lt |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Sorts an array of gk_idxkv_t in decreasing order */ |
||||||
|
/*************************************************************************/ |
||||||
|
void gk_idxkvsortd(size_t n, gk_idxkv_t *base) |
||||||
|
{ |
||||||
|
#define idxkey_gt(a, b) ((a)->key > (b)->key) |
||||||
|
GK_MKQSORT(gk_idxkv_t, base, n, idxkey_gt); |
||||||
|
#undef idxkey_gt |
||||||
|
} |
||||||
@ -0,0 +1,530 @@ |
|||||||
|
/************************************************************************/ |
||||||
|
/*! \file
|
||||||
|
|
||||||
|
\brief Functions for manipulating strings. |
||||||
|
|
||||||
|
Various functions for manipulating strings. Some of these functions
|
||||||
|
provide new functionality, whereas others are drop-in replacements |
||||||
|
of standard functions (but with enhanced functionality). |
||||||
|
|
||||||
|
\date Started 11/1/99 |
||||||
|
\author George |
||||||
|
\version $Id: string.c 14330 2013-05-18 12:15:15Z karypis $ |
||||||
|
*/ |
||||||
|
/************************************************************************/ |
||||||
|
|
||||||
|
/* the following is for strptime() */ |
||||||
|
#define _XOPEN_SOURCE |
||||||
|
#include <time.h> |
||||||
|
#undef _XOPEN_SOURCE |
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************************************************************/ |
||||||
|
/*! \brief Replaces certain characters in a string.
|
||||||
|
|
||||||
|
This function takes a string and replaces all the characters in the |
||||||
|
\c fromlist with the corresponding characters from the \c tolist.
|
||||||
|
That is, each occurence of <tt>fromlist[i]</tt> is replaced by
|
||||||
|
<tt>tolist[i]</tt>.
|
||||||
|
If the \c tolist is shorter than \c fromlist, then the corresponding
|
||||||
|
characters are deleted. The modifications on \c str are done in place.
|
||||||
|
It tries to provide a functionality similar to Perl's \b tr// function.
|
||||||
|
|
||||||
|
\param str is the string whose characters will be replaced. |
||||||
|
\param fromlist is the set of characters to be replaced. |
||||||
|
\param tolist is the set of replacement characters . |
||||||
|
\returns A pointer to \c str itself. |
||||||
|
*/ |
||||||
|
/************************************************************************/ |
||||||
|
char *gk_strchr_replace(char *str, char *fromlist, char *tolist) |
||||||
|
{ |
||||||
|
ssize_t i, j, k, len, fromlen, tolen; |
||||||
|
|
||||||
|
len = strlen(str); |
||||||
|
fromlen = strlen(fromlist); |
||||||
|
tolen = strlen(tolist); |
||||||
|
|
||||||
|
for (i=j=0; i<len; i++) { |
||||||
|
for (k=0; k<fromlen; k++) { |
||||||
|
if (str[i] == fromlist[k]) { |
||||||
|
if (k < tolen)
|
||||||
|
str[j++] = tolist[k]; |
||||||
|
break; |
||||||
|
} |
||||||
|
} |
||||||
|
if (k == fromlen) |
||||||
|
str[j++] = str[i]; |
||||||
|
} |
||||||
|
str[j] = '\0'; |
||||||
|
|
||||||
|
return str; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************************************************************/ |
||||||
|
/*! \brief Regex-based search-and-replace function
|
||||||
|
|
||||||
|
This function is a C implementation of Perl's <tt> s//</tt> regular-expression
|
||||||
|
based substitution function. |
||||||
|
|
||||||
|
\param str
|
||||||
|
is the input string on which the operation will be performed. |
||||||
|
\param pattern |
||||||
|
is the regular expression for the pattern to be matched for substitution. |
||||||
|
\param replacement |
||||||
|
is the replacement string, in which the possible captured pattern substrings |
||||||
|
are referred to as $1, $2, ..., $9. The entire matched pattern is refered |
||||||
|
to as $0. |
||||||
|
\param options |
||||||
|
is a string specified options for the substitution operation. Currently the |
||||||
|
<tt>"i"</tt> (case insensitive) and <tt>"g"</tt> (global substitution) are
|
||||||
|
supported. |
||||||
|
\param new_str
|
||||||
|
is a reference to a pointer that will store a pointer to the newly created
|
||||||
|
string that results from the substitutions. This string is allocated via
|
||||||
|
gk_malloc() and needs to be freed using gk_free(). The string is returned
|
||||||
|
even if no substitutions were performed. |
||||||
|
\returns |
||||||
|
If successful, it returns 1 + the number of substitutions that were performed. |
||||||
|
Thus, if no substitutions were performed, the returned value will be 1. |
||||||
|
Otherwise it returns 0. In case of error, a meaningful error message is
|
||||||
|
returned in <tt>newstr</tt>, which also needs to be freed afterwards. |
||||||
|
*/ |
||||||
|
/************************************************************************/ |
||||||
|
int gk_strstr_replace(char *str, char *pattern, char *replacement, char *options, |
||||||
|
char **new_str) |
||||||
|
{ |
||||||
|
ssize_t i, len, rlen, nlen, offset, noffset; |
||||||
|
int j, rc, flags, global, nmatches; |
||||||
|
regex_t re; |
||||||
|
regmatch_t matches[10]; |
||||||
|
|
||||||
|
|
||||||
|
/* Parse the options */ |
||||||
|
flags = REG_EXTENDED; |
||||||
|
if (strchr(options, 'i') != NULL) |
||||||
|
flags = flags | REG_ICASE; |
||||||
|
global = (strchr(options, 'g') != NULL ? 1 : 0); |
||||||
|
|
||||||
|
|
||||||
|
/* Compile the regex */ |
||||||
|
if ((rc = regcomp(&re, pattern, flags)) != 0) {
|
||||||
|
len = regerror(rc, &re, NULL, 0); |
||||||
|
*new_str = gk_cmalloc(len, "gk_strstr_replace: new_str"); |
||||||
|
regerror(rc, &re, *new_str, len); |
||||||
|
return 0; |
||||||
|
} |
||||||
|
|
||||||
|
/* Prepare the output string */ |
||||||
|
len = strlen(str); |
||||||
|
nlen = 2*len; |
||||||
|
noffset = 0; |
||||||
|
*new_str = gk_cmalloc(nlen+1, "gk_strstr_replace: new_str"); |
||||||
|
|
||||||
|
|
||||||
|
/* Get into the matching-replacing loop */ |
||||||
|
rlen = strlen(replacement); |
||||||
|
offset = 0; |
||||||
|
nmatches = 0; |
||||||
|
do { |
||||||
|
rc = regexec(&re, str+offset, 10, matches, 0); |
||||||
|
|
||||||
|
if (rc == REG_ESPACE) { |
||||||
|
gk_free((void **)new_str, LTERM); |
||||||
|
*new_str = gk_strdup("regexec ran out of memory."); |
||||||
|
regfree(&re); |
||||||
|
return 0; |
||||||
|
} |
||||||
|
else if (rc == REG_NOMATCH) { |
||||||
|
if (nlen-noffset < len-offset) { |
||||||
|
nlen += (len-offset) - (nlen-noffset); |
||||||
|
*new_str = (char *)gk_realloc(*new_str, (nlen+1)*sizeof(char), "gk_strstr_replace: new_str"); |
||||||
|
} |
||||||
|
strcpy(*new_str+noffset, str+offset); |
||||||
|
noffset += (len-offset); |
||||||
|
break; |
||||||
|
} |
||||||
|
else { /* A match was found! */ |
||||||
|
nmatches++; |
||||||
|
|
||||||
|
/* Copy the left unmatched portion of the string */ |
||||||
|
if (matches[0].rm_so > 0) { |
||||||
|
if (nlen-noffset < matches[0].rm_so) { |
||||||
|
nlen += matches[0].rm_so - (nlen-noffset); |
||||||
|
*new_str = (char *)gk_realloc(*new_str, (nlen+1)*sizeof(char), "gk_strstr_replace: new_str"); |
||||||
|
} |
||||||
|
strncpy(*new_str+noffset, str+offset, matches[0].rm_so); |
||||||
|
noffset += matches[0].rm_so; |
||||||
|
} |
||||||
|
|
||||||
|
/* Go and append the replacement string */ |
||||||
|
for (i=0; i<rlen; i++) { |
||||||
|
switch (replacement[i]) { |
||||||
|
case '\\': |
||||||
|
if (i+1 < rlen) { |
||||||
|
if (nlen-noffset < 1) { |
||||||
|
nlen += nlen + 1; |
||||||
|
*new_str = (char *)gk_realloc(*new_str, (nlen+1)*sizeof(char), "gk_strstr_replace: new_str"); |
||||||
|
} |
||||||
|
*new_str[noffset++] = replacement[++i]; |
||||||
|
} |
||||||
|
else { |
||||||
|
gk_free((void **)new_str, LTERM); |
||||||
|
*new_str = gk_strdup("Error in replacement string. Missing character following '\'."); |
||||||
|
regfree(&re); |
||||||
|
return 0; |
||||||
|
} |
||||||
|
break; |
||||||
|
|
||||||
|
case '$': |
||||||
|
if (i+1 < rlen) { |
||||||
|
j = (int)(replacement[++i] - '0'); |
||||||
|
if (j < 0 || j > 9) { |
||||||
|
gk_free((void **)new_str, LTERM); |
||||||
|
*new_str = gk_strdup("Error in captured subexpression specification."); |
||||||
|
regfree(&re); |
||||||
|
return 0; |
||||||
|
} |
||||||
|
|
||||||
|
if (nlen-noffset < matches[j].rm_eo-matches[j].rm_so) { |
||||||
|
nlen += nlen + (matches[j].rm_eo-matches[j].rm_so); |
||||||
|
*new_str = (char *)gk_realloc(*new_str, (nlen+1)*sizeof(char), "gk_strstr_replace: new_str"); |
||||||
|
} |
||||||
|
|
||||||
|
strncpy(*new_str+noffset, str+offset+matches[j].rm_so, matches[j].rm_eo); |
||||||
|
noffset += matches[j].rm_eo-matches[j].rm_so; |
||||||
|
} |
||||||
|
else { |
||||||
|
gk_free((void **)new_str, LTERM); |
||||||
|
*new_str = gk_strdup("Error in replacement string. Missing subexpression number folloing '$'."); |
||||||
|
regfree(&re); |
||||||
|
return 0; |
||||||
|
} |
||||||
|
break; |
||||||
|
|
||||||
|
default: |
||||||
|
if (nlen-noffset < 1) { |
||||||
|
nlen += nlen + 1; |
||||||
|
*new_str = (char *)gk_realloc(*new_str, (nlen+1)*sizeof(char), "gk_strstr_replace: new_str"); |
||||||
|
} |
||||||
|
(*new_str)[noffset++] = replacement[i]; |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
/* Update the offset of str for the next match */ |
||||||
|
offset += matches[0].rm_eo; |
||||||
|
|
||||||
|
if (!global) { |
||||||
|
/* Copy the right portion of the string if no 'g' option */ |
||||||
|
if (nlen-noffset < len-offset) { |
||||||
|
nlen += (len-offset) - (nlen-noffset); |
||||||
|
*new_str = (char *)gk_realloc(*new_str, (nlen+1)*sizeof(char), "gk_strstr_replace: new_str"); |
||||||
|
} |
||||||
|
strcpy(*new_str+noffset, str+offset); |
||||||
|
noffset += (len-offset); |
||||||
|
} |
||||||
|
} |
||||||
|
} while (global); |
||||||
|
|
||||||
|
(*new_str)[noffset] = '\0'; |
||||||
|
|
||||||
|
regfree(&re); |
||||||
|
return nmatches + 1; |
||||||
|
|
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************************************************************/ |
||||||
|
/*! \brief Prunes characters from the end of the string.
|
||||||
|
|
||||||
|
This function removes any trailing characters that are included in the |
||||||
|
\c rmlist. The trimming stops at the last character (i.e., first character
|
||||||
|
from the end) that is not in \c rmlist.
|
||||||
|
This function can be used to removed trailing spaces, newlines, etc. |
||||||
|
This is a distructive operation as it modifies the string. |
||||||
|
|
||||||
|
\param str is the string that will be trimmed. |
||||||
|
\param rmlist contains the set of characters that will be removed. |
||||||
|
\returns A pointer to \c str itself. |
||||||
|
\sa gk_strhprune() |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
char *gk_strtprune(char *str, char *rmlist) |
||||||
|
{ |
||||||
|
ssize_t i, j, len; |
||||||
|
|
||||||
|
len = strlen(rmlist); |
||||||
|
|
||||||
|
for (i=strlen(str)-1; i>=0; i--) { |
||||||
|
for (j=0; j<len; j++) { |
||||||
|
if (str[i] == rmlist[j]) |
||||||
|
break; |
||||||
|
} |
||||||
|
if (j == len) |
||||||
|
break; |
||||||
|
} |
||||||
|
|
||||||
|
str[i+1] = '\0'; |
||||||
|
|
||||||
|
return str; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/************************************************************************/ |
||||||
|
/*! \brief Prunes characters from the beginning of the string.
|
||||||
|
|
||||||
|
This function removes any starting characters that are included in the |
||||||
|
\c rmlist. The trimming stops at the first character that is not in
|
||||||
|
\c rmlist. |
||||||
|
This function can be used to removed leading spaces, tabs, etc. |
||||||
|
This is a distructive operation as it modifies the string. |
||||||
|
|
||||||
|
\param str is the string that will be trimmed. |
||||||
|
\param rmlist contains the set of characters that will be removed. |
||||||
|
\returns A pointer to \c str itself. |
||||||
|
\sa gk_strtprune() |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
char *gk_strhprune(char *str, char *rmlist) |
||||||
|
{ |
||||||
|
ssize_t i, j, len; |
||||||
|
|
||||||
|
len = strlen(rmlist); |
||||||
|
|
||||||
|
for (i=0; str[i]; i++) { |
||||||
|
for (j=0; j<len; j++) { |
||||||
|
if (str[i] == rmlist[j]) |
||||||
|
break; |
||||||
|
} |
||||||
|
if (j == len) |
||||||
|
break; |
||||||
|
} |
||||||
|
|
||||||
|
if (i>0) { /* If something needs to be removed */ |
||||||
|
for (j=0; str[i]; i++, j++) |
||||||
|
str[j] = str[i]; |
||||||
|
str[j] = '\0'; |
||||||
|
} |
||||||
|
|
||||||
|
return str; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/************************************************************************/ |
||||||
|
/*! \brief Converts a string to upper case.
|
||||||
|
|
||||||
|
This function converts a string to upper case. This operation modifies the
|
||||||
|
string itself. |
||||||
|
|
||||||
|
\param str is the string whose case will be changed. |
||||||
|
\returns A pointer to \c str itself. |
||||||
|
\sa gk_strtolower() |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
char *gk_strtoupper(char *str) |
||||||
|
{ |
||||||
|
int i; |
||||||
|
|
||||||
|
for (i=0; str[i]!='\0'; str[i]=toupper(str[i]), i++);
|
||||||
|
return str; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/************************************************************************/ |
||||||
|
/*! \brief Converts a string to lower case.
|
||||||
|
|
||||||
|
This function converts a string to lower case. This operation modifies the
|
||||||
|
string itself. |
||||||
|
|
||||||
|
\param str is the string whose case will be changed. |
||||||
|
\returns A pointer to \c str itself. |
||||||
|
\sa gk_strtoupper() |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
char *gk_strtolower(char *str) |
||||||
|
{ |
||||||
|
int i; |
||||||
|
|
||||||
|
for (i=0; str[i]!='\0'; str[i]=tolower(str[i]), i++);
|
||||||
|
return str; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/************************************************************************/ |
||||||
|
/*! \brief Duplicates a string
|
||||||
|
|
||||||
|
This function is a replacement for C's standard <em>strdup()</em> function. |
||||||
|
The key differences between the two are that gk_strdup(): |
||||||
|
- uses the dynamic memory allocation routines of \e GKlib.
|
||||||
|
- it correctly handles NULL input strings. |
||||||
|
|
||||||
|
The string that is returned must be freed by gk_free(). |
||||||
|
|
||||||
|
\param orgstr is the string that will be duplicated. |
||||||
|
\returns A pointer to the newly created string. |
||||||
|
\sa gk_free() |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
char *gk_strdup(char *orgstr) |
||||||
|
{ |
||||||
|
int len; |
||||||
|
char *str=NULL; |
||||||
|
|
||||||
|
if (orgstr != NULL) { |
||||||
|
len = strlen(orgstr)+1; |
||||||
|
str = gk_malloc(len*sizeof(char), "gk_strdup: str"); |
||||||
|
strcpy(str, orgstr); |
||||||
|
} |
||||||
|
|
||||||
|
return str; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/************************************************************************/ |
||||||
|
/*! \brief Case insensitive string comparison.
|
||||||
|
|
||||||
|
This function compares two strings for equality by ignoring the case of the |
||||||
|
strings.
|
||||||
|
|
||||||
|
\warning This function is \b not equivalent to a case-insensitive
|
||||||
|
<em>strcmp()</em> function, as it does not return ordering
|
||||||
|
information. |
||||||
|
|
||||||
|
\todo Remove the above warning. |
||||||
|
|
||||||
|
\param s1 is the first string to be compared. |
||||||
|
\param s2 is the second string to be compared. |
||||||
|
\retval 1 if the strings are identical, |
||||||
|
\retval 0 otherwise. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
int gk_strcasecmp(char *s1, char *s2) |
||||||
|
{ |
||||||
|
int i=0; |
||||||
|
|
||||||
|
if (strlen(s1) != strlen(s2)) |
||||||
|
return 0; |
||||||
|
|
||||||
|
while (s1[i] != '\0') { |
||||||
|
if (tolower(s1[i]) != tolower(s2[i])) |
||||||
|
return 0; |
||||||
|
i++; |
||||||
|
} |
||||||
|
|
||||||
|
return 1; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/************************************************************************/ |
||||||
|
/*! \brief Compare two strings in revere order
|
||||||
|
|
||||||
|
This function is similar to strcmp but it performs the comparison as |
||||||
|
if the two strings were reversed. |
||||||
|
|
||||||
|
\param s1 is the first string to be compared. |
||||||
|
\param s2 is the second string to be compared. |
||||||
|
\retval -1, 0, 1, if the s1 < s2, s1 == s2, or s1 > s2. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
int gk_strrcmp(char *s1, char *s2) |
||||||
|
{ |
||||||
|
int i1 = strlen(s1)-1; |
||||||
|
int i2 = strlen(s2)-1; |
||||||
|
|
||||||
|
while ((i1 >= 0) && (i2 >= 0)) { |
||||||
|
if (s1[i1] != s2[i2]) |
||||||
|
return (s1[i1] - s2[i2]); |
||||||
|
i1--; |
||||||
|
i2--; |
||||||
|
} |
||||||
|
|
||||||
|
/* i1 == -1 and/or i2 == -1 */ |
||||||
|
|
||||||
|
if (i1 < i2) |
||||||
|
return -1; |
||||||
|
if (i1 > i2) |
||||||
|
return 1; |
||||||
|
return 0; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/************************************************************************/ |
||||||
|
/*! \brief Converts a time_t time into a string
|
||||||
|
|
||||||
|
This function takes a time_t-specified time and returns a string-formated |
||||||
|
representation of the corresponding time. The format of the string is |
||||||
|
<em>mm/dd/yyyy hh:mm:ss</em>, in which the hours are in military time. |
||||||
|
|
||||||
|
\param time is the time to be converted. |
||||||
|
\return It returns a pointer to a statically allocated string that is
|
||||||
|
over-written in successive calls of this function. If the
|
||||||
|
conversion failed, it returns NULL. |
||||||
|
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
char *gk_time2str(time_t time) |
||||||
|
{ |
||||||
|
static char datestr[128]; |
||||||
|
struct tm *tm; |
||||||
|
|
||||||
|
tm = localtime(&time); |
||||||
|
|
||||||
|
if (strftime(datestr, 128, "%m/%d/%Y %H:%M:%S", tm) == 0) |
||||||
|
return NULL; |
||||||
|
else |
||||||
|
return datestr; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
#if !defined(WIN32) && !defined(__MINGW32__) |
||||||
|
/************************************************************************/ |
||||||
|
/*! \brief Converts a date/time string into its equivalent time_t value
|
||||||
|
|
||||||
|
This function takes date and/or time specification and converts it in |
||||||
|
the equivalent time_t representation. The conversion is done using the |
||||||
|
strptime() function. The format that gk_str2time() understands is |
||||||
|
<em>mm/dd/yyyy hh:mm:ss</em>, in which the hours are in military time. |
||||||
|
|
||||||
|
\param str is the date/time string to be converted. |
||||||
|
\return If the conversion was successful it returns the time, otherwise
|
||||||
|
it returns -1. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
time_t gk_str2time(char *str) |
||||||
|
{ |
||||||
|
struct tm time; |
||||||
|
time_t rtime; |
||||||
|
|
||||||
|
memset(&time, '\0', sizeof(time)); |
||||||
|
|
||||||
|
if (strptime(str, "%m/%d/%Y %H:%M:%S", &time) == NULL) |
||||||
|
return -1; |
||||||
|
|
||||||
|
rtime = mktime(&time); |
||||||
|
return (rtime < 0 ? 0 : rtime); |
||||||
|
} |
||||||
|
#endif |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************
|
||||||
|
* This function returns the ID of a particular string based on the
|
||||||
|
* supplied StringMap array |
||||||
|
**************************************************************************/ |
||||||
|
int gk_GetStringID(gk_StringMap_t *strmap, char *key) |
||||||
|
{ |
||||||
|
int i; |
||||||
|
|
||||||
|
for (i=0; strmap[i].name; i++) { |
||||||
|
if (gk_strcasecmp(key, strmap[i].name)) |
||||||
|
return strmap[i].id; |
||||||
|
} |
||||||
|
|
||||||
|
return -1; |
||||||
|
} |
||||||
@ -0,0 +1,19 @@ |
|||||||
|
# Build program. |
||||||
|
add_executable(strings strings.c) |
||||||
|
add_executable(gksort gksort.c) |
||||||
|
add_executable(fis fis.c) |
||||||
|
add_executable(gkrw rw.c) |
||||||
|
add_executable(gkgraph gkgraph.c) |
||||||
|
add_executable(csrcnv csrcnv.c) |
||||||
|
add_executable(grKx grKx.c) |
||||||
|
add_executable(m2mnbrs m2mnbrs.c) |
||||||
|
add_executable(cmpnbrs cmpnbrs.c) |
||||||
|
add_executable(splatt2svd splatt2svd.c) |
||||||
|
add_executable(gkuniq gkuniq.c) |
||||||
|
|
||||||
|
foreach(prog strings gksort fis gkrw gkgraph csrcnv grKx m2mnbrs cmpnbrs splatt2svd gkuniq) |
||||||
|
target_link_libraries(${prog} GKlib) |
||||||
|
endforeach(prog) |
||||||
|
|
||||||
|
# Install a subset of them |
||||||
|
install(TARGETS csrcnv RUNTIME DESTINATION bin) |
||||||
@ -0,0 +1,301 @@ |
|||||||
|
/*!
|
||||||
|
\file
|
||||||
|
\brief It takes as input two CSR matrices A and B and computes how |
||||||
|
similar AA' and A'A are to BB' and B'B, respectively in terms |
||||||
|
of the cosine similarity of the corresponding rows. |
||||||
|
|
||||||
|
\date 11/09/2015 |
||||||
|
\author George |
||||||
|
\version \verbatim $Id: m2mnbrs.c 17699 2014-09-27 18:05:31Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Data structures for the code */ |
||||||
|
/*************************************************************************/ |
||||||
|
typedef struct { |
||||||
|
int simtype; /*!< The similarity type to use */ |
||||||
|
int verbosity; /*!< The reporting verbosity level */ |
||||||
|
|
||||||
|
char *afile; /*!< The file storing the query documents */ |
||||||
|
char *bfile; /*!< The file storing the collection documents */ |
||||||
|
|
||||||
|
/* timers */ |
||||||
|
double timer_global; |
||||||
|
} params_t; |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Constants */ |
||||||
|
/*************************************************************************/ |
||||||
|
/* Versions */ |
||||||
|
#define VER_MAJOR 0 |
||||||
|
#define VER_MINOR 1 |
||||||
|
#define VER_SUBMINOR 0 |
||||||
|
|
||||||
|
/* Command-line option codes */ |
||||||
|
#define CMD_SIMTYPE 10 |
||||||
|
#define CMD_VERBOSITY 70 |
||||||
|
#define CMD_HELP 100 |
||||||
|
|
||||||
|
/* The text labels for the different simtypes */ |
||||||
|
static char simtypenames[][10] = {"", "dotp", "cos", "jac", ""}; |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Local variables */ |
||||||
|
/*************************************************************************/ |
||||||
|
static struct gk_option long_options[] = { |
||||||
|
{"simtype", 1, 0, CMD_SIMTYPE}, |
||||||
|
{"verbosity", 1, 0, CMD_VERBOSITY}, |
||||||
|
|
||||||
|
{"help", 0, 0, CMD_HELP}, |
||||||
|
{0, 0, 0, 0} |
||||||
|
}; |
||||||
|
|
||||||
|
static gk_StringMap_t simtype_options[] = { |
||||||
|
{"dotp", GK_CSR_DOTP}, |
||||||
|
{"cos", GK_CSR_COS}, |
||||||
|
{"jac", GK_CSR_JAC}, |
||||||
|
{NULL, 0} |
||||||
|
}; |
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------------
|
||||||
|
* Mini help |
||||||
|
*-------------------------------------------------------------------*/ |
||||||
|
static char helpstr[][100] = |
||||||
|
{ |
||||||
|
" ", |
||||||
|
"Usage: cmpnbrs [options] afile bfile", |
||||||
|
" ", |
||||||
|
" Options", |
||||||
|
" -simtype=string", |
||||||
|
" Specifies the type of similarity to use. Possible values are:", |
||||||
|
" dotp - Dot-product similarity [default]", |
||||||
|
" cos - Cosine similarity", |
||||||
|
" jac - Jacquard similarity",
|
||||||
|
" ", |
||||||
|
" -verbosity=int", |
||||||
|
" Specifies the level of debugging information to be displayed.", |
||||||
|
" Default value is 0.", |
||||||
|
" ", |
||||||
|
" -help", |
||||||
|
" Prints this message.", |
||||||
|
"" |
||||||
|
}; |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Function prototypes */ |
||||||
|
/*************************************************************************/ |
||||||
|
params_t *parse_cmdline(int argc, char *argv[]); |
||||||
|
double ComputeNeighborhoodSimilarity(params_t *params, gk_csr_t *amat, gk_csr_t *bmat); |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This is the entry point of the command-line argument parser */ |
||||||
|
/*************************************************************************/ |
||||||
|
params_t *parse_cmdline(int argc, char *argv[]) |
||||||
|
{ |
||||||
|
int i; |
||||||
|
int c, option_index; |
||||||
|
params_t *params; |
||||||
|
|
||||||
|
params = (params_t *)gk_malloc(sizeof(params_t), "parse_cmdline: params"); |
||||||
|
|
||||||
|
/* initialize the params data structure */ |
||||||
|
params->simtype = GK_CSR_DOTP; |
||||||
|
params->verbosity = -1; |
||||||
|
params->afile = NULL; |
||||||
|
params->bfile = NULL; |
||||||
|
|
||||||
|
|
||||||
|
/* Parse the command line arguments */ |
||||||
|
while ((c = gk_getopt_long_only(argc, argv, "", long_options, &option_index)) != -1) { |
||||||
|
switch (c) { |
||||||
|
case CMD_SIMTYPE: |
||||||
|
if (gk_optarg) { |
||||||
|
if ((params->simtype = gk_GetStringID(simtype_options, gk_optarg)) == -1) |
||||||
|
errexit("Invalid simtype of %s.\n", gk_optarg); |
||||||
|
} |
||||||
|
break; |
||||||
|
|
||||||
|
case CMD_VERBOSITY: |
||||||
|
if (gk_optarg) params->verbosity = atoi(gk_optarg); |
||||||
|
break; |
||||||
|
|
||||||
|
case CMD_HELP: |
||||||
|
for (i=0; strlen(helpstr[i]) > 0; i++) |
||||||
|
printf("%s\n", helpstr[i]); |
||||||
|
exit(EXIT_SUCCESS); |
||||||
|
break; |
||||||
|
|
||||||
|
case '?': |
||||||
|
default: |
||||||
|
printf("Illegal command-line option(s)\nUse %s -help for a summary of the options.\n", argv[0]); |
||||||
|
exit(EXIT_FAILURE); |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
/* Get the input/output file info */ |
||||||
|
if (argc-gk_optind != 2) { |
||||||
|
printf("Missing input file info.\n Use %s -help for a summary of the options.\n", argv[0]); |
||||||
|
exit(EXIT_FAILURE); |
||||||
|
} |
||||||
|
|
||||||
|
params->afile = gk_strdup(argv[gk_optind++]); |
||||||
|
params->bfile = gk_strdup(argv[gk_optind++]); |
||||||
|
|
||||||
|
if (!gk_fexists(params->afile)) |
||||||
|
errexit("input file %s does not exist.\n", params->afile); |
||||||
|
if (!gk_fexists(params->bfile)) |
||||||
|
errexit("input file %s does not exist.\n", params->bfile); |
||||||
|
|
||||||
|
return params; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This is the entry point of the program */ |
||||||
|
/**************************************************************************/ |
||||||
|
int main(int argc, char *argv[]) |
||||||
|
{ |
||||||
|
params_t *params; |
||||||
|
gk_csr_t *amat, *bmat, *amatt, *bmatt; |
||||||
|
int rc = EXIT_SUCCESS; |
||||||
|
|
||||||
|
params = parse_cmdline(argc, argv); |
||||||
|
|
||||||
|
amat = gk_csr_Read(params->afile, GK_CSR_FMT_CSR, 1, 0); |
||||||
|
bmat = gk_csr_Read(params->bfile, GK_CSR_FMT_CSR, 1, 0); |
||||||
|
|
||||||
|
/* make the matrices of similar dimensions (if neccessary) */ |
||||||
|
GKASSERT(amat->nrows == bmat->nrows); |
||||||
|
amat->ncols = gk_max(amat->ncols, bmat->ncols); |
||||||
|
bmat->ncols = amat->ncols; |
||||||
|
|
||||||
|
/* create the transpose matrices */ |
||||||
|
amatt = gk_csr_Transpose(amat); |
||||||
|
bmatt = gk_csr_Transpose(bmat); |
||||||
|
|
||||||
|
printf("********************************************************************************\n"); |
||||||
|
printf("cmpnbrs (%d.%d.%d) Copyright 2015, GK.\n", VER_MAJOR, VER_MINOR, VER_SUBMINOR); |
||||||
|
printf(" simtype=%s\n", |
||||||
|
simtypenames[params->simtype]); |
||||||
|
printf(" afile=%s, nrows=%d, ncols=%d, nnz=%zd\n", |
||||||
|
params->afile, amat->nrows, amat->ncols, amat->rowptr[amat->nrows]); |
||||||
|
printf(" bfile=%s, nrows=%d, ncols=%d, nnz=%zd\n", |
||||||
|
params->bfile, bmat->nrows, bmat->ncols, bmat->rowptr[bmat->nrows]); |
||||||
|
|
||||||
|
gk_clearwctimer(params->timer_global); |
||||||
|
gk_startwctimer(params->timer_global); |
||||||
|
|
||||||
|
printf("SIM(AA', BB'): %.5lf\t", ComputeNeighborhoodSimilarity(params, amat, bmat)); |
||||||
|
printf("SIM(A'A, B'B): %.5lf\n", ComputeNeighborhoodSimilarity(params, amatt, bmatt)); |
||||||
|
|
||||||
|
gk_stopwctimer(params->timer_global); |
||||||
|
|
||||||
|
printf(" wclock: %.2lfs\n", gk_getwctimer(params->timer_global)); |
||||||
|
printf("********************************************************************************\n"); |
||||||
|
|
||||||
|
gk_csr_Free(&amat); |
||||||
|
gk_csr_Free(&bmat); |
||||||
|
gk_csr_Free(&amatt); |
||||||
|
gk_csr_Free(&bmatt); |
||||||
|
|
||||||
|
exit(rc); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Compares the neighbors of AA' vs BB' */ |
||||||
|
/**************************************************************************/ |
||||||
|
double ComputeNeighborhoodSimilarity(params_t *params, gk_csr_t *amat,
|
||||||
|
gk_csr_t *bmat) |
||||||
|
{ |
||||||
|
int iR, iH, nahits, nbhits, ncmps; |
||||||
|
int32_t *marker; |
||||||
|
gk_fkv_t *ahits, *bhits, *cand; |
||||||
|
double tabsim, abdot, anorm2, bnorm2, *avec, *bvec; |
||||||
|
|
||||||
|
/* if cosine, make rows unit length */ |
||||||
|
if (params->simtype == GK_CSR_COS) { |
||||||
|
gk_csr_Normalize(amat, GK_CSR_ROW, 2); |
||||||
|
gk_csr_Normalize(bmat, GK_CSR_ROW, 2); |
||||||
|
} |
||||||
|
|
||||||
|
/* create the inverted index */ |
||||||
|
gk_csr_CreateIndex(amat, GK_CSR_COL); |
||||||
|
gk_csr_CreateIndex(bmat, GK_CSR_COL); |
||||||
|
|
||||||
|
/* compute the row squared norms */ |
||||||
|
gk_csr_ComputeSquaredNorms(amat, GK_CSR_ROW); |
||||||
|
gk_csr_ComputeSquaredNorms(bmat, GK_CSR_ROW); |
||||||
|
|
||||||
|
|
||||||
|
/* allocate memory for the necessary working arrays */ |
||||||
|
ahits = gk_fkvmalloc(amat->nrows, "ComputeNeighborhoodSimilarity: ahits"); |
||||||
|
bhits = gk_fkvmalloc(bmat->nrows, "ComputeNeighborhoodSimilarity: bhits"); |
||||||
|
marker = gk_i32smalloc(amat->nrows, -1, "ComputeNeighborhoodSimilarity: marker"); |
||||||
|
cand = gk_fkvmalloc(amat->nrows, "ComputeNeighborhoodSimilarity: cand"); |
||||||
|
avec = gk_dsmalloc(amat->nrows, 0.0, "ComputeNeighborhoodSimilarity: avec"); |
||||||
|
bvec = gk_dsmalloc(bmat->nrows, 0.0, "ComputeNeighborhoodSimilarity: bvec"); |
||||||
|
|
||||||
|
|
||||||
|
/* find the best neighbors for each row in the two matrices and compute
|
||||||
|
the cosine similarity between them. */ |
||||||
|
tabsim = 0.0; |
||||||
|
ncmps = 0; |
||||||
|
for (iR=0; iR<amat->nrows; iR++) { |
||||||
|
if (params->verbosity > 1) |
||||||
|
printf("Working on row %7d\n", iR); |
||||||
|
|
||||||
|
if (amat->rowptr[iR+1]-amat->rowptr[iR] == 0 || |
||||||
|
bmat->rowptr[iR+1]-bmat->rowptr[iR] == 0) |
||||||
|
continue; |
||||||
|
|
||||||
|
nahits = gk_csr_GetSimilarRows(amat,
|
||||||
|
amat->rowptr[iR+1]-amat->rowptr[iR],
|
||||||
|
amat->rowind+amat->rowptr[iR],
|
||||||
|
amat->rowval+amat->rowptr[iR],
|
||||||
|
params->simtype, amat->nrows, 0.0, |
||||||
|
ahits, marker, cand); |
||||||
|
|
||||||
|
nbhits = gk_csr_GetSimilarRows(bmat,
|
||||||
|
bmat->rowptr[iR+1]-bmat->rowptr[iR],
|
||||||
|
bmat->rowind+bmat->rowptr[iR],
|
||||||
|
bmat->rowval+bmat->rowptr[iR],
|
||||||
|
params->simtype, bmat->nrows, 0.0, |
||||||
|
bhits, marker, cand); |
||||||
|
|
||||||
|
if (params->verbosity > 0) |
||||||
|
printf("Row %7d %7d %7d %8zd %8zd\n", iR, nahits, nbhits,
|
||||||
|
amat->rowptr[iR+1]-amat->rowptr[iR], bmat->rowptr[iR+1]-bmat->rowptr[iR]); |
||||||
|
|
||||||
|
for (iH=0; iH<nahits; iH++)
|
||||||
|
avec[ahits[iH].val] = ahits[iH].key; |
||||||
|
for (iH=0; iH<nbhits; iH++)
|
||||||
|
bvec[bhits[iH].val] = bhits[iH].key; |
||||||
|
|
||||||
|
for (abdot=anorm2=bnorm2=0.0, iH=0; iH<amat->nrows; iH++) { |
||||||
|
abdot += avec[iH]*bvec[iH]; |
||||||
|
anorm2 += avec[iH]*avec[iH]; |
||||||
|
bnorm2 += bvec[iH]*bvec[iH]; |
||||||
|
} |
||||||
|
tabsim += (abdot > 0 ? abdot/sqrt(anorm2*bnorm2) : 0.0); |
||||||
|
ncmps++; |
||||||
|
|
||||||
|
for (iH=0; iH<nahits; iH++)
|
||||||
|
avec[ahits[iH].val] = 0.0; |
||||||
|
for (iH=0; iH<nbhits; iH++)
|
||||||
|
bvec[bhits[iH].val] = 0.0; |
||||||
|
} |
||||||
|
|
||||||
|
gk_free((void **)&ahits, &bhits, &marker, &cand, &avec, &bvec, LTERM); |
||||||
|
|
||||||
|
return tabsim/ncmps; |
||||||
|
} |
||||||
|
|
||||||
@ -0,0 +1,397 @@ |
|||||||
|
/*!
|
||||||
|
\file
|
||||||
|
\brief A simple program to convert between different matrix formats that are supported |
||||||
|
by the gk_csr_Read/gk_csr_Write functions. |
||||||
|
|
||||||
|
\date 5/30/2013 |
||||||
|
\author George |
||||||
|
\version \verbatim $Id: csrcnv.c 15314 2013-10-05 16:50:50Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Data structures for the code */ |
||||||
|
/*************************************************************************/ |
||||||
|
typedef struct { |
||||||
|
int inf, outf; /* input/output format */ |
||||||
|
int numbering; /* input numbering (output when applicable) */ |
||||||
|
int readvals; /* input values (output when applicable) */ |
||||||
|
int writevals; /* output values */ |
||||||
|
int rshuf, cshuf; /* random shuffle of rows/columns */ |
||||||
|
int symmetric; /* a symmetric shuffle */ |
||||||
|
int mincolfreq; /* column prunning */ |
||||||
|
int maxcolfreq; /* column prunning */ |
||||||
|
int minrowfreq; /* row prunning */ |
||||||
|
int maxrowfreq; /* row prunning */ |
||||||
|
float rownrmfltr; /* row-lowfilter threshold */ |
||||||
|
int compactcols; /* if to renumber columns to eliminate empty ones */ |
||||||
|
int transpose; /* transpose the output matrix */ |
||||||
|
char *srenumber; /* the iperm file for the symmetric renumbering */ |
||||||
|
char *infile; /* input file */ |
||||||
|
char *outfile; /* output file */ |
||||||
|
} params_t; |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Constants */ |
||||||
|
/*************************************************************************/ |
||||||
|
#define CMD_NUMONE 1 |
||||||
|
#define CMD_NOREADVALS 2 |
||||||
|
#define CMD_NOWRITEVALS 3 |
||||||
|
#define CMD_RSHUF 4 |
||||||
|
#define CMD_CSHUF 5 |
||||||
|
#define CMD_SYMMETRIC 6 |
||||||
|
#define CMD_MINCOLFREQ 7 |
||||||
|
#define CMD_MAXCOLFREQ 8 |
||||||
|
#define CMD_MINROWFREQ 9 |
||||||
|
#define CMD_MAXROWFREQ 10 |
||||||
|
#define CMD_ROWNRMFLTR 11 |
||||||
|
#define CMD_COMPACTCOLS 12 |
||||||
|
#define CMD_TRANSPOSE 13 |
||||||
|
#define CMD_SRENUMBER 14 |
||||||
|
#define CMD_HELP 100 |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Local variables */ |
||||||
|
/*************************************************************************/ |
||||||
|
static struct gk_option long_options[] = { |
||||||
|
{"numone", 0, 0, CMD_NUMONE}, |
||||||
|
{"noreadvals", 0, 0, CMD_NOREADVALS}, |
||||||
|
{"nowritevals", 0, 0, CMD_NOWRITEVALS}, |
||||||
|
{"rshuf", 0, 0, CMD_RSHUF}, |
||||||
|
{"cshuf", 0, 0, CMD_CSHUF}, |
||||||
|
{"symmetric", 0, 0, CMD_SYMMETRIC}, |
||||||
|
{"mincolfreq", 1, 0, CMD_MINCOLFREQ}, |
||||||
|
{"maxcolfreq", 1, 0, CMD_MAXCOLFREQ}, |
||||||
|
{"minrowfreq", 1, 0, CMD_MINROWFREQ}, |
||||||
|
{"maxrowfreq", 1, 0, CMD_MAXROWFREQ}, |
||||||
|
{"rownrmfltr", 1, 0, CMD_ROWNRMFLTR}, |
||||||
|
{"compactcols", 0, 0, CMD_COMPACTCOLS}, |
||||||
|
{"transpose", 0, 0, CMD_TRANSPOSE}, |
||||||
|
{"srenumber", 1, 0, CMD_SRENUMBER}, |
||||||
|
{"help", 0, 0, CMD_HELP}, |
||||||
|
{0, 0, 0, 0} |
||||||
|
}; |
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------------*/ |
||||||
|
/* Mini help */ |
||||||
|
/*-------------------------------------------------------------------*/ |
||||||
|
static char helpstr[][100] = { |
||||||
|
" ", |
||||||
|
"Usage: csrconv [options] <infile> <inf> <outfile> <outf>", |
||||||
|
" ", |
||||||
|
" Required parameters", |
||||||
|
" infile, outfile", |
||||||
|
" The name of the input/output CSR file.", |
||||||
|
" ", |
||||||
|
" inf/outf", |
||||||
|
" The format of the input/output file.", |
||||||
|
" Supported values are:", |
||||||
|
" 1 GK_CSR_FMT_CLUTO", |
||||||
|
" 2 GK_CSR_FMT_CSR", |
||||||
|
" 3 GK_CSR_FMT_METIS", |
||||||
|
" 4 GK_CSR_FMT_BINROW", |
||||||
|
" 6 GK_CSR_FMT_IJV", |
||||||
|
" 7 GK_CSR_FMT_BIJV", |
||||||
|
" ", |
||||||
|
" Optional parameters", |
||||||
|
" -numone", |
||||||
|
" Specifies that the numbering of the input file starts from 1. ", |
||||||
|
" It only applies to CSR/IJV formats.", |
||||||
|
" ", |
||||||
|
" -nowritevals", |
||||||
|
" Specifies that no values will be output.", |
||||||
|
" ", |
||||||
|
" -noreadvals", |
||||||
|
" Specifies that the values will not be read when applicable.", |
||||||
|
" ", |
||||||
|
" -rshuf", |
||||||
|
" Specifies that the rows will be randmly shuffled prior to output.", |
||||||
|
" ", |
||||||
|
" -cshuf", |
||||||
|
" Specifies that the columns will be randmly shuffled prior to output.", |
||||||
|
" ", |
||||||
|
" -symmetric", |
||||||
|
" Specifies that the row+column shuffling will be symmetric.", |
||||||
|
" ", |
||||||
|
" -mincolfreq=int", |
||||||
|
" Used to prune infrequent columns.", |
||||||
|
" ", |
||||||
|
" -maxcolfreq=int", |
||||||
|
" Used to prune frequent columns.", |
||||||
|
" ", |
||||||
|
" -minrowfreq=int", |
||||||
|
" Used to prune infrequent rows.", |
||||||
|
" ", |
||||||
|
" -maxrowfreq=int", |
||||||
|
" Used to prune frequent.", |
||||||
|
" ", |
||||||
|
" -rownrmfltr=float", |
||||||
|
" The parameter to use for the row-wise low filter.", |
||||||
|
" ", |
||||||
|
" -compactcols", |
||||||
|
" Specifies if empty columns will be removed and the columns renumbered.", |
||||||
|
" ", |
||||||
|
" -transpose", |
||||||
|
" Specifies that the transposed matrix will be written.", |
||||||
|
" ", |
||||||
|
" -srenumber=iperm-file", |
||||||
|
" Performs a symmetric renumbering based on the provided iperm file.", |
||||||
|
" ", |
||||||
|
" -help", |
||||||
|
" Prints this message.", |
||||||
|
"" |
||||||
|
}; |
||||||
|
|
||||||
|
static char shorthelpstr[][100] = { |
||||||
|
" ", |
||||||
|
" Usage: csrconv [options] <infile> <inf> <outfile> <outf>", |
||||||
|
" use 'csrconv -help' for a summary of the options.", |
||||||
|
"" |
||||||
|
}; |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This is the entry point of the command-line argument parser */ |
||||||
|
/*************************************************************************/ |
||||||
|
params_t *parse_cmdline(int argc, char *argv[]) |
||||||
|
{ |
||||||
|
int i; |
||||||
|
int c, option_index; |
||||||
|
params_t *params; |
||||||
|
|
||||||
|
params = (params_t *)gk_malloc(sizeof(params_t), "parse_cmdline: params"); |
||||||
|
|
||||||
|
/* initialize the params data structure */ |
||||||
|
params->numbering = 0; |
||||||
|
params->readvals = 1; |
||||||
|
params->writevals = 1; |
||||||
|
params->rshuf = 0; |
||||||
|
params->cshuf = 0; |
||||||
|
params->symmetric = 0; |
||||||
|
params->transpose = 0; |
||||||
|
params->srenumber = NULL; |
||||||
|
|
||||||
|
params->mincolfreq = -1; |
||||||
|
params->minrowfreq = -1; |
||||||
|
params->maxcolfreq = -1; |
||||||
|
params->maxrowfreq = -1; |
||||||
|
params->rownrmfltr = -1; |
||||||
|
params->compactcols = 0; |
||||||
|
|
||||||
|
params->inf = -1; |
||||||
|
params->outf = -1; |
||||||
|
params->infile = NULL; |
||||||
|
params->outfile = NULL; |
||||||
|
|
||||||
|
|
||||||
|
/* Parse the command line arguments */ |
||||||
|
while ((c = gk_getopt_long_only(argc, argv, "", long_options, &option_index)) != -1) { |
||||||
|
switch (c) { |
||||||
|
case CMD_NUMONE: |
||||||
|
params->numbering = 1; |
||||||
|
break; |
||||||
|
case CMD_NOREADVALS: |
||||||
|
params->readvals = 0; |
||||||
|
break; |
||||||
|
case CMD_NOWRITEVALS: |
||||||
|
params->writevals = 0; |
||||||
|
break; |
||||||
|
case CMD_RSHUF: |
||||||
|
params->rshuf = 1; |
||||||
|
break; |
||||||
|
case CMD_CSHUF: |
||||||
|
params->cshuf = 1; |
||||||
|
break; |
||||||
|
case CMD_SYMMETRIC: |
||||||
|
params->symmetric = 1; |
||||||
|
break; |
||||||
|
case CMD_TRANSPOSE: |
||||||
|
params->transpose = 1; |
||||||
|
break; |
||||||
|
|
||||||
|
|
||||||
|
case CMD_MINCOLFREQ: |
||||||
|
if (gk_optarg) params->mincolfreq = atoi(gk_optarg); |
||||||
|
break; |
||||||
|
case CMD_MINROWFREQ: |
||||||
|
if (gk_optarg) params->minrowfreq = atoi(gk_optarg); |
||||||
|
break; |
||||||
|
case CMD_MAXCOLFREQ: |
||||||
|
if (gk_optarg) params->maxcolfreq = atoi(gk_optarg); |
||||||
|
break; |
||||||
|
case CMD_MAXROWFREQ: |
||||||
|
if (gk_optarg) params->maxrowfreq = atoi(gk_optarg); |
||||||
|
break; |
||||||
|
case CMD_ROWNRMFLTR: |
||||||
|
if (gk_optarg) params->rownrmfltr = atof(gk_optarg); |
||||||
|
break; |
||||||
|
case CMD_COMPACTCOLS: |
||||||
|
params->compactcols = 1; |
||||||
|
break; |
||||||
|
|
||||||
|
case CMD_SRENUMBER: |
||||||
|
if (gk_optarg) { |
||||||
|
params->srenumber = gk_strdup(gk_optarg); |
||||||
|
if (!gk_fexists(params->srenumber)) |
||||||
|
errexit("srenumber file %s does not exist.\n", params->srenumber); |
||||||
|
} |
||||||
|
break; |
||||||
|
|
||||||
|
case CMD_HELP: |
||||||
|
for (i=0; strlen(helpstr[i]) > 0; i++) |
||||||
|
printf("%s\n", helpstr[i]); |
||||||
|
exit(0); |
||||||
|
break; |
||||||
|
case '?': |
||||||
|
default: |
||||||
|
printf("Illegal command-line option(s)\nUse %s -help for a summary of the options.\n", argv[0]); |
||||||
|
exit(0); |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
if (argc-gk_optind != 4) { |
||||||
|
printf("Unrecognized parameters."); |
||||||
|
for (i=0; strlen(shorthelpstr[i]) > 0; i++) |
||||||
|
printf("%s\n", shorthelpstr[i]); |
||||||
|
exit(0); |
||||||
|
} |
||||||
|
|
||||||
|
params->infile = gk_strdup(argv[gk_optind++]); |
||||||
|
params->inf = atoi(argv[gk_optind++]); |
||||||
|
params->outfile = gk_strdup(argv[gk_optind++]); |
||||||
|
params->outf = atoi(argv[gk_optind++]); |
||||||
|
|
||||||
|
if (!gk_fexists(params->infile)) |
||||||
|
errexit("input file %s does not exist.\n", params->infile); |
||||||
|
|
||||||
|
return params; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! the entry point */ |
||||||
|
/**************************************************************************/ |
||||||
|
int main(int argc, char *argv[]) |
||||||
|
{ |
||||||
|
int what; |
||||||
|
params_t *params; |
||||||
|
gk_csr_t *mat, *mat1, *smat; |
||||||
|
|
||||||
|
/* get command-line options */ |
||||||
|
params = parse_cmdline(argc, argv); |
||||||
|
|
||||||
|
/* read the data */ |
||||||
|
mat = gk_csr_Read(params->infile, params->inf, params->readvals, params->numbering); |
||||||
|
|
||||||
|
/* deal with weird transformations */ |
||||||
|
if (params->mincolfreq != -1 || params->maxcolfreq != -1) { |
||||||
|
params->mincolfreq = (params->mincolfreq == -1 ? 0 : params->mincolfreq); |
||||||
|
params->maxcolfreq = (params->maxcolfreq == -1 ? mat->nrows : params->maxcolfreq); |
||||||
|
|
||||||
|
printf("Column prune: %d %d; nnz: %zd => ",
|
||||||
|
params->mincolfreq, params->maxcolfreq, mat->rowptr[mat->nrows]); |
||||||
|
mat1 = gk_csr_Prune(mat, GK_CSR_COL, params->mincolfreq, params->maxcolfreq); |
||||||
|
gk_csr_Free(&mat); |
||||||
|
mat = mat1; |
||||||
|
mat1 = NULL; |
||||||
|
|
||||||
|
printf("%zd\n", mat->rowptr[mat->nrows]); |
||||||
|
} |
||||||
|
|
||||||
|
if (params->minrowfreq != -1 || params->maxrowfreq != -1) { |
||||||
|
params->minrowfreq = (params->minrowfreq == -1 ? 0 : params->minrowfreq); |
||||||
|
params->maxrowfreq = (params->maxrowfreq == -1 ? mat->ncols : params->maxrowfreq); |
||||||
|
|
||||||
|
printf("Row prune: %d %d; nnz: %zd => ",
|
||||||
|
params->minrowfreq, params->maxrowfreq, mat->rowptr[mat->nrows]); |
||||||
|
mat1 = gk_csr_Prune(mat, GK_CSR_ROW, params->minrowfreq, params->maxrowfreq); |
||||||
|
gk_csr_Free(&mat); |
||||||
|
mat = mat1; |
||||||
|
mat1 = NULL; |
||||||
|
|
||||||
|
printf("%zd\n", mat->rowptr[mat->nrows]); |
||||||
|
} |
||||||
|
|
||||||
|
if (params->rownrmfltr >= 0.0) { |
||||||
|
//gk_csr_Scale(mat, GK_CSR_LOG);
|
||||||
|
//gk_csr_Scale(mat, GK_CSR_IDF2);
|
||||||
|
|
||||||
|
printf("Row low filter: %f; nnz: %zd => ", params->rownrmfltr, mat->rowptr[mat->nrows]); |
||||||
|
mat1 = gk_csr_LowFilter(mat, GK_CSR_ROW, 2, params->rownrmfltr); |
||||||
|
gk_csr_Normalize(mat1, GK_CSR_ROW, 2); |
||||||
|
|
||||||
|
gk_csr_Free(&mat); |
||||||
|
mat = mat1; |
||||||
|
mat1 = NULL; |
||||||
|
|
||||||
|
printf("%zd\n", mat->rowptr[mat->nrows]); |
||||||
|
} |
||||||
|
|
||||||
|
if (params->compactcols) { |
||||||
|
printf("Compacting columns: %d => ", mat->ncols); |
||||||
|
gk_csr_CompactColumns(mat); |
||||||
|
printf("%d\n", mat->ncols); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
if (params->rshuf || params->cshuf) { |
||||||
|
if (params->rshuf && params->cshuf) |
||||||
|
what = GK_CSR_ROWCOL; |
||||||
|
else if (params->rshuf) |
||||||
|
what = GK_CSR_ROW; |
||||||
|
else |
||||||
|
what = GK_CSR_COL; |
||||||
|
|
||||||
|
smat = gk_csr_Shuffle(mat, what, params->symmetric); |
||||||
|
gk_csr_Free(&mat); |
||||||
|
mat = smat; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
if (params->srenumber) { |
||||||
|
int32_t i; |
||||||
|
size_t nlines; |
||||||
|
int32_t *iperm; |
||||||
|
gk_csr_t *smat; |
||||||
|
|
||||||
|
iperm = gk_i32readfile(params->srenumber, &nlines); |
||||||
|
if (nlines != mat->nrows && nlines != mat->ncols) |
||||||
|
errexit("The nlines=%zud of srenumber file does not match nrows: %d, ncols: %d\n", nlines, mat->nrows, mat->ncols); |
||||||
|
|
||||||
|
if (gk_i32max(nlines, iperm, 1) >= nlines && gk_i32min(nlines, iperm, 1) <= 0)
|
||||||
|
errexit("The srenumber iperm seems to be wrong.\n"); |
||||||
|
|
||||||
|
if (gk_i32max(nlines, iperm, 1) == nlines) { /* need to renumber */ |
||||||
|
for (i=0; i<nlines; i++) |
||||||
|
iperm[i]--; |
||||||
|
} |
||||||
|
|
||||||
|
smat = gk_csr_ReorderSymmetric(mat, iperm, NULL); |
||||||
|
gk_csr_Free(&mat); |
||||||
|
mat = smat; |
||||||
|
|
||||||
|
gk_free((void **)&iperm, LTERM); |
||||||
|
} |
||||||
|
|
||||||
|
if (params->writevals && mat->rowval == NULL)
|
||||||
|
mat->rowval = gk_fsmalloc(mat->rowptr[mat->nrows], 1.0, "mat->rowval"); |
||||||
|
|
||||||
|
if (params->transpose) { |
||||||
|
mat1 = gk_csr_Transpose(mat); |
||||||
|
gk_csr_Free(&mat); |
||||||
|
mat = mat1; |
||||||
|
mat1 = NULL; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
gk_csr_Write(mat, params->outfile, params->outf, params->writevals, 0); |
||||||
|
|
||||||
|
gk_csr_Free(&mat); |
||||||
|
|
||||||
|
} |
||||||
|
|
||||||
@ -0,0 +1,286 @@ |
|||||||
|
/*!
|
||||||
|
\file
|
||||||
|
\brief A simple frequent itemset discovery program to test GKlib's routines |
||||||
|
|
||||||
|
\date 6/12/2008 |
||||||
|
\author George |
||||||
|
\version \verbatim $Id: fis.c 11075 2011-11-11 22:31:52Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Data structures for the code */ |
||||||
|
/*************************************************************************/ |
||||||
|
typedef struct { |
||||||
|
ssize_t minlen, maxlen; |
||||||
|
ssize_t minfreq, maxfreq; |
||||||
|
char *filename; |
||||||
|
int silent; |
||||||
|
ssize_t nitemsets; |
||||||
|
char *clabelfile; |
||||||
|
char **clabels; |
||||||
|
} params_t; |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Constants */ |
||||||
|
/*************************************************************************/ |
||||||
|
#define CMD_MINLEN 1 |
||||||
|
#define CMD_MAXLEN 2 |
||||||
|
#define CMD_MINFREQ 3 |
||||||
|
#define CMD_MAXFREQ 4 |
||||||
|
#define CMD_SILENT 5 |
||||||
|
#define CMD_CLABELFILE 6 |
||||||
|
#define CMD_HELP 10 |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Local variables */ |
||||||
|
/*************************************************************************/ |
||||||
|
static struct gk_option long_options[] = { |
||||||
|
{"minlen", 1, 0, CMD_MINLEN}, |
||||||
|
{"maxlen", 1, 0, CMD_MAXLEN}, |
||||||
|
{"minfreq", 1, 0, CMD_MINFREQ}, |
||||||
|
{"maxfreq", 1, 0, CMD_MAXFREQ}, |
||||||
|
{"silent", 0, 0, CMD_SILENT}, |
||||||
|
{"clabels", 1, 0, CMD_CLABELFILE}, |
||||||
|
{"help", 0, 0, CMD_HELP}, |
||||||
|
{0, 0, 0, 0} |
||||||
|
}; |
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------------*/ |
||||||
|
/* Mini help */ |
||||||
|
/*-------------------------------------------------------------------*/ |
||||||
|
static char helpstr[][100] = { |
||||||
|
" ", |
||||||
|
"Usage: fis [options] <mat-file>", |
||||||
|
" ", |
||||||
|
" Required parameters", |
||||||
|
" mat-file", |
||||||
|
" The name of the file storing the transactions. The file is in ", |
||||||
|
" Cluto's .mat format.", |
||||||
|
" ", |
||||||
|
" Optional parameters", |
||||||
|
" -minlen=int", |
||||||
|
" Specifies the minimum length of the patterns. [default: 1]", |
||||||
|
" ", |
||||||
|
" -maxlen=int", |
||||||
|
" Specifies the maximum length of the patterns. [default: none]", |
||||||
|
" ", |
||||||
|
" -minfreq=int", |
||||||
|
" Specifies the minimum frequency of the patterns. [default: 10]", |
||||||
|
" ", |
||||||
|
" -maxfreq=int", |
||||||
|
" Specifies the maximum frequency of the patterns. [default: none]", |
||||||
|
" ", |
||||||
|
" -silent", |
||||||
|
" Does not print the discovered itemsets.", |
||||||
|
" ", |
||||||
|
" -clabels=filename", |
||||||
|
" Specifies the name of the file that stores the column labels.", |
||||||
|
" ", |
||||||
|
" -help", |
||||||
|
" Prints this message.", |
||||||
|
"" |
||||||
|
}; |
||||||
|
|
||||||
|
static char shorthelpstr[][100] = { |
||||||
|
" ", |
||||||
|
" Usage: fis [options] <mat-file>", |
||||||
|
" use 'fis -help' for a summary of the options.", |
||||||
|
"" |
||||||
|
}; |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Function prototypes */ |
||||||
|
/*************************************************************************/ |
||||||
|
void print_init_info(params_t *params, gk_csr_t *mat); |
||||||
|
void print_final_info(params_t *params); |
||||||
|
params_t *parse_cmdline(int argc, char *argv[]); |
||||||
|
void print_an_itemset(void *stateptr, int nitems, int *itemind,
|
||||||
|
int ntrans, int *tranind); |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! the entry point */ |
||||||
|
/**************************************************************************/ |
||||||
|
int main(int argc, char *argv[]) |
||||||
|
{ |
||||||
|
ssize_t i; |
||||||
|
char line[8192]; |
||||||
|
FILE *fpin; |
||||||
|
params_t *params; |
||||||
|
gk_csr_t *mat; |
||||||
|
|
||||||
|
params = parse_cmdline(argc, argv); |
||||||
|
params->nitemsets = 0; |
||||||
|
|
||||||
|
/* read the data */ |
||||||
|
mat = gk_csr_Read(params->filename, GK_CSR_FMT_CLUTO, 1, 1); |
||||||
|
gk_csr_CreateIndex(mat, GK_CSR_COL); |
||||||
|
|
||||||
|
/* read the column labels */ |
||||||
|
params->clabels = (char **)gk_malloc(mat->ncols*sizeof(char *), "main: clabels"); |
||||||
|
if (params->clabelfile == NULL) { |
||||||
|
for (i=0; i<mat->ncols; i++) { |
||||||
|
sprintf(line, "%zd", i); |
||||||
|
params->clabels[i] = gk_strdup(line); |
||||||
|
} |
||||||
|
} |
||||||
|
else { |
||||||
|
fpin = gk_fopen(params->clabelfile, "r", "main: fpin"); |
||||||
|
for (i=0; i<mat->ncols; i++) { |
||||||
|
if (fgets(line, 8192, fpin) == NULL) |
||||||
|
errexit("Failed on fgets.\n"); |
||||||
|
params->clabels[i] = gk_strdup(gk_strtprune(line, " \n\t")); |
||||||
|
} |
||||||
|
gk_fclose(fpin); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
print_init_info(params, mat); |
||||||
|
|
||||||
|
gk_find_frequent_itemsets(mat->nrows, mat->rowptr, mat->rowind, |
||||||
|
params->minfreq, params->maxfreq, params->minlen, params->maxlen, |
||||||
|
&print_an_itemset, (void *)params); |
||||||
|
|
||||||
|
printf("Total itemsets found: %zd\n", params->nitemsets); |
||||||
|
|
||||||
|
print_final_info(params); |
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function prints run parameters */ |
||||||
|
/*************************************************************************/ |
||||||
|
void print_init_info(params_t *params, gk_csr_t *mat) |
||||||
|
{ |
||||||
|
printf("*******************************************************************************\n"); |
||||||
|
printf(" fis\n\n"); |
||||||
|
printf("Matrix Information ---------------------------------------------------------\n"); |
||||||
|
printf(" input file=%s, [%d, %d, %zd]\n",
|
||||||
|
params->filename, mat->nrows, mat->ncols, mat->rowptr[mat->nrows]); |
||||||
|
|
||||||
|
printf("\n"); |
||||||
|
printf("Options --------------------------------------------------------------------\n"); |
||||||
|
printf(" minlen=%zd, maxlen=%zd, minfeq=%zd, maxfreq=%zd\n", |
||||||
|
params->minlen, params->maxlen, params->minfreq, params->maxfreq); |
||||||
|
|
||||||
|
printf("\n"); |
||||||
|
printf("Finding patterns... -----------------------------------------------------\n"); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function prints final statistics */ |
||||||
|
/*************************************************************************/ |
||||||
|
void print_final_info(params_t *params) |
||||||
|
{ |
||||||
|
printf("\n"); |
||||||
|
printf("Memory Usage Information -----------------------------------------------------\n"); |
||||||
|
printf(" Maximum memory used: %10zd bytes\n", (ssize_t) gk_GetMaxMemoryUsed()); |
||||||
|
printf(" Current memory used: %10zd bytes\n", (ssize_t) gk_GetCurMemoryUsed()); |
||||||
|
printf("********************************************************************************\n"); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This is the entry point of the command-line argument parser */ |
||||||
|
/*************************************************************************/ |
||||||
|
params_t *parse_cmdline(int argc, char *argv[]) |
||||||
|
{ |
||||||
|
int i; |
||||||
|
int c, option_index; |
||||||
|
params_t *params; |
||||||
|
|
||||||
|
params = (params_t *)gk_malloc(sizeof(params_t), "parse_cmdline: params"); |
||||||
|
|
||||||
|
/* initialize the params data structure */ |
||||||
|
params->minlen = 1; |
||||||
|
params->maxlen = -1; |
||||||
|
params->minfreq = 10; |
||||||
|
params->maxfreq = -1; |
||||||
|
params->silent = 0; |
||||||
|
params->filename = NULL; |
||||||
|
params->clabelfile = NULL; |
||||||
|
|
||||||
|
|
||||||
|
/* Parse the command line arguments */ |
||||||
|
while ((c = gk_getopt_long_only(argc, argv, "", long_options, &option_index)) != -1) { |
||||||
|
switch (c) { |
||||||
|
case CMD_MINLEN: |
||||||
|
if (gk_optarg) params->minlen = atoi(gk_optarg); |
||||||
|
break; |
||||||
|
case CMD_MAXLEN: |
||||||
|
if (gk_optarg) params->maxlen = atoi(gk_optarg); |
||||||
|
break; |
||||||
|
case CMD_MINFREQ: |
||||||
|
if (gk_optarg) params->minfreq = atoi(gk_optarg); |
||||||
|
break; |
||||||
|
case CMD_MAXFREQ: |
||||||
|
if (gk_optarg) params->maxfreq = atoi(gk_optarg); |
||||||
|
break; |
||||||
|
|
||||||
|
case CMD_SILENT: |
||||||
|
params->silent = 1; |
||||||
|
break; |
||||||
|
|
||||||
|
case CMD_CLABELFILE: |
||||||
|
if (gk_optarg) params->clabelfile = gk_strdup(gk_optarg); |
||||||
|
break; |
||||||
|
|
||||||
|
case CMD_HELP: |
||||||
|
for (i=0; strlen(helpstr[i]) > 0; i++) |
||||||
|
printf("%s\n", helpstr[i]); |
||||||
|
exit(0); |
||||||
|
break; |
||||||
|
case '?': |
||||||
|
default: |
||||||
|
printf("Illegal command-line option(s)\nUse %s -help for a summary of the options.\n", argv[0]); |
||||||
|
exit(0); |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
if (argc-gk_optind != 1) { |
||||||
|
printf("Unrecognized parameters."); |
||||||
|
for (i=0; strlen(shorthelpstr[i]) > 0; i++) |
||||||
|
printf("%s\n", shorthelpstr[i]); |
||||||
|
exit(0); |
||||||
|
} |
||||||
|
|
||||||
|
params->filename = gk_strdup(argv[gk_optind++]); |
||||||
|
|
||||||
|
if (!gk_fexists(params->filename)) |
||||||
|
errexit("input file %s does not exist.\n", params->filename); |
||||||
|
|
||||||
|
return params; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This is the callback function for the itemset discovery routine */ |
||||||
|
/*************************************************************************/ |
||||||
|
void print_an_itemset(void *stateptr, int nitems, int *itemids, int ntrans,
|
||||||
|
int *transids) |
||||||
|
{ |
||||||
|
ssize_t i; |
||||||
|
params_t *params; |
||||||
|
|
||||||
|
params = (params_t *)stateptr; |
||||||
|
params->nitemsets++; |
||||||
|
|
||||||
|
if (!params->silent) { |
||||||
|
printf("%4zd %4d %4d => ", params->nitemsets, nitems, ntrans); |
||||||
|
for (i=0; i<nitems; i++) |
||||||
|
printf(" %s", params->clabels[itemids[i]]); |
||||||
|
printf("\n"); |
||||||
|
for (i=0; i<ntrans; i++) |
||||||
|
printf(" %d\n", transids[i]); |
||||||
|
printf("\n"); |
||||||
|
} |
||||||
|
} |
||||||
@ -0,0 +1,845 @@ |
|||||||
|
/*!
|
||||||
|
\file
|
||||||
|
\brief A simple program to try out some graph routines |
||||||
|
|
||||||
|
\date 6/12/2008 |
||||||
|
\author George |
||||||
|
\version \verbatim $Id: gkgraph.c 17700 2014-09-27 18:10:02Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Data structures for the code */ |
||||||
|
/*************************************************************************/ |
||||||
|
typedef struct { |
||||||
|
int lnbits; |
||||||
|
int cnbits; |
||||||
|
int type; |
||||||
|
int niter; |
||||||
|
float eps; |
||||||
|
float lamda; |
||||||
|
int nosort; |
||||||
|
int write; |
||||||
|
|
||||||
|
char *infile; |
||||||
|
char *outfile; |
||||||
|
} params_t; |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Constants */ |
||||||
|
/*************************************************************************/ |
||||||
|
#define CMD_NITER 1 |
||||||
|
#define CMD_EPS 2 |
||||||
|
#define CMD_LAMDA 3 |
||||||
|
#define CMD_TYPE 4 |
||||||
|
#define CMD_NOSORT 5 |
||||||
|
#define CMD_WRITE 6 |
||||||
|
#define CMD_LNBITS 7 |
||||||
|
#define CMD_CNBITS 8 |
||||||
|
#define CMD_HELP 10 |
||||||
|
|
||||||
|
#define CLINE32 16 |
||||||
|
#define CLINE64 8 |
||||||
|
#define MAXRCLOCKSPAN (1<<20) |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Local variables */ |
||||||
|
/*************************************************************************/ |
||||||
|
static struct gk_option long_options[] = { |
||||||
|
{"lnbits", 1, 0, CMD_LNBITS}, |
||||||
|
{"cnbits", 1, 0, CMD_CNBITS}, |
||||||
|
{"type", 1, 0, CMD_TYPE}, |
||||||
|
{"niter", 1, 0, CMD_NITER}, |
||||||
|
{"lamda", 1, 0, CMD_LAMDA}, |
||||||
|
{"eps", 1, 0, CMD_EPS}, |
||||||
|
{"nosort", 0, 0, CMD_NOSORT}, |
||||||
|
{"write", 0, 0, CMD_WRITE}, |
||||||
|
{"help", 0, 0, CMD_HELP}, |
||||||
|
{0, 0, 0, 0} |
||||||
|
}; |
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------------*/ |
||||||
|
/* Mini help */ |
||||||
|
/*-------------------------------------------------------------------*/ |
||||||
|
static char helpstr[][100] = { |
||||||
|
" ", |
||||||
|
"Usage: gkgraph [options] <graph-file> [<out-file>]", |
||||||
|
" ", |
||||||
|
" Required parameters", |
||||||
|
" graph-file", |
||||||
|
" The name of the file storing the graph. The file is in ", |
||||||
|
" Metis' graph format.", |
||||||
|
" ", |
||||||
|
" Optional parameters", |
||||||
|
" -niter=int", |
||||||
|
" Specifies the maximum number of iterations. [default: 100]", |
||||||
|
" ", |
||||||
|
" -lnbits=int", |
||||||
|
" Specifies the number of address bits indexing the cacheline. [default: 6]", |
||||||
|
" ", |
||||||
|
" -cnbits=int", |
||||||
|
" Specifies the number of address bits indexing the cache. [default: 13]", |
||||||
|
" ", |
||||||
|
" -lamda=float", |
||||||
|
" Specifies the follow-the-adjacent-links probability. [default: 0.80]", |
||||||
|
" ", |
||||||
|
" -eps=float", |
||||||
|
" Specifies the error tollerance. [default: 1e-10]", |
||||||
|
" ", |
||||||
|
" -nosort", |
||||||
|
" Does not sort the adjacency lists.", |
||||||
|
" ", |
||||||
|
" -write", |
||||||
|
" Output the reordered graphs.", |
||||||
|
" ", |
||||||
|
" -help", |
||||||
|
" Prints this message.", |
||||||
|
"" |
||||||
|
}; |
||||||
|
|
||||||
|
static char shorthelpstr[][100] = { |
||||||
|
" ", |
||||||
|
" Usage: gkgraph [options] <graph-file> [<out-file>]", |
||||||
|
" use 'gkgraph -help' for a summary of the options.", |
||||||
|
"" |
||||||
|
}; |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Function prototypes */ |
||||||
|
/*************************************************************************/ |
||||||
|
void test_spmv(params_t *params); |
||||||
|
void test_tc(params_t *params); |
||||||
|
void sort_adjacencies(params_t *params, gk_graph_t *graph); |
||||||
|
double compute_spmvstats(params_t *params, gk_graph_t *graph); |
||||||
|
double compute_tcstats(params_t *params, gk_graph_t *graph, int32_t *iperm); |
||||||
|
int32_t *reorder_degrees(params_t *params, gk_graph_t *graph); |
||||||
|
int32_t *reorder_freqlpn(params_t *params, gk_graph_t *graph); |
||||||
|
int32_t *reorder_freqlpn_db(params_t *params, gk_graph_t *graph); |
||||||
|
int32_t *reorder_minlpn(params_t *params, gk_graph_t *graph); |
||||||
|
int32_t *reorder_minlpn_db(params_t *params, gk_graph_t *graph); |
||||||
|
void print_init_info(params_t *params, gk_graph_t *graph); |
||||||
|
void print_final_info(params_t *params); |
||||||
|
params_t *parse_cmdline(int argc, char *argv[]); |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! the entry point */ |
||||||
|
/**************************************************************************/ |
||||||
|
int main(int argc, char *argv[]) |
||||||
|
{ |
||||||
|
params_t *params; |
||||||
|
|
||||||
|
/* get command-line options */ |
||||||
|
params = parse_cmdline(argc, argv); |
||||||
|
|
||||||
|
test_tc(params); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! various spmv-related tests */ |
||||||
|
/**************************************************************************/ |
||||||
|
void test_spmv(params_t *params) |
||||||
|
{ |
||||||
|
ssize_t i, j, v; |
||||||
|
gk_graph_t *graph, *pgraph; |
||||||
|
int32_t *perm; |
||||||
|
|
||||||
|
/* read the data */ |
||||||
|
graph = gk_graph_Read(params->infile, GK_GRAPH_FMT_METIS, -1, -1, 0, 0, 0); |
||||||
|
|
||||||
|
/* display some basic stats */ |
||||||
|
print_init_info(params, graph); |
||||||
|
|
||||||
|
sort_adjacencies(params, graph); |
||||||
|
if (params->write) gk_graph_Write(graph, "original.ijv", GK_GRAPH_FMT_IJV, 1); |
||||||
|
printf("Input SPMV HitRate: %.4lf\n", compute_spmvstats(params, graph)); |
||||||
|
|
||||||
|
|
||||||
|
v = RandomInRange(graph->nvtxs); |
||||||
|
gk_graph_ComputeBFSOrdering(graph, v, &perm, NULL); |
||||||
|
pgraph = gk_graph_Reorder(graph, perm, NULL); |
||||||
|
sort_adjacencies(params, pgraph); |
||||||
|
if (params->write) gk_graph_Write(pgraph, "bfs.ijv", GK_GRAPH_FMT_IJV, 1); |
||||||
|
printf("BFS SPMV HitRate: %.4lf\n", compute_spmvstats(params, pgraph)); |
||||||
|
gk_graph_Free(&pgraph); |
||||||
|
gk_free((void **)&perm, LTERM); |
||||||
|
|
||||||
|
|
||||||
|
perm = reorder_degrees(params, graph); |
||||||
|
pgraph = gk_graph_Reorder(graph, perm, NULL); |
||||||
|
sort_adjacencies(params, pgraph); |
||||||
|
if (params->write) gk_graph_Write(pgraph, "degrees.ijv", GK_GRAPH_FMT_IJV, 1); |
||||||
|
printf("Degrees SPMV HitRate: %.4lf\n", compute_spmvstats(params, pgraph)); |
||||||
|
gk_graph_Free(&pgraph); |
||||||
|
gk_free((void **)&perm, LTERM); |
||||||
|
|
||||||
|
|
||||||
|
perm = reorder_freqlpn(params, graph); |
||||||
|
pgraph = gk_graph_Reorder(graph, perm, NULL); |
||||||
|
sort_adjacencies(params, pgraph); |
||||||
|
if (params->write) gk_graph_Write(pgraph, "freqlpn.ijv", GK_GRAPH_FMT_IJV, 1); |
||||||
|
printf("FreqLabelPropN SPMV HitRate: %.4lf\n", compute_spmvstats(params, pgraph)); |
||||||
|
gk_graph_Free(&pgraph); |
||||||
|
gk_free((void **)&perm, LTERM); |
||||||
|
|
||||||
|
perm = reorder_freqlpn_db(params, graph); |
||||||
|
pgraph = gk_graph_Reorder(graph, perm, NULL); |
||||||
|
sort_adjacencies(params, pgraph); |
||||||
|
if (params->write) gk_graph_Write(pgraph, "freqlpn-db.ijv", GK_GRAPH_FMT_IJV, 1); |
||||||
|
printf("DBFreqLabelPropN SPMV HitRate: %.4lf\n", compute_spmvstats(params, pgraph)); |
||||||
|
gk_graph_Free(&pgraph); |
||||||
|
gk_free((void **)&perm, LTERM); |
||||||
|
|
||||||
|
perm = reorder_minlpn(params, graph); |
||||||
|
pgraph = gk_graph_Reorder(graph, perm, NULL); |
||||||
|
sort_adjacencies(params, pgraph); |
||||||
|
if (params->write) gk_graph_Write(pgraph, "minlpn.ijv", GK_GRAPH_FMT_IJV, 1); |
||||||
|
printf("MinLabelPropN SPMV HitRate: %.4lf\n", compute_spmvstats(params, pgraph)); |
||||||
|
gk_graph_Free(&pgraph); |
||||||
|
gk_free((void **)&perm, LTERM); |
||||||
|
|
||||||
|
perm = reorder_minlpn_db(params, graph); |
||||||
|
pgraph = gk_graph_Reorder(graph, perm, NULL); |
||||||
|
sort_adjacencies(params, pgraph); |
||||||
|
if (params->write) gk_graph_Write(pgraph, "minlpn-db.ijv", GK_GRAPH_FMT_IJV, 1); |
||||||
|
printf("DBMinLabelPropN SPMV HitRate: %.4lf\n", compute_spmvstats(params, pgraph)); |
||||||
|
gk_graph_Free(&pgraph); |
||||||
|
gk_free((void **)&perm, LTERM); |
||||||
|
|
||||||
|
gk_graph_Free(&graph); |
||||||
|
|
||||||
|
print_final_info(params); |
||||||
|
|
||||||
|
return; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! various tc-related tests */ |
||||||
|
/**************************************************************************/ |
||||||
|
void test_tc(params_t *params) |
||||||
|
{ |
||||||
|
ssize_t i, j, v; |
||||||
|
gk_graph_t *graph, *pgraph; |
||||||
|
int32_t *perm, *iperm; |
||||||
|
|
||||||
|
/* read the data */ |
||||||
|
graph = gk_graph_Read(params->infile, GK_GRAPH_FMT_METIS, -1, -1, 0, 0, 0); |
||||||
|
|
||||||
|
/* display some basic stats */ |
||||||
|
print_init_info(params, graph); |
||||||
|
|
||||||
|
perm = reorder_degrees(params, graph); |
||||||
|
pgraph = gk_graph_Reorder(graph, perm, NULL); |
||||||
|
gk_free((void **)&perm, LTERM); |
||||||
|
sort_adjacencies(params, pgraph); |
||||||
|
iperm = gk_i32incset(graph->nvtxs, 0, gk_i32malloc(graph->nvtxs, "iperm")); |
||||||
|
printf("Degrees TC HitRate: %.4lf\n", compute_tcstats(params, pgraph, iperm)); |
||||||
|
|
||||||
|
|
||||||
|
sort_adjacencies(params, pgraph); |
||||||
|
v = RandomInRange(pgraph->nvtxs); |
||||||
|
gk_graph_ComputeBFSOrdering(pgraph, v, &perm, NULL); |
||||||
|
for (i=0; i<graph->nvtxs; i++) iperm[perm[i]] = i; |
||||||
|
gk_free((void **)&perm, LTERM); |
||||||
|
printf("BFS TC HitRate: %.4lf\n", compute_tcstats(params, pgraph, iperm)); |
||||||
|
|
||||||
|
|
||||||
|
sort_adjacencies(params, pgraph); |
||||||
|
perm = reorder_freqlpn(params, pgraph); |
||||||
|
for (i=0; i<graph->nvtxs; i++) iperm[perm[i]] = i; |
||||||
|
gk_free((void **)&perm, LTERM); |
||||||
|
printf("FreqLabelPropN TC HitRate: %.4lf\n", compute_tcstats(params, pgraph, iperm)); |
||||||
|
|
||||||
|
sort_adjacencies(params, pgraph); |
||||||
|
perm = reorder_freqlpn_db(params, pgraph); |
||||||
|
for (i=0; i<graph->nvtxs; i++) iperm[perm[i]] = i; |
||||||
|
gk_free((void **)&perm, LTERM); |
||||||
|
printf("DBFreqLabelPropN TC HitRate: %.4lf\n", compute_tcstats(params, pgraph, iperm)); |
||||||
|
|
||||||
|
|
||||||
|
#ifdef XXX |
||||||
|
perm = reorder_minlpn(params, graph); |
||||||
|
pgraph = gk_graph_Reorder(graph, perm, NULL); |
||||||
|
sort_adjacencies(params, pgraph); |
||||||
|
if (params->write) gk_graph_Write(pgraph, "minlpn.ijv", GK_GRAPH_FMT_IJV, 1); |
||||||
|
printf("MinLabelPropN SPMV HitRate: %.4lf\n", compute_spmvstats(params, pgraph)); |
||||||
|
gk_graph_Free(&pgraph); |
||||||
|
gk_free((void **)&perm, LTERM); |
||||||
|
|
||||||
|
perm = reorder_minlpn_db(params, graph); |
||||||
|
pgraph = gk_graph_Reorder(graph, perm, NULL); |
||||||
|
sort_adjacencies(params, pgraph); |
||||||
|
if (params->write) gk_graph_Write(pgraph, "minlpn-db.ijv", GK_GRAPH_FMT_IJV, 1); |
||||||
|
printf("DBMinLabelPropN SPMV HitRate: %.4lf\n", compute_spmvstats(params, pgraph)); |
||||||
|
gk_graph_Free(&pgraph); |
||||||
|
gk_free((void **)&perm, LTERM); |
||||||
|
#endif |
||||||
|
|
||||||
|
gk_free((void **)&iperm, LTERM); |
||||||
|
gk_graph_Free(&graph); |
||||||
|
|
||||||
|
print_final_info(params); |
||||||
|
|
||||||
|
return; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function sorts the adjacency lists of the vertices in increasing
|
||||||
|
order. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
void sort_adjacencies(params_t *params, gk_graph_t *graph) |
||||||
|
{ |
||||||
|
uint64_t i, nvtxs; |
||||||
|
ssize_t *xadj;
|
||||||
|
int32_t *adjncy; |
||||||
|
|
||||||
|
if (params->nosort) |
||||||
|
return; |
||||||
|
|
||||||
|
nvtxs = graph->nvtxs; |
||||||
|
xadj = graph->xadj; |
||||||
|
adjncy = graph->adjncy; |
||||||
|
|
||||||
|
for (i=0; i<nvtxs; i++)
|
||||||
|
gk_i32sorti(xadj[i+1]-xadj[i], adjncy+xadj[i]); |
||||||
|
|
||||||
|
return; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function analyzes the cache locality of an SPMV operation using
|
||||||
|
GKlib's cache simulator and returns the cache's hit rate. |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
double compute_spmvstats(params_t *params, gk_graph_t *graph) |
||||||
|
{ |
||||||
|
uint64_t i, nvtxs; |
||||||
|
ssize_t *xadj;
|
||||||
|
int32_t *adjncy, *vec; |
||||||
|
|
||||||
|
gk_cache_t *cache = gk_cacheCreate(16, params->lnbits, params->cnbits); /* 8MB total; i7 spec */ |
||||||
|
|
||||||
|
nvtxs = graph->nvtxs; |
||||||
|
xadj = graph->xadj; |
||||||
|
adjncy = graph->adjncy; |
||||||
|
|
||||||
|
vec = gk_i32malloc(nvtxs, "vec"); |
||||||
|
for (i=0; i<xadj[nvtxs]; i++) { |
||||||
|
gk_cacheLoad(cache, (size_t)(&adjncy[i])); |
||||||
|
gk_cacheLoad(cache, (size_t)(&vec[adjncy[i]])); |
||||||
|
} |
||||||
|
|
||||||
|
gk_free((void **)&vec, LTERM); |
||||||
|
|
||||||
|
double hitrate = gk_cacheGetHitRate(cache); |
||||||
|
gk_cacheDestroy(&cache); |
||||||
|
|
||||||
|
return hitrate; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! The hash-map-based triangle-counting routine that uses the JIK
|
||||||
|
triangle enumeration scheme. |
||||||
|
|
||||||
|
This version implements the following: |
||||||
|
- It does not store location information in L |
||||||
|
- Reverts the order within U's adjancency lists to allow ++ traversal |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
double compute_tcstats(params_t *params, gk_graph_t *graph, int32_t *iperm) |
||||||
|
{ |
||||||
|
int32_t vi, vj, vjj, vk, vl, nvtxs; |
||||||
|
ssize_t ei, eiend, eistart, ej, ejend, ejstart; |
||||||
|
int64_t ntriangles; |
||||||
|
ssize_t *xadj, *uxadj; |
||||||
|
int32_t *adjncy; |
||||||
|
int32_t l, hmsize, *hmap; |
||||||
|
|
||||||
|
gk_cache_t *cache = gk_cacheCreate(16, params->lnbits, params->cnbits);
|
||||||
|
|
||||||
|
nvtxs = graph->nvtxs; |
||||||
|
xadj = graph->xadj; |
||||||
|
adjncy = graph->adjncy; |
||||||
|
|
||||||
|
/* determine the starting location of the upper trianglular part */ |
||||||
|
uxadj = gk_zmalloc(nvtxs, "uxadj"); |
||||||
|
for (vi=0; vi<nvtxs; vi++) { |
||||||
|
for (ei=xadj[vi], eiend=xadj[vi+1]; ei<eiend && adjncy[ei]<vi; ei++);
|
||||||
|
uxadj[vi] = ei; |
||||||
|
/* flip the order of Adj(vi)'s upper triangular adjacency list */ |
||||||
|
for (ej=xadj[vi+1]-1; ei<ej; ei++, ej--) { |
||||||
|
vj = adjncy[ei]; |
||||||
|
adjncy[ei] = adjncy[ej]; |
||||||
|
adjncy[ej] = vj; |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
/* determine the size of the hash-map and convert it into a format
|
||||||
|
that is compatible with a bitwise AND operation */ |
||||||
|
for (hmsize=0, vi=0; vi<nvtxs; vi++)
|
||||||
|
hmsize = gk_max(hmsize, (int32_t)(xadj[vi+1]-uxadj[vi])); |
||||||
|
for (l=1; hmsize>(1<<l); l++); |
||||||
|
hmsize = (1<<(l+4))-1; |
||||||
|
hmap = gk_i32smalloc(hmsize+1, 0, "hmap"); |
||||||
|
|
||||||
|
for (ntriangles=0, vjj=0; vjj<nvtxs; vjj++) { |
||||||
|
vj = iperm[vjj]; |
||||||
|
|
||||||
|
gk_cacheLoad(cache, (size_t)(&xadj[vj])); |
||||||
|
gk_cacheLoad(cache, (size_t)(&xadj[vj+1])); |
||||||
|
gk_cacheLoad(cache, (size_t)(&uxadj[vj])); |
||||||
|
|
||||||
|
if (xadj[vj+1]-uxadj[vj] == 0 || uxadj[vj] == xadj[vj]) |
||||||
|
continue; |
||||||
|
|
||||||
|
/* hash Adj(vj) */ |
||||||
|
gk_cacheLoad(cache, (size_t)(&uxadj[vj])); |
||||||
|
gk_cacheLoad(cache, (size_t)(&xadj[vj+1])); |
||||||
|
for (ej=uxadj[vj], ejend=xadj[vj+1]; ej<ejend; ej++) { |
||||||
|
gk_cacheLoad(cache, (size_t)(&adjncy[ej])); |
||||||
|
vk = adjncy[ej]; |
||||||
|
for (l=(vk&hmsize);
|
||||||
|
gk_cacheLoad(cache, (size_t)(&hmap[l])) && hmap[l]!=0;
|
||||||
|
l=((l+1)&hmsize)); |
||||||
|
hmap[l] = vk; |
||||||
|
} |
||||||
|
|
||||||
|
/* find intersections */ |
||||||
|
gk_cacheLoad(cache, (size_t)(&xadj[vj])); |
||||||
|
gk_cacheLoad(cache, (size_t)(&uxadj[vj])); |
||||||
|
for (ej=xadj[vj], ejend=uxadj[vj]; ej<ejend; ej++) { |
||||||
|
gk_cacheLoad(cache, (size_t)(&adjncy[ej])); |
||||||
|
gk_cacheLoad(cache, (size_t)(&uxadj[vi])); |
||||||
|
vi = adjncy[ej]; |
||||||
|
for (ei=uxadj[vi]; gk_cacheLoad(cache, (size_t)(&adjncy[ei])) && adjncy[ei]>vj; ei++) { |
||||||
|
vk = adjncy[ei]; |
||||||
|
for (l=vk&hmsize;
|
||||||
|
gk_cacheLoad(cache, (size_t)(&hmap[l])) && hmap[l]!=0 && hmap[l]!=vk;
|
||||||
|
l=((l+1)&hmsize)); |
||||||
|
gk_cacheLoad(cache, (size_t)(&hmap[l])); |
||||||
|
if (hmap[l] == vk)
|
||||||
|
ntriangles++; |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
/* reset hash */ |
||||||
|
gk_cacheLoad(cache, (size_t)(&uxadj[vj])); |
||||||
|
gk_cacheLoad(cache, (size_t)(&xadj[vj+1])); |
||||||
|
for (ej=uxadj[vj], ejend=xadj[vj+1]; ej<ejend; ej++) { |
||||||
|
gk_cacheLoad(cache, (size_t)(&adjncy[ej])); |
||||||
|
vk = adjncy[ej]; |
||||||
|
for (l=(vk&hmsize);
|
||||||
|
gk_cacheLoad(cache, (size_t)(&hmap[l])) && hmap[l]!=vk;
|
||||||
|
l=((l+1)&hmsize)); |
||||||
|
hmap[l] = 0; |
||||||
|
} |
||||||
|
} |
||||||
|
printf("& compatible hmsize: %"PRId32" #triangles: %"PRIu64"\n", hmsize, ntriangles); |
||||||
|
|
||||||
|
gk_free((void **)&uxadj, &hmap, LTERM); |
||||||
|
|
||||||
|
//printf("%zd %zd\n", (ssize_t)cache->nhits, (ssize_t)cache->clock);
|
||||||
|
|
||||||
|
double hitrate = gk_cacheGetHitRate(cache); |
||||||
|
gk_cacheDestroy(&cache); |
||||||
|
|
||||||
|
return hitrate; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function computes an increasing degree ordering
|
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
int32_t *reorder_degrees(params_t *params, gk_graph_t *graph) |
||||||
|
{ |
||||||
|
int i, v, u, nvtxs, range; |
||||||
|
ssize_t j, *xadj;
|
||||||
|
int32_t *counts, *perm; |
||||||
|
|
||||||
|
nvtxs = graph->nvtxs; |
||||||
|
xadj = graph->xadj; |
||||||
|
|
||||||
|
for (range=0, i=0; i<nvtxs; i++)
|
||||||
|
range = gk_max(range, xadj[i+1]-xadj[i]); |
||||||
|
range++; |
||||||
|
|
||||||
|
counts = gk_i32smalloc(range+1, 0, "counts"); |
||||||
|
for (i=0; i<nvtxs; i++) |
||||||
|
counts[xadj[i+1]-xadj[i]]++; |
||||||
|
MAKECSR(i, range, counts); |
||||||
|
|
||||||
|
perm = gk_i32malloc(nvtxs, "perm"); |
||||||
|
for (i=0; i<nvtxs; i++) |
||||||
|
perm[i] = counts[xadj[i+1]-xadj[i]]++; |
||||||
|
|
||||||
|
gk_free((void **)&counts, LTERM); |
||||||
|
|
||||||
|
return perm; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function re-orders the graph by:
|
||||||
|
- performing a fixed number of most-popular label propagation iterations |
||||||
|
- locally renumbers the vertices with the same label |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
int32_t *reorder_freqlpn(params_t *params, gk_graph_t *graph) |
||||||
|
{ |
||||||
|
int32_t i, ii, k, nvtxs, maxlbl; |
||||||
|
ssize_t j, *xadj;
|
||||||
|
int32_t *adjncy, *labels, *freq, *perm; |
||||||
|
gk_i32kv_t *cand; |
||||||
|
|
||||||
|
nvtxs = graph->nvtxs; |
||||||
|
xadj = graph->xadj; |
||||||
|
adjncy = graph->adjncy; |
||||||
|
|
||||||
|
labels = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "labels")); |
||||||
|
freq = gk_i32smalloc(nvtxs, 0, "freq"); |
||||||
|
perm = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "perm")); |
||||||
|
|
||||||
|
for (k=0; k<params->niter; k++) { |
||||||
|
gk_i32randArrayPermuteFine(nvtxs, perm, 0); |
||||||
|
for (ii=0; ii<nvtxs; ii++) { |
||||||
|
i = perm[ii]; |
||||||
|
maxlbl = labels[adjncy[xadj[i]]]; |
||||||
|
freq[maxlbl] = 1; |
||||||
|
for (j=xadj[i]+1; j<xadj[i+1]; j++) { |
||||||
|
freq[labels[adjncy[j]]]++; |
||||||
|
if (freq[maxlbl] < freq[labels[adjncy[j]]]) |
||||||
|
maxlbl = labels[adjncy[j]]; |
||||||
|
else if (freq[maxlbl] == freq[labels[adjncy[j]]]) { |
||||||
|
if (RandomInRange(2)) |
||||||
|
maxlbl = labels[adjncy[j]]; |
||||||
|
} |
||||||
|
} |
||||||
|
for (j=xadj[i]; j<xadj[i+1]; j++)
|
||||||
|
freq[labels[adjncy[j]]] = 0; |
||||||
|
labels[i] = maxlbl; |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
cand = gk_i32kvmalloc(nvtxs, "cand"); |
||||||
|
for (i=0; i<nvtxs; i++) { |
||||||
|
cand[i].key = labels[i]; |
||||||
|
cand[i].val = i; |
||||||
|
} |
||||||
|
gk_i32kvsorti(nvtxs, cand); |
||||||
|
|
||||||
|
for (i=0; i<nvtxs; i++) |
||||||
|
perm[cand[i].val] = i; |
||||||
|
|
||||||
|
gk_free((void **)&labels, &freq, &cand, LTERM); |
||||||
|
|
||||||
|
return perm; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function re-orders the graph by:
|
||||||
|
- performing a fixed number of most-popular label propagation iterations |
||||||
|
- restricts that propagation to take place within similar degree buckets |
||||||
|
of vertices |
||||||
|
- locally renumbers the vertices with the same label |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
int32_t *reorder_freqlpn_db(params_t *params, gk_graph_t *graph) |
||||||
|
{ |
||||||
|
int32_t i, ii, k, nvtxs, maxlbl; |
||||||
|
ssize_t j, *xadj;
|
||||||
|
int32_t *adjncy, *labels, *freq, *perm, *dbucket; |
||||||
|
gk_i32kv_t *cand; |
||||||
|
|
||||||
|
nvtxs = graph->nvtxs; |
||||||
|
xadj = graph->xadj; |
||||||
|
adjncy = graph->adjncy; |
||||||
|
|
||||||
|
labels = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "labels")); |
||||||
|
freq = gk_i32smalloc(nvtxs, 0, "freq"); |
||||||
|
perm = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "perm")); |
||||||
|
dbucket = gk_i32malloc(nvtxs, "dbucket"); |
||||||
|
|
||||||
|
for (i=0; i<nvtxs; i++) |
||||||
|
dbucket[i] = ((xadj[i+1]-xadj[i])>>3); |
||||||
|
|
||||||
|
for (k=0; k<params->niter; k++) { |
||||||
|
gk_i32randArrayPermuteFine(nvtxs, perm, 0); |
||||||
|
for (ii=0; ii<nvtxs; ii++) { |
||||||
|
i = perm[ii]; |
||||||
|
maxlbl = labels[i]; |
||||||
|
for (j=xadj[i]; j<xadj[i+1]; j++) { |
||||||
|
if (dbucket[i] != dbucket[adjncy[j]]) |
||||||
|
continue; |
||||||
|
|
||||||
|
freq[labels[adjncy[j]]]++; |
||||||
|
if (freq[maxlbl] < freq[labels[adjncy[j]]]) |
||||||
|
maxlbl = labels[adjncy[j]]; |
||||||
|
else if (freq[maxlbl] == freq[labels[adjncy[j]]]) { |
||||||
|
if (RandomInRange(2)) |
||||||
|
maxlbl = labels[adjncy[j]]; |
||||||
|
} |
||||||
|
} |
||||||
|
for (j=xadj[i]; j<xadj[i+1]; j++)
|
||||||
|
freq[labels[adjncy[j]]] = 0; |
||||||
|
labels[i] = maxlbl; |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
cand = gk_i32kvmalloc(nvtxs, "cand"); |
||||||
|
for (i=0; i<nvtxs; i++) { |
||||||
|
cand[i].key = labels[i]; |
||||||
|
cand[i].val = i; |
||||||
|
} |
||||||
|
gk_i32kvsorti(nvtxs, cand); |
||||||
|
|
||||||
|
for (i=0; i<nvtxs; i++) |
||||||
|
perm[cand[i].val] = i; |
||||||
|
|
||||||
|
gk_free((void **)&labels, &freq, &dbucket, &cand, LTERM); |
||||||
|
|
||||||
|
return perm; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function re-orders the graph by:
|
||||||
|
- performing a fixed number of min-label propagation iterations |
||||||
|
- locally renumbers the vertices with the same label |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
int32_t *reorder_minlpn(params_t *params, gk_graph_t *graph) |
||||||
|
{ |
||||||
|
int32_t i, ii, k, nvtxs, minlbl; |
||||||
|
ssize_t j, *xadj;
|
||||||
|
int32_t *adjncy, *labels, *perm; |
||||||
|
gk_i32kv_t *cand; |
||||||
|
|
||||||
|
nvtxs = graph->nvtxs; |
||||||
|
xadj = graph->xadj; |
||||||
|
adjncy = graph->adjncy; |
||||||
|
|
||||||
|
labels = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "labels")); |
||||||
|
perm = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "perm")); |
||||||
|
|
||||||
|
for (k=0; k<params->niter; k++) { |
||||||
|
for (i=0; i<nvtxs; i++) { |
||||||
|
minlbl = labels[i]; |
||||||
|
for (j=xadj[i]; j<xadj[i+1]; j++) { |
||||||
|
if (minlbl > labels[adjncy[j]]) |
||||||
|
minlbl = labels[adjncy[j]]; |
||||||
|
} |
||||||
|
labels[i] = minlbl; |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
cand = gk_i32kvmalloc(nvtxs, "cand"); |
||||||
|
for (i=0; i<nvtxs; i++) { |
||||||
|
cand[i].key = labels[i]; |
||||||
|
cand[i].val = i; |
||||||
|
} |
||||||
|
gk_i32kvsorti(nvtxs, cand); |
||||||
|
|
||||||
|
for (i=0; i<nvtxs; i++) { |
||||||
|
perm[cand[i].val] = i; |
||||||
|
//if (i>0 && cand[i].key != cand[i-1].key)
|
||||||
|
// printf("%10d %10d\n", i-1, cand[i-1].key);
|
||||||
|
} |
||||||
|
//printf("%10d %10d\n", i-1, cand[i-1].key);
|
||||||
|
|
||||||
|
gk_free((void **)&labels, &cand, LTERM); |
||||||
|
|
||||||
|
return perm; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function re-orders the graph by:
|
||||||
|
- performing a fixed number of min-label propagation iterations
|
||||||
|
- restricts that propagation to take place within similar degree buckets |
||||||
|
of vertices |
||||||
|
- locally renumbers the vertices with the same label |
||||||
|
*/ |
||||||
|
/*************************************************************************/ |
||||||
|
int32_t *reorder_minlpn_db(params_t *params, gk_graph_t *graph) |
||||||
|
{ |
||||||
|
int32_t i, ii, k, nvtxs, minlbl; |
||||||
|
ssize_t j, *xadj;
|
||||||
|
int32_t *adjncy, *labels, *perm, *dbucket; |
||||||
|
gk_i32kv_t *cand; |
||||||
|
|
||||||
|
nvtxs = graph->nvtxs; |
||||||
|
xadj = graph->xadj; |
||||||
|
adjncy = graph->adjncy; |
||||||
|
|
||||||
|
labels = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "labels")); |
||||||
|
perm = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "perm")); |
||||||
|
dbucket = gk_i32malloc(nvtxs, "dbucket"); |
||||||
|
|
||||||
|
for (i=0; i<nvtxs; i++) |
||||||
|
dbucket[i] = ((xadj[i+1]-xadj[i])>>3); |
||||||
|
|
||||||
|
for (k=0; k<params->niter; k++) { |
||||||
|
for (i=0; i<nvtxs; i++) { |
||||||
|
minlbl = labels[i]; |
||||||
|
for (j=xadj[i]; j<xadj[i+1]; j++) { |
||||||
|
if (dbucket[i] != dbucket[adjncy[j]]) |
||||||
|
continue; |
||||||
|
|
||||||
|
if (minlbl > labels[adjncy[j]]) |
||||||
|
minlbl = labels[adjncy[j]]; |
||||||
|
} |
||||||
|
labels[i] = minlbl; |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
cand = gk_i32kvmalloc(nvtxs, "cand"); |
||||||
|
for (i=0; i<nvtxs; i++) { |
||||||
|
cand[i].key = labels[i]; |
||||||
|
cand[i].val = i; |
||||||
|
} |
||||||
|
gk_i32kvsorti(nvtxs, cand); |
||||||
|
|
||||||
|
for (i=0; i<nvtxs; i++) { |
||||||
|
perm[cand[i].val] = i; |
||||||
|
//if (i>0 && cand[i].key != cand[i-1].key)
|
||||||
|
// printf("%10d %10d\n", i-1, cand[i-1].key);
|
||||||
|
} |
||||||
|
//printf("%10d %10d\n", i-1, cand[i-1].key);
|
||||||
|
|
||||||
|
gk_free((void **)&labels, &dbucket, &cand, LTERM); |
||||||
|
|
||||||
|
return perm; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function prints run parameters */ |
||||||
|
/*************************************************************************/ |
||||||
|
void print_init_info(params_t *params, gk_graph_t *graph) |
||||||
|
{ |
||||||
|
printf("*******************************************************************************\n"); |
||||||
|
printf(" gkgraph\n\n"); |
||||||
|
printf("Graph Information ----------------------------------------------------------\n"); |
||||||
|
printf(" input file=%s, [%d, %zd]\n",
|
||||||
|
params->infile, graph->nvtxs, graph->xadj[graph->nvtxs]); |
||||||
|
|
||||||
|
printf("\n"); |
||||||
|
printf("Options --------------------------------------------------------------------\n"); |
||||||
|
printf(" lnbits=%d, cnbits=%d, type=%d, niter=%d, lamda=%f, eps=%e\n", |
||||||
|
params->lnbits, params->cnbits, params->type, params->niter,
|
||||||
|
params->lamda, params->eps); |
||||||
|
|
||||||
|
printf("\n"); |
||||||
|
printf("Working... -----------------------------------------------------------------\n"); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function prints final statistics */ |
||||||
|
/*************************************************************************/ |
||||||
|
void print_final_info(params_t *params) |
||||||
|
{ |
||||||
|
printf("\n"); |
||||||
|
printf("Memory Usage Information -----------------------------------------------------\n"); |
||||||
|
printf(" Maximum memory used: %10zd bytes\n", (ssize_t) gk_GetMaxMemoryUsed()); |
||||||
|
printf(" Current memory used: %10zd bytes\n", (ssize_t) gk_GetCurMemoryUsed()); |
||||||
|
printf("********************************************************************************\n"); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This is the entry point of the command-line argument parser */ |
||||||
|
/*************************************************************************/ |
||||||
|
params_t *parse_cmdline(int argc, char *argv[]) |
||||||
|
{ |
||||||
|
int i; |
||||||
|
int c, option_index; |
||||||
|
params_t *params; |
||||||
|
|
||||||
|
params = (params_t *)gk_malloc(sizeof(params_t), "parse_cmdline: params"); |
||||||
|
|
||||||
|
/* initialize the params data structure */ |
||||||
|
params->lnbits = 6; |
||||||
|
params->cnbits = 13; |
||||||
|
params->type = 1; |
||||||
|
params->niter = 1; |
||||||
|
params->eps = 1e-10; |
||||||
|
params->lamda = 0.20; |
||||||
|
params->nosort = 0; |
||||||
|
params->write = 0; |
||||||
|
params->infile = NULL; |
||||||
|
|
||||||
|
|
||||||
|
/* Parse the command line arguments */ |
||||||
|
while ((c = gk_getopt_long_only(argc, argv, "", long_options, &option_index)) != -1) { |
||||||
|
switch (c) { |
||||||
|
case CMD_LNBITS: |
||||||
|
if (gk_optarg) params->lnbits = atoi(gk_optarg); |
||||||
|
break; |
||||||
|
case CMD_CNBITS: |
||||||
|
if (gk_optarg) params->cnbits = atoi(gk_optarg); |
||||||
|
break; |
||||||
|
case CMD_TYPE: |
||||||
|
if (gk_optarg) params->type = atoi(gk_optarg); |
||||||
|
break; |
||||||
|
case CMD_NITER: |
||||||
|
if (gk_optarg) params->niter = atoi(gk_optarg); |
||||||
|
break; |
||||||
|
case CMD_EPS: |
||||||
|
if (gk_optarg) params->eps = atof(gk_optarg); |
||||||
|
break; |
||||||
|
case CMD_LAMDA: |
||||||
|
if (gk_optarg) params->lamda = atof(gk_optarg); |
||||||
|
break; |
||||||
|
case CMD_NOSORT: |
||||||
|
params->nosort = 1; |
||||||
|
break; |
||||||
|
case CMD_WRITE: |
||||||
|
params->write = 1; |
||||||
|
break; |
||||||
|
|
||||||
|
case CMD_HELP: |
||||||
|
for (i=0; strlen(helpstr[i]) > 0; i++) |
||||||
|
printf("%s\n", helpstr[i]); |
||||||
|
exit(0); |
||||||
|
break; |
||||||
|
case '?': |
||||||
|
default: |
||||||
|
printf("Illegal command-line option(s)\nUse %s -help for a summary of the options.\n", argv[0]); |
||||||
|
exit(0); |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
if (argc-gk_optind != 1) { |
||||||
|
printf("Unrecognized parameters."); |
||||||
|
for (i=0; strlen(shorthelpstr[i]) > 0; i++) |
||||||
|
printf("%s\n", shorthelpstr[i]); |
||||||
|
exit(0); |
||||||
|
} |
||||||
|
|
||||||
|
params->infile = gk_strdup(argv[gk_optind++]); |
||||||
|
|
||||||
|
if (argc-gk_optind > 0)
|
||||||
|
params->outfile = gk_strdup(argv[gk_optind++]); |
||||||
|
else |
||||||
|
params->outfile = gk_strdup("gkgraph.out"); |
||||||
|
|
||||||
|
if (!gk_fexists(params->infile)) |
||||||
|
errexit("input file %s does not exist.\n", params->infile); |
||||||
|
|
||||||
|
return params; |
||||||
|
} |
||||||
|
|
||||||
@ -0,0 +1,346 @@ |
|||||||
|
/*!
|
||||||
|
\file gksort.c |
||||||
|
\brief Testing module for the various sorting routines in GKlib |
||||||
|
|
||||||
|
\date Started 4/4/2007 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: gksort.c 11058 2011-11-10 00:02:50Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
#define N 10000 |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Testing module for gk_?isort() routine */ |
||||||
|
/*************************************************************************/ |
||||||
|
void test_isort() |
||||||
|
{ |
||||||
|
gk_idx_t i; |
||||||
|
int array[N]; |
||||||
|
|
||||||
|
/* test the increasing sort */ |
||||||
|
printf("Testing iisort...\n"); |
||||||
|
for (i=0; i<N; i++) |
||||||
|
array[i] = RandomInRange(123432); |
||||||
|
|
||||||
|
gk_isorti(N, array); |
||||||
|
|
||||||
|
for (i=0; i<N-1; i++) { |
||||||
|
if (array[i] > array[i+1]) |
||||||
|
printf("gk_isorti error at index %jd [%d %d]\n", (intmax_t)i, array[i], array[i+1]); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/* test the decreasing sort */ |
||||||
|
printf("Testing disort...\n"); |
||||||
|
for (i=0; i<N; i++) |
||||||
|
array[i] = RandomInRange(123432); |
||||||
|
|
||||||
|
gk_isortd(N, array); |
||||||
|
|
||||||
|
for (i=0; i<N-1; i++) { |
||||||
|
if (array[i] < array[i+1]) |
||||||
|
printf("gk_isortd error at index %jd [%d %d]\n", (intmax_t)i, array[i], array[i+1]); |
||||||
|
} |
||||||
|
|
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Testing module for gk_?fsort() routine */ |
||||||
|
/*************************************************************************/ |
||||||
|
void test_fsort() |
||||||
|
{ |
||||||
|
gk_idx_t i; |
||||||
|
float array[N]; |
||||||
|
|
||||||
|
/* test the increasing sort */ |
||||||
|
printf("Testing ifsort...\n"); |
||||||
|
for (i=0; i<N; i++) |
||||||
|
array[i] = RandomInRange(123432)/(1.0+RandomInRange(645323)); |
||||||
|
|
||||||
|
gk_fsorti(N, array); |
||||||
|
|
||||||
|
for (i=0; i<N-1; i++) { |
||||||
|
if (array[i] > array[i+1]) |
||||||
|
printf("gk_fsorti error at index %jd [%f %f]\n", (intmax_t)i, array[i], array[i+1]); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/* test the decreasing sort */ |
||||||
|
printf("Testing dfsort...\n"); |
||||||
|
for (i=0; i<N; i++) |
||||||
|
array[i] = RandomInRange(123432)/(1.0+RandomInRange(645323)); |
||||||
|
|
||||||
|
gk_fsortd(N, array); |
||||||
|
|
||||||
|
for (i=0; i<N-1; i++) { |
||||||
|
if (array[i] < array[i+1]) |
||||||
|
printf("gk_fsortd error at index %jd [%f %f]\n", (intmax_t)i, array[i], array[i+1]); |
||||||
|
} |
||||||
|
|
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Testing module for gk_?idxsort() routine */ |
||||||
|
/*************************************************************************/ |
||||||
|
void test_idxsort() |
||||||
|
{ |
||||||
|
gk_idx_t i; |
||||||
|
gk_idx_t array[N]; |
||||||
|
|
||||||
|
/* test the increasing sort */ |
||||||
|
printf("Testing idxsorti...\n"); |
||||||
|
for (i=0; i<N; i++) |
||||||
|
array[i] = RandomInRange(123432); |
||||||
|
|
||||||
|
gk_idxsorti(N, array); |
||||||
|
|
||||||
|
for (i=0; i<N-1; i++) { |
||||||
|
if (array[i] > array[i+1]) |
||||||
|
printf("gk_idxsorti error at index %zd [%zd %zd]\n", (ssize_t)i, (ssize_t)array[i], (ssize_t)array[i+1]); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/* test the decreasing sort */ |
||||||
|
printf("Testing idxsortd...\n"); |
||||||
|
for (i=0; i<N; i++) |
||||||
|
array[i] = RandomInRange(123432); |
||||||
|
|
||||||
|
gk_idxsortd(N, array); |
||||||
|
|
||||||
|
for (i=0; i<N-1; i++) { |
||||||
|
if (array[i] < array[i+1]) |
||||||
|
printf("gk_idxsortd error at index %zd [%zd %zd]\n", (ssize_t)i, (ssize_t)array[i], (ssize_t)array[i+1]); |
||||||
|
} |
||||||
|
|
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Testing module for gk_?ikvsort() routine */ |
||||||
|
/*************************************************************************/ |
||||||
|
void test_ikvsort() |
||||||
|
{ |
||||||
|
gk_idx_t i; |
||||||
|
gk_ikv_t array[N]; |
||||||
|
|
||||||
|
/* test the increasing sort */ |
||||||
|
printf("Testing ikvsorti...\n"); |
||||||
|
for (i=0; i<N; i++) { |
||||||
|
array[i].key = RandomInRange(123432); |
||||||
|
array[i].val = i; |
||||||
|
} |
||||||
|
|
||||||
|
gk_ikvsorti(N, array); |
||||||
|
|
||||||
|
for (i=0; i<N-1; i++) { |
||||||
|
if (array[i].key > array[i+1].key) |
||||||
|
printf("gk_ikvsorti error at index %jd [%d %d] [%jd %jd]\n", (intmax_t)i, array[i].key, array[i+1].key, (intmax_t)array[i].val, (intmax_t)array[i+1].val); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/* test the decreasing sort */ |
||||||
|
printf("Testing ikvsortd...\n"); |
||||||
|
for (i=0; i<N; i++) { |
||||||
|
array[i].key = RandomInRange(123432); |
||||||
|
array[i].val = i; |
||||||
|
} |
||||||
|
|
||||||
|
gk_ikvsortd(N, array); |
||||||
|
|
||||||
|
for (i=0; i<N-1; i++) { |
||||||
|
if (array[i].key < array[i+1].key) |
||||||
|
printf("gk_ikvsortd error at index %jd [%d %d] [%jd %jd]\n", (intmax_t)i, array[i].key, array[i+1].key, (intmax_t)array[i].val, (intmax_t)array[i+1].val); |
||||||
|
} |
||||||
|
|
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Testing module for gk_?fkvsort() routine */ |
||||||
|
/*************************************************************************/ |
||||||
|
void test_fkvsort() |
||||||
|
{ |
||||||
|
gk_idx_t i; |
||||||
|
gk_fkv_t array[N]; |
||||||
|
|
||||||
|
/* test the increasing sort */ |
||||||
|
printf("Testing fkvsorti...\n"); |
||||||
|
for (i=0; i<N; i++) { |
||||||
|
array[i].key = RandomInRange(123432)/(1.0+RandomInRange(645323)); |
||||||
|
array[i].val = i; |
||||||
|
} |
||||||
|
|
||||||
|
gk_fkvsorti(N, array); |
||||||
|
|
||||||
|
for (i=0; i<N-1; i++) { |
||||||
|
if (array[i].key > array[i+1].key) |
||||||
|
printf("gk_fkvsorti error at index %jd [%f %f] [%jd %jd]\n", (intmax_t)i, array[i].key, array[i+1].key, (intmax_t)array[i].val, (intmax_t)array[i+1].val); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/* test the decreasing sort */ |
||||||
|
printf("Testing fkvsortd...\n"); |
||||||
|
for (i=0; i<N; i++) { |
||||||
|
array[i].key = RandomInRange(123432)/(1.0+RandomInRange(645323)); |
||||||
|
array[i].val = i; |
||||||
|
} |
||||||
|
|
||||||
|
gk_fkvsortd(N, array); |
||||||
|
|
||||||
|
for (i=0; i<N-1; i++) { |
||||||
|
if (array[i].key < array[i+1].key) |
||||||
|
printf("gk_fkvsortd error at index %jd [%f %f] [%jd %jd]\n", (intmax_t)i, array[i].key, array[i+1].key, (intmax_t)array[i].val, (intmax_t)array[i+1].val); |
||||||
|
} |
||||||
|
|
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Testing module for gk_?dkvsort() routine */ |
||||||
|
/*************************************************************************/ |
||||||
|
void test_dkvsort() |
||||||
|
{ |
||||||
|
gk_idx_t i; |
||||||
|
gk_dkv_t array[N]; |
||||||
|
|
||||||
|
/* test the increasing sort */ |
||||||
|
printf("Testing dkvsorti...\n"); |
||||||
|
for (i=0; i<N; i++) { |
||||||
|
array[i].key = RandomInRange(123432)/(1.0+RandomInRange(645323)); |
||||||
|
array[i].val = i; |
||||||
|
} |
||||||
|
|
||||||
|
gk_dkvsorti(N, array); |
||||||
|
|
||||||
|
for (i=0; i<N-1; i++) { |
||||||
|
if (array[i].key > array[i+1].key) |
||||||
|
printf("gk_dkvsorti error at index %jd [%lf %lf] [%jd %jd]\n", (intmax_t)i, array[i].key, array[i+1].key, (intmax_t)array[i].val, (intmax_t)array[i+1].val); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/* test the decreasing sort */ |
||||||
|
printf("Testing dkvsortd...\n"); |
||||||
|
for (i=0; i<N; i++) { |
||||||
|
array[i].key = RandomInRange(123432)/(1.0+RandomInRange(645323)); |
||||||
|
array[i].val = i; |
||||||
|
} |
||||||
|
|
||||||
|
gk_dkvsortd(N, array); |
||||||
|
|
||||||
|
for (i=0; i<N-1; i++) { |
||||||
|
if (array[i].key < array[i+1].key) |
||||||
|
printf("gk_dkvsortd error at index %jd [%lf %lf] [%jd %jd]\n", (intmax_t)i, array[i].key, array[i+1].key, (intmax_t)array[i].val, (intmax_t)array[i+1].val); |
||||||
|
} |
||||||
|
|
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Testing module for gk_?skvsort() routine */ |
||||||
|
/*************************************************************************/ |
||||||
|
void test_skvsort() |
||||||
|
{ |
||||||
|
gk_idx_t i; |
||||||
|
gk_skv_t array[N]; |
||||||
|
char line[256]; |
||||||
|
|
||||||
|
/* test the increasing sort */ |
||||||
|
printf("Testing skvsorti...\n"); |
||||||
|
for (i=0; i<N; i++) { |
||||||
|
sprintf(line, "%d", RandomInRange(123432)); |
||||||
|
array[i].key = gk_strdup(line); |
||||||
|
array[i].val = i; |
||||||
|
} |
||||||
|
|
||||||
|
gk_skvsorti(N, array); |
||||||
|
|
||||||
|
for (i=0; i<N-1; i++) { |
||||||
|
if (strcmp(array[i].key, array[i+1].key) > 0) |
||||||
|
printf("gk_skvsorti error at index %jd [%s %s] [%jd %jd]\n", (intmax_t)i, array[i].key, array[i+1].key, (intmax_t)array[i].val, (intmax_t)array[i+1].val); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/* test the decreasing sort */ |
||||||
|
printf("Testing skvsortd...\n"); |
||||||
|
for (i=0; i<N; i++) { |
||||||
|
sprintf(line, "%d", RandomInRange(123432)); |
||||||
|
array[i].key = gk_strdup(line); |
||||||
|
array[i].val = i; |
||||||
|
} |
||||||
|
|
||||||
|
gk_skvsortd(N, array); |
||||||
|
|
||||||
|
for (i=0; i<N-1; i++) { |
||||||
|
/*printf("%s\n", array[i].key);*/ |
||||||
|
if (strcmp(array[i].key, array[i+1].key) < 0) |
||||||
|
printf("gk_skvsortd error at index %jd [%s %s] [%jd %jd]\n", (intmax_t)i, array[i].key, array[i+1].key, (intmax_t)array[i].val, (intmax_t)array[i+1].val); |
||||||
|
} |
||||||
|
|
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Testing module for gk_?idxkvsort() routine */ |
||||||
|
/*************************************************************************/ |
||||||
|
void test_idxkvsort() |
||||||
|
{ |
||||||
|
gk_idx_t i; |
||||||
|
gk_idxkv_t array[N]; |
||||||
|
|
||||||
|
/* test the increasing sort */ |
||||||
|
printf("Testing idxkvsorti...\n"); |
||||||
|
for (i=0; i<N; i++) { |
||||||
|
array[i].key = RandomInRange(123432); |
||||||
|
array[i].val = i; |
||||||
|
} |
||||||
|
|
||||||
|
gk_idxkvsorti(N, array); |
||||||
|
|
||||||
|
for (i=0; i<N-1; i++) { |
||||||
|
if (array[i].key > array[i+1].key) |
||||||
|
printf("gk_idxkvsorti error at index %zd [%zd %zd] [%zd %zd]\n",
|
||||||
|
(ssize_t)i, (ssize_t)array[i].key, (ssize_t)array[i+1].key,
|
||||||
|
(ssize_t)array[i].val, (ssize_t)array[i+1].val); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/* test the decreasing sort */ |
||||||
|
printf("Testing idxkvsortd...\n"); |
||||||
|
for (i=0; i<N; i++) { |
||||||
|
array[i].key = RandomInRange(123432); |
||||||
|
array[i].val = i; |
||||||
|
} |
||||||
|
|
||||||
|
gk_idxkvsortd(N, array); |
||||||
|
|
||||||
|
for (i=0; i<N-1; i++) { |
||||||
|
if (array[i].key < array[i+1].key) |
||||||
|
printf("gk_idxkvsortd error at index %zd [%zd %zd] [%zd %zd]\n",
|
||||||
|
(ssize_t)i, (ssize_t)array[i].key, (ssize_t)array[i+1].key,
|
||||||
|
(ssize_t)array[i].val, (ssize_t)array[i+1].val); |
||||||
|
} |
||||||
|
|
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
int main() |
||||||
|
{ |
||||||
|
test_isort(); |
||||||
|
test_fsort(); |
||||||
|
test_idxsort(); |
||||||
|
|
||||||
|
test_ikvsort(); |
||||||
|
test_fkvsort(); |
||||||
|
test_dkvsort(); |
||||||
|
test_skvsort(); |
||||||
|
test_idxkvsort(); |
||||||
|
} |
||||||
|
|
||||||
@ -0,0 +1,268 @@ |
|||||||
|
/*!
|
||||||
|
\file
|
||||||
|
\brief A program to test various implementations for unique. |
||||||
|
|
||||||
|
\date 10/8/2020 |
||||||
|
\author George |
||||||
|
*/ |
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Data structures for the code */ |
||||||
|
/*************************************************************************/ |
||||||
|
typedef struct { |
||||||
|
ssize_t length, dupfactor; |
||||||
|
} params_t; |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Constants */ |
||||||
|
/*************************************************************************/ |
||||||
|
#define CMD_HELP 10 |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Local variables */ |
||||||
|
/*************************************************************************/ |
||||||
|
static struct gk_option long_options[] = { |
||||||
|
{"help", 0, 0, CMD_HELP}, |
||||||
|
{0, 0, 0, 0} |
||||||
|
}; |
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------------*/ |
||||||
|
/* Mini help */ |
||||||
|
/*-------------------------------------------------------------------*/ |
||||||
|
static char helpstr[][100] = { |
||||||
|
" ", |
||||||
|
"Usage: gkuniq length dupfactor", |
||||||
|
" ", |
||||||
|
" Required parameters", |
||||||
|
" length", |
||||||
|
" The length of the base array.", |
||||||
|
" ", |
||||||
|
" dupfactor", |
||||||
|
" The number of times the initial array is replicated.", |
||||||
|
" ", |
||||||
|
" Optional parameters", |
||||||
|
" -help", |
||||||
|
" Prints this message.", |
||||||
|
"" |
||||||
|
}; |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Function prototypes */ |
||||||
|
/*************************************************************************/ |
||||||
|
params_t *parse_cmdline(int argc, char *argv[]); |
||||||
|
int unique_v1(int n, int *input, int *output); |
||||||
|
int unique_v2(int n, int *input, int *output); |
||||||
|
int unique_v3(int n, int *input, int *output, int *r_maxsize, int **r_hmap); |
||||||
|
void mem_flush(const void *p, unsigned int allocation_size); |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! A function to flush the cache associated with an array */ |
||||||
|
/**************************************************************************/ |
||||||
|
void mem_flush(const void *p, unsigned int allocation_size) |
||||||
|
{ |
||||||
|
#ifndef NO_X86 |
||||||
|
const size_t cache_line = 64; |
||||||
|
const char *cp = (const char *)p; |
||||||
|
size_t i = 0; |
||||||
|
|
||||||
|
if (p == NULL || allocation_size <= 0) |
||||||
|
return; |
||||||
|
|
||||||
|
for (i = 0; i < allocation_size; i += cache_line) { |
||||||
|
__asm__ volatile("clflush (%0)\n\t" |
||||||
|
: |
||||||
|
: "r"(&cp[i]) |
||||||
|
: "memory"); |
||||||
|
} |
||||||
|
|
||||||
|
__asm__ volatile("sfence\n\t" |
||||||
|
: |
||||||
|
: |
||||||
|
: "memory"); |
||||||
|
#endif |
||||||
|
} |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! the entry point */ |
||||||
|
/**************************************************************************/ |
||||||
|
int main(int argc, char *argv[]) |
||||||
|
{ |
||||||
|
int i, j, k; |
||||||
|
params_t *params; |
||||||
|
double tmr; |
||||||
|
int n, nunique, *input, *output; |
||||||
|
int maxsize=0, *hmap=NULL;
|
||||||
|
|
||||||
|
params = parse_cmdline(argc, argv); |
||||||
|
|
||||||
|
/* create the input data */ |
||||||
|
n = params->length*params->dupfactor; |
||||||
|
input = gk_imalloc(n, "input"); |
||||||
|
output = gk_imalloc(n, "output"); |
||||||
|
for (i=0; i<params->length; i++) { |
||||||
|
k = RandomInRange(n); |
||||||
|
for (j=0; j<params->dupfactor; j++) |
||||||
|
input[j*params->length+i] = k; |
||||||
|
} |
||||||
|
|
||||||
|
gk_clearwctimer(tmr); |
||||||
|
gk_startwctimer(tmr); |
||||||
|
mem_flush(input, n*sizeof(int)); |
||||||
|
mem_flush(output, n*sizeof(int)); |
||||||
|
nunique = unique_v1(n, input, output); |
||||||
|
gk_stopwctimer(tmr); |
||||||
|
printf(" V1: nunique: %d, timer: %.5lf\n", nunique, gk_getwctimer(tmr)); |
||||||
|
|
||||||
|
gk_clearwctimer(tmr); |
||||||
|
gk_startwctimer(tmr); |
||||||
|
mem_flush(input, n*sizeof(int)); |
||||||
|
mem_flush(output, n*sizeof(int)); |
||||||
|
nunique = unique_v2(n, input, output); |
||||||
|
gk_stopwctimer(tmr); |
||||||
|
printf(" V2: nunique: %d, timer: %.5lf\n", nunique, gk_getwctimer(tmr)); |
||||||
|
|
||||||
|
gk_clearwctimer(tmr); |
||||||
|
gk_startwctimer(tmr); |
||||||
|
mem_flush(input, n*sizeof(int)); |
||||||
|
mem_flush(output, n*sizeof(int)); |
||||||
|
nunique = unique_v3(n, input, output, &maxsize, &hmap); |
||||||
|
gk_stopwctimer(tmr); |
||||||
|
printf("V3c: nunique: %d, timer: %.5lf\n", nunique, gk_getwctimer(tmr)); |
||||||
|
|
||||||
|
gk_clearwctimer(tmr); |
||||||
|
gk_startwctimer(tmr); |
||||||
|
mem_flush(input, n*sizeof(int)); |
||||||
|
mem_flush(output, n*sizeof(int)); |
||||||
|
nunique = unique_v3(n, input, output, &maxsize, &hmap); |
||||||
|
gk_stopwctimer(tmr); |
||||||
|
printf("V3w: nunique: %d, timer: %.5lf\n", nunique, gk_getwctimer(tmr)); |
||||||
|
|
||||||
|
gk_free((void **)&input, &output, &hmap, LTERM); |
||||||
|
|
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This is the entry point of the command-line argument parser */ |
||||||
|
/*************************************************************************/ |
||||||
|
params_t *parse_cmdline(int argc, char *argv[]) |
||||||
|
{ |
||||||
|
int i; |
||||||
|
int c, option_index; |
||||||
|
params_t *params; |
||||||
|
|
||||||
|
params = (params_t *)gk_malloc(sizeof(params_t), "parse_cmdline: params"); |
||||||
|
|
||||||
|
/* Parse the command line arguments */ |
||||||
|
while ((c = gk_getopt_long_only(argc, argv, "", long_options, &option_index)) != -1) { |
||||||
|
switch (c) { |
||||||
|
case CMD_HELP: |
||||||
|
for (i=0; strlen(helpstr[i]) > 0; i++) |
||||||
|
printf("%s\n", helpstr[i]); |
||||||
|
exit(0); |
||||||
|
break; |
||||||
|
case '?': |
||||||
|
default: |
||||||
|
printf("Illegal command-line option(s)\nUse %s -help for a summary of the options.\n", argv[0]); |
||||||
|
exit(0); |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
if (argc-gk_optind != 2) { |
||||||
|
printf("Unrecognized parameters."); |
||||||
|
for (i=0; strlen(helpstr[i]) > 0; i++) |
||||||
|
printf("%s\n", helpstr[i]); |
||||||
|
exit(0); |
||||||
|
} |
||||||
|
|
||||||
|
params->length = atoi(argv[gk_optind++]); |
||||||
|
params->dupfactor = atoi(argv[gk_optind++]); |
||||||
|
|
||||||
|
return params; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! gklib-sort based approach */ |
||||||
|
/*************************************************************************/ |
||||||
|
int unique_v1(int n, int *input, int *output) |
||||||
|
{ |
||||||
|
int i, j; |
||||||
|
|
||||||
|
gk_isorti(n, input); |
||||||
|
|
||||||
|
output[0] = input[0]; |
||||||
|
for (j=0, i=1; i<n; i++) { |
||||||
|
if (output[j] != input[i])
|
||||||
|
output[++j] = input[i]; |
||||||
|
} |
||||||
|
return j+1; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! hash-table based approach */ |
||||||
|
/*************************************************************************/ |
||||||
|
int unique_v2(int n, int *input, int *output) |
||||||
|
{ |
||||||
|
int i, j, k, nuniq, size, mask; |
||||||
|
int *hmap; |
||||||
|
|
||||||
|
for (size=1; size<2*n; size*=2); |
||||||
|
mask = size-1; |
||||||
|
//printf("size: %d, mask: %x\n", size, mask);
|
||||||
|
hmap = gk_ismalloc(size, -1, "hmap"); |
||||||
|
|
||||||
|
for (nuniq=0, i=0; i<n; i++) { |
||||||
|
k = input[i]; |
||||||
|
for (j=(k&mask); hmap[j]!=-1 && hmap[j]!=k; j=((j+1)&mask)); |
||||||
|
if (hmap[j] == -1) { |
||||||
|
hmap[j] = k; |
||||||
|
output[nuniq++] = k; |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
gk_free((void **)&hmap, LTERM); |
||||||
|
return nuniq; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! hash-table based approach, where the htable is most likely pre-allocated */ |
||||||
|
/*************************************************************************/ |
||||||
|
int unique_v3(int n, int *input, int *output, int *r_maxsize, int **r_hmap) |
||||||
|
{ |
||||||
|
int i, j, k, nuniq, size, mask; |
||||||
|
int *hmap; |
||||||
|
|
||||||
|
for (size=1; size<2*n; size*=2); |
||||||
|
mask = size-1; |
||||||
|
//printf("size: %d, mask: %x\n", size, mask);
|
||||||
|
if (size > *r_maxsize) { |
||||||
|
gk_free((void **)r_hmap, LTERM); |
||||||
|
hmap = *r_hmap = gk_ismalloc(size, -1, "hmap"); |
||||||
|
*r_maxsize = size; |
||||||
|
} |
||||||
|
else { |
||||||
|
hmap = *r_hmap; |
||||||
|
gk_iset(size, -1, hmap); |
||||||
|
} |
||||||
|
|
||||||
|
for (nuniq=0, i=0; i<n; i++) { |
||||||
|
k = input[i]; |
||||||
|
for (j=(k&mask); hmap[j]!=-1 && hmap[j]!=k; j=((j+1)&mask)); |
||||||
|
if (hmap[j] == -1) { |
||||||
|
hmap[j] = k; |
||||||
|
output[nuniq++] = k; |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
return nuniq; |
||||||
|
} |
||||||
@ -0,0 +1,256 @@ |
|||||||
|
/*!
|
||||||
|
\file
|
||||||
|
\brief A simple program to create multiple copies of an input matrix. |
||||||
|
|
||||||
|
\date 5/30/2013 |
||||||
|
\author George |
||||||
|
\version \verbatim $Id: grKx.c 17699 2014-09-27 18:05:31Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Data structures for the code */ |
||||||
|
/*************************************************************************/ |
||||||
|
typedef struct { |
||||||
|
int inf, outf; |
||||||
|
int numbering; /* input numbering (output when applicable) */ |
||||||
|
int readvals; /* input values (output when applicable) */ |
||||||
|
int writevals; /* output values */ |
||||||
|
int rshuf, cshuf; /* random shuffle of rows/columns */ |
||||||
|
int symmetric; /* a symmetric shuffle */ |
||||||
|
int ncopies; /* the copies of the graph to create */ |
||||||
|
char *infile; /* input file */ |
||||||
|
char *outfile; /* output file */ |
||||||
|
} params_t; |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Constants */ |
||||||
|
/*************************************************************************/ |
||||||
|
#define CMD_NUMONE 1 |
||||||
|
#define CMD_NOREADVALS 2 |
||||||
|
#define CMD_NOWRITEVALS 3 |
||||||
|
#define CMD_RSHUF 4 |
||||||
|
#define CMD_CSHUF 5 |
||||||
|
#define CMD_SYMMETRIC 6 |
||||||
|
#define CMD_HELP 100 |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Local variables */ |
||||||
|
/*************************************************************************/ |
||||||
|
static struct gk_option long_options[] = { |
||||||
|
{"numone", 0, 0, CMD_NUMONE}, |
||||||
|
{"noreadvals", 0, 0, CMD_NOREADVALS}, |
||||||
|
{"nowritevals", 0, 0, CMD_NOWRITEVALS}, |
||||||
|
{"rshuf", 0, 0, CMD_RSHUF}, |
||||||
|
{"cshuf", 0, 0, CMD_CSHUF}, |
||||||
|
{"symmetric", 0, 0, CMD_SYMMETRIC}, |
||||||
|
{"help", 0, 0, CMD_HELP}, |
||||||
|
{0, 0, 0, 0} |
||||||
|
}; |
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------------*/ |
||||||
|
/* Mini help */ |
||||||
|
/*-------------------------------------------------------------------*/ |
||||||
|
static char helpstr[][100] = { |
||||||
|
" ", |
||||||
|
"Usage: grKx [options] <infile> <inf> <outfile> <outf> <ncopies>", |
||||||
|
" ", |
||||||
|
" Required parameters", |
||||||
|
" infile, outfile", |
||||||
|
" The name of the input/output CSR file.", |
||||||
|
" ", |
||||||
|
" inf/outf", |
||||||
|
" The format of the input/output file.", |
||||||
|
" Supported values are:", |
||||||
|
" 1 GK_CSR_FMT_CLUTO", |
||||||
|
" 2 GK_CSR_FMT_CSR", |
||||||
|
" 3 GK_CSR_FMT_METIS", |
||||||
|
" 4 GK_CSR_FMT_BINROW", |
||||||
|
" 6 GK_CSR_FMT_IJV", |
||||||
|
" 7 GK_CSR_FMT_BIJV", |
||||||
|
" ", |
||||||
|
" Optional parameters", |
||||||
|
" -numone", |
||||||
|
" Specifies that the numbering of the input file starts from 1. ", |
||||||
|
" It only applies to CSR/IJV formats.", |
||||||
|
" ", |
||||||
|
" -nowritevals", |
||||||
|
" Specifies that no values will be output.", |
||||||
|
" ", |
||||||
|
" -noreadvals", |
||||||
|
" Specifies that the values will not be read when applicable.", |
||||||
|
" ", |
||||||
|
" -rshuf", |
||||||
|
" Specifies that the rows will be randmly shuffled prior to output.", |
||||||
|
" ", |
||||||
|
" -cshuf", |
||||||
|
" Specifies that the columns will be randmly shuffled prior to output.", |
||||||
|
" ", |
||||||
|
" -symmetric", |
||||||
|
" Specifies that the row+column shuffling will be symmetric.", |
||||||
|
" ", |
||||||
|
" -help", |
||||||
|
" Prints this message.", |
||||||
|
"" |
||||||
|
}; |
||||||
|
|
||||||
|
static char shorthelpstr[][100] = { |
||||||
|
" ", |
||||||
|
" Usage: grKx [options] <infile> <inf> <outfile> <outf> <ncopies>", |
||||||
|
" use 'csrconv -help' for a summary of the options.", |
||||||
|
"" |
||||||
|
}; |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This is the entry point of the command-line argument parser */ |
||||||
|
/*************************************************************************/ |
||||||
|
params_t *parse_cmdline(int argc, char *argv[]) |
||||||
|
{ |
||||||
|
int i; |
||||||
|
int c, option_index; |
||||||
|
params_t *params; |
||||||
|
|
||||||
|
params = (params_t *)gk_malloc(sizeof(params_t), "parse_cmdline: params"); |
||||||
|
|
||||||
|
/* initialize the params data structure */ |
||||||
|
params->numbering = 0; |
||||||
|
params->readvals = 1; |
||||||
|
params->writevals = 1; |
||||||
|
params->rshuf = 0; |
||||||
|
params->cshuf = 0; |
||||||
|
params->symmetric = 0; |
||||||
|
|
||||||
|
params->inf = -1; |
||||||
|
params->outf = -1; |
||||||
|
params->infile = NULL; |
||||||
|
params->outfile = NULL; |
||||||
|
|
||||||
|
|
||||||
|
/* Parse the command line arguments */ |
||||||
|
while ((c = gk_getopt_long_only(argc, argv, "", long_options, &option_index)) != -1) { |
||||||
|
switch (c) { |
||||||
|
case CMD_NUMONE: |
||||||
|
params->numbering = 1; |
||||||
|
break; |
||||||
|
case CMD_NOREADVALS: |
||||||
|
params->readvals = 0; |
||||||
|
break; |
||||||
|
case CMD_NOWRITEVALS: |
||||||
|
params->writevals = 0; |
||||||
|
break; |
||||||
|
case CMD_RSHUF: |
||||||
|
params->rshuf = 1; |
||||||
|
break; |
||||||
|
case CMD_CSHUF: |
||||||
|
params->cshuf = 1; |
||||||
|
break; |
||||||
|
case CMD_SYMMETRIC: |
||||||
|
params->symmetric = 1; |
||||||
|
break; |
||||||
|
|
||||||
|
case CMD_HELP: |
||||||
|
for (i=0; strlen(helpstr[i]) > 0; i++) |
||||||
|
printf("%s\n", helpstr[i]); |
||||||
|
exit(0); |
||||||
|
break; |
||||||
|
case '?': |
||||||
|
default: |
||||||
|
printf("Illegal command-line option(s)\nUse %s -help for a summary of the options.\n", argv[0]); |
||||||
|
exit(0); |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
if (argc-gk_optind != 5) { |
||||||
|
printf("Unrecognized parameters."); |
||||||
|
for (i=0; strlen(shorthelpstr[i]) > 0; i++) |
||||||
|
printf("%s\n", shorthelpstr[i]); |
||||||
|
exit(0); |
||||||
|
} |
||||||
|
|
||||||
|
params->infile = gk_strdup(argv[gk_optind++]); |
||||||
|
params->inf = atoi(argv[gk_optind++]); |
||||||
|
params->outfile = gk_strdup(argv[gk_optind++]); |
||||||
|
params->outf = atoi(argv[gk_optind++]); |
||||||
|
params->ncopies = atoi(argv[gk_optind++]); |
||||||
|
|
||||||
|
if (!gk_fexists(params->infile)) |
||||||
|
errexit("input file %s does not exist.\n", params->infile); |
||||||
|
|
||||||
|
return params; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! the entry point */ |
||||||
|
/**************************************************************************/ |
||||||
|
int main(int argc, char *argv[]) |
||||||
|
{ |
||||||
|
ssize_t i, j, k, knnz, nrows, ncols, ncopies; |
||||||
|
int what; |
||||||
|
params_t *params; |
||||||
|
gk_csr_t *mat, *kmat, *smat; |
||||||
|
|
||||||
|
/* get command-line options */ |
||||||
|
params = parse_cmdline(argc, argv); |
||||||
|
|
||||||
|
/* read the data */ |
||||||
|
mat = gk_csr_Read(params->infile, params->inf, params->readvals, params->numbering); |
||||||
|
|
||||||
|
/* create the copies */ |
||||||
|
ncopies = params->ncopies; |
||||||
|
|
||||||
|
nrows = mat->nrows; |
||||||
|
ncols = mat->ncols; |
||||||
|
knnz = mat->rowptr[nrows]*ncopies; |
||||||
|
|
||||||
|
kmat = gk_csr_Create(); |
||||||
|
kmat->nrows = nrows*ncopies; |
||||||
|
kmat->ncols = ncols*ncopies; |
||||||
|
kmat->rowptr = gk_zmalloc(kmat->nrows+1, "rowptr"); |
||||||
|
kmat->rowind = gk_imalloc(knnz, "rowind"); |
||||||
|
if (mat->rowval) |
||||||
|
kmat->rowval = gk_fmalloc(knnz, "rowval"); |
||||||
|
|
||||||
|
kmat->rowptr[0] = knnz = 0; |
||||||
|
for (k=0; k<ncopies; k++) { |
||||||
|
for (i=0; i<nrows; i++) { |
||||||
|
for (j=mat->rowptr[i]; j<mat->rowptr[i+1]; j++, knnz++) { |
||||||
|
kmat->rowind[knnz] = mat->rowind[j] + k*ncols; |
||||||
|
if (mat->rowval) |
||||||
|
kmat->rowval[knnz] = mat->rowval[j]; |
||||||
|
} |
||||||
|
kmat->rowptr[k*nrows+i+1] = knnz; |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
gk_csr_Free(&mat); |
||||||
|
mat = kmat; |
||||||
|
|
||||||
|
|
||||||
|
if (params->rshuf || params->cshuf) { |
||||||
|
if (params->rshuf && params->cshuf) |
||||||
|
what = GK_CSR_ROWCOL; |
||||||
|
else if (params->rshuf) |
||||||
|
what = GK_CSR_ROW; |
||||||
|
else |
||||||
|
what = GK_CSR_COL; |
||||||
|
|
||||||
|
smat = gk_csr_Shuffle(mat, what, params->symmetric); |
||||||
|
gk_csr_Free(&mat); |
||||||
|
mat = smat; |
||||||
|
} |
||||||
|
|
||||||
|
if (params->writevals && mat->rowval == NULL)
|
||||||
|
mat->rowval = gk_fsmalloc(mat->rowptr[mat->nrows], 1.0, "mat->rowval"); |
||||||
|
|
||||||
|
gk_csr_Write(mat, params->outfile, params->outf, params->writevals, 0); |
||||||
|
|
||||||
|
gk_csr_Free(&mat); |
||||||
|
|
||||||
|
} |
||||||
|
|
||||||
@ -0,0 +1,304 @@ |
|||||||
|
/*!
|
||||||
|
\file
|
||||||
|
\brief It takes as input two CSR matrices and finds for each row of the
|
||||||
|
first matrix the most similar rows in the second matrix. |
||||||
|
|
||||||
|
\date 9/27/2014 |
||||||
|
\author George |
||||||
|
\version \verbatim $Id: m2mnbrs.c 17699 2014-09-27 18:05:31Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Data structures for the code */ |
||||||
|
/*************************************************************************/ |
||||||
|
typedef struct { |
||||||
|
int simtype; /*!< The similarity type to use */ |
||||||
|
int nnbrs; /*!< The maximum number of nearest neighbots to output */ |
||||||
|
float minsim; /*!< The minimum similarity to use for keeping neighbors */ |
||||||
|
|
||||||
|
int verbosity; /*!< The reporting verbosity level */ |
||||||
|
|
||||||
|
char *qfile; /*!< The file storing the query documents */ |
||||||
|
char *cfile; /*!< The file storing the collection documents */ |
||||||
|
char *outfile; /*!< The file where the output will be stored */ |
||||||
|
|
||||||
|
/* timers */ |
||||||
|
double timer_global; |
||||||
|
double timer_1; |
||||||
|
double timer_2; |
||||||
|
double timer_3; |
||||||
|
double timer_4; |
||||||
|
} params_t; |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Constants */ |
||||||
|
/*************************************************************************/ |
||||||
|
/* Versions */ |
||||||
|
#define VER_MAJOR 0 |
||||||
|
#define VER_MINOR 1 |
||||||
|
#define VER_SUBMINOR 0 |
||||||
|
|
||||||
|
/* Command-line option codes */ |
||||||
|
#define CMD_SIMTYPE 10 |
||||||
|
#define CMD_NNBRS 20 |
||||||
|
#define CMD_MINSIM 22 |
||||||
|
#define CMD_VERBOSITY 70 |
||||||
|
#define CMD_HELP 100 |
||||||
|
|
||||||
|
/* The text labels for the different simtypes */ |
||||||
|
static char simtypenames[][10] = {"", "dotp", "cos", "jac", ""}; |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Local variables */ |
||||||
|
/*************************************************************************/ |
||||||
|
static struct gk_option long_options[] = { |
||||||
|
{"simtype", 1, 0, CMD_SIMTYPE}, |
||||||
|
{"nnbrs", 1, 0, CMD_NNBRS}, |
||||||
|
{"minsim", 1, 0, CMD_MINSIM}, |
||||||
|
{"verbosity", 1, 0, CMD_VERBOSITY}, |
||||||
|
|
||||||
|
{"help", 0, 0, CMD_HELP}, |
||||||
|
{0, 0, 0, 0} |
||||||
|
}; |
||||||
|
|
||||||
|
static gk_StringMap_t simtype_options[] = { |
||||||
|
{"cos", GK_CSR_COS}, |
||||||
|
{"jac", GK_CSR_JAC}, |
||||||
|
{NULL, 0} |
||||||
|
}; |
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------------
|
||||||
|
* Mini help |
||||||
|
*-------------------------------------------------------------------*/ |
||||||
|
static char helpstr[][100] = |
||||||
|
{ |
||||||
|
" ", |
||||||
|
"Usage: m2mnbrs [options] qfile cfile [outfile]", |
||||||
|
" ", |
||||||
|
" Options", |
||||||
|
" -simtype=string", |
||||||
|
" Specifies the type of similarity to use. Possible values are:", |
||||||
|
" cos - Cosine similarity", |
||||||
|
" jac - Jacquard similarity [default]",
|
||||||
|
" ", |
||||||
|
" -nnbrs=int", |
||||||
|
" Specifies the maximum number of nearest neighbors.", |
||||||
|
" A value of -1 indicates that all neighbors will be considered.", |
||||||
|
" Default value is 100.", |
||||||
|
" ", |
||||||
|
" -minsim=float", |
||||||
|
" The minimum allowed similarity between neighbors. ", |
||||||
|
" Default value is .25.", |
||||||
|
" ", |
||||||
|
" -verbosity=int", |
||||||
|
" Specifies the level of debugging information to be displayed.", |
||||||
|
" Default value is 0.", |
||||||
|
" ", |
||||||
|
" -help", |
||||||
|
" Prints this message.", |
||||||
|
"" |
||||||
|
}; |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Function prototypes */ |
||||||
|
/*************************************************************************/ |
||||||
|
params_t *parse_cmdline(int argc, char *argv[]); |
||||||
|
void FindNeighbors(params_t *params, gk_csr_t *qmat, gk_csr_t *cmat); |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This is the entry point of the command-line argument parser */ |
||||||
|
/*************************************************************************/ |
||||||
|
params_t *parse_cmdline(int argc, char *argv[]) |
||||||
|
{ |
||||||
|
int i; |
||||||
|
int c, option_index; |
||||||
|
params_t *params; |
||||||
|
|
||||||
|
params = (params_t *)gk_malloc(sizeof(params_t), "parse_cmdline: params"); |
||||||
|
|
||||||
|
/* initialize the params data structure */ |
||||||
|
params->simtype = GK_CSR_JAC; |
||||||
|
params->nnbrs = 100; |
||||||
|
params->minsim = .25; |
||||||
|
params->verbosity = -1; |
||||||
|
params->qfile = NULL; |
||||||
|
params->cfile = NULL; |
||||||
|
params->outfile = NULL; |
||||||
|
|
||||||
|
|
||||||
|
/* Parse the command line arguments */ |
||||||
|
while ((c = gk_getopt_long_only(argc, argv, "", long_options, &option_index)) != -1) { |
||||||
|
switch (c) { |
||||||
|
case CMD_SIMTYPE: |
||||||
|
if (gk_optarg) { |
||||||
|
if ((params->simtype = gk_GetStringID(simtype_options, gk_optarg)) == -1) |
||||||
|
errexit("Invalid simtype of %s.\n", gk_optarg); |
||||||
|
} |
||||||
|
break; |
||||||
|
|
||||||
|
case CMD_NNBRS: |
||||||
|
if (gk_optarg) params->nnbrs = atoi(gk_optarg); |
||||||
|
break; |
||||||
|
|
||||||
|
case CMD_MINSIM: |
||||||
|
if (gk_optarg) params->minsim = atof(gk_optarg); |
||||||
|
break; |
||||||
|
|
||||||
|
case CMD_VERBOSITY: |
||||||
|
if (gk_optarg) params->verbosity = atoi(gk_optarg); |
||||||
|
break; |
||||||
|
|
||||||
|
case CMD_HELP: |
||||||
|
for (i=0; strlen(helpstr[i]) > 0; i++) |
||||||
|
printf("%s\n", helpstr[i]); |
||||||
|
exit(EXIT_SUCCESS); |
||||||
|
break; |
||||||
|
|
||||||
|
case '?': |
||||||
|
default: |
||||||
|
printf("Illegal command-line option(s)\nUse %s -help for a summary of the options.\n", argv[0]); |
||||||
|
exit(EXIT_FAILURE); |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
/* Get the input/output file info */ |
||||||
|
if (argc-gk_optind < 1) { |
||||||
|
printf("Missing input/output file info.\n Use %s -help for a summary of the options.\n", argv[0]); |
||||||
|
exit(EXIT_FAILURE); |
||||||
|
} |
||||||
|
|
||||||
|
params->qfile = gk_strdup(argv[gk_optind++]); |
||||||
|
params->cfile = gk_strdup(argv[gk_optind++]); |
||||||
|
params->outfile = (gk_optind < argc ? gk_strdup(argv[gk_optind++]) : NULL); |
||||||
|
|
||||||
|
if (!gk_fexists(params->qfile)) |
||||||
|
errexit("input file %s does not exist.\n", params->qfile); |
||||||
|
if (!gk_fexists(params->cfile)) |
||||||
|
errexit("input file %s does not exist.\n", params->cfile); |
||||||
|
|
||||||
|
return params; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This is the entry point of the program */ |
||||||
|
/**************************************************************************/ |
||||||
|
int main(int argc, char *argv[]) |
||||||
|
{ |
||||||
|
params_t *params; |
||||||
|
gk_csr_t *qmat, *cmat; |
||||||
|
int rc = EXIT_SUCCESS; |
||||||
|
|
||||||
|
params = parse_cmdline(argc, argv); |
||||||
|
|
||||||
|
qmat = gk_csr_Read(params->qfile, GK_CSR_FMT_CSR, 1, 0); |
||||||
|
cmat = gk_csr_Read(params->cfile, GK_CSR_FMT_CSR, 1, 0); |
||||||
|
|
||||||
|
|
||||||
|
printf("********************************************************************************\n"); |
||||||
|
printf("sd (%d.%d.%d) Copyright 2014, GK.\n", VER_MAJOR, VER_MINOR, VER_SUBMINOR); |
||||||
|
printf(" simtype=%s, nnbrs=%d, minsim=%.2f\n", |
||||||
|
simtypenames[params->simtype], params->nnbrs, params->minsim); |
||||||
|
printf(" qfile=%s, nrows=%d, ncols=%d, nnz=%zd\n", |
||||||
|
params->qfile, qmat->nrows, qmat->ncols, qmat->rowptr[qmat->nrows]); |
||||||
|
printf(" cfile=%s, nrows=%d, ncols=%d, nnz=%zd\n", |
||||||
|
params->cfile, cmat->nrows, cmat->ncols, cmat->rowptr[cmat->nrows]); |
||||||
|
|
||||||
|
gk_clearwctimer(params->timer_global); |
||||||
|
gk_clearwctimer(params->timer_1); |
||||||
|
gk_clearwctimer(params->timer_2); |
||||||
|
gk_clearwctimer(params->timer_3); |
||||||
|
gk_clearwctimer(params->timer_4); |
||||||
|
|
||||||
|
gk_startwctimer(params->timer_global); |
||||||
|
|
||||||
|
FindNeighbors(params, qmat, cmat); |
||||||
|
|
||||||
|
gk_stopwctimer(params->timer_global); |
||||||
|
|
||||||
|
printf(" wclock: %.2lfs\n", gk_getwctimer(params->timer_global)); |
||||||
|
printf(" timer1: %.2lfs\n", gk_getwctimer(params->timer_1)); |
||||||
|
printf(" timer2: %.2lfs\n", gk_getwctimer(params->timer_2)); |
||||||
|
printf(" timer3: %.2lfs\n", gk_getwctimer(params->timer_3)); |
||||||
|
printf(" timer4: %.2lfs\n", gk_getwctimer(params->timer_4)); |
||||||
|
printf("********************************************************************************\n"); |
||||||
|
|
||||||
|
gk_csr_Free(&qmat); |
||||||
|
gk_csr_Free(&cmat); |
||||||
|
|
||||||
|
exit(rc); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Reads and computes the neighbors of each query document against the
|
||||||
|
collection of documents */ |
||||||
|
/**************************************************************************/ |
||||||
|
void FindNeighbors(params_t *params, gk_csr_t *qmat, gk_csr_t *cmat) |
||||||
|
{ |
||||||
|
int iQ, iH, nhits; |
||||||
|
int32_t *marker; |
||||||
|
gk_fkv_t *hits, *cand; |
||||||
|
FILE *fpout; |
||||||
|
|
||||||
|
GKASSERT(qmat->ncols <= cmat->ncols); |
||||||
|
|
||||||
|
/* if cosine, make rows unit length */ |
||||||
|
if (params->simtype == GK_CSR_COS) { |
||||||
|
gk_csr_Normalize(qmat, GK_CSR_ROW, 2); |
||||||
|
gk_csr_Normalize(cmat, GK_CSR_ROW, 2); |
||||||
|
} |
||||||
|
|
||||||
|
/* create the inverted index */ |
||||||
|
gk_csr_CreateIndex(cmat, GK_CSR_COL); |
||||||
|
|
||||||
|
/* compute the row norms */ |
||||||
|
gk_csr_ComputeSquaredNorms(cmat, GK_CSR_ROW); |
||||||
|
|
||||||
|
/* create the output file */ |
||||||
|
fpout = (params->outfile ? gk_fopen(params->outfile, "w", "FindNeighbors: fpout") : NULL); |
||||||
|
|
||||||
|
/* allocate memory for the necessary working arrays */ |
||||||
|
hits = gk_fkvmalloc(cmat->nrows, "FindNeighbors: hits"); |
||||||
|
marker = gk_i32smalloc(cmat->nrows, -1, "FindNeighbors: marker"); |
||||||
|
cand = gk_fkvmalloc(cmat->nrows, "FindNeighbors: cand"); |
||||||
|
|
||||||
|
|
||||||
|
/* find the best neighbors for each query document */ |
||||||
|
gk_startwctimer(params->timer_1); |
||||||
|
for (iQ=0; iQ<qmat->nrows; iQ++) { |
||||||
|
if (params->verbosity > 0) |
||||||
|
printf("Working on query %7d\n", iQ); |
||||||
|
|
||||||
|
/* find the neighbors of the ith document */
|
||||||
|
nhits = gk_csr_GetSimilarRows(cmat,
|
||||||
|
qmat->rowptr[iQ+1]-qmat->rowptr[iQ],
|
||||||
|
qmat->rowind+qmat->rowptr[iQ],
|
||||||
|
qmat->rowval+qmat->rowptr[iQ],
|
||||||
|
params->simtype, params->nnbrs, params->minsim,
|
||||||
|
hits, marker, cand); |
||||||
|
|
||||||
|
/* write the results in the file */ |
||||||
|
if (fpout) { |
||||||
|
for (iH=0; iH<nhits; iH++)
|
||||||
|
fprintf(fpout, "%8d %8zd %.3f\n", iQ, hits[iH].val, hits[iH].key); |
||||||
|
} |
||||||
|
} |
||||||
|
gk_stopwctimer(params->timer_1); |
||||||
|
|
||||||
|
|
||||||
|
/* cleanup and exit */ |
||||||
|
if (fpout) gk_fclose(fpout); |
||||||
|
|
||||||
|
gk_free((void **)&hits, &marker, &cand, LTERM); |
||||||
|
} |
||||||
|
|
||||||
@ -0,0 +1,306 @@ |
|||||||
|
/*!
|
||||||
|
\file
|
||||||
|
\brief A simple (personalized) random walk program to test GKlib's routines |
||||||
|
|
||||||
|
\date 6/12/2008 |
||||||
|
\author George |
||||||
|
\version \verbatim $Id$ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Data structures for the code */ |
||||||
|
/*************************************************************************/ |
||||||
|
typedef struct { |
||||||
|
int niter; |
||||||
|
int ntvs; |
||||||
|
int ppr; |
||||||
|
float eps; |
||||||
|
float lamda; |
||||||
|
char *infile; |
||||||
|
char *outfile; |
||||||
|
} params_t; |
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Constants */ |
||||||
|
/*************************************************************************/ |
||||||
|
#define CMD_NITER 1 |
||||||
|
#define CMD_EPS 2 |
||||||
|
#define CMD_LAMDA 3 |
||||||
|
#define CMD_PPR 4 |
||||||
|
#define CMD_NTVS 5 |
||||||
|
#define CMD_HELP 10 |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Local variables */ |
||||||
|
/*************************************************************************/ |
||||||
|
static struct gk_option long_options[] = { |
||||||
|
{"niter", 1, 0, CMD_NITER}, |
||||||
|
{"lamda", 1, 0, CMD_LAMDA}, |
||||||
|
{"eps", 1, 0, CMD_EPS}, |
||||||
|
{"ppr", 1, 0, CMD_PPR}, |
||||||
|
{"ntvs", 1, 0, CMD_NTVS}, |
||||||
|
{"help", 0, 0, CMD_HELP}, |
||||||
|
{0, 0, 0, 0} |
||||||
|
}; |
||||||
|
|
||||||
|
|
||||||
|
/*-------------------------------------------------------------------*/ |
||||||
|
/* Mini help */ |
||||||
|
/*-------------------------------------------------------------------*/ |
||||||
|
static char helpstr[][100] = { |
||||||
|
" ", |
||||||
|
"Usage: rw [options] <graph-file> <out-file>", |
||||||
|
" ", |
||||||
|
" Required parameters", |
||||||
|
" graph-file", |
||||||
|
" The name of the file storing the transactions. The file is in ", |
||||||
|
" Metis' graph format.", |
||||||
|
" ", |
||||||
|
" Optional parameters", |
||||||
|
" -niter=int", |
||||||
|
" Specifies the maximum number of iterations. [default: 100]", |
||||||
|
" ", |
||||||
|
" -lamda=float", |
||||||
|
" Specifies the follow-the-adjacent-links probability. [default: 0.80]", |
||||||
|
" ", |
||||||
|
" -eps=float", |
||||||
|
" Specifies the error tollerance. [default: 1e-10]", |
||||||
|
" ", |
||||||
|
" -ppr=int", |
||||||
|
" Specifies the source of the personalized PR. [default: -1]", |
||||||
|
" ", |
||||||
|
" -ntvs=int", |
||||||
|
" Specifies the number of test-vectors to compute. [default: -1]", |
||||||
|
" ", |
||||||
|
" -help", |
||||||
|
" Prints this message.", |
||||||
|
"" |
||||||
|
}; |
||||||
|
|
||||||
|
static char shorthelpstr[][100] = { |
||||||
|
" ", |
||||||
|
" Usage: rw [options] <graph-file> <out-file>", |
||||||
|
" use 'rw -help' for a summary of the options.", |
||||||
|
"" |
||||||
|
}; |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Function prototypes */ |
||||||
|
/*************************************************************************/ |
||||||
|
void print_init_info(params_t *params, gk_csr_t *mat); |
||||||
|
void print_final_info(params_t *params); |
||||||
|
params_t *parse_cmdline(int argc, char *argv[]); |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! the entry point */ |
||||||
|
/**************************************************************************/ |
||||||
|
int main(int argc, char *argv[]) |
||||||
|
{ |
||||||
|
ssize_t i, j, niter; |
||||||
|
params_t *params; |
||||||
|
gk_csr_t *mat; |
||||||
|
FILE *fpout; |
||||||
|
|
||||||
|
/* get command-line options */ |
||||||
|
params = parse_cmdline(argc, argv); |
||||||
|
|
||||||
|
/* read the data */ |
||||||
|
mat = gk_csr_Read(params->infile, GK_CSR_FMT_METIS, 1, 1); |
||||||
|
|
||||||
|
/* display some basic stats */ |
||||||
|
print_init_info(params, mat); |
||||||
|
|
||||||
|
|
||||||
|
if (params->ntvs != -1) { |
||||||
|
/* compute the pr for different randomly generated restart-distribution vectors */ |
||||||
|
float **prs; |
||||||
|
|
||||||
|
prs = gk_fAllocMatrix(params->ntvs, mat->nrows, 0.0, "main: prs"); |
||||||
|
|
||||||
|
/* generate the random restart vectors */ |
||||||
|
for (j=0; j<params->ntvs; j++) { |
||||||
|
for (i=0; i<mat->nrows; i++) |
||||||
|
prs[j][i] = RandomInRange(931); |
||||||
|
gk_fscale(mat->nrows, 1.0/gk_fsum(mat->nrows, prs[j], 1), prs[j], 1); |
||||||
|
|
||||||
|
niter = gk_rw_PageRank(mat, params->lamda, params->eps, params->niter, prs[j]); |
||||||
|
printf("tvs#: %zd; niters: %zd\n", j, niter); |
||||||
|
} |
||||||
|
|
||||||
|
/* output the computed pr scores */ |
||||||
|
fpout = gk_fopen(params->outfile, "w", "main: outfile"); |
||||||
|
for (i=0; i<mat->nrows; i++) { |
||||||
|
for (j=0; j<params->ntvs; j++)
|
||||||
|
fprintf(fpout, "%.4e ", prs[j][i]); |
||||||
|
fprintf(fpout, "\n"); |
||||||
|
} |
||||||
|
gk_fclose(fpout); |
||||||
|
|
||||||
|
gk_fFreeMatrix(&prs, params->ntvs, mat->nrows); |
||||||
|
} |
||||||
|
else if (params->ppr != -1) { |
||||||
|
/* compute the personalized pr from the specified vertex */ |
||||||
|
float *pr; |
||||||
|
|
||||||
|
pr = gk_fsmalloc(mat->nrows, 0.0, "main: pr"); |
||||||
|
|
||||||
|
pr[params->ppr-1] = 1.0; |
||||||
|
|
||||||
|
niter = gk_rw_PageRank(mat, params->lamda, params->eps, params->niter, pr); |
||||||
|
printf("ppr: %d; niters: %zd\n", params->ppr, niter); |
||||||
|
|
||||||
|
/* output the computed pr scores */ |
||||||
|
fpout = gk_fopen(params->outfile, "w", "main: outfile"); |
||||||
|
for (i=0; i<mat->nrows; i++)
|
||||||
|
fprintf(fpout, "%.4e\n", pr[i]); |
||||||
|
gk_fclose(fpout); |
||||||
|
|
||||||
|
gk_free((void **)&pr, LTERM); |
||||||
|
} |
||||||
|
else { |
||||||
|
/* compute the standard pr */ |
||||||
|
int jmax; |
||||||
|
float diff, maxdiff; |
||||||
|
float *pr; |
||||||
|
|
||||||
|
pr = gk_fsmalloc(mat->nrows, 1.0/mat->nrows, "main: pr"); |
||||||
|
|
||||||
|
niter = gk_rw_PageRank(mat, params->lamda, params->eps, params->niter, pr); |
||||||
|
printf("pr; niters: %zd\n", niter); |
||||||
|
|
||||||
|
/* output the computed pr scores */ |
||||||
|
fpout = gk_fopen(params->outfile, "w", "main: outfile"); |
||||||
|
for (i=0; i<mat->nrows; i++) { |
||||||
|
for (jmax=i, maxdiff=0.0, j=mat->rowptr[i]; j<mat->rowptr[i+1]; j++) { |
||||||
|
if ((diff = fabs(pr[i]-pr[mat->rowind[j]])) > maxdiff) { |
||||||
|
maxdiff = diff; |
||||||
|
jmax = mat->rowind[j]; |
||||||
|
} |
||||||
|
} |
||||||
|
fprintf(fpout, "%.4e %10zd %.4e %10d\n", pr[i],
|
||||||
|
mat->rowptr[i+1]-mat->rowptr[i], maxdiff, jmax+1); |
||||||
|
} |
||||||
|
gk_fclose(fpout); |
||||||
|
|
||||||
|
gk_free((void **)&pr, LTERM); |
||||||
|
} |
||||||
|
|
||||||
|
gk_csr_Free(&mat); |
||||||
|
|
||||||
|
/* display some final stats */ |
||||||
|
print_final_info(params); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function prints run parameters */ |
||||||
|
/*************************************************************************/ |
||||||
|
void print_init_info(params_t *params, gk_csr_t *mat) |
||||||
|
{ |
||||||
|
printf("*******************************************************************************\n"); |
||||||
|
printf(" fis\n\n"); |
||||||
|
printf("Matrix Information ---------------------------------------------------------\n"); |
||||||
|
printf(" input file=%s, [%d, %d, %zd]\n",
|
||||||
|
params->infile, mat->nrows, mat->ncols, mat->rowptr[mat->nrows]); |
||||||
|
|
||||||
|
printf("\n"); |
||||||
|
printf("Options --------------------------------------------------------------------\n"); |
||||||
|
printf(" niter=%d, ntvs=%d, ppr=%d, lamda=%f, eps=%e\n", |
||||||
|
params->niter, params->ntvs, params->ppr, params->lamda, params->eps); |
||||||
|
|
||||||
|
printf("\n"); |
||||||
|
printf("Performing random walks... ----------------------------------------------\n"); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This function prints final statistics */ |
||||||
|
/*************************************************************************/ |
||||||
|
void print_final_info(params_t *params) |
||||||
|
{ |
||||||
|
printf("\n"); |
||||||
|
printf("Memory Usage Information -----------------------------------------------------\n"); |
||||||
|
printf(" Maximum memory used: %10zd bytes\n", (ssize_t) gk_GetMaxMemoryUsed()); |
||||||
|
printf(" Current memory used: %10zd bytes\n", (ssize_t) gk_GetCurMemoryUsed()); |
||||||
|
printf("********************************************************************************\n"); |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! This is the entry point of the command-line argument parser */ |
||||||
|
/*************************************************************************/ |
||||||
|
params_t *parse_cmdline(int argc, char *argv[]) |
||||||
|
{ |
||||||
|
int i; |
||||||
|
int c, option_index; |
||||||
|
params_t *params; |
||||||
|
|
||||||
|
params = (params_t *)gk_malloc(sizeof(params_t), "parse_cmdline: params"); |
||||||
|
|
||||||
|
/* initialize the params data structure */ |
||||||
|
params->niter = 100; |
||||||
|
params->ppr = -1; |
||||||
|
params->ntvs = -1; |
||||||
|
params->eps = 1e-10; |
||||||
|
params->lamda = 0.80; |
||||||
|
params->infile = NULL; |
||||||
|
params->outfile = NULL; |
||||||
|
|
||||||
|
|
||||||
|
/* Parse the command line arguments */ |
||||||
|
while ((c = gk_getopt_long_only(argc, argv, "", long_options, &option_index)) != -1) { |
||||||
|
switch (c) { |
||||||
|
case CMD_NITER: |
||||||
|
if (gk_optarg) params->niter = atoi(gk_optarg); |
||||||
|
break; |
||||||
|
case CMD_NTVS: |
||||||
|
if (gk_optarg) params->ntvs = atoi(gk_optarg); |
||||||
|
break; |
||||||
|
case CMD_PPR: |
||||||
|
if (gk_optarg) params->ppr = atoi(gk_optarg); |
||||||
|
break; |
||||||
|
case CMD_EPS: |
||||||
|
if (gk_optarg) params->eps = atof(gk_optarg); |
||||||
|
break; |
||||||
|
case CMD_LAMDA: |
||||||
|
if (gk_optarg) params->lamda = atof(gk_optarg); |
||||||
|
break; |
||||||
|
|
||||||
|
case CMD_HELP: |
||||||
|
for (i=0; strlen(helpstr[i]) > 0; i++) |
||||||
|
printf("%s\n", helpstr[i]); |
||||||
|
exit(0); |
||||||
|
break; |
||||||
|
case '?': |
||||||
|
default: |
||||||
|
printf("Illegal command-line option(s)\nUse %s -help for a summary of the options.\n", argv[0]); |
||||||
|
exit(0); |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
if (argc-gk_optind != 2) { |
||||||
|
printf("Unrecognized parameters."); |
||||||
|
for (i=0; strlen(shorthelpstr[i]) > 0; i++) |
||||||
|
printf("%s\n", shorthelpstr[i]); |
||||||
|
exit(0); |
||||||
|
} |
||||||
|
|
||||||
|
params->infile = gk_strdup(argv[gk_optind++]); |
||||||
|
params->outfile = gk_strdup(argv[gk_optind++]); |
||||||
|
|
||||||
|
if (!gk_fexists(params->infile)) |
||||||
|
errexit("input file %s does not exist.\n", params->infile); |
||||||
|
|
||||||
|
if (params->ppr != -1 && params->ntvs != -1) |
||||||
|
errexit("Only one of the -ppr and -ntvs options can be specified.\n"); |
||||||
|
|
||||||
|
return params; |
||||||
|
} |
||||||
|
|
||||||
@ -0,0 +1,98 @@ |
|||||||
|
/*!
|
||||||
|
\file
|
||||||
|
\brief A simple program to convert a tensor in coordinate format into an unfolded
|
||||||
|
matrix |
||||||
|
|
||||||
|
\author George |
||||||
|
*/ |
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
|
||||||
|
int main(int argc, char *argv[]) |
||||||
|
{ |
||||||
|
size_t nnz, i, j, k, nI, nJ, nK, nrows, ncols; |
||||||
|
int32_t *I, *J, *K, *rowind, *colind; |
||||||
|
ssize_t *rowptr, *colptr; |
||||||
|
float *V, *rowval, *colval; |
||||||
|
|
||||||
|
if (argc != 2)
|
||||||
|
errexit("Usage %s <infile> [%d]\n", argv[0], argc); |
||||||
|
|
||||||
|
if (!gk_fexists(argv[1])) |
||||||
|
errexit("File %s does not exist.\n", argv[1]); |
||||||
|
|
||||||
|
gk_getfilestats(argv[1], &nnz, NULL, NULL, NULL); |
||||||
|
I = gk_i32malloc(nnz, "I"); |
||||||
|
J = gk_i32malloc(nnz, "J"); |
||||||
|
K = gk_i32malloc(nnz, "K"); |
||||||
|
V = gk_fmalloc(nnz, "V"); |
||||||
|
|
||||||
|
fprintf(stderr, "Input nnz: %zd\n", nnz); |
||||||
|
|
||||||
|
FILE *fpin = gk_fopen(argv[1], "r", "infile"); |
||||||
|
for (i=0; i<nnz; i++) { |
||||||
|
if (4 != fscanf(fpin, "%d %d %d %f", K+i, I+i, J+i, V+i)) |
||||||
|
errexit("Failed to read 4 values in line %zd\n", i); |
||||||
|
K[i]--; I[i]--; J[i]--; |
||||||
|
} |
||||||
|
gk_fclose(fpin); |
||||||
|
|
||||||
|
nI = gk_i32max(nnz, I, 1)+1; |
||||||
|
nJ = gk_i32max(nnz, J, 1)+1; |
||||||
|
nK = gk_i32max(nnz, K, 1)+1; |
||||||
|
|
||||||
|
fprintf(stderr, "nI: %zd, nJ: %zd, nK: %zd\n", nI, nJ, nK); |
||||||
|
|
||||||
|
nrows = nK*nI; |
||||||
|
ncols = nJ; |
||||||
|
rowptr = gk_zsmalloc(nrows+1, 0, "rowptr"); |
||||||
|
for (i=0; i<nnz; i++)
|
||||||
|
rowptr[K[i]*nI+I[i]]++; |
||||||
|
MAKECSR(i, nrows, rowptr); |
||||||
|
|
||||||
|
rowind = gk_i32malloc(nnz, "rowind"); |
||||||
|
rowval = gk_fmalloc(nnz, "rowval"); |
||||||
|
for (i=0; i<nnz; i++) { |
||||||
|
rowind[rowptr[K[i]*nI+I[i]]] = J[i]; |
||||||
|
rowval[rowptr[K[i]*nI+I[i]]] = V[i]; |
||||||
|
rowptr[K[i]*nI+I[i]]++; |
||||||
|
} |
||||||
|
SHIFTCSR(i, nrows, rowptr); |
||||||
|
|
||||||
|
gk_free((void **)&I, &J, &K, &V, LTERM); |
||||||
|
|
||||||
|
colptr = gk_zsmalloc(ncols+1, 0, "colptr"); |
||||||
|
colind = gk_i32malloc(nnz, "colind"); |
||||||
|
colval = gk_fmalloc(nnz, "colval"); |
||||||
|
for (i=0; i<nrows; i++) { |
||||||
|
for (j=rowptr[i]; j<rowptr[i+1]; j++) |
||||||
|
colptr[rowind[j]]++; |
||||||
|
} |
||||||
|
MAKECSR(i, ncols, colptr); |
||||||
|
for (i=0; i<nrows; i++) { |
||||||
|
for (j=rowptr[i]; j<rowptr[i+1]; j++) { |
||||||
|
colind[colptr[rowind[j]]] = i; |
||||||
|
colval[colptr[rowind[j]]] = rowval[j]; |
||||||
|
colptr[rowind[j]]++; |
||||||
|
} |
||||||
|
} |
||||||
|
SHIFTCSR(i, ncols, colptr); |
||||||
|
|
||||||
|
/* sanity check */ |
||||||
|
for (i=0; i<ncols; i++) { |
||||||
|
for (j=colptr[i]+1; j<colptr[i+1]; j++) { |
||||||
|
if (colind[j-1] == colind[j]) |
||||||
|
fprintf(stderr, "Duplicate row indices: %d %d %d\n", (int)i, colind[j], colind[j-1]); |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
printf("%zd %zd %zd\n", nrows, ncols, nnz); |
||||||
|
for (i=0; i<ncols; i++) { |
||||||
|
printf("%zd\n", colptr[i+1]-colptr[i]); |
||||||
|
for (j=colptr[i]; j<colptr[i+1]; j++) |
||||||
|
printf("%d %.3f\n", colind[j], colval[j]); |
||||||
|
} |
||||||
|
|
||||||
|
} |
||||||
|
|
||||||
@ -0,0 +1,82 @@ |
|||||||
|
/*!
|
||||||
|
\file strings.c |
||||||
|
\brief Testing module for the string functions in GKlib |
||||||
|
|
||||||
|
\date Started 3/5/2007 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: strings.c 10711 2011-08-31 22:23:04Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************/ |
||||||
|
/*! Testing module for gk_strstr_replace() */ |
||||||
|
/*************************************************************************/ |
||||||
|
void test_strstr_replace() |
||||||
|
{ |
||||||
|
char *new_str; |
||||||
|
int rc; |
||||||
|
|
||||||
|
rc = gk_strstr_replace("This is a simple string", "s", "S", "", &new_str); |
||||||
|
printf("%d, %s.\n", rc, new_str); |
||||||
|
gk_free((void **)&new_str, LTERM); |
||||||
|
|
||||||
|
|
||||||
|
rc = gk_strstr_replace("This is a simple string", "s", "S", "g", &new_str); |
||||||
|
printf("%d, %s.\n", rc, new_str); |
||||||
|
gk_free((void **)&new_str, LTERM); |
||||||
|
|
||||||
|
|
||||||
|
rc = gk_strstr_replace("This is a simple SS & ss string", "s", "T", "g", &new_str); |
||||||
|
printf("%d, %s.\n", rc, new_str); |
||||||
|
gk_free((void **)&new_str, LTERM); |
||||||
|
|
||||||
|
|
||||||
|
rc = gk_strstr_replace("This is a simple SS & ss string", "s", "T", "ig", &new_str); |
||||||
|
printf("%d, %s.\n", rc, new_str); |
||||||
|
gk_free((void **)&new_str, LTERM); |
||||||
|
|
||||||
|
rc = gk_strstr_replace("This is a simple SS & ss string", "\\b\\w(\\w+)\\w\\b", "$1", "ig", &new_str); |
||||||
|
printf("%d, %s.\n", rc, new_str); |
||||||
|
gk_free((void **)&new_str, LTERM); |
||||||
|
|
||||||
|
rc = gk_strstr_replace("This is a simple SS & ss string", "\\b\\w+\\b", "word", "ig", &new_str); |
||||||
|
printf("%d, %s.\n", rc, new_str); |
||||||
|
gk_free((void **)&new_str, LTERM); |
||||||
|
|
||||||
|
rc = gk_strstr_replace("http://www.cs.umn.edu/This-is-something-T12323?pp=20&page=4", |
||||||
|
"(http://www\\.cs\\.umn\\.edu/)(.*)-T(\\d+)", "$1$2-P$3", "g", &new_str); |
||||||
|
printf("%d, %s.\n", rc, new_str); |
||||||
|
gk_free((void **)&new_str, LTERM); |
||||||
|
|
||||||
|
rc = gk_strstr_replace("http://www.cs.umn.edu/This-is-something-T12323?pp=20&page=4", |
||||||
|
"(\\d+)", "number:$1", "ig", &new_str); |
||||||
|
printf("%d, %s.\n", rc, new_str); |
||||||
|
gk_free((void **)&new_str, LTERM); |
||||||
|
|
||||||
|
|
||||||
|
rc = gk_strstr_replace("http://www.cs.umn.edu/This-is-something-T12323?pp=20&page=4", |
||||||
|
"(http://www\\.cs\\.umn\\.edu/)", "[$1]", "g", &new_str); |
||||||
|
printf("%d, %s.\n", rc, new_str); |
||||||
|
gk_free((void **)&new_str, LTERM); |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
int main() |
||||||
|
{ |
||||||
|
test_strstr_replace(); |
||||||
|
|
||||||
|
/*
|
||||||
|
{ |
||||||
|
int i; |
||||||
|
for (i=0; i<1000; i++) |
||||||
|
printf("%d\n", RandomInRange(3)); |
||||||
|
} |
||||||
|
*/ |
||||||
|
} |
||||||
|
|
||||||
@ -0,0 +1,52 @@ |
|||||||
|
/*!
|
||||||
|
\file timers.c |
||||||
|
\brief Various timing functions
|
||||||
|
|
||||||
|
\date Started 4/12/2007 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: timers.c 10711 2011-08-31 22:23:04Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************
|
||||||
|
* This function returns the CPU seconds |
||||||
|
**************************************************************************/ |
||||||
|
double gk_WClockSeconds(void) |
||||||
|
{ |
||||||
|
#ifdef __GNUC__ |
||||||
|
struct timeval ctime; |
||||||
|
|
||||||
|
gettimeofday(&ctime, NULL); |
||||||
|
|
||||||
|
return (double)ctime.tv_sec + (double).000001*ctime.tv_usec; |
||||||
|
#else |
||||||
|
return (double)time(NULL); |
||||||
|
#endif |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/*************************************************************************
|
||||||
|
* This function returns the CPU seconds |
||||||
|
**************************************************************************/ |
||||||
|
double gk_CPUSeconds(void) |
||||||
|
{ |
||||||
|
//#ifdef __OPENMP__
|
||||||
|
#ifdef __OPENMPXXXX__ |
||||||
|
return omp_get_wtime(); |
||||||
|
#else |
||||||
|
#if defined(WIN32) || defined(__MINGW32__) |
||||||
|
return((double) clock()/CLOCKS_PER_SEC); |
||||||
|
#else |
||||||
|
struct rusage r; |
||||||
|
|
||||||
|
getrusage(RUSAGE_SELF, &r); |
||||||
|
return ((r.ru_utime.tv_sec + r.ru_stime.tv_sec) + 1.0e-6*(r.ru_utime.tv_usec + r.ru_stime.tv_usec)); |
||||||
|
#endif |
||||||
|
#endif |
||||||
|
} |
||||||
|
|
||||||
@ -0,0 +1,77 @@ |
|||||||
|
/*!
|
||||||
|
\file tokenizer.c |
||||||
|
\brief String tokenization routines |
||||||
|
|
||||||
|
This file contains various routines for splitting an input string into |
||||||
|
tokens and returning them in form of a list. The goal is to mimic perl's
|
||||||
|
split function. |
||||||
|
|
||||||
|
\date Started 11/23/04 |
||||||
|
\author George |
||||||
|
\version\verbatim $Id: tokenizer.c 10711 2011-08-31 22:23:04Z karypis $ \endverbatim |
||||||
|
*/ |
||||||
|
|
||||||
|
|
||||||
|
#include <GKlib.h> |
||||||
|
|
||||||
|
|
||||||
|
/************************************************************************
|
||||||
|
* This function tokenizes a string based on the user-supplied delimiters |
||||||
|
* list. The resulting tokens are returned into an array of strings. |
||||||
|
*************************************************************************/ |
||||||
|
void gk_strtokenize(char *str, char *delim, gk_Tokens_t *tokens) |
||||||
|
{ |
||||||
|
int i, ntoks, slen; |
||||||
|
|
||||||
|
tokens->strbuf = gk_strdup(str); |
||||||
|
|
||||||
|
slen = strlen(str); |
||||||
|
str = tokens->strbuf; |
||||||
|
|
||||||
|
/* Scan once to determine the number of tokens */ |
||||||
|
for (ntoks=0, i=0; i<slen;) { |
||||||
|
/* Consume all the consecutive characters from the delimiters list */ |
||||||
|
while (i<slen && strchr(delim, str[i]))
|
||||||
|
i++; |
||||||
|
|
||||||
|
if (i == slen) |
||||||
|
break; |
||||||
|
|
||||||
|
ntoks++; |
||||||
|
|
||||||
|
/* Consume all the consecutive characters from the token */ |
||||||
|
while (i<slen && !strchr(delim, str[i]))
|
||||||
|
i++; |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
tokens->ntoks = ntoks; |
||||||
|
tokens->list = (char **)gk_malloc(ntoks*sizeof(char *), "strtokenize: tokens->list"); |
||||||
|
|
||||||
|
|
||||||
|
/* Scan a second time to mark and link the tokens */ |
||||||
|
for (ntoks=0, i=0; i<slen;) { |
||||||
|
/* Consume all the consecutive characters from the delimiters list */ |
||||||
|
while (i<slen && strchr(delim, str[i]))
|
||||||
|
str[i++] = '\0'; |
||||||
|
|
||||||
|
if (i == slen) |
||||||
|
break; |
||||||
|
|
||||||
|
tokens->list[ntoks++] = str+i; |
||||||
|
|
||||||
|
/* Consume all the consecutive characters from the token */ |
||||||
|
while (i<slen && !strchr(delim, str[i]))
|
||||||
|
i++; |
||||||
|
} |
||||||
|
} |
||||||
|
|
||||||
|
|
||||||
|
/************************************************************************
|
||||||
|
* This function frees the memory associated with a gk_Tokens_t |
||||||
|
*************************************************************************/ |
||||||
|
void gk_freetokenslist(gk_Tokens_t *tokens) |
||||||
|
{ |
||||||
|
gk_free((void *)&tokens->list, &tokens->strbuf, LTERM); |
||||||
|
} |
||||||
|
|
||||||
@ -0,0 +1,11 @@ |
|||||||
|
/*
|
||||||
|
\file win32/adapt.c |
||||||
|
\brief Implementation of Win32 adaptation of libc functions |
||||||
|
*/ |
||||||
|
|
||||||
|
#include "adapt.h" |
||||||
|
|
||||||
|
pid_t getpid(void) |
||||||
|
{ |
||||||
|
return GetCurrentProcessId(); |
||||||
|
} |
||||||
@ -0,0 +1,14 @@ |
|||||||
|
/*
|
||||||
|
\file win32/adapt.h |
||||||
|
\brief Declaration of Win32 adaptation of POSIX functions and types |
||||||
|
*/ |
||||||
|
#ifndef _WIN32_ADAPT_H_ |
||||||
|
#define _WIN32_ADAPT_H_ |
||||||
|
|
||||||
|
#include <windows.h> |
||||||
|
|
||||||
|
typedef DWORD pid_t; |
||||||
|
|
||||||
|
pid_t getpid(void); |
||||||
|
|
||||||
|
#endif /* _WIN32_ADAPT_H_ */ |
||||||
Loading…
Reference in new issue