Merge pull request #1701 from danielpeter/devel

SPECFEM · Jun 5, 2024 · 1f01888 · 1f01888
2 parents ee3b095 + 2652225
commit 1f01888
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diff --git a/.github/scripts/run_build.sh b/.github/scripts/run_build.sh
@@ -29,13 +29,25 @@ 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
 
 # configuration
 echo
-echo "configuration: default"
+echo "configuration:"
 echo
 
-./configure FC=gfortran MPIFC=mpif90 CC=gcc ${TESTFLAGS}
+./configure \
+${adios[@]} \
+FC=gfortran MPIFC=mpif90 CC=gcc ${TESTFLAGS}
 
 # checks
 if [[ $? -ne 0 ]]; then echo "configuration failed:"; cat config.log; echo ""; echo "exiting..."; exit 1; fi

diff --git a/.github/scripts/run_install.sh b/.github/scripts/run_install.sh
@@ -38,6 +38,12 @@ fi
 if [[ $? -ne 0 ]]; then exit 1; fi
 echo
 
+# 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
+if [[ $? -ne 0 ]]; then exit 1; fi
+echo
+
 # python script needs numpy
 #sudo apt-get install -qq python-numpy # not working, likely installed on older python version
 pip install --user --upgrade pip setuptools wheel
@@ -68,6 +74,39 @@ 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 zxf 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

diff --git a/.github/scripts/run_tests.sh b/.github/scripts/run_tests.sh
@@ -117,6 +117,12 @@ if [[ "${TEST}" == *"with-hdf5"* ]]; then
   cp -v run_this_example_HDF5_IO_server.sh run_this_example.sh
 fi
 
+# adios
+if [ "${ADIOS2}" == "true" ]; then
+  # turns on ADIOS
+  sed -i "s:^ADIOS_ENABLED .*:ADIOS_ENABLED = .true.:" DATA/Par_file
+fi
+
 # default script
 ./run_this_example.sh
 

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Check for changes
       id: diff
@@ -86,7 +86,7 @@ jobs:
     needs: changesCheck
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install dependencies
       run: |
@@ -104,10 +104,11 @@ jobs:
         echo ""
         ## avoids sed -i '' issue on MacOS, using gnu sed to have the same sed command lines as in linux
         brew install gnu-sed
-        echo "PATH=/usr/local/opt/gnu-sed/libexec/gnubin:$PATH" >> $GITHUB_ENV
+        echo "PATH=/opt/homebrew/opt/gnu-sed/libexec/gnubin:$PATH" >> $GITHUB_ENV
         ## OpenMP
         echo "OMP_NUM_THREADS=2" >> $GITHUB_ENV
         ## MPI
+        echo
         echo "MPI environment:"
         echo "mpif90 on path: $(which mpif90)"
         echo
@@ -149,7 +150,7 @@ jobs:
         os: [ubuntu-latest,ubuntu-20.04]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -168,7 +169,7 @@ jobs:
     needs: changesCheck
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Cache Intel oneapi packages
       id: cache-intel-oneapi
@@ -303,7 +304,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -322,7 +323,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -346,7 +347,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -370,7 +371,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -395,7 +396,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -419,7 +420,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -444,7 +445,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -469,7 +470,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -495,7 +496,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -520,7 +521,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -544,7 +545,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -568,7 +569,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -592,7 +593,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -616,7 +617,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -640,7 +641,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -664,7 +665,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -688,7 +689,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -712,7 +713,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       run: ./.github/scripts/run_install.sh
@@ -736,7 +737,7 @@ jobs:
     needs: [linuxCheck]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install packages
       env:
@@ -758,3 +759,31 @@ jobs:
       run: ./.github/scripts/run_tests.sh
       shell: bash
 
+  linuxTest_19:
+    name: Test run example 19 - meshfem3D simple model w/ 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: --with-mpi --enable-vectorization
+        ADIOS2: true
+      run: ./.github/scripts/run_build.sh
+      shell: bash
+
+    - name: Run test
+      env:
+        TESTDIR: EXAMPLES/applications/meshfem3D_examples/simple_model/
+        ADIOS2: true
+      run: ./.github/scripts/run_tests.sh
+      shell: bash
+
diff --git a/src/generate_databases/save_arrays_solver_adios.F90 b/src/generate_databases/save_arrays_solver_adios.F90
@@ -208,7 +208,7 @@ subroutine save_arrays_solver_mesh_adios()
 
 
   ! calling wrapper instead to compile without mpi
-  call max_allreduce_i(max_global_values,num_vars)
+  call max_all_all_veci(max_global_values,num_vars)
 
   nglob_wmax                          = max_global_values(1)
   nspec_wmax                          = max_global_values(2)

diff --git a/src/generate_databases/save_moho_adios.F90 b/src/generate_databases/save_moho_adios.F90
@@ -61,8 +61,8 @@ subroutine crm_save_moho_adios()
   ! ADIOS write equally sized chunks for each processor.            |
   !-----------------------------------------------------------------'
   ! determines maximum values for nspec over all partition slices
-  call max_allreduce_singlei(NSPEC_AB,NSPEC_wmax)
-  call max_allreduce_singlei(nspec2d_moho,nspec2d_moho_wmax)
+  call max_all_all_i(NSPEC_AB,NSPEC_wmax)
+  call max_all_all_i(nspec2d_moho,nspec2d_moho_wmax)
 
   !-----------------------------------.
   ! Setup ADIOS for the current group |

diff --git a/src/inverse_problem_for_model/input_output/Teleseismic_IO.f90 b/src/inverse_problem_for_model/input_output/Teleseismic_IO.f90
@@ -39,6 +39,8 @@ module Teleseismic_IO_mod
                                         calc_delta_dist_baz, calc_dist_baz_cart, lowcase, &
                                         write_binary_data
   use signal_processing, only: taper_window_W
+
+  implicit none
   integer, private :: NEVENT
 
 contains
@@ -50,8 +52,8 @@ module Teleseismic_IO_mod
   subroutine read_acqui_teleseismic_file(acqui_file, acqui_simu, myrank)
 
     use my_mpi             !! module from specfem
-    include "precision.h"  !! from specfem
 
+    implicit none
     character(len=MAX_LEN_STRING),           intent(in)    ::  acqui_file
     integer,                                 intent(in)    ::  myrank
     type(acqui),  dimension(:), allocatable, intent(inout) ::  acqui_simu
@@ -437,7 +439,7 @@ subroutine setup_teleseismic_stations(acqui_simu, myrank)
     !! hgamma, hpgamma
     !!
     !! ------------------------------------------------------------------------------
-
+    implicit none
     type(acqui), dimension(:),              intent(inout)  :: acqui_simu
     integer,                                intent(in)     :: myrank
     ! local