adds github action test for adios2

.github/scripts/run_build.sh

@@ -29,6 +29,17 @@ 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="$ADIOS2_CONFIG" )
+else
+  adios=()
+fi
+
 ## NetCDF
 if [ "${NETCDF}" == "true" ]; then
   echo
@@ -39,7 +50,7 @@ else
   netcdf=()
 fi
 
-# PETSc
+## PETSc
 if [ "${PETSC}" == "true" ]; then
   echo
   echo "enabling PETSc"
@@ -55,6 +66,7 @@ echo "configuration:"
 echo
 
 ./configure \
+${adios[@]} \
 ${netcdf[@]} \
 ${petsc[@]} \
 FC=gfortran MPIFC=mpif90 CC=gcc "${TESTFLAGS}"

.github/scripts/run_install.sh

@@ -18,7 +18,7 @@ sudo apt-get install -yq --no-install-recommends gfortran g++ openmpi-bin libope
 if [[ $? -ne 0 ]]; then exit 1; fi
 echo
 
-# NetCDF
+## NetCDF
 if [ "${NETCDF}" == "true" ]; then
   echo
   echo "NETCDF installation:"
@@ -27,10 +27,10 @@ if [ "${NETCDF}" == "true" ]; then
   sudo apt-get install -yq --no-install-recommends libnetcdff-dev
   # checks exit code
   if [[ $? -ne 0 ]]; then exit 1; fi
-  echo "done"; echo
+  echo; echo "done netCDF"; echo
 fi
 
-# PETSc
+## PETSc
 if [ "${PETSC}" == "true" ]; then
   echo
   echo "PETSc installation:"
@@ -43,7 +43,7 @@ if [ "${PETSC}" == "true" ]; then
   sudo apt-get install -yq --no-install-recommends petsc-dev
   # checks exit code
   if [[ $? -ne 0 ]]; then exit 1; fi
-  echo "done"; echo
+  echo; echo "done PETSc"; echo
 fi
 
 # python3 pip upgrade might complain: "ERROR: launchpadlib 1.10.13 requires testresources"
@@ -88,6 +88,39 @@ 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 zxvf 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

@@ -62,9 +62,20 @@ if [ "${FULL_GRAVITY}" == "true" ]; then
   echo "NSTEP = 2" >> DATA/Par_file
 fi
 
-# default script
-./run_this_example.sh
+# full gravity
+if [ "${ADIOS2}" == "true" ]; then
+  # turns on ADIOS
+  sed -i "s:^ADIOS_ENABLED .*:ADIOS_ENABLED = .true.:" DATA/Par_file
+fi
 
+# use kernel script
+if [ "${RUN_KERNEL}" == "true" ]; then
+  # use kernel script
+  ./run_this_example.kernel.sh
+else
+  # default script
+  ./run_this_example.sh
+fi
 # checks exit code
 if [[ $? -ne 0 ]]; then exit 1; fi
 
@@ -75,7 +86,7 @@ echo `date`
 echo
 
 # seismogram comparison
-if [ "${DEBUG}" == "true" ] || [ "${FULL_GRAVITY}" == "true" ]; then
+if [ "${DEBUG}" == "true" ] || [ "${FULL_GRAVITY}" == "true" ] || [ "${RUN_KERNEL}" == "true" ]; then
   # no comparisons
   :     # do nothing
 else

.github/workflows/CI.yml

@@ -511,7 +511,7 @@ jobs:
 
     - name: Run build
       env:
-        TESTFLAGS: --enable-vectorization
+        TESTFLAGS:  # no extra flags
         PETSC: true
       run: ./.github/scripts/run_build.sh
       shell: bash
@@ -523,3 +523,32 @@ jobs:
         PETSC: true
       run: ./.github/scripts/run_tests.sh
       shell: bash
+
+  linuxTest_10:
+    name: Test run example 10 - regional_Greece_small_LDDRK kernel 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: # no extra flags
+        ADIOS2: true
+      run: ./.github/scripts/run_build.sh
+      shell: bash
+
+    - name: Run test
+      env:
+        TESTDIR: EXAMPLES/regional_Greece_small_LDDRK
+        ADIOS2: true
+        RUN_KERNEL: true
+      run: ./.github/scripts/run_tests.sh
+      shell: bash

src/tomography/postprocess_sensitivity_kernels/convert_model_file_adios.f90

@@ -90,6 +90,10 @@ program convert_model_file_adios
   call world_size(sizeprocs)
   call world_rank(myrank)
 
+  ! initialization
+  is_model_file_conversion = .false.
+  convert_format = 0
+
   ! reads input arguments
   do i = 1, 4
     call get_command_argument(i,arg)