Added DEPENDENCIES

.github/workflows/build_external_lib.yml

@@ -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() }}

.github/workflows/build_netcdf_no_hdf5.yml

@@ -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() }}

.github/workflows/build_test.yml

@@ -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() }}

.github/workflows/build_variant.yml

@@ -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') }}

.github/workflows/ci-build.sh

@@ -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

.github/workflows/cla.yml

@@ -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
-

.github/workflows/coverity-scan.yml

@@ -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() }}

.github/workflows/docker-exodus.yml

@@ -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'

.github/workflows/docker-seacas.yml

@@ -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'

.github/workflows/intel-build.yml

@@ -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

.github/workflows/msys2.yml

@@ -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

.github/workflows/python-linting.yml

@@ -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

.github/workflows/stale.yml

@@ -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'

.github/workflows/trailing.yml

@@ -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

.gitignore

@@ -0,0 +1,4 @@
+/build/
+/lib/
+/include/
+SeacasRepoVersion.txt

DEPENDENCIES

@@ -1,2 +1,2 @@
-netcdf-c >= 4.6.1
-hdf5 >= 1.10.3
+NetCDF-C >= 4.6.1
+HDF5 >= 1.10.3