Merge branch 'master' into discontinuous-galerkin

.appveyor.yml

@@ -57,16 +57,16 @@ build_script:
      -DNetCDF_ROOT:PATH=%LIB_ROOT% ^
      -DSEACASExodus_ENABLE_THREADSAFE:BOOL=OFF ^
      -DSEACASIoss_ENABLE_THREADSAFE:BOOL=OFF ^
-     -DSEACASProj_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON ^
-     -DSEACASProj_ENABLE_ALL_PACKAGES:BOOL=ON ^
-     -DSEACASProj_ENABLE_DOXYGEN:BOOL=OFF ^
-     -DSEACASProj_ENABLE_Fortran=OFF ^
-     -DSEACASProj_ENABLE_SEACAS:BOOL=ON ^
-     -DSEACASProj_ENABLE_SECONDARY_TESTED_CODE:BOOL=ON ^
-     -DSEACASProj_ENABLE_TESTS=ON ^
-     -DSEACASProj_ENABLE_Zoltan:BOOL=OFF ^
-     -DSEACASProj_HIDE_DEPRECATED_CODE:BOOL=ON ^
-     -DSEACASProj_SKIP_FORTRANCINTERFACE_VERIFY_TEST:BOOL=ON ^
+     -DSeacas_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON ^
+     -DSeacas_ENABLE_ALL_PACKAGES:BOOL=ON ^
+     -DSeacas_ENABLE_DOXYGEN:BOOL=OFF ^
+     -DSeacas_ENABLE_Fortran=OFF ^
+     -DSeacas_ENABLE_SEACAS:BOOL=ON ^
+     -DSeacas_ENABLE_SECONDARY_TESTED_CODE:BOOL=ON ^
+     -DSeacas_ENABLE_TESTS=ON ^
+     -DSeacas_ENABLE_Zoltan:BOOL=OFF ^
+     -DSeacas_HIDE_DEPRECATED_CODE:BOOL=ON ^
+     -DSeacas_SKIP_FORTRANCINTERFACE_VERIFY_TEST:BOOL=ON ^
      -DTPL_ENABLE_ADIOS2:BOOL=OFF ^
      -DTPL_ENABLE_CGNS:BOOL=OFF ^
      -DTPL_ENABLE_Kokkos:BOOL=OFF ^

.github/workflows/build_external_lib.yml

@@ -0,0 +1,57 @@
+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

@@ -0,0 +1,130 @@
+# 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

@@ -1,26 +1,28 @@
 name: Build and run SEACAS tests
 
-on: 
+on:
   push:
-    branches-ignore:
-      - 'coverity'
+    branches:
+    - master
   pull_request:
+    branches:
+    - master
 
 jobs:
 
   build-deps:
 
     runs-on: ubuntu-latest
-    
+
     strategy:
       matrix:
         compiler: [ gnu, clang, mpi ]
-        hdf5: [ V18, V110, V112 ]
-        netcdf: [ 4.8.1 ]
-        cgns: [ 4.2.0 ]
+        hdf5: [ V18, V110, V114 ]
+        netcdf: [ 4.9.2 ]
+        cgns: [ 4.3.0 ]
     steps:
 
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Install System dependencies
         shell: bash -l {0}
@@ -31,10 +33,10 @@ jobs:
         ###
       - name: Cache TPL-${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
         id: cache-TPL
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ~/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
-          key: TPL-v5-${{ runner.os }}-${{ 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'
@@ -49,30 +51,30 @@ jobs:
 ###
 
   seacas-build:
-  
+
     needs: build-deps
     runs-on: ubuntu-latest
 
     strategy:
       matrix:
         compiler: [ gnu, clang, mpi ]
-        hdf5: [ V18, V110, V112 ]
-        netcdf: [ 4.8.1 ]
-        cgns: [ 4.2.0 ]
+        hdf5: [ V18, V110, V114 ]
+        netcdf: [ 4.9.2 ]
+        cgns: [ 4.3.0 ]
     steps:
 
-      - uses: actions/checkout@v2
+      - 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@v2
+        uses: actions/cache@v3
         with:
           path: ~/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }}
-          key: TPL-v5-${{ runner.os }}-${{ 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}
@@ -81,6 +83,15 @@ jobs:
 ###
 # 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: |
@@ -89,17 +100,17 @@ jobs:
           cd build
           NUMPROCS=2 COMPILER=${{ matrix.compiler }} INSTALL_PATH=${HOME}/environments/${{ matrix.compiler }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-${{ matrix.cgns }} bash ../cmake-config
 
-      - name: Build 
+      - name: Build
         shell: bash -l {0}
         run: |
-          cd build 
+          cd build
           make -j 4
         if: ${{ success() }}
 
       - name: Install
         shell: bash -l {0}
         run: |
-          cd build 
+          cd build
           make -j 4 install
         if: ${{ success() }}
 
@@ -109,3 +120,10 @@ jobs:
           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() }}