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438 lines
16 KiB
<!-------- @HEADER
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!
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! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
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!
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! Zoltan Toolkit for Load-balancing, Partitioning, Ordering and Coloring
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! Copyright 2012 Sandia Corporation
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!
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! Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
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! the U.S. Government retains certain rights in this software.
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!
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! Redistribution and use in source and binary forms, with or without
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! modification, are permitted provided that the following conditions are
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! met:
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!
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! 1. Redistributions of source code must retain the above copyright
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! notice, this list of conditions and the following disclaimer.
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!
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! 2. Redistributions in binary form must reproduce the above copyright
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! notice, this list of conditions and the following disclaimer in the
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! documentation and/or other materials provided with the distribution.
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!
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! 3. Neither the name of the Corporation nor the names of the
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! contributors may be used to endorse or promote products derived from
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! this software without specific prior written permission.
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!
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! THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
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! EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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! IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
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! PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
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! CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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! EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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! PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
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! PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
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! LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
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! NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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! SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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!
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! Questions? Contact Karen Devine kddevin@sandia.gov
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! Erik Boman egboman@sandia.gov
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!
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! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
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!
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! @HEADER
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------->
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<!DOCTYPE html PUBLIC "-//w3c//dtd html 4.0 transitional//en">
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<html>
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<head>
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<meta http-equiv="Content-Type"
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content="text/html; charset=iso-8859-1">
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<meta name="GENERATOR"
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content="Mozilla/4.76 [en] (X11; U; Linux 2.4.2-2smp i686) [Netscape]">
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<meta name="sandia.approval_type" content="formal">
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<meta name="sandia.approved" content="SAND2007-4748W">
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<meta name="author" content="Zoltan PI">
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<title>Zoltan User's Guide: ParMETIS Interface</title>
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</head>
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<body bgcolor="#ffffff">
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<div align="right"><b><i><a href="ug.html">Zoltan User's Guide</a>
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| <a href="ug_alg_ptscotch.html">Next</a> | <a
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href="ug_graph_vs_hg.html">Previous</a></i></b></div>
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<h2>
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<a name="ParMETIS"></a>ParMETIS - Parallel Graph Partitioning</h2>
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<a href="https://www-users.cs.umn.edu/%7Ekarypis/metis/parmetis/">ParMETIS</a>
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is a parallel library for graph partitioning (for static load
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balancing)
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and repartitioning (for dynamic load balancing) developed at the
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University
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of Minnesota by Karypis, Schloegel and Kumar [<a
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href="ug_refs.html#parmetis">Karypis
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and Kumar</a>]. Note that ParMetis must be obtained separately and has a different license than Zoltan (see page 31 of <a
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href="https://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/manual.pdf">
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this manual</a>). ParMETIS is strictly speaking not a method but
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rather a collection of methods. In the Zoltan context, ParMETIS is a
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method
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with many sub-methods. Zoltan provides an interface to all the ParMETIS
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(sub-)methods. The user selects which ParMETIS method to use
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through
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the parameter PARMETIS_METHOD. Most of the ParMETIS methods are based
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on
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either multilevel Kernighan-Lin partitioning or a diffusion algorithm.
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The names of the ParMETIS methods used by Zoltan are identical to those
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in the ParMETIS library. For further information about the various <a
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href="https://www-users.cs.umn.edu/%7Ekarypis/metis/parmetis/">ParMETIS</a>
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methods and parameters, please consult the <a
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href="https://www-users.cs.umn.edu/%7Ekarypis/metis/parmetis/">ParMETIS</a>
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User's Guide.
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<p>Graph partitioning is a useful abstraction for load balancing. The
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main
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idea is to represent the computational application as a weighted graph.
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The nodes or vertices in the graph correspond to objects in
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Zoltan.
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Each object may have a weight that normally represents the amount of
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computation.
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The edges or arcs in the graph usually correspond to communication
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costs.
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In graph partitioning, the problem is to find a partition of the
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graph
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(that is, each vertex is assigned to one out of <i>k</i>
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possible
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sets called parts) that minimizes the cut size (weight) subject to
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the parts having approximately equal size (weight). In
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repartitioning,
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it is assumed that a partition already exists. The problem is to
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find
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a good partition that is also "similar" in some sense to the
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existing
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partition. This keeps the migration cost low. All the problems
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described
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above are NP-hard so no efficient exact algorithm is known, but
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heuristics work well in practice.<br>
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</p>
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<p>We give only a brief summary of the various ParMETIS methods here;
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for
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more details see the <a
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href="https://www-users.cs.umn.edu/%7Ekarypis/metis/parmetis/">ParMETIS</a>
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documentation. The methods fall into three categories:
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</p>
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<ol>
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<li>
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Part* - Perform graph partitioning without consideration of the initial
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distribution. (LB_APPROACH=partition)<br>
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</li>
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<li>
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AdaptiveRepart - Incremental
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algorithms with small migration cost. (LB_APPROACH=repartition)</li>
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<li>
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Refine* - Refines a given partition (balance). Can be applied
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multiple times to reduce the communication cost (cut weight) if
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desired. (LB_APPROACH=refine)</li>
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</ol>
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As a rule of thumb, use one of the Part* methods if you have a poor
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initial
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balance and you are willing to spend some time doing migration. One
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such
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case is static load balancing; that is, you need to balance only once.
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Use AdaptiveRepart or the Repart* methods when you have a reasonably
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good
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load balance that you wish to update incrementally. These methods are
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well
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suited for dynamic load balancing (for example, adaptive
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mesh
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refinement). A reasonable strategy is to call PartKway once to obtain a
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good initial balance and later update this balance using
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AdaptiveRepart.
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<p>
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Zoltan supports the multiconstraint partitioning
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feature of ParMETIS through multiple object weights (see <i><a
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href="ug_param.html#General_Parameters">OBJ_WEIGHT_DIM</a></i>).
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</p>
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<p>The graph given to Zoltan/ParMETIS must be symmetric. Any self edges
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(loops) will be ignored. Multiple edges between a pair of vertices is
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not allowed. All weights must be non-negative. The graph does not have to
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be connected.
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</p>
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<p>Zoltan is currently compatible with ParMETIS version 3.1 and 4.0.x.
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The ParMETIS source code can be obtained from
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the <a href="https://glaros.dtc.umn.edu/gkhome/views/metis/parmetis">
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ParMETIS home page</a>. ParMETIS has a separate license:
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<i>'PARMETIS can be freely used for educational and research purposes by non-profit institutions and US government agencies only. Other organizations are allowed to
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use PARMETIS only for evaluation purposes, and any further uses will require prior approval from <a href="https://www.license.umn.edu/Products/ParMETIS---Mesh-Graph-Partitioning-Algorithm__Z09041.aspx">the technology transfer office at the University of Minnesota</a>'
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</i> <br>
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If you do not wish to install ParMETIS, it
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is possible to compile Zoltan without any references to ParMETIS;
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(when you 'make' Zoltan, comment out the PARMETIS_LIBPATH variable in
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the
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configuration file <i><a href="ug_usage.html#Building%20the%20Library">Utilities/Config/Config.<platform></a></i>).
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</p>
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<br>
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<table nosave="" width="100%">
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<tbody>
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<tr>
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<td valign="top"><b>Value of LB_METHOD:</b></td>
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<td><b>GRAPH</b></td>
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</tr>
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<tr>
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<td valign="top"><b>Value of GRAPH_PACKAGE:</b></td>
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<td><b>Parmetis</b></td>
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</tr>
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<tr>
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<td><b>Parameters:</b></td>
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<td><br>
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</td>
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</tr>
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<tr>
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<td valign="top"><i> LB_APPROACH<br>
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</i></td>
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<td>The load balancing approach:. <br>
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<i>PARTITION</i> - partition from scratch, not taking
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the current data distribution into account<br>
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<i>REPARTITION</i> - partition but try to stay close to the
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current partition/distribution
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<br>
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<i>REFINE</i> - refine the current partition/distribution;
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assumes only small changes
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</td>
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</tr>
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<tr>
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<td valign="top"><i> PARMETIS_METHOD</i></td>
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<td>The specific ParMETIS method to be used (see below).
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Note: See also <a href="ug_alg.html#LB_APPROACH">LB_APPROACH</a>,
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which is a simpler way to specify the overall load balance approach.
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Only use <i>PARMETIS_METHOD</i> if you really need a specific
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implementation.<br>
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<i>PartKway</i> - multilevel Kernighan-Lin partitioning
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<br>
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<i>PartGeom</i> - space filling curves (coordinate based)
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<br>
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<i>PartGeomKway</i> - hybrid method based on PartKway and
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PartGeom
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(needs both graph data and coordinates)
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<br>
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<i>AdaptiveRepart - </i>adaptive repartitioning (only in
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ParMETIS 3.0
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and higher)
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<br>
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<i>RefineKway</i> - refine the current partition (balance)</td>
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</tr>
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<tr>
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<td><br>
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</td>
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<td>The method names are case insensitive.</td>
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</tr>
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<tr>
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<td valign="top"> <i>PARMETIS_OUTPUT_LEVEL</i></td>
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<td>Amount of output the load-balancing algorithm should
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produce.
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<br>
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0 = no output, 1 = print timing info. Turning on more bits displays
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more information (for example, 3=1+2, 5=1+4, 7=1+2+4).</td>
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</tr>
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<tr>
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<td> <i>PARMETIS_COARSE_ALG</i></td>
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<td>Coarse algorithm for PartKway. 1 = serial, 2 = parallel.
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(ParMETIS
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2 only)</td>
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</tr>
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<tr>
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<td> <i>PARMETIS_SEED</i></td>
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<td>Random seed for ParMETIS.</td>
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</tr>
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<tr nosave="" valign="top">
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<td> <i>PARMETIS_ITR</i></td>
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<td nosave="">Ratio of interprocessor communication time to
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redistribution
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time. A high value will emphasize reducing the edge cut, while a small
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value will try to keep the change in the new partition (distribution)
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small.
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This parameter is used only by AdaptiveRepart. A value of between 100
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and
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1000 is good for most problems.</td>
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</tr>
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<tr nosave="" valign="top">
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<td> <i>CHECK_GRAPH</i></td>
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<td nosave="">Level of error checking for graph input: 0 = no
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checking, 1
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= on-processor checking, 2 = full checking. (CHECK_GRAPH==2 is very
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slow
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and should be used only during debugging).</td>
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</tr>
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<tr nosave="" valign="top">
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<td> <i>SCATTER_GRAPH</i></td>
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<td nosave="">Scatter graph data by distributing contiguous
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chunks of objects
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(vertices) of roughly equal size to each processor before calling the
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partitioner.
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0 = don't scatter;
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1 = scatter only if all objects are on a single processor;
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2 = scatter if at least one processor owns no objects;
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3 = always scatter. </td>
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</tr>
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<tr nosave="" valign="top">
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<td> <i>GRAPH_SYMMETRIZE</i></td>
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<td nosave="">How to symmetrize the graph:
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NONE = graph is symmetric and no symmetrization is needed <br/>
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TRANSPOSE = if M is adjacency matrix of the input graph, output will be the graph representation of M+M<sup>T</sup> <br/>
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BIPARTITE = graph is symmetrized in a bipartite way : [[ 0 M ][M<sup>t</sup> 0]]
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</td>
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</tr>
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<tr nosave="" valign="top">
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<td> <i>GRAPH_SYM_WEIGHT</i></td>
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<td nosave="">How edge weights are handled during symmetrization:
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ADD = weights of each arc are added <br/>
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MAX = only the heaviest arc weight is kept <br/>
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<p>See more informations about graph build options on this <a href="ug_graph_build.html">page</a></p>
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<!-- ERROR = fail if complementary arcs don't have the same weight. -->
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</td>
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</tr>
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<!-- <tr nosave="" valign="top"> -->
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<!-- <td> <i>GRAPH_BIPARTITE_TYPE</i></td> -->
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<!-- <td nosave=""> In the case of a bipartite symmetrization, -->
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<!-- NONE = graph is symmetric and no symmetrization is needed <br/> -->
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<!-- TRANSPOSE = if M is adjacency matrix of the input graph, output will be the graph representation of M+M<sup>T</sup> <br/> -->
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<!-- BIPARTITE = graph is symmetrized in a bipartite way : [[ 0 M ][M<sup>t</sup> 0]] -->
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<!-- </td> -->
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<!-- </tr> -->
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<tr>
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<td valign="top"><b>Default values:</b></td>
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<td><br>
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</td>
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</tr>
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<tr>
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<td><br>
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</td>
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<td><i>LB_APPROACH</i> = Repartition</td>
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</tr>
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<tr>
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<td><br>
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</td>
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<td><i>PARMETIS_METHOD</i> = AdaptiveRepart</td>
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</tr>
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<tr>
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<td><br>
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</td>
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<td><i>PARMETIS_OUTPUT_LEVEL</i> = 0</td>
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</tr>
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<tr>
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<td><br>
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</td>
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<td><i>PARMETIS_COARSE_ALG </i>= 2</td>
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</tr>
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<tr>
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<td><br>
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</td>
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<td><i>PARMETIS_SEED </i>= 15</td>
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</tr>
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<tr>
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<td><br>
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</td>
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<td><i>PARMETIS_ITR </i>= 100</td>
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</tr>
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<tr>
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<td><br>
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</td>
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<td><i>USE_OBJ_SIZE </i>= 1</td>
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</tr>
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<tr>
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<td><br>
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</td>
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<td><i>CHECK_GRAPH</i> = 1</td>
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</tr>
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<tr>
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<td><br>
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</td>
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<td><i>SCATTER_GRAPH </i>= 1</td>
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</tr>
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<tr>
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<td><br>
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</td>
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<td><i>GRAPH_SYMMETRIZE </i>= NONE</td>
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</tr>
|
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<tr>
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<td><br>
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</td>
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<td><i>GRAPH_SYM_WEIGHT </i>= ADD</td>
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</tr>
|
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|
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<tr>
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<td valign="top"><b>Required Query Functions:</b></td>
|
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<td><br>
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</td>
|
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</tr>
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<tr>
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<td>For all submethods:</td>
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<td><b><a href="ug_query_lb.html#ZOLTAN_NUM_OBJ_FN">ZOLTAN_NUM_OBJ_FN</a></b></td>
|
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</tr>
|
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<tr>
|
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<td><br>
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</td>
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<td><b><a href="ug_query_lb.html#ZOLTAN_OBJ_LIST_FN">ZOLTAN_OBJ_LIST_FN</a></b>
|
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</td>
|
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</tr>
|
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<tr>
|
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<td>Only PartGeom & PartGeomKway:</td>
|
|
<td><b><a href="ug_query_lb.html#ZOLTAN_NUM_GEOM_FN">ZOLTAN_NUM_GEOM_FN</a></b></td>
|
|
</tr>
|
|
<tr>
|
|
<td><br>
|
|
</td>
|
|
<td>
|
|
<b><a href="ug_query_lb.html#ZOLTAN_GEOM_MULTI_FN">ZOLTAN_GEOM_MULTI_FN</a></b>
|
|
or <b><a href="ug_query_lb.html#ZOLTAN_GEOM_FN">ZOLTAN_GEOM_FN</a></b>
|
|
</td>
|
|
</tr>
|
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<tr nosave="" valign="top">
|
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<td>All but PartGeom:</td>
|
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<td nosave="">
|
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<b><a href="ug_query_lb.html#ZOLTAN_NUM_EDGES_MULTI_FN">ZOLTAN_NUM_EDGES_MULTI_FN</a></b>
|
|
or
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<b><a href="ug_query_lb.html#ZOLTAN_NUM_EDGES_FN">ZOLTAN_NUM_EDGES_FN</a></b>
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|
<br>
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<b><a href="ug_query_lb.html#ZOLTAN_EDGE_LIST_MULTI_FN">ZOLTAN_EDGE_LIST_MULTI_FN</a></b>
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or
|
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<b><a href="ug_query_lb.html#ZOLTAN_EDGE_LIST_FN">ZOLTAN_EDGE_LIST_FN</a></b>
|
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</td>
|
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</tr>
|
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<tr>
|
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<td valign="top"><b>Optional Query Functions:</b></td>
|
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<td><br>
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</td>
|
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</tr>
|
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<tr>
|
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<td><br>
|
|
</td>
|
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<td>
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<b><a href="ug_query_mig.html#ZOLTAN_OBJ_SIZE_MULTI_FN">ZOLTAN_OBJ_SIZE_MULTI_FN</a></b>
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|
or
|
|
<b><a href="ug_query_mig.html#ZOLTAN_OBJ_SIZE_FN">ZOLTAN_OBJ_SIZE_FN</a></b> for <i>PARMETIS_METHOD</i>=<i>AdaptiveRepart</i>
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</td>
|
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</tr>
|
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<tr>
|
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<td><br>
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</td>
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<td>
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<b><a href="ug_query_lb.html#ZOLTAN_PART_MULTI_FN">ZOLTAN_PART_MULTI_FN</a></b>
|
|
or
|
|
<b><a href="ug_query_lb.html#ZOLTAN_PART_FN">ZOLTAN_PART_FN</a></b> for part remapping in ParMETIS.
|
|
</td>
|
|
</tr>
|
|
|
|
</tbody>
|
|
</table>
|
|
</p>
|
|
<hr width="100%">[<a href="ug.html">Table of Contents</a> | <a
|
|
href="ug_alg_ptscotch.html">Next:
|
|
PT-Scotch</a> | <a href="ug_graph_vs_hg.html">Previous:
|
|
Graph vs. Hypergraph Partitioning</a> | <a href="https://www.sandia.gov/general/privacy-security/index.html">Privacy and Security</a>]
|
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</body>
|
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</html>
|
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