Merge branch 'develop' into sunspot

brtnfld · Apr 1, 2024 · 9041c03 · 9041c03
2 parents 7bc94b9 + a314a7a
commit 9041c03
Show file tree

Hide file tree

Showing 86 changed files with 2,140 additions and 921 deletions.
diff --git a/.github/workflows/aocc-auto.yml b/.github/workflows/aocc-auto.yml
@@ -28,43 +28,43 @@ jobs:
           sudo apt install -y zlib1g-dev libcurl4-openssl-dev libjpeg-dev wget curl bzip2
           sudo apt install -y m4 flex bison cmake libzip-dev openssl build-essential
 
-      - name: Install AOCC 4.1.0
+      - name: Install AOCC 4.2.0
         shell: bash
         run: |
-          wget https://download.amd.com/developer/eula/aocc/aocc-4-1/aocc-compiler-4.1.0.tar
-          tar -xvf aocc-compiler-4.1.0.tar
-          cd aocc-compiler-4.1.0
+          wget https://download.amd.com/developer/eula/aocc/aocc-4-2/aocc-compiler-4.2.0.tar
+          tar -xvf aocc-compiler-4.2.0.tar
+          cd aocc-compiler-4.2.0
           bash install.sh
           source /home/runner/work/hdf5/hdf5/setenv_AOCC.sh
           which clang
           which flang
           clang -v
 
-      - name: Cache OpenMPI 4.1.5 installation
-        id: cache-openmpi-4_1_5
+      - name: Cache OpenMPI 4.1.6 installation
+        id: cache-openmpi-4_1_6
         uses: actions/cache@v4
         with:
-          path: /home/runner/work/hdf5/hdf5/openmpi-4.1.5-install
-          key: ${{ runner.os }}-${{ runner.arch }}-openmpi-4_1_5-cache
+          path: /home/runner/work/hdf5/hdf5/openmpi-4.1.6-install
+          key: ${{ runner.os }}-${{ runner.arch }}-openmpi-4_1_6-cache
 
-      - name: Install OpenMPI 4.1.5
-        if: ${{ steps.cache-openmpi-4_1_5.outputs.cache-hit != 'true' }}
+      - name: Install OpenMPI 4.1.6
+        if: ${{ steps.cache-openmpi-4_1_6.outputs.cache-hit != 'true' }}
         run: |
-          export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/usr/local/lib
-          wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.5.tar.gz
-          tar zxvf openmpi-4.1.5.tar.gz
-          cd openmpi-4.1.5
-          ./configure CC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/bin/clang FC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/bin/flang --prefix=/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install
+          export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/lib:/usr/local/lib
+          wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.6.tar.gz
+          tar zxvf openmpi-4.1.6.tar.gz
+          cd openmpi-4.1.6
+          ./configure CC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/bin/clang FC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/bin/flang --prefix=/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install
           make
           make install
 
       - name: Autotools Configure
         env:
           NPROCS: 2
         run: |
-          export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/lib:/usr/local/lib
-          export LD_RUN_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/lib:/usr/local/lib
-          export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/bin:/usr/local/bin:$PATH
+          export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/lib:/usr/local/lib
+          export LD_RUN_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/lib:/usr/local/lib
+          export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/bin:/usr/local/bin:$PATH
           sh ./autogen.sh
           mkdir "${{ runner.workspace }}/build"
           cd "${{ runner.workspace }}/build"
@@ -73,30 +73,30 @@ jobs:
             --enable-build-mode=${{ inputs.build_mode }} \
             --enable-shared \
             --enable-parallel \
-            LDFLAGS="-L/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib \
-            -L/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/lib"
+            LDFLAGS="-L/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/lib \
+            -L/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/lib"
 
       - name: Autotools Build
         shell: bash
         env:
           NPROCS: 2
         run: |
-          export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/bin:/usr/local/bin:$PATH
+          export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/bin:/usr/local/bin:$PATH
           make -j3
         working-directory: ${{ runner.workspace }}/build
 
       - name: Autotools Run Tests
         env:
           NPROCS: 2
         run: |
-          export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/bin:/usr/local/bin:$PATH
+          export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/bin:/usr/local/bin:$PATH
           make check -j
         working-directory: ${{ runner.workspace }}/build
 
       - name: Autotools Install
         env:
           NPROCS: 2
         run: |
-          export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/bin:/usr/local/bin:$PATH
+          export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/bin:/usr/local/bin:$PATH
           make install
         working-directory: ${{ runner.workspace }}/build
diff --git a/.github/workflows/aocc-cmake.yml b/.github/workflows/aocc-cmake.yml
@@ -28,42 +28,42 @@ jobs:
           sudo apt install -y zlib1g-dev libcurl4-openssl-dev libjpeg-dev wget curl bzip2
           sudo apt install -y m4 flex bison cmake libzip-dev openssl build-essential
 
-      - name: Install AOCC 4.1.0
+      - name: Install AOCC 4.2.0
         shell: bash
         run: |
-          wget https://download.amd.com/developer/eula/aocc/aocc-4-1/aocc-compiler-4.1.0.tar
-          tar -xvf aocc-compiler-4.1.0.tar
-          cd aocc-compiler-4.1.0
+          wget https://download.amd.com/developer/eula/aocc/aocc-4-2/aocc-compiler-4.2.0.tar
+          tar -xvf aocc-compiler-4.2.0.tar
+          cd aocc-compiler-4.2.0
           bash install.sh
           source /home/runner/work/hdf5/hdf5/setenv_AOCC.sh
           which clang
           which flang
           clang -v
 
-      - name: Cache OpenMPI 4.1.5 installation
-        id: cache-openmpi-4_1_5
+      - name: Cache OpenMPI 4.1.6 installation
+        id: cache-openmpi-4_1_6
         uses: actions/cache@v4
         with:
-          path: /home/runner/work/hdf5/hdf5/openmpi-4.1.5-install
-          key: ${{ runner.os }}-${{ runner.arch }}-openmpi-4_1_5-cache
+          path: /home/runner/work/hdf5/hdf5/openmpi-4.1.6-install
+          key: ${{ runner.os }}-${{ runner.arch }}-openmpi-4_1_6-cache
 
-      - name: Install OpenMPI 4.1.5
-        if: ${{ steps.cache-openmpi-4_1_5.outputs.cache-hit != 'true' }}
+      - name: Install OpenMPI 4.1.6
+        if: ${{ steps.cache-openmpi-4_1_6.outputs.cache-hit != 'true' }}
         run: |
-          export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/usr/local/lib
-          wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.5.tar.gz
-          tar zxvf openmpi-4.1.5.tar.gz
-          cd openmpi-4.1.5
-          ./configure CC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/bin/clang FC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/bin/flang --prefix=/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install
+          export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/lib:/usr/local/lib
+          wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.6.tar.gz
+          tar zxvf openmpi-4.1.6.tar.gz
+          cd openmpi-4.1.6
+          ./configure CC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/bin/clang FC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/bin/flang --prefix=/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install
           make
           make install
 
       - name: CMake Configure
         shell: bash
         run: |
-          export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/lib:/usr/local/lib
-          export LD_RUN_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/lib:/usr/local/lib
-          export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/bin:/usr/local/bin:$PATH
+          export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/lib:/usr/local/lib
+          export LD_RUN_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.2.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/lib:/usr/local/lib
+          export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.6-install/bin:/usr/local/bin:$PATH
           mkdir "${{ runner.workspace }}/build"
           cd "${{ runner.workspace }}/build"
           CC=mpicc cmake -C $GITHUB_WORKSPACE/config/cmake/cacheinit.cmake -G Ninja \

diff --git a/.github/workflows/cmake-bintest.yml b/.github/workflows/cmake-bintest.yml
@@ -98,7 +98,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Install CMake Dependencies (Linux)
-        run: sudo apt-get install ninja-build doxygen graphviz
+        run: |
+          sudo apt-get update
+          sudo apt-get install ninja-build doxygen graphviz
 
       - name: Set up JDK 19
         uses: actions/setup-java@v4

diff --git a/.github/workflows/cmake-ctest.yml b/.github/workflows/cmake-ctest.yml
@@ -122,7 +122,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Install CMake Dependencies (Linux)
-        run: sudo apt-get install ninja-build graphviz
+        run: |
+          sudo apt-get update
+          sudo apt-get install ninja-build graphviz
 
       - name: Install Dependencies
         uses: ssciwr/doxygen-install@v1
@@ -330,8 +332,9 @@ jobs:
     steps:
       - name: Install CMake Dependencies (Linux S3)
         run: |
-           sudo apt-get install ninja-build doxygen graphviz
-           sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
+          sudo apt-get update
+          sudo apt-get install ninja-build doxygen graphviz
+          sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
 
       - name: Set file base name (Linux S3)
         id: set-file-base
@@ -493,7 +496,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Install CMake Dependencies (Linux_intel)
-        run: sudo apt-get install ninja-build doxygen graphviz
+        run: |
+          sudo apt-get update
+          sudo apt-get install ninja-build doxygen graphviz
 
       - name: add oneAPI to env
         uses: fortran-lang/setup-fortran@v1

diff --git a/.github/workflows/intel-cmake.yml b/.github/workflows/intel-cmake.yml
@@ -22,7 +22,7 @@ jobs:
       - name: Install Dependencies (Linux)
         shell: bash
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
 

diff --git a/.github/workflows/julia-cmake.yml b/.github/workflows/julia-cmake.yml
@@ -22,7 +22,7 @@ jobs:
       - name: Install Dependencies
         shell: bash
         run: |
-          sudo apt update
+          sudo apt-get update
           sudo apt-get install ninja-build doxygen graphviz
           sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
           sudo apt install -y libaec-dev zlib1g-dev wget curl bzip2 flex bison cmake libzip-dev openssl build-essential

diff --git a/.github/workflows/main-auto-par-spc.yml b/.github/workflows/main-auto-par-spc.yml
@@ -28,7 +28,7 @@ jobs:
       # libssl, etc. are needed for the ros3 VFD
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12
@@ -86,7 +86,7 @@ jobs:
       # libssl, etc. are needed for the ros3 VFD
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12

diff --git a/.github/workflows/main-auto-par.yml b/.github/workflows/main-auto-par.yml
@@ -36,7 +36,7 @@ jobs:
       # SETUP
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12

diff --git a/.github/workflows/main-auto-spc.yml b/.github/workflows/main-auto-spc.yml
@@ -28,7 +28,7 @@ jobs:
       # libssl, etc. are needed for the ros3 VFD
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12
@@ -89,7 +89,7 @@ jobs:
       # libssl, etc. are needed for the ros3 VFD
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12
@@ -150,7 +150,7 @@ jobs:
       # libssl, etc. are needed for the ros3 VFD
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12
@@ -211,7 +211,7 @@ jobs:
       # libssl, etc. are needed for the ros3 VFD
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12
@@ -272,7 +272,7 @@ jobs:
       # libssl, etc. are needed for the ros3 VFD
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12
@@ -333,7 +333,7 @@ jobs:
       # libssl, etc. are needed for the ros3 VFD
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12
@@ -394,7 +394,7 @@ jobs:
       # libssl, etc. are needed for the ros3 VFD
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12
@@ -457,7 +457,7 @@ jobs:
       # libssl, etc. are needed for the ros3 VFD
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12

diff --git a/.github/workflows/main-auto.yml b/.github/workflows/main-auto.yml
@@ -37,7 +37,7 @@ jobs:
       # SETUP
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12

diff --git a/.github/workflows/main-cmake-par.yml b/.github/workflows/main-cmake-par.yml
@@ -27,7 +27,7 @@ jobs:
 
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12

diff --git a/.github/workflows/main-cmake-spc.yml b/.github/workflows/main-cmake-spc.yml
@@ -26,7 +26,7 @@ jobs:
       # SETUP
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12
@@ -86,7 +86,7 @@ jobs:
       # SETUP
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12
@@ -146,7 +146,7 @@ jobs:
       # SETUP
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12
@@ -206,7 +206,7 @@ jobs:
       # SETUP
       - name: Install Linux Dependencies
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build doxygen graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12

diff --git a/.github/workflows/main-cmake.yml b/.github/workflows/main-cmake.yml
@@ -124,7 +124,7 @@ jobs:
 
       - name: Install CMake Dependencies (Linux)
         run: |
-           sudo apt update
+           sudo apt-get update
            sudo apt-get install ninja-build graphviz
            sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
            sudo apt install gcc-12 g++-12 gfortran-12

diff --git a/.github/workflows/nvhpc-cmake.yml b/.github/workflows/nvhpc-cmake.yml
@@ -22,7 +22,7 @@ jobs:
       - name: Install Dependencies
         shell: bash
         run: |
-          sudo apt update
+          sudo apt-get update
           sudo apt-get install ninja-build doxygen graphviz
           sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
           sudo apt install -y libaec-dev zlib1g-dev wget curl bzip2 flex bison cmake libzip-dev openssl build-essential