Merge pull request #842 from danielpeter/devel

updates SIEM configuration and routines; adds github action tests for ADIOS2 and full gravity w/ PETSc

.github/scripts/run_build.sh

@@ -29,13 +29,47 @@ 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
+  echo "enabling NetCDF"
+  echo
+  netcdf=(--with-netcdf NETCDF_INC="/usr/include" NETCDF_LIBS="-lnetcdff" )
+else
+  netcdf=()
+fi
+
+## PETSc
+if [ "${PETSC}" == "true" ]; then
+  echo
+  echo "enabling PETSc"
+  echo
+  petsc=(--with-petsc PETSC_INC="/usr/include/petsc" )
+else
+  petsc=()
+fi
 
 # configuration
 echo
-echo "configuration: default"
+echo "configuration:"
 echo
 
-./configure FC=gfortran MPIFC=mpif90 CC=gcc "${TESTFLAGS}"
+./configure \
+${adios[@]} \
+${netcdf[@]} \
+${petsc[@]} \
+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

@@ -18,6 +18,34 @@ sudo apt-get install -yq --no-install-recommends gfortran g++ openmpi-bin libope
 if [[ $? -ne 0 ]]; then exit 1; fi
 echo
 
+## NetCDF
+if [ "${NETCDF}" == "true" ]; then
+  echo
+  echo "NETCDF installation:"
+  echo
+  # installs fortran netcdf
+  sudo apt-get install -yq --no-install-recommends libnetcdff-dev
+  # checks exit code
+  if [[ $? -ne 0 ]]; then exit 1; fi
+  echo; echo "done netCDF"; echo
+fi
+
+## PETSc
+if [ "${PETSC}" == "true" ]; then
+  echo
+  echo "PETSc installation:"
+  echo
+  # requires gfortran version 10 as default
+  #mv -v /usr/local/bin/gfortran /usr/local/bin/gfortran-9
+  #sudo update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-10 60
+  #sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-10 60
+  # installs petsc
+  sudo apt-get install -yq --no-install-recommends petsc-dev
+  # checks exit code
+  if [[ $? -ne 0 ]]; then exit 1; fi
+  echo; echo "done PETSc"; echo
+fi
+
 # python3 pip upgrade might complain: "ERROR: launchpadlib 1.10.13 requires testresources"
 sudo apt-get install -yq --no-install-recommends python3-testresources
 # checks exit code
@@ -60,6 +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
@@ -116,8 +177,6 @@ echo "OMPI_MCA_rmaps_base_inherit=1" >> $GITHUB_ENV
 # exports for xterm output (for make tests)
 echo "TERM=xterm" >> $GITHUB_ENV
 
-
-
 echo
 echo "exports:"
 export

.github/scripts/run_tests.sh

@@ -34,10 +34,12 @@ my_test(){
 cd $dir
 
 # default setup
-# limit number of time steps
-sed -i "s:^RECORD_LENGTH_IN_MINUTES .*:RECORD_LENGTH_IN_MINUTES = 0.5:" DATA/Par_file
-# shortens output interval to avoid timeouts
-sed -i "s:^NTSTEP_BETWEEN_OUTPUT_INFO .*:NTSTEP_BETWEEN_OUTPUT_INFO    = 50:" DATA/Par_file
+if [ ! "${RUN_KERNEL}" == "true" ]; then
+  # limit number of time steps
+  sed -i "s:^RECORD_LENGTH_IN_MINUTES .*:RECORD_LENGTH_IN_MINUTES = 0.5:" DATA/Par_file
+  # shortens output interval to avoid timeouts
+  sed -i "s:^NTSTEP_BETWEEN_OUTPUT_INFO .*:NTSTEP_BETWEEN_OUTPUT_INFO    = 50:" DATA/Par_file
+fi
 
 # specific example setups
 if [ "${TESTDIR}" == "EXAMPLES/global_small" ]; then
@@ -50,9 +52,33 @@ if [ "${DEBUG}" == "true" ]; then
   sed -i "s:^RECORD_LENGTH_IN_MINUTES .*:RECORD_LENGTH_IN_MINUTES = 0.0:" DATA/Par_file
 fi
 
-# default script
-./run_this_example.sh
+# full gravity
+if [ "${FULL_GRAVITY}" == "true" ]; then
+  # turns on full gravity
+  sed -i "s:^FULL_GRAVITY .*:FULL_GRAVITY = .true.:" DATA/Par_file
+  # PETSc
+  if [ "${PETSC}" == "true" ]; then
+    # switch to PETSc Poisson solver
+    sed -i "s:^POISSON_SOLVER .*:POISSON_SOLVER = 1:" DATA/Par_file
+  fi
+  # set NSTEP for short checks only
+  echo "NSTEP = 2" >> DATA/Par_file
+fi
+
+# adios
+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
 
@@ -63,7 +89,7 @@ echo `date`
 echo
 
 # seismogram comparison
-if [ "${DEBUG}" == "true" ]; then
+if [ "${DEBUG}" == "true" ] || [ "${FULL_GRAVITY}" == "true" ] || [ "${RUN_KERNEL}" == "true" ]; then
   # no comparisons
   :     # do nothing
 else

.github/workflows/CI.yml

@@ -442,3 +442,113 @@ jobs:
         TESTDIR: EXAMPLES/mars_regional
       run: ./.github/scripts/run_tests.sh
       shell: bash
+
+  linuxTest_7:
+    name: Test run example 7 - global_small
+    runs-on: ubuntu-latest
+    needs: [linuxCheck]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install packages
+      run: ./.github/scripts/run_install.sh
+      shell: bash
+
+    - name: Run build
+      env:
+        TESTFLAGS: --enable-vectorization
+      run: ./.github/scripts/run_build.sh
+      shell: bash
+
+    - name: Run test
+      env:
+        TESTDIR: EXAMPLES/global_small
+      run: ./.github/scripts/run_tests.sh
+      shell: bash
+
+  linuxTest_8:
+    name: Test run example 8 - global_small w/ FULL_GRAVITY netCDF
+    runs-on: ubuntu-latest
+    needs: [linuxCheck]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install packages
+      env:
+        NETCDF: true
+      run: ./.github/scripts/run_install.sh
+      shell: bash
+
+    - name: Run build
+      env:
+        TESTFLAGS: --enable-debug
+        NETCDF: true
+      run: ./.github/scripts/run_build.sh
+      shell: bash
+
+    - name: Run test
+      env:
+        TESTDIR: EXAMPLES/global_small
+        FULL_GRAVITY: true
+      run: ./.github/scripts/run_tests.sh
+      shell: bash
+
+  linuxTest_9:
+    name: Test run example 9 - global_small w/ FULL_GRAVITY PETSc
+    runs-on: ubuntu-latest
+    needs: [linuxCheck]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install packages
+      env:
+        PETSC: true
+      run: ./.github/scripts/run_install.sh
+      shell: bash
+
+    - name: Run build
+      env:
+        TESTFLAGS:  # no extra flags
+        PETSC: true
+      run: ./.github/scripts/run_build.sh
+      shell: bash
+
+    - name: Run test
+      env:
+        TESTDIR: EXAMPLES/global_small
+        FULL_GRAVITY: true
+        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

EXAMPLES/global_small/run_mesher_solver.bash

@@ -1,18 +1,22 @@
 #!/bin/bash
 
 # DATABASES directory
-BASEMPIDIR=`grep ^LOCAL_PATH DATA/Par_file | cut -d = -f 2 `
+BASEMPIDIR=`grep ^LOCAL_PATH DATA/Par_file | cut -d = -f 2`
 
 # script to run the mesher and the solver
 # read DATA/Par_file to get information about the run
 # compute total number of nodes needed
-NPROC_XI=`grep ^NPROC_XI DATA/Par_file | cut -d = -f 2 `
+NPROC_XI=`grep ^NPROC_XI DATA/Par_file | cut -d = -f 2`
 NPROC_ETA=`grep ^NPROC_ETA DATA/Par_file | cut -d = -f 2`
-NCHUNKS=`grep ^NCHUNKS DATA/Par_file | cut -d = -f 2 `
+NCHUNKS=`grep ^NCHUNKS DATA/Par_file | cut -d = -f 2`
 
 # total number of nodes is the product of the values read
 numnodes=$(( $NCHUNKS * $NPROC_XI * $NPROC_ETA ))
 
+# full gravity option
+FULL_GRAVITY=`grep ^FULL_GRAVITY DATA/Par_file | cut -d = -f 2 | tr -d '[:space:]'`
+
+
 mkdir -p OUTPUT_FILES
 mkdir -p $BASEMPIDIR
 
@@ -43,6 +47,26 @@ echo
 cp OUTPUT_FILES/*.txt $BASEMPIDIR/
 
 
+## full gravity
+if [ "$FULL_GRAVITY" == ".true." ]; then
+  ##
+  ## gindex3D
+  ##
+  echo
+  echo "running xgindex3D..."
+  echo
+  if [ ! -e $PWD/bin/xgindex3D ]; then echo "xgindex3D was not compiled, aborting..."; exit 1; fi
+
+  mpirun -np 1 $PWD/bin/xgindex3D $numnodes
+
+  # checks exit code
+  if [[ $? -ne 0 ]]; then exit 1; fi
+
+  echo
+  echo "  gindex3D done: `date`"
+  echo
+fi
+
 ##
 ## forward simulation
 ##

EXAMPLES/global_small/run_this_example.sh

@@ -58,10 +58,7 @@ fi
 # copy executables
 mkdir -p bin
 rm -rf bin/*
-cp ../../bin/xmeshfem3D ./bin/
-cp ../../bin/xspecfem3D ./bin/
-cp ../../bin/xcombine_vol_data ./bin/
-cp ../../bin/xcombine_vol_data_vtk ./bin/
+cp ../../bin/x* ./bin/
 
 # links data directories needed to run example in this current directory with s362ani
 cd DATA/

configure

@@ -11843,7 +11843,7 @@ printf %s "checking PETSc linking with PetscInitialize in -lpetsc... " >&6; }
   use petscksp
   implicit none
   PetscErrorCode :: ierr
-  call PetscInitialize(ierr)
+  call PetscInitialize(PETSC_NULL_CHARACTER,ierr)
   call PetscFinalize(ierr)
 
       end

configure.ac

@@ -922,7 +922,7 @@ AS_IF([test x"$want_petsc" != xno], [
   use petscksp
   implicit none
   PetscErrorCode :: ierr
-  call PetscInitialize(ierr)
+  call PetscInitialize(PETSC_NULL_CHARACTER,ierr)
   call PetscFinalize(ierr)
       ]])
     ], [