updates testing w/ HDF5

.github/scripts/run_build.sh

@@ -40,6 +40,16 @@ else
   adios=()
 fi
 
+## HDF5
+if [ "${HDF5}" == "true" ]; then
+  echo
+  echo "enabling HDF5"
+  echo
+  hdf=(--with-hdf5 HDF5_INC="/usr/include/hdf5/openmpi/" HDF5_LIBS="-L/usr/lib/x86_64-linux-gnu/hdf5/openmpi")
+else
+  hdf=()
+fi
+
 ## HIP
 if [ "${HIP}" == "true" ]; then
   echo
@@ -55,10 +65,14 @@ echo
 echo "configuration:"
 echo
 
+# split TESTFLAGS into individual items
+set -- ${TESTFLAGS}
+
 ./configure \
 "${adios[@]}" \
+"${hdf[@]}" \
 "${hip[@]}" \
-FC=gfortran MPIFC=mpif90 CC=gcc ${TESTFLAGS}
+FC=gfortran MPIFC=mpif90 CC=gcc "$@"
 
 # checks
 if [[ $? -ne 0 ]]; then echo "configuration failed:"; cat config.log; echo ""; echo "exiting..."; exit 1; fi

.github/scripts/run_install.sh

@@ -15,10 +15,10 @@ if [[ $? -ne 0 ]]; then exit 1; fi
 # fortran/openMPI compiler
 sudo apt-get install -yq --no-install-recommends gfortran g++ openmpi-bin libopenmpi-dev
 
-# parallel hdf5
-if [[ "${TEST}" == *"with-hdf5"* ]]; then
+## parallel HDF5
+if [ "${HDF5}" == "true" ]; then
   echo
-  echo "additional installation: ${TEST}"
+  echo "HDF5 additional installation:"
   echo
   sudo apt-get install -yq --no-install-recommends libhdf5-mpi-dev
   ## checks installation paths

.github/scripts/run_tests.sh

@@ -160,10 +160,10 @@ if [ "$TESTDIR" == "EXAMPLES/applications/meshfem3D_examples/sep_bathymetry/" ];
   sed -i "s:^NSTEP .*:NSTEP    = 1000:" DATA/Par_file
 fi
 
-## hdf5 i/o example
-if [[ "${TEST}" == *"with-hdf5"* ]]; then
+## HDF5 - i/o example
+if [ "${HDF5}" == "true" ]; then
   echo
-  echo "test run: ${TEST}"
+  echo "test run w/ HDF5"
   echo
   # turns on HDF5
   echo "turning on HDF5"

.github/workflows/CI.yml

@@ -626,7 +626,7 @@ jobs:
 
     - name: Run build
       env:
-        TESTFLAGS: 'FLAGS_CHECK="-O3 -mcmodel=medium -std=f2008 -Wall -Wno-do-subscript -Wno-conversion -Wno-maybe-uninitialized"'
+        TESTFLAGS: FLAGS_CHECK="-O3 -mcmodel=medium -std=f2008 -Wall -Wno-do-subscript -Wno-conversion -Wno-maybe-uninitialized"
       run: ./.github/scripts/run_build.sh
       shell: bash
 
@@ -805,7 +805,7 @@ jobs:
       shell: bash
 
   linuxTest_20:
-    name: Test 20 - socal1D hdf5 i/o
+    name: Test 20 - socal1D HDF5 I/O
     runs-on: ubuntu-latest
     needs: [linuxCheck]
 
@@ -814,21 +814,22 @@ jobs:
 
     - name: Install packages
       env:
-        TEST: with-hdf5
+        HDF5: true
       run: ./.github/scripts/run_install.sh
       shell: bash
 
     - name: Run build
       env:
-        TESTFLAGS: --with-mpi --with-hdf5 HDF5_INC=/usr/include/hdf5/openmpi/ HDF5_LIBS=-L/usr/lib/x86_64-linux-gnu/hdf5/openmpi
+        TESTFLAGS: --with-mpi
+        HDF5: true
       run: ./.github/scripts/run_build.sh
       shell: bash
 
     - name: Run test
       env:
-        TEST: with-hdf5
         TESTDIR: EXAMPLES/applications/meshfem3D_examples/socal1D/
         TESTID: 0
+        HDF5: true
       run: ./.github/scripts/run_tests.sh
       shell: bash