Recreated: Debug/updates for hdf5 routines

.github/scripts/run_build.sh

@@ -29,13 +29,25 @@ echo "mpif90 --version"
 mpif90 --version
 echo
 
+## ADIOS2
+if [ "${ADIOS2}" == "true" ]; then
+  echo
+  echo "enabling ADIOS2"
+  echo
+  ADIOS2_CONFIG="${ADIOS2_DIR}/bin/adios2-config"
+  adios=(--with-adios2 ADIOS2_CONFIG="$ADIOS2_CONFIG" )
+else
+  adios=()
+fi
 
 # configuration
 echo
-echo "configuration: default"
+echo "configuration:"
 echo
 
-./configure FC=gfortran MPIFC=mpif90 CC=gcc ${TESTFLAGS}
+./configure \
+${adios[@]} \
+FC=gfortran MPIFC=mpif90 CC=gcc ${TESTFLAGS}
 
 # checks
 if [[ $? -ne 0 ]]; then echo "configuration failed:"; cat config.log; echo ""; echo "exiting..."; exit 1; fi

.github/scripts/run_install.sh

@@ -38,6 +38,12 @@ fi
 if [[ $? -ne 0 ]]; then exit 1; fi
 echo
 
+# python3 pip upgrade might complain: "ERROR: launchpadlib 1.10.13 requires testresources"
+sudo apt-get install -yq --no-install-recommends python3-testresources
+# checks exit code
+if [[ $? -ne 0 ]]; then exit 1; fi
+echo
+
 # python script needs numpy
 #sudo apt-get install -qq python-numpy # not working, likely installed on older python version
 pip install --user --upgrade pip setuptools wheel
@@ -68,6 +74,39 @@ echo "mpif90 --version"
 mpif90 --version
 echo
 
+## ADIOS2
+if [ "${ADIOS2}" == "true" ]; then
+  echo
+  echo "ADIOS2 installation:"
+  echo
+  # installs cmake wget
+  sudo apt-get install -yq --no-install-recommends cmake wget
+  # checks exit code
+  if [[ $? -ne 0 ]]; then exit 1; fi
+  # uses /opt as installation directory
+  mkdir -p /opt; cd /opt
+  # download source
+  wget https://github.com/ornladios/ADIOS2/archive/refs/tags/v2.10.1.tar.gz
+  tar zxf v2.10.1.tar.gz
+  cd ADIOS2-2.10.1/
+  # build source
+  mkdir -p build; cd build/
+  CC=gcc CXX=g++ FC=gfortran cmake -DADIOS2_USE_Fortran=ON \
+    -DADIOS2_USE_HDF5=OFF -DADIOS2_BUILD_EXAMPLES=OFF -DBUILD_TESTING=OFF \
+    -DCMAKE_INSTALL_PREFIX=/opt/ADIOS2 ../
+  # checks exit code
+  if [[ $? -ne 0 ]]; then exit 1; fi
+  make -j4
+  # checks exit code
+  if [[ $? -ne 0 ]]; then exit 1; fi
+  make install
+  # checks exit code
+  if [[ $? -ne 0 ]]; then exit 1; fi
+  # environment for directory
+  echo "ADIOS2_DIR=/opt/ADIOS2" >> $GITHUB_ENV
+  echo; echo "done ADIOS2"; echo
+fi
+
 # MPI
 # github actions uses for Linux virtual machines a 2-core CPU environment
 # see: https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources

.github/scripts/run_tests.sh

@@ -117,6 +117,12 @@ if [[ "${TEST}" == *"with-hdf5"* ]]; then
   cp -v run_this_example_HDF5_IO_server.sh run_this_example.sh
 fi
 
+# adios
+if [ "${ADIOS2}" == "true" ]; then
+  # turns on ADIOS
+  sed -i "s:^ADIOS_ENABLED .*:ADIOS_ENABLED = .true.:" DATA/Par_file
+fi
+
 # default script
 ./run_this_example.sh
 

.github/workflows/CI.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Check for changes
       id: diff
@@ -86,7 +86,7 @@ jobs:
     needs: changesCheck
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install dependencies
       run: |
@@ -104,9 +104,16 @@ jobs:
         echo ""
         ## avoids sed -i '' issue on MacOS, using gnu sed to have the same sed command lines as in linux
         brew install gnu-sed
-        echo "PATH=/usr/local/opt/gnu-sed/libexec/gnubin:$PATH" >> $GITHUB_ENV
+        echo "PATH=/opt/homebrew/opt/gnu-sed/libexec/gnubin:$PATH" >> $GITHUB_ENV
         ## OpenMP
         echo "OMP_NUM_THREADS=2" >> $GITHUB_ENV
+        ## MPI
+        echo
+        echo "MPI environment:"
+        echo "mpif90 on path: $(which mpif90)"
+        echo
+        # add OpenMPI path to have ./configure detect mpi.h
+        echo "MPI_INC=/opt/homebrew/include" >> $GITHUB_ENV
         ## avoids MPI issue with number of slots
         echo "OMPI_MCA_rmaps_base_oversubscribe=1" >> $GITHUB_ENV
         echo "OMPI_MCA_rmaps_base_inherit=1" >> $GITHUB_ENV
@@ -121,7 +128,8 @@ jobs:
 
     - name: configure
       run: |
-        ./configure
+        ./configure ; if [[ $? -ne 0 ]]; then cat config.log; exit 1; fi
+        # changes SCOTCH Makefile for macOS
         echo "modifying external_libs/scotch/src/Makefile.inc"
         cp -v external_libs/scotch/src/Make.inc/Makefile.inc.i686_mac_darwin8 external_libs/scotch/src/Makefile.inc
 
@@ -142,7 +150,7 @@ jobs:
         os: [ubuntu-latest,ubuntu-20.04]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -161,7 +169,7 @@ jobs:
     needs: changesCheck
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Cache Intel oneapi packages
       id: cache-intel-oneapi
@@ -296,7 +304,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -315,7 +323,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -339,7 +347,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -363,7 +371,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -388,7 +396,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -412,7 +420,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -437,7 +445,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -462,7 +470,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -488,7 +496,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -513,7 +521,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -537,7 +545,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -561,7 +569,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -585,7 +593,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -609,7 +617,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -633,7 +641,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -657,7 +665,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -681,7 +689,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -705,7 +713,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -729,7 +737,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       env:
@@ -751,3 +759,31 @@ jobs:
       run: ./.github/scripts/run_tests.sh
       shell: bash
 
+  linuxTest_19:
+    name: Test run example 19 - meshfem3D simple model w/ ADIOS2
+    runs-on: ubuntu-latest
+    needs: [linuxCheck]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install packages
+      env:
+        ADIOS2: true
+      run: ./.github/scripts/run_install.sh
+      shell: bash
+
+    - name: Run build
+      env:
+        TESTFLAGS: --with-mpi --enable-vectorization
+        ADIOS2: true
+      run: ./.github/scripts/run_build.sh
+      shell: bash
+
+    - name: Run test
+      env:
+        TESTDIR: EXAMPLES/applications/meshfem3D_examples/simple_model/
+        ADIOS2: true
+      run: ./.github/scripts/run_tests.sh
+      shell: bash
+

.gitignore

@@ -24,6 +24,7 @@ src/generate_databases/*.mod
 src/meshfem3D/*.mod
 src/specfem3D/*.mod
 *__genmod.f90
+my_mpi.mod
 
 # documentation
 manual_SPECFEM3D_Cartesian.aux