Merge pull request #1665 from danielpeter/devel

updates tests; fixes LTS arrays for surface points and shakemaps; adds blender visualization scripts
SPECFEM · Dec 20, 2023 · 89d1601 · 89d1601
2 parents 0321f61 + c836576
commit 89d1601
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Showing 22 changed files with 4,073 additions and 95 deletions.
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -179,31 +179,67 @@ jobs:
         sudo echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
         sudo apt-get update
         echo ""
-        echo "packages intel oneapi:"
-        sudo apt-get install -y intel-oneapi-compiler-fortran intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic intel-oneapi-mpi intel-oneapi-mpi-devel
+        # info
+        #sudo -E apt-cache pkgnames intel | grep intel-oneapi
+        #echo ""
+        echo "installing packages intel oneapi:"
+        sudo apt-get install -y intel-oneapi-compiler-fortran-2023.2.2 intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic-2023.2.2 intel-oneapi-mpi intel-oneapi-mpi-devel
+        echo ""
 
     - name: compiler infos
       run: |
         echo ""
         source /opt/intel/oneapi/setvars.sh
         echo ""
         echo "compiler versions:"
+        echo "icx --version"
+        which icx
+        icx --version
+        echo ""
         echo "icc --version"
+        which icc
         icc --version
+        echo ""
+        echo "ifx --version"
+        which ifx
+        ifx --version
+        echo ""
         echo "ifort --version"
+        which ifort
         ifort --version
+        echo ""
         echo "mpiifort --version"
+        which mpiifort
         mpiifort --version
+        echo ""
         echo "mpif90 --version"
+        which mpif90
         mpif90 --version
         echo ""
+        # infos
+        which ifort
+        which icc
+        which mpiifort
+        echo "mpirun:"
+        which mpirun
+        echo ""
+        # intel setup for running tests
+        echo ""
+        echo "replacing mpif90 with mpiifort link:"
+        sudo ln -sf $(which mpiifort) $(which mpif90)
+        mpif90 --version
+        echo ""
+        # debug
+        #export I_MPI_DEBUG=5,pid,host
+        #export I_MPI_LIBRARY_KIND=debug
+        # remove -ftrapuv which leads to issues for running tests
+        sed -i "s/-ftrapuv//g" flags.guess
+        # environment setting
         export TERM=xterm
+        # export info
         echo "exports:"
         export
         echo ""
-        which ifort
-        which icc
-        which mpiifort
         echo ""
         printenv >> $GITHUB_ENV
         echo "CXX=icpc" >> $GITHUB_ENV
@@ -212,7 +248,8 @@ jobs:
         echo ""
 
     - name: configure serial debug
-      run: ./configure --enable-debug --without-mpi FC=ifort CC=icc
+      run: |
+        ./configure --enable-debug --without-mpi FC=ifort CC=icc
 
     - name: make serial debug
       run: |
@@ -221,15 +258,17 @@ jobs:
         make clean
 
     - name: configure serial
-      run: ./configure --without-mpi FC=ifort CC=icc
+      run: |
+        ./configure --without-mpi FC=ifort CC=icc
 
     - name: make serial
       run: |
         make -j2 all
         make clean
 
     - name: configure parallel debug
-      run: ./configure --enable-debug --with-mpi FC=ifort CC=icc MPIFC=mpiifort MPI_INC="${I_MPI_ROOT}/include"
+      run: |
+        ./configure --enable-debug --with-mpi FC=ifort CC=icc MPIFC=mpiifort MPI_INC="${I_MPI_ROOT}/include"
 
     - name: make parallel debug
       run: |
@@ -238,16 +277,18 @@ jobs:
         make clean
 
     - name: configure parallel
-      run: ./configure --with-mpi FC=ifort CC=icc MPIFC=mpiifort MPI_INC="${I_MPI_ROOT}/include"
+      run: |
+        ./configure --with-mpi FC=ifort CC=icc MPIFC=mpiifort MPI_INC="${I_MPI_ROOT}/include"
 
     - name: make parallel
       run: |
         make -j2 all
         make clean
 
-    # check: fails due to intel MPI issue with mpif90 using gfortran as default on virtual nodes
-    #- name: make tests
-    #  run: make tests
+    # note: fails with -ftrapuv flag due to MPI issue on virtual nodes
+    - name: make tests
+      run: |
+        make tests
 
   linuxTest_0:
     name: Test run example 0 - make tests

diff --git a/EXAMPLES/applications/coffee_mug_with_fluid_inside/run_boundary_definition.py b/EXAMPLES/applications/coffee_mug_with_fluid_inside/run_boundary_definition.py
@@ -28,7 +28,9 @@
 
 ###### This is boundary_definition.py of GEOCUBIT
 #..... which extracts the bounding faces and defines them into blocks
-reload(boundary_definition)
+import importlib
+importlib.reload(boundary_definition)
+
 boundary_definition.entities=['face']
 boundary_definition.define_bc(boundary_definition.entities,parallel=True)
 

diff --git a/EXAMPLES/applications/coffee_mug_with_fluid_inside/run_cubit2specfem3d.py b/EXAMPLES/applications/coffee_mug_with_fluid_inside/run_cubit2specfem3d.py
@@ -27,15 +27,18 @@
 
 ###### This is boundary_definition.py of GEOCUBIT
 #..... which extracts the bounding faces and defines them into blocks
-#reload(boundary_definition)
+#import importlib
+#importlib.(boundary_definition)
 #boundary_definition.entities=['face']
 #boundary_definition.define_bc(boundary_definition.entities,parallel=True)
 
 
 #### Export to SESAME format using cubit2specfem3d.py of GEOCUBIT
 os.system('mkdir -p MESH')
 
-reload(cubit2specfem3d)
+import importlib
+importlib.reload(cubit2specfem3d)
+
 cubit2specfem3d.export2SPECFEM3D('MESH')
 
 # all files needed by SCOTCH are now in directory MESH

diff --git a/doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.pdf b/doc/USER_MANUAL/manual_SPECFEM3D_Cartesian.pdf
diff --git a/flags.guess b/flags.guess
@@ -92,12 +92,11 @@ case $my_FC in
         #
         # warnings about external function calls can be suppressed by "-warn all,noexternal" for version > 2018
         # optimization report: "-vec-report0" is old and will be replaced by "-qopt-report0 -qopt-report-phase=vec" for v >=15.0
-        DEF_FFLAGS="-xHost -fpe0 -ftz -assume buffered_io -assume byterecl -align sequence -std08 -diag-disable 6477 -implicitnone -gen-interfaces -warn all" # -mcmodel=medium -shared-intel
+        DEF_FFLAGS="-xHost -fpe0 -ftz -assume buffered_io -assume byterecl -align sequence -std08 -diag-disable 6477 -implicitnone -gen-interfaces -warn all,noexternal" # -mcmodel=medium -shared-intel
         OPT_FFLAGS="-O3 -check nobounds"
         DEBUG_FFLAGS="-check all -debug -g -O0 -fp-stack-check -traceback -ftrapuv"
         # option "-openmp" is soon deprecated and replaced by "-qopenmp" for versions > 17.x
         OMP_FFLAGS="-qopenmp"
-        #
         ;;
     gfortran|*/gfortran|f95|*/f95)
         #

diff --git a/src/auxiliaries/combine_surf_data.f90 b/src/auxiliaries/combine_surf_data.f90
@@ -277,7 +277,7 @@ program combine_surf_data
     read(27) zstore
     close(27)
 
-    do ispec_surf=1,nspec_surf
+    do ispec_surf = 1,nspec_surf
       ispec = ibelm_surf(ispec_surf)
       k = 1
       do j = 1, NGLLY, iny
@@ -345,7 +345,7 @@ program combine_surf_data
 
     np = npoint * (it-1)
 
-! surface file
+    ! surface file
     local_ibool_surf_file = trim(prname) // 'ibelm_' //trim(surfname)// '.bin'
     open(unit = 28,file = trim(local_ibool_surf_file),status='old', iostat = ier, form='unformatted')
     read(28) nspec_surf
@@ -354,7 +354,7 @@ program combine_surf_data
     read(28) ibelm_surf
     close(28)
 
-! ibool file
+    ! ibool file
     local_ibool_file = trim(prname) // 'ibool' // '.bin'
     open(unit = 28,file = trim(local_ibool_file),status='old', iostat = ier, form='unformatted')
     read(28) ibool

diff --git a/src/generate_databases/create_regions_mesh.f90 b/src/generate_databases/create_regions_mesh.f90
@@ -1857,7 +1857,7 @@ subroutine crm_setup_mesh_surface()
     nfaces_surface = NSPEC2D_TOP
   endif
 
-! number of surface faces for all partitions together
+  ! number of surface faces for all partitions together
   call sum_all_i(nfaces_surface,nfaces_surface_glob_ext_mesh)
 
   deallocate(ibool_interfaces_ext_mesh_dummy)