updates GPU source kernels; adds GPU kernel testing in github actions

.github/scripts/run_build.sh

@@ -40,14 +40,52 @@ 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
+  echo "enabling HIP"
+  echo
+  hip=(--with-hip HIPCC=g++ HIP_FLAGS="-O2 -g -std=c++17" HIP_PLATFORM=cpu HIP_INC=./external_libs/ROCm-HIP-CPU/include HIP_LIBS="-ltbb -lpthread -lstdc++")
+else
+  hip=()
+fi
+
+## special testflags
+if [ "${TESTFLAGS}" == "check-mcmodel-medium" ]; then
+  # note: this is a work-around as using the 'env:' parameter in the workflow 'CI.yml' with TESTFLAGS: FLAGS_CHECK=".."
+  #       won't work as the FLAGS_CHECK string will then get split up and ./configure .. complains about unknown parameters.
+  #       here, we re-define TESTFLAGS with a single quote around FLAGS_CHECK=".." to avoid the splitting.
+  # use FLAGS_CHECK
+  flags=(FLAGS_CHECK="-O3 -mcmodel=medium -std=f2008 -Wall -Wno-do-subscript -Wno-conversion -Wno-maybe-uninitialized")
+  TESTFLAGS=""  # reset
+else
+  flags=()
+fi
+
 # configuration
 echo
 echo "configuration:"
 echo
 
+# split TESTFLAGS into individual items
+set -- ${TESTFLAGS}
+
 ./configure \
-${adios[@]} \
-FC=gfortran MPIFC=mpif90 CC=gcc ${TESTFLAGS}
+"${adios[@]}" \
+"${hdf[@]}" \
+"${hip[@]}" \
+"${flags[@]}" \
+FC=gfortran MPIFC=mpif90 CC=gcc "$@"
 
 # checks
 if [[ $? -ne 0 ]]; then echo "configuration failed:"; cat config.log; echo ""; echo "exiting..."; exit 1; fi
@@ -62,8 +100,14 @@ sed -i "s:IMAIN .*:IMAIN = ISTANDARD_OUTPUT:" setup/constants.h
 
 # compilation
 echo
-echo "compilation:"
-make clean; make -j2 all
+echo "clean"
+echo
+make clean
+
+echo
+echo "compilation"
+echo
+make -j4 all
 
 # checks
 if [[ $? -ne 0 ]]; then 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: ${TEST}"
+  echo "HDF5 additional installation:"
   echo
   sudo apt-get install -yq --no-install-recommends libhdf5-mpi-dev
   ## checks installation paths
@@ -34,6 +34,14 @@ if [[ "${TEST}" == *"with-hdf5"* ]]; then
   #echo
 fi
 
+## HIP
+if [ "${HIP}" == "true" ]; then
+  echo
+  echo "HIP additionals installation:"
+  echo
+  sudo apt-get install -yq --no-install-recommends libtbb-dev
+fi
+
 # checks exit code
 if [[ $? -ne 0 ]]; then exit 1; fi
 echo

.github/scripts/run_tests.sh

@@ -22,12 +22,67 @@ echo
 
 # bash function for checking seismogram output with reference solutions
 my_test(){
-  echo "testing seismograms:"
+  echo "######################################################################################################################"
+  echo "testing seismograms"
   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;}}'
   if [[ $? -ne 0 ]]; then exit 1; fi
+  echo "######################################################################################################################"
+}
+
+my_kernel_test(){
+  # kernel value test - checks rho/kappa/mu kernel value outputs
+  echo "######################################################################################################################"
+  echo "testing kernel values"
+  file_ref=REF_KERNEL/output_solver.txt
+  file_out=output.log        # captures the OUTPUT_FILES/output_solver.txt when running solver since IMAIN was set to standard out
+  if [ ! -e $file_ref ]; then echo "Please check if file $file_ref exists..."; ls -alR ./; exit 1; fi
+  if [ ! -e $file_out ]; then echo "Please check if file $file_out exists..."; ls -alR ./; exit 1; fi
+  # gets reference expected kernel values from REF_KERNEL/ folder
+  RHO=`grep -E 'maximum value of rho[[:space:]]+kernel' $file_ref | cut -d = -f 2 | tr -d ' '`
+  KAPPA=`grep -E 'maximum value of kappa[[:space:]]+kernel' $file_ref | cut -d = -f 2 | tr -d ' '`
+  MU=`grep -E 'maximum value of mu[[:space:]]+kernel' $file_ref | cut -d = -f 2 | tr -d ' '`
+  # need at least rho & kappa (for acoustic kernels)
+  if [ "$RHO" == "" ] || [ "$KAPPA" == "" ]; then
+    echo "  missing reference kernel values: RHO=$RHO KAPPA=$KAPPA MU=$MU"
+    echo
+    exit 1
+  else
+    echo "  reference kernel values: RHO=$RHO KAPPA=$KAPPA MU=$MU"
+  fi
+  # compares with test output - using a relative tolerance of 0.001 (1 promille) with respect to expected value
+  # final test result
+  PASSED=0
+  # checks rho kernel value
+  if [ "$RHO" != "" ]; then
+    VAL=`grep -E 'maximum value of rho[[:space:]]+kernel' $file_out | cut -d = -f 2 | tr -d ' '`
+    echo "kernel rho   : $VAL"
+    echo "" | awk '{diff=ex-val;diff_abs=(diff >= 0)? diff:-diff;diff_rel=diff_abs/ex;print "  value: expected = "ex" gotten = "val" - difference absolute = "diff_abs" relative = "diff_rel; if (diff_rel>0.001){print "  failed"; exit 1;}else{print "  good"; exit 0;} }' ex=$RHO val=$VAL
+    if [[ $? -ne 0 ]]; then PASSED=1; fi
+  fi
+  # checks kappa kernel value
+  if [ "$KAPPA" != "" ]; then
+    VAL=`grep -E 'maximum value of kappa[[:space:]]+kernel' $file_out | cut -d = -f 2 | tr -d ' '`
+    echo "kernel kappa : $VAL"
+    echo "" | awk '{diff=ex-val;diff_abs=(diff >= 0)? diff:-diff;diff_rel=diff_abs/ex;print "  value: expected = "ex" gotten = "val" - difference absolute = "diff_abs" relative = "diff_rel; if (diff_rel>0.001){print "  failed"; exit 1;}else{print "  good"; exit 0;} }' ex=$KAPPA val=$VAL
+    if [[ $? -ne 0 ]]; then PASSED=1; fi
+  fi
+  # checks mu kernel value (if available for elastic kernel)
+  if [ "$MU" != "" ]; then
+    VAL=`grep -E 'maximum value of mu[[:space:]]+kernel' $file_out | cut -d = -f 2 | tr -d ' '`
+    echo "kernel mu    : $VAL"
+    echo "" | awk '{diff=ex-val;diff_abs=(diff >= 0)? diff:-diff;diff_rel=diff_abs/ex;print "  value: expected = "ex" gotten = "val" - difference absolute = "diff_abs" relative = "diff_rel; if (diff_rel>0.001){print "  failed"; exit 1;}else{print "  good"; exit 0;} }' ex=$MU val=$VAL
+    if [[ $? -ne 0 ]]; then PASSED=1; fi
+  fi
+  # overall pass
+  if [[ $PASSED -ne 0 ]]; then
+    echo "testing kernel values: failed"; exit 1;
+  else
+    echo "testing kernel values: all good"
+  fi
+  echo "######################################################################################################################"
 }
 
 # test example
@@ -37,7 +92,7 @@ cd $dir
 # limit time steps for testing
 sed -i "s:^NSTEP .*:NSTEP    = 200:" DATA/Par_file
 # shortens output interval to avoid timeouts
-sed -i "s:^NTSTEP_BETWEEN_OUTPUT_INFO .*:NTSTEP_BETWEEN_OUTPUT_INFO    = 50:" DATA/Par_file
+sed -i "s:^NTSTEP_BETWEEN_OUTPUT_INFO .*:NTSTEP_BETWEEN_OUTPUT_INFO    = 100:" DATA/Par_file
 
 # limit time steps for specific examples
 # simple mesh example
@@ -105,27 +160,45 @@ 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"
   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
+## adios
 if [ "${ADIOS2}" == "true" ]; then
   # turns on ADIOS
+  echo "turning on ADIOS"
   sed -i "s:^ADIOS_ENABLED .*:ADIOS_ENABLED = .true.:" DATA/Par_file
 fi
 
-# default script
-./run_this_example.sh
+## GPU
+if [ "${GPU}" == "true" ]; then
+  # turns on GPU
+  echo "turning on GPU"
+  sed -i "s:^GPU_MODE .*:GPU_MODE = .true.:" DATA/Par_file
+fi
+
+# save Par_file state
+cp -v DATA/Par_file DATA/Par_file.bak
 
+# use kernel script
+if [ "${RUN_KERNEL}" == "true" ]; then
+  # use kernel script
+  ./run_this_example_kernel.sh | tee output.log
+else
+  # default script
+  ./run_this_example.sh
+fi
 # checks exit code
 if [[ $? -ne 0 ]]; then exit 1; fi
 
@@ -136,15 +209,52 @@ echo `date`
 echo
 
 # seismogram comparison
-if [ "${DEBUG}" == "true" ]; then
+if [ "${DEBUG}" == "true" ] || [ "${RUN_KERNEL}" == "true" ]; then
   # no comparisons
-  continue
+  :     # do nothing
 else
   my_test
 fi
+# checks exit code
+if [[ $? -ne 0 ]]; then exit 1; fi
+
+# kernel test
+if [ "${RUN_KERNEL}" == "true" ]; then
+  # check kernel values
+  my_kernel_test
+  # checks exit code
+  if [[ $? -ne 0 ]]; then exit 1; fi
+  # clean up
+  rm -rf OUTPUT_FILES/ SEM/ output.log
+
+  # re-run kernel test w/ UNDO_ATT
+  echo
+  echo "*****************************************"
+  echo "run kernel w/ UNDO_ATTENUATION_AND_OR_PML"
+  echo "*****************************************"
+  echo
+
+  # turns on UNDO_ATTENUATION_AND_OR_PML
+  echo "turning on UNDO_ATTENUATION_AND_OR_PML"
+  sed -i "s:^UNDO_ATTENUATION_AND_OR_PML .*:UNDO_ATTENUATION_AND_OR_PML = .true.:" DATA/Par_file
+
+  # use kernel script
+  ./run_this_example_kernel.sh | tee output.log
+  # checks exit code
+  if [[ $? -ne 0 ]]; then exit 1; fi
+  # kernel test
+  my_kernel_test
+  # checks exit code
+  if [[ $? -ne 0 ]]; then exit 1; fi
+fi
+
+# restore original Par_file
+cp -v DATA/Par_file.bak DATA/Par_file
 
 # cleanup
-rm -rf OUTPUT_FILES/ DATABASES_MPI/
+rm -rf OUTPUT_FILES/
+if [ -e DATABASES_MPI ]; then rm -rf DATABASES_MPI/; fi
+if [ -e SEM ]; then rm -rf SEM/; fi
 
 echo
 echo "all good"