updates github scripts (for hdf5); sets hdf5 Par_file defaults to .fa…

…lse.

.github/scripts/run_build.sh

@@ -60,6 +60,16 @@ else
   petsc=()
 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
+
 # configuration
 echo
 echo "configuration:"
@@ -68,8 +78,9 @@ echo
 ./configure \
 ${adios[@]} \
 ${netcdf[@]} \
+${hdf[@]} \
 ${petsc[@]} \
-FC=gfortran MPIFC=mpif90 CC=gcc ${TESTFLAGS}
+FC=gfortran MPIFC=mpif90 CC=gcc "${TESTFLAGS}"
 
 # checks
 if [[ $? -ne 0 ]]; then echo "configuration failed:"; cat config.log; echo ""; echo "exiting..."; exit 1; fi

.github/scripts/run_install.sh

@@ -19,9 +19,9 @@ if [[ $? -ne 0 ]]; then exit 1; fi
 echo
 
 # parallel hdf5
-if [[ "${TEST}" == *"with-hdf5"* ]]; then
+if [ "${HDF5}" == "true" ]; then
   echo
-  echo "additional installation: ${TEST}"
+  echo "HDF5 installation:"
   echo
   sudo apt-get install -yq --no-install-recommends libhdf5-mpi-dev
   ## checks installation paths

.github/scripts/run_tests.sh

@@ -66,9 +66,9 @@ if [ "${FULL_GRAVITY}" == "true" ]; then
 fi
 
 # hdf5 i/o example
-if [[ "${TEST}" == *"with-hdf5"* ]]; then
+if [ "${HDF5}" == "true" ]; then
   echo
-  echo "test run: ${TEST}"
+  echo "HDF5 enabled test run"
   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

.github/workflows/CI.yml

@@ -563,19 +563,20 @@ jobs:
 
     - name: Install packages
       env:
-        TEST: with-hdf5
+        HDF5: true
       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
+        TESTFLAGS: # no extra flags
+        HDF5: true
       run: ./.github/scripts/run_build.sh
       shell: bash
 
     - name: Run test
       env:
-        TEST: with-hdf5
         TESTDIR: EXAMPLES/regional_Greece_small
+        HDF5: true
       run: ./.github/scripts/run_tests.sh
       shell: bash

EXAMPLES/regional_s40rts/DATA/Par_file

@@ -433,5 +433,5 @@ ADIOS_FOR_UNDO_ATTENUATION      = .true.
 
 # HDF5 Database I/O
 # (note the flags for HDF5 and ADIOS are mutually exclusive, only one can be used)
-HDF5_ENABLED                    = .true.
+HDF5_ENABLED                    = .false.
 

EXAMPLES/regional_small_adjoint/DATA/Par_file

@@ -433,5 +433,5 @@ ADIOS_FOR_UNDO_ATTENUATION      = .true.
 
 # HDF5 Database I/O
 # (note the flags for HDF5 and ADIOS are mutually exclusive, only one can be used)
-HDF5_ENABLED                    = .true.
+HDF5_ENABLED                    = .false.
 

src/shared/read_parameter_file.F90

@@ -437,5 +437,4 @@ subroutine read_parameter_file()
   endif
 #endif
 
-
   end subroutine read_parameter_file