diff --git a/.github/workflows/build_external_lib.yml b/.github/workflows/build_external_lib.yml deleted file mode 100644 index b3a01b8..0000000 --- a/.github/workflows/build_external_lib.yml +++ /dev/null @@ -1,57 +0,0 @@ -name: Build Using Ubuntu-installed libraries - -on: - push: - branches: - - master - pull_request: - branches: - - master - workflow_dispatch: - -jobs: - - build-deps: - - runs-on: ubuntu-22.04 - - strategy: - matrix: - compiler: [ gnu, clang ] - steps: - - - uses: actions/checkout@v3 - - - name: Install System dependencies - shell: bash -l {0} - run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev openmpi-bin libopenmpi-dev libnetcdf-dev libhdf5-dev libcgns-dev libmatio-dev libfmt-dev - - - name: Run cmake - shell: bash -l {0} - run: | - echo $HOME - find /usr/include -name cgnslib.h - mkdir build - cd build - NETCDF_PATH=/usr MODERN=YES NUMPROCS=2 COMPILER=${{ matrix.compiler }} INSTALL_PATH=${HOME} bash ../cmake-config - - - name: Build - shell: bash -l {0} - run: | - cd build - make -j 4 - if: ${{ success() }} - - - name: Install - shell: bash -l {0} - run: | - cd build - make -j 4 install - if: ${{ success() }} - - - name: Run Tests - shell: bash -l {0} - run: | - cd build - ctest -j 4 --output-on-failure - if: ${{ success() }} diff --git a/.github/workflows/build_netcdf_no_hdf5.yml b/.github/workflows/build_netcdf_no_hdf5.yml deleted file mode 100644 index 06560b7..0000000 --- a/.github/workflows/build_netcdf_no_hdf5.yml +++ /dev/null @@ -1,130 +0,0 @@ -# This is a basic workflow to help you get started with Actions -name: SEACAS no-hdf5-netcdf builds - -# Controls when the action will run. Triggers the workflow on push -on: - push: - branches: - - master - pull_request: - branches: - - master - -jobs: - - build-deps: - - runs-on: ubuntu-latest - - strategy: - matrix: - compiler: [ gnu, clang, mpi ] - netcdf: [ 4.9.2 ] - steps: - - - uses: actions/checkout@v3 - - - name: Install System dependencies - shell: bash -l {0} - run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev openmpi-bin libopenmpi-dev - - ### - # Installing TPL - ### - - name: Cache TPL-${{ matrix.compiler }}-${{ matrix.netcdf }} - id: cache-TPL-mpi - uses: actions/cache@v3 - with: - path: ~/environments/${{ matrix.compiler }}-${{ matrix.netcdf }} - key: TPL-v4-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.netcdf }} - - - name: Build TPL-${{ matrix.compiler }}-${{ matrix.netcdf }} - if: steps.cache-TPL.outputs.cache-hit != 'true' - run: | - set -x - COMPILER=${{ matrix.compiler }} HDF5=NO GNU_PARALLEL=OFF INSTALL_PATH=${HOME}/environments/${{ matrix.compiler }}-${{ matrix.netcdf }} ./install-tpl.sh - ls ${HOME} && ls ${HOME}/environments && ls ${HOME}/environments/${{ matrix.compiler }}-${{ matrix.netcdf }} && ls ${HOME}/environments/${{ matrix.compiler }}-${{ matrix.netcdf }}/lib - - - build: - needs: build-deps - - # The type of runner that the job will run on - name: ${{ matrix.config.name }} - runs-on: ${{ matrix.config.os }} - strategy: - fail-fast: false - matrix: - netcdf: [ 4.9.2 ] - config: - - { - name: "Debug serial build", - os: ubuntu-latest, - compiler: "gnu", - debug: "YES", - extra: "", - } - - { - name: "Debug parallel build", - os: ubuntu-latest, - compiler: "mpi", - debug: "YES", - extra: "", - } - - { - name: "Use modern CMake configure of netCDF package", - os: ubuntu-latest, - compiler: "mpi", - debug: "NO", - extra: "MODERN=YES", - } - steps: - - - uses: actions/checkout@v3 - - - name: Install System dependencies - shell: bash -l {0} - run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev openmpi-bin libopenmpi-dev - - - name: Fetch TPL Cache - id: cache-TPL - uses: actions/cache@v3 - with: - path: ~/environments/${{ matrix.config.compiler }}-${{ matrix.netcdf }} - key: TPL-v4-${{ runner.os }}-${{ matrix.config.compiler }}-${{ matrix.netcdf }} - - - name: Check Cache - shell: bash -l {0} - run: ls ${HOME} && ls ${HOME}/environments && ls ${HOME}/environments/${{ matrix.config.compiler }}-${{ matrix.netcdf }} && ls ${HOME}/environments/${{ matrix.config.compiler }}-${{ matrix.netcdf }}/lib - -### -# Configure and build -### - - name: Run cmake - shell: bash -l {0} - run: | - echo $HOME - mkdir build - cd build - NUMPROCS=2 ${{ matrix.config.extra }} DEBUG=${{ matrix.config.debug }} COMPILER=${{ matrix.config.compiler }} INSTALL_PATH=${HOME}/environments/${{ matrix.config.compiler }}-${{ matrix.netcdf }} bash ../cmake-config - - - name: Build - shell: bash -l {0} - run: | - cd build - make -j 4 - if: ${{ success() }} - - - name: Install - shell: bash -l {0} - run: | - cd build - make -j 4 install - if: ${{ success() }} - - - name: Run Tests - shell: bash -l {0} - run: | - cd build - ctest -j 4 --output-on-failure - if: ${{ success() }} diff --git a/.github/workflows/build_test.yml b/.github/workflows/build_test.yml deleted file mode 100644 index 5f5de18..0000000 --- a/.github/workflows/build_test.yml +++ /dev/null @@ -1,129 +0,0 @@ -name: Build and run SEACAS tests - -on: - push: - branches: - - master - pull_request: - branches: - - master - -jobs: - - build-deps: - - runs-on: ubuntu-latest - - strategy: - matrix: - compiler: [ gnu, clang, mpi ] - hdf5: [ V18, V110, V114 ] - netcdf: [ 4.9.2 ] - cgns: [ 4.3.0 ] - steps: - - - uses: actions/checkout@v3 - - - name: Install System dependencies - shell: bash -l {0} - run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev openmpi-bin libopenmpi-dev - - ### - # Installing TPL - ### - - name: Cache TPL-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} - id: cache-TPL - uses: actions/cache@v3 - with: - path: ~/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} - key: TPL-v4-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} - - - name: Build TPL-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} - if: steps.cache-TPL.outputs.cache-hit != 'true' - run: | - echo $HOME - set -x - COMPILER=${{ matrix.compiler }} H5VERSION=${{ matrix.hdf5}} GNU_PARALLEL=OFF INSTALL_PATH=${HOME}/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} ./install-tpl.sh - ls ${HOME} && ls ${HOME}/environments && ls ${HOME}/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} && ls ${HOME}/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}/lib - -### -# Fetch Cache -### - - seacas-build: - - needs: build-deps - runs-on: ubuntu-latest - - strategy: - matrix: - compiler: [ gnu, clang, mpi ] - hdf5: [ V18, V110, V114 ] - netcdf: [ 4.9.2 ] - cgns: [ 4.3.0 ] - steps: - - - uses: actions/checkout@v3 - - - name: Install System dependencies - shell: bash -l {0} - run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev openmpi-bin libopenmpi-dev - - - name: Fetch TPL Cache - id: cache-TPL - uses: actions/cache@v3 - with: - path: ~/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} - key: TPL-v4-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} - - - name: Check Cache - shell: bash -l {0} - run: ls ${HOME} && ls ${HOME}/environments && ls ${HOME}/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} && ls ${HOME}/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}/lib - -### -# Configure and build -### - - name: Setup Python - uses: actions/setup-python@v3 - with: - python-version: '3.11' - - - name: Install NumPy - shell: bash -l {0} - run: pip install numpy - - - name: Run cmake - shell: bash -l {0} - run: | - echo $HOME - mkdir build - cd build - NUMPROCS=2 COMPILER=${{ matrix.compiler }} INSTALL_PATH=${HOME}/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} bash ../cmake-config - - - name: Build - shell: bash -l {0} - run: | - cd build - make -j 4 - if: ${{ success() }} - - - name: Install - shell: bash -l {0} - run: | - cd build - make -j 4 install - if: ${{ success() }} - - - name: Run Tests - shell: bash -l {0} - run: | - cd build - ctest -j 4 --output-on-failure - if: ${{ success() }} - - - name: Run SEACAS-Test - shell: bash -l {0} - run: | - cd SEACAS-Test - make BASE=${HOME}/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} test - if: ${{ success() }} diff --git a/.github/workflows/build_variant.yml b/.github/workflows/build_variant.yml deleted file mode 100644 index c6360cf..0000000 --- a/.github/workflows/build_variant.yml +++ /dev/null @@ -1,309 +0,0 @@ -# This is a basic workflow to help you get started with Actions -name: SEACAS Variant builds - -# Controls when the action will run. Triggers the workflow on push -on: - push: - branches: - - master - pull_request: - branches: - - master - -jobs: - - build-deps: - - runs-on: ubuntu-latest - - strategy: - matrix: - compiler: [ gnu, clang, mpi ] - hdf5: [ V110 ] - netcdf: [ 4.9.2 ] - cgns: [ 4.3.0 ] - steps: - - - uses: actions/checkout@v3 - - - name: Install System dependencies - shell: bash -l {0} - run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev openmpi-bin libopenmpi-dev - - ### - # Installing TPL - ### - - name: Cache TPL-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} - id: cache-TPL-mpi - uses: actions/cache@v3 - with: - path: ~/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} - key: TPL-v4-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} - - - name: Build TPL-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} - if: steps.cache-TPL.outputs.cache-hit != 'true' - run: | - set -x - COMPILER=${{ matrix.compiler }} H5VERSION=${{ matrix.hdf5}} GNU_PARALLEL=OFF INSTALL_PATH=${HOME}/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} ./install-tpl.sh - ls ${HOME} && ls ${HOME}/environments && ls ${HOME}/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} && ls ${HOME}/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}/lib - - - build: - needs: build-deps - - # The type of runner that the job will run on - name: ${{ matrix.config.name }} - runs-on: ${{ matrix.config.os }} - strategy: - fail-fast: false - matrix: - hdf5: [ V110 ] - netcdf: [ 4.9.2 ] - cgns: [ 4.3.0 ] - config: - - { - name: "Debug serial build", - os: ubuntu-latest, - compiler: "gnu", - debug: "YES", - threadsafe: "NO", - fortran: "YES", - use_kokkos: "NO", - use_adios2: "NO", - use_catalyst2: "NO", - gtest: "NO", - extra: "", - sanitizer: "NO" # address, integer, thread, memory, undefined - } - - { - name: "Debug parallel build", - os: ubuntu-latest, - compiler: "mpi", - debug: "YES", - threadsafe: "NO", - fortran: "YES", - use_kokkos: "NO", - use_adios2: "NO", - use_catalyst2: "NO", - gtest: "NO", - extra: "", - sanitizer: "NO" # address, integer, thread, memory, undefined - } - - { - name: "Threadsafe ON, No Fortran", - os: ubuntu-latest, - compiler: "gnu", - debug: "YES", - threadsafe: "YES", - fortran: "NO", - use_kokkos: "NO", - use_adios2: "NO", - use_catalyst2: "NO", - gtest: "NO", - extra: "", - sanitizer: "thread" # address, integer, thread, memory, undefined - } - - { - name: "Threadsafe ON, Parallel, No Fortran", - os: ubuntu-latest, - compiler: "mpi", - debug: "YES", - threadsafe: "YES", - fortran: "NO", - use_kokkos: "NO", - use_adios2: "NO", - use_catalyst2: "NO", - gtest: "NO", - extra: "", - sanitizer: "thread" # address, integer, thread, memory, undefined - } - - { - name: "Sanitize address, no fortran", - os: ubuntu-latest, - compiler: "clang", - debug: "YES", - threadsafe: "NO", - fortran: "NO", - use_kokkos: "NO", - use_adios2: "NO", - use_catalyst2: "NO", - gtest: "NO", - extra: "", - sanitizer: "address" # address, integer, thread, memory, undefined - } - - { - name: "Sanitize undefined", - os: ubuntu-latest, - compiler: "clang", - debug: "YES", - threadsafe: "NO", - fortran: "YES", - use_kokkos: "NO", - use_adios2: "NO", - use_catalyst2: "NO", - gtest: "NO", - extra: "", - sanitizer: "undefined" # address, integer, thread, memory, undefined - } - - { - name: "Sanitize integer", - os: ubuntu-latest, - compiler: "clang", - debug: "YES", - threadsafe: "NO", - fortran: "NO", - use_kokkos: "NO", - use_adios2: "NO", - use_catalyst2: "NO", - gtest: "NO", - extra: "", - sanitizer: "integer" # address, integer, thread, memory, undefined - } - - { - name: "GTest Enabled", - os: ubuntu-latest, - compiler: "gnu", - debug: "YES", - threadsafe: "NO", - fortran: "YES", - use_kokkos: "NO", - use_adios2: "NO", - use_catalyst2: "NO", - gtest: "YES", - extra: "", - sanitizer: "NO" # address, integer, thread, memory, undefined - } - - { - name: "No applications, legacy, or fortran", - os: ubuntu-latest, - compiler: "clang", - debug: "NO", - threadsafe: "NO", - fortran: "NO", - use_kokkos: "NO", - use_adios2: "NO", - use_catalyst2: "NO", - gtest: "NO", - extra: "APPLICATIONS=NO LEGACY=NO", - sanitizer: "NO" # address, integer, thread, memory, undefined - } - - { - name: "CATALYST2, serial", - os: ubuntu-latest, - compiler: "clang", - debug: "NO", - threadsafe: "NO", - fortran: "YES", - use_kokkos: "NO", - use_adios2: "NO", - use_catalyst2: "YES", - gtest: "NO", - extra: "", - sanitizer: "NO" # address, integer, thread, memory, undefined - } - - { - name: "KOKKOS, parallel", - os: ubuntu-latest, - compiler: "mpi", - debug: "NO", - threadsafe: "NO", - fortran: "YES", - use_kokkos: "YES", - use_adios2: "NO", - use_catalyst2: "NO", - gtest: "NO", - extra: "", - sanitizer: "NO" # address, integer, thread, memory, undefined - } - - { - name: "No deprecated exodus functions", - os: ubuntu-latest, - compiler: "mpi", - debug: "NO", - threadsafe: "NO", - fortran: "YES", - use_kokkos: "NO", - use_adios2: "NO", - use_catalyst2: "NO", - gtest: "NO", - extra: "OMIT_DEPRECATED=YES", - sanitizer: "NO" # address, integer, thread, memory, undefined - } - - { - name: "Use modern CMake configure of netCDF and HDF5 packages", - os: ubuntu-latest, - compiler: "mpi", - debug: "NO", - threadsafe: "NO", - fortran: "YES", - use_kokkos: "NO", - use_adios2: "NO", - use_catalyst2: "NO", - gtest: "NO", - extra: "MODERN=YES", - sanitizer: "NO" # address, integer, thread, memory, undefined - } - steps: - - - uses: actions/checkout@v3 - - - name: Install System dependencies - shell: bash -l {0} - run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev openmpi-bin libopenmpi-dev - - - name: Fetch TPL Cache - id: cache-TPL - uses: actions/cache@v3 - with: - path: ~/environments/${{ matrix.config.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} - key: TPL-v4-${{ runner.os }}-${{ matrix.config.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} - - - name: Check Cache - shell: bash -l {0} - run: ls ${HOME} && ls ${HOME}/environments && ls ${HOME}/environments/${{ matrix.config.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} && ls ${HOME}/environments/${{ matrix.config.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}/lib - - - name: install additional TPL - if: ${{ matrix.config.use_kokkos == 'YES' || matrix.config.use_adios2 == 'YES' || matrix.config.gtest == 'YES' || matrix.config.use_catalyst == 'YES' }} - run: | - set -x - COMPILER=${{ matrix.config.compiler }} KOKKOS=${{ matrix.config.use_kokkos }} ADIOS2=${{ matrix.config.use_adios2 }} CATALYST2=${{ matrix.config.use_catalyst2 }} GNU_PARALLEL=OFF GTEST=${{ matrix.config.gtest }} INSTALL_PATH=${HOME}/environments/${{ matrix.config.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} ./install-tpl.sh - ls ${HOME} && ls ${HOME}/environments && ls ${HOME}/environments/${{ matrix.config.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} && ls ${HOME}/environments/${{ matrix.config.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}/lib - -### -# Configure and build -### - - name: Run cmake - shell: bash -l {0} - run: | - echo $HOME - mkdir build - cd build - NUMPROCS=2 ${{ matrix.config.extra }} THREADSAFE=${{ matrix.config.threadsafe }} DEBUG=${{ matrix.config.debug }} FORTRAN=${{ matrix.config.fortran }} SANITIZER=${{ matrix.config.sanitizer }} COMPILER=${{ matrix.config.compiler }} INSTALL_PATH=${HOME}/environments/${{ matrix.config.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} bash ../cmake-config - - - name: Build - shell: bash -l {0} - run: | - cd build - make -j 4 - if: ${{ success() }} - - - name: Install - shell: bash -l {0} - run: | - cd build - make -j 4 install - if: ${{ success() }} - - - name: Run Non-sanitized Tests - shell: bash -l {0} - run: | - cd build - ctest -j 4 --output-on-failure - if: ${{ success() && matrix.config.sanitizer == 'NO' && matrix.config.threadsafe == 'NO' }} - - - name: Run sanitized/threadsafe Tests - shell: bash -l {0} - run: | - cd build - ctest -j 4 --output-on-failure --exclude-regex test_exo - if: ${{ success() && (matrix.config.sanitizer != 'NO' || matrix.config.threadsafe != 'NO') }} diff --git a/.github/workflows/ci-build.sh b/.github/workflows/ci-build.sh deleted file mode 100644 index 7c57c1e..0000000 --- a/.github/workflows/ci-build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/bash -set -e -pwd - -echo "$HOME" -mkdir build -cd build -bash ../cmake-config -make -j4 -ctest -j 4 --output-on-failure diff --git a/.github/workflows/cla.yml b/.github/workflows/cla.yml deleted file mode 100644 index caa749b..0000000 --- a/.github/workflows/cla.yml +++ /dev/null @@ -1,35 +0,0 @@ -name: "CLA Assistant" -on: - pull_request_target: - types: [opened,closed,synchronize] - -jobs: - CLAssistant: - runs-on: ubuntu-latest - steps: - - name: "CLA Assistant" - if: (github.event.comment.body == 'recheck' || github.event.comment.body == 'I have read the CLA Document and I hereby sign the CLA') || github.event_name == 'pull_request_target' - # Beta Release - uses: cla-assistant/github-action@v2.1.3-beta - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - # the below token should have repo scope and must be manually added by you in the repository's secret - PERSONAL_ACCESS_TOKEN : ${{ secrets.PERSONAL_ACCESS_TOKEN }} - with: - path-to-signatures: 'signatures/version1/cla.json' - path-to-document: 'https://github.com/sandialabs/seacas/blob/master/SEACAS-CLA.md' - # branch should not be protected - branch: 'master' - allowlist: user1,bot*,*@sandia.gov - - #below are the optional inputs - If the optional inputs are not given, then default values will be taken - #remote-organization-name: enter the remote organization name where the signatures should be stored (Default is storing the signatures in the same repository) - #remote-repository-name: enter the remote repository name where the signatures should be stored (Default is storing the signatures in the same repository) - #create-file-commit-message: 'For example: Creating file for storing CLA Signatures' - #signed-commit-message: 'For example: $contributorName has signed the CLA in #$pullRequestNo' - #custom-notsigned-prcomment: 'pull request comment with Introductory message to ask new contributors to sign' - #custom-pr-sign-comment: 'The signature to be committed in order to sign the CLA' - #custom-allsigned-prcomment: 'pull request comment when all contributors has signed, defaults to **CLA Assistant Lite bot** All Contributors have signed the CLA.' - #lock-pullrequest-aftermerge: false - if you don't want this bot to automatically lock the pull request after merging (default - true) - #use-dco-flag: true - If you are using DCO instead of CLA - diff --git a/.github/workflows/coverity-scan.yml b/.github/workflows/coverity-scan.yml deleted file mode 100644 index e3b633a..0000000 --- a/.github/workflows/coverity-scan.yml +++ /dev/null @@ -1,119 +0,0 @@ -name: coverity-scan -on: - push: - branches: - - coverity -jobs: - - build-deps: - - runs-on: ubuntu-latest - - strategy: - matrix: - compiler: [ gnu ] - hdf5: [ V110 ] - netcdf: [ 4.9.2 ] - cgns: [ 4.3.0 ] - steps: - - - uses: actions/checkout@v3 - - - name: Install System dependencies - shell: bash -l {0} - run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev openmpi-bin libopenmpi-dev - - ### - # Installing TPL - ### - - name: Cache TPL-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} - id: cache-TPL - uses: actions/cache@v3 - with: - path: ~/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} - key: TPL-v2-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} - - - name: Build TPL-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} - if: steps.cache-TPL.outputs.cache-hit != 'true' - run: | - echo $HOME - set -x - COMPILER=${{ matrix.compiler }} H5VERSION=${{ matrix.hdf5}} GNU_PARALLEL=OFF INSTALL_PATH=${HOME}/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} ./install-tpl.sh - ls ${HOME} && ls ${HOME}/environments && ls ${HOME}/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} && ls ${HOME}/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}/lib - -### -# Fetch Cache -### - - seacas-build: - - needs: build-deps - runs-on: ubuntu-latest - - strategy: - matrix: - compiler: [ gnu ] - hdf5: [ V110 ] - netcdf: [ 4.9.2 ] - cgns: [ 4.3.0 ] - steps: - - - uses: actions/checkout@v3 - - - name: Install System dependencies - shell: bash -l {0} - run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev openmpi-bin libopenmpi-dev - - - name: Fetch TPL Cache - id: cache-TPL - uses: actions/cache@v3 - with: - path: ~/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} - key: TPL-v2-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} - - - name: Check Cache - shell: bash -l {0} - run: ls ${HOME} && ls ${HOME}/environments && ls ${HOME}/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} && ls ${HOME}/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}/lib - -### -# Configure and build -### - - name: Download Coverity Build Tool - run: | - wget -q https://scan.coverity.com/download/linux64 --post-data "token=$TOKEN&project=gsjaardema%2Fseacas" -O coverity_tool.tgz - mkdir cov-analysis-linux64 - tar xzf coverity_tool.tgz --strip 1 -C cov-analysis-linux64 - env: - TOKEN: ${{ secrets.COVERITY_SCAN_TOKEN }} - - - name: Run cmake - shell: bash -l {0} - run: | - echo $HOME - mkdir build - cd build - ZOLTAN=NO INSTALL_PATH=${HOME}/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} bash ../cmake-config coverity - - - name: Build - shell: bash -l {0} - run: | - cd build - mkdir cov-int - ../cov-analysis-linux64/bin/cov-build --dir cov-int make -j 4 - if: ${{ success() }} - - - name: Submit the result to Coverity Scan - run: | - cd build - tail cov-int/build-log.txt - tar czf seacas.tgz cov-int - curl \ - --form token="$TOKEN" \ - --form email=gsjaardema@gmail.com \ - --form file=@seacas.tgz \ - --form version="master" \ - --form description="SEACAS Github Actions Coverity Scan" \ - https://scan.coverity.com/builds?project=gsjaardema%2Fseacas - env: - TOKEN: ${{ secrets.COVERITY_SCAN_TOKEN }} - if: ${{ success() }} diff --git a/.github/workflows/docker-exodus.yml b/.github/workflows/docker-exodus.yml deleted file mode 100644 index dcdeca9..0000000 --- a/.github/workflows/docker-exodus.yml +++ /dev/null @@ -1,30 +0,0 @@ -name: docker-exodus -on: - push: - branches: [ "master" ] -jobs: - build-latest: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - - name: Docker login - uses: docker/login-action@v2 - with: - username: ${{ secrets.DOCKERHUB_USERNAME }} - password: ${{ secrets.DOCKERHUB_TOKEN }} - - name: Docker build and push - uses: docker/build-push-action@v3 - with: - context: docker/exodus - push: true - tags: mrbuche/exodus:latest - - name: Delay before pull - run: sleep 234s - test-latest: - needs: build-latest - runs-on: ubuntu-latest - container: mrbuche/exodus - steps: - - name: Docker pull and test - run: | - python -c 'import exodus3 as exodus' diff --git a/.github/workflows/docker-seacas.yml b/.github/workflows/docker-seacas.yml deleted file mode 100644 index 7f61b22..0000000 --- a/.github/workflows/docker-seacas.yml +++ /dev/null @@ -1,32 +0,0 @@ -name: docker-seacas -on: - push: - branches: [ "master" ] -jobs: - build-latest: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - - name: Docker login - uses: docker/login-action@v2 - with: - username: ${{ secrets.DOCKERHUB_USERNAME }} - password: ${{ secrets.DOCKERHUB_TOKEN }} - - name: Docker build and push - uses: docker/build-push-action@v3 - with: - context: docker/seacas - push: true - tags: mrbuche/seacas:latest - - name: Delay before pull - run: sleep 234s - test-latest: - needs: build-latest - runs-on: ubuntu-latest - container: mrbuche/seacas - steps: - - name: Docker pull and test - run: | - cd /seacas/build/ && ctest --output-on-failure && cd - cd /seacas/SEACAS-Test/ && make test && cd - python -c 'import exodus3 as exodus' diff --git a/.github/workflows/intel-build.yml b/.github/workflows/intel-build.yml deleted file mode 100644 index 2879081..0000000 --- a/.github/workflows/intel-build.yml +++ /dev/null @@ -1,169 +0,0 @@ -name: Intel OneAPI build - -on: - push: - branches: - - master - pull_request: - branches: - - master - -jobs: - build-deps: - - runs-on: ubuntu-latest - - strategy: - matrix: - compiler: [ intel, mpi ] - hdf5: [ V114 ] - netcdf: [ 4.9.2 ] - cgns: [ 4.3.0 ] - - defaults: - run: - shell: bash --noprofile --norc {0} - - steps: - - uses: actions/checkout@v3 - - name: setup repo - run: | - wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB - sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB - rm GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB - sudo echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list - sudo apt-get update - - name: install - run: | - sudo apt-get install -y intel-oneapi-common-vars - sudo apt-get install -y intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic - sudo apt-get install -y intel-oneapi-compiler-fortran - sudo apt-get install -y intel-oneapi-mpi - sudo apt-get install -y intel-oneapi-mpi-devel - sudo apt-get install -y intel-oneapi-mkl - sudo apt-get install -y ninja-build - - - name: Install System dependencies - shell: bash -l {0} - run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev - - ### - # Installing TPL - ### - - name: Cache TPL-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} - id: cache-TPL - uses: actions/cache@v3 - with: - path: ~/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} - key: TPL-v5intel-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} - - - name: Build TPL-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} - if: steps.cache-TPL.outputs.cache-hit != 'true' - run: | - echo $HOME - set -x - source /opt/intel/oneapi/setvars.sh - printenv >> $GITHUB_ENV - COMPILER=${{ matrix.compiler }} H5VERSION=${{ matrix.hdf5}} GNU_PARALLEL=OFF INSTALL_PATH=${HOME}/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} ./install-tpl.sh - ls ${HOME} && ls ${HOME}/environments && ls ${HOME}/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} && ls ${HOME}/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}/lib - - seacas-build: - - needs: build-deps - runs-on: ubuntu-latest - - strategy: - matrix: - compiler: [ intel, mpi ] - hdf5: [ V114 ] - netcdf: [ 4.9.2 ] - cgns: [ 4.3.0 ] - steps: - - - uses: actions/checkout@v3 - - name: setup repo - run: | - wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB - sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB - rm GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB - sudo echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list - sudo apt-get update - - name: install - run: | - sudo apt-get install -y intel-oneapi-common-vars - sudo apt-get install -y intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic - sudo apt-get install -y intel-oneapi-compiler-fortran - sudo apt-get install -y intel-oneapi-mpi - sudo apt-get install -y intel-oneapi-mpi-devel - sudo apt-get install -y intel-oneapi-mkl - sudo apt-get install -y ninja-build - - - name: Install System dependencies - shell: bash -l {0} - run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev - - - name: Fetch TPL Cache - id: cache-TPL - uses: actions/cache@v3 - with: - path: ~/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} - key: TPL-v5intel-${{ runner.os }}-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} - - - name: Check Cache - shell: bash -l {0} - run: ls ${HOME} && ls ${HOME}/environments && ls ${HOME}/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} && ls ${HOME}/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}/lib - -### -# Configure and build -### - - name: List directory - shell: bash -l {0} - run: | - echo $HOME - ls ${HOME}/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}/lib - ls ${HOME}/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}/include - - - name: Run cmake - shell: bash -l {0} - run: | - echo $HOME - mkdir build - cd build - source /opt/intel/oneapi/setvars.sh - printenv >> $GITHUB_ENV - NUMPROCS=2 COMPILER=${{ matrix.compiler }} INSTALL_PATH=${HOME}/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} bash ../cmake-config - - - name: Build - shell: bash -l {0} - run: | - cd build - make -j 4 - if: ${{ success() }} - - - name: Install - shell: bash -l {0} - run: | - cd build - make -j 4 install - if: ${{ success() }} - - - name: Run Tests - shell: bash -l {0} - run: | - cd build - ctest -j 4 --output-on-failure - if: ${{ success() }} - -# - name: Compile -# run: | -# source /opt/intel/oneapi/setvars.sh -# printenv >> $GITHUB_ENV -# ifort test.f90 -o test_program -# mpiifort test2.f90 -o mpitest - -# - name: "Test the code" -# run: | -# echo "Running the tests using the Intel oneapi fortran compiler" -# cd tests/test01 -# mpirun -np 1 $HOME/work/reponame/reponame/mpitest -# ./$HOME/work/reponame/reponame/test_program diff --git a/.github/workflows/msys2.yml b/.github/workflows/msys2.yml deleted file mode 100644 index 2af9345..0000000 --- a/.github/workflows/msys2.yml +++ /dev/null @@ -1,26 +0,0 @@ -name: SEACAS MSYS2 Build -on: - push: - branches: - - master - pull_request: - branches: - - master - -jobs: - build: - runs-on: windows-latest - defaults: - run: - shell: msys2 {0} - steps: - - uses: actions/checkout@v3 - - uses: msys2/setup-msys2@v2 - with: - msystem: MINGW64 - update: true - install: git mingw-w64-x86_64-toolchain make mingw-w64-x86_64-hdf5 mingw-w64-x86_64-cgns mingw-w64-x86_64-netcdf mingw-w64-x86_64-zlib mingw-w64-x86_64-gcc-fortran mingw-w64-x86_64-gcc-libgfortran mingw-w64-x86_64-cmake mingw-w64-x86_64-fmt - - name: CI-Build - run: | - echo 'Running in MSYS2!' - ./ci-msys2-build.sh diff --git a/.github/workflows/python-linting.yml b/.github/workflows/python-linting.yml deleted file mode 100644 index a5cbb80..0000000 --- a/.github/workflows/python-linting.yml +++ /dev/null @@ -1,34 +0,0 @@ -name: Python Linting -on: - push: - branches: - - master - pull_request: - branches: - - master - workflow_dispatch: -jobs: - build: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: '3.10' - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install flake8 - pip install pylint - - name: Lint exodus.py - run: | - flake8 --ignore E501,W503 packages/seacas/scripts/exodus3.in.py - - name: Lint exomerge.py - if: success() || failure() - run: | - flake8 --ignore E501,W503,W504 packages/seacas/scripts/exomerge3.py - - name: Lint exodus tests - if: success() || failure() - run: | - flake8 --ignore E501,E402,W503,W605 packages/seacas/scripts/tests diff --git a/.github/workflows/stale.yml b/.github/workflows/stale.yml deleted file mode 100644 index 3404517..0000000 --- a/.github/workflows/stale.yml +++ /dev/null @@ -1,19 +0,0 @@ -name: Mark stale issues and pull requests - -on: - schedule: - - cron: "30 1 * * *" - -jobs: - stale: - - runs-on: ubuntu-latest - - steps: - - uses: actions/stale@v1 - with: - repo-token: ${{ secrets.GITHUB_TOKEN }} - stale-issue-message: 'Stale issue message' - stale-pr-message: 'Stale pull request message' - stale-issue-label: 'no-issue-activity' - stale-pr-label: 'no-pr-activity' diff --git a/.github/workflows/trailing.yml b/.github/workflows/trailing.yml deleted file mode 100644 index 2fd3c7b..0000000 --- a/.github/workflows/trailing.yml +++ /dev/null @@ -1,11 +0,0 @@ -name: CI Formatting -on: - workflow_dispatch: - -jobs: - trailing: - name: Find Trailing Whitespace - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - - uses: harupy/find-trailing-whitespace@master diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..f6cc3cc --- /dev/null +++ b/.gitignore @@ -0,0 +1,4 @@ +/build/ +/lib/ +/include/ +SeacasRepoVersion.txt diff --git a/DEPENDENCIES b/DEPENDENCIES index 0989292..c716988 100644 --- a/DEPENDENCIES +++ b/DEPENDENCIES @@ -1,2 +1,2 @@ -netcdf-c >= 4.6.1 -hdf5 >= 1.10.3 +NetCDF-C >= 4.6.1 +HDF5 >= 1.10.3