adds github actions hdf5 compilation test

Author: danielpeter

.github/scripts/run_install.sh

@@ -18,6 +18,25 @@ sudo apt-get install -yq --no-install-recommends gfortran g++ openmpi-bin libope
 if [[ $? -ne 0 ]]; then exit 1; fi
 echo
 
+# parallel hdf5
+if [[ "${TEST}" == *"with-hdf5"* ]]; then
+  echo
+  echo "additional installation: ${TEST}"
+  echo
+  sudo apt-get install -yq --no-install-recommends libhdf5-mpi-dev
+  ## checks installation paths
+  #echo
+  #dpkg -L libhdf5-mpi-dev
+  #echo
+  #dpkg -L libhdf5-openmpi-dev
+  #echo
+  #echo "hdf5 module paths:"
+  #find /usr/ -iname 'hdf5.mod'
+  #echo "hdf5 library paths:"
+  #find /usr/ -iname 'libhdf5hl_fortran*'
+  #echo
+fi
+
 ## NetCDF
 if [ "${NETCDF}" == "true" ]; then
   echo

.github/scripts/run_tests.sh

@@ -23,7 +23,7 @@ echo
 # bash function for checking seismogram output with reference solutions
 my_test(){
   echo "testing seismograms:"
-  ln -s $WORKDIR/utils/compare_seismogram_correlations.py
+  ln -s $WORKDIR/utils/scripts/compare_seismogram_correlations.py
   ./compare_seismogram_correlations.py REF_SEIS/ OUTPUT_FILES/
   if [[ $? -ne 0 ]]; then exit 1; fi
   ./compare_seismogram_correlations.py REF_SEIS/ OUTPUT_FILES/ | grep min/max | cut -d \| -f 3 | awk '{print "correlation:",$1; if ($1 < 0.999 ){print $1,"failed"; exit 1;}else{ print $1,"good"; exit 0;}}'
@@ -65,6 +65,18 @@ if [ "${FULL_GRAVITY}" == "true" ]; then
   echo "NSTEP = 2" >> DATA/Par_file
 fi
 
+# hdf5 i/o example
+if [[ "${TEST}" == *"with-hdf5"* ]]; then
+  echo
+  echo "test run: ${TEST}"
+  echo
+  sed -i "s:^HDF5_ENABLED .*:HDF5_ENABLED    = .true.:" DATA/Par_file
+  #sed -i "s:^HDF5_FOR_MOVIES .*:HDF5_FOR_MOVIES    = .true.:" DATA/Par_file
+  #sed -i "s:^HDF5_IO_NODES .*:HDF5_IO_NODES    = 1:" DATA/Par_file
+  # replaces run script
+  #cp -v run_this_example_HDF5_IO_server.sh run_this_example.sh
+fi
+
 # adios
 if [ "${ADIOS2}" == "true" ]; then
   # turns on ADIOS

.github/workflows/CI.yml

@@ -552,3 +552,30 @@ jobs:
         RUN_KERNEL: true
       run: ./.github/scripts/run_tests.sh
       shell: bash
+
+  linuxTest_11:
+    name: Test run example 11 - regional_Greece_small hdf5 i/o
+    runs-on: ubuntu-latest
+    needs: [linuxCheck]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install packages
+      env:
+        TEST: with-hdf5
+      run: ./.github/scripts/run_install.sh
+      shell: bash
+
+    - name: Run build
+      env:
+        TESTFLAGS: --with-hdf5 HDF5_INC=/usr/include/hdf5/openmpi/ HDF5_LIBS=-L/usr/lib/x86_64-linux-gnu/hdf5/openmpi
+      run: ./.github/scripts/run_build.sh
+      shell: bash
+
+    - name: Run test
+      env:
+        TEST: with-hdf5
+        TESTDIR: EXAMPLES/regional_Greece_small
+      run: ./.github/scripts/run_tests.sh
+      shell: bash