Merge pull request #854 from danielpeter/devel

.github/scripts/run_build.sh

@@ -60,6 +60,16 @@ else
   petsc=()
 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
+
 # configuration
 echo
 echo "configuration:"
@@ -68,6 +78,7 @@ echo
 ./configure \
 ${adios[@]} \
 ${netcdf[@]} \
+${hdf[@]} \
 ${petsc[@]} \
 FC=gfortran MPIFC=mpif90 CC=gcc "${TESTFLAGS}"
 

.github/scripts/run_install.sh

@@ -18,6 +18,25 @@ sudo apt-get install -yq --no-install-recommends gfortran g++ openmpi-bin libope
 if [[ $? -ne 0 ]]; then exit 1; fi
 echo
 
+# parallel hdf5
+if [ "${HDF5}" == "true" ]; then
+  echo
+  echo "HDF5 installation:"
+  echo
+  sudo apt-get install -yq --no-install-recommends libhdf5-mpi-dev
+  ## checks installation paths
+  #echo
+  #dpkg -L libhdf5-mpi-dev
+  #echo
+  #dpkg -L libhdf5-openmpi-dev
+  #echo
+  #echo "hdf5 module paths:"
+  #find /usr/ -iname 'hdf5.mod'
+  #echo "hdf5 library paths:"
+  #find /usr/ -iname 'libhdf5hl_fortran*'
+  #echo
+fi
+
 ## NetCDF
 if [ "${NETCDF}" == "true" ]; then
   echo

.github/scripts/run_tests.sh

@@ -23,7 +23,7 @@ echo
 # bash function for checking seismogram output with reference solutions
 my_test(){
   echo "testing seismograms:"
-  ln -s $WORKDIR/utils/compare_seismogram_correlations.py
+  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 $1,"good"; exit 0;}}'
@@ -65,6 +65,18 @@ if [ "${FULL_GRAVITY}" == "true" ]; then
   echo "NSTEP = 2" >> DATA/Par_file
 fi
 
+# hdf5 i/o example
+if [ "${HDF5}" == "true" ]; then
+  echo
+  echo "HDF5 enabled test run"
+  echo
+  sed -i "s:^HDF5_ENABLED .*:HDF5_ENABLED    = .true.:" DATA/Par_file
+  #sed -i "s:^HDF5_FOR_MOVIES .*:HDF5_FOR_MOVIES    = .true.:" DATA/Par_file
+  #sed -i "s:^HDF5_IO_NODES .*:HDF5_IO_NODES    = 1:" DATA/Par_file
+  # replaces run script
+  #cp -v run_this_example_HDF5_IO_server.sh run_this_example.sh
+fi
+
 # adios
 if [ "${ADIOS2}" == "true" ]; then
   # turns on ADIOS

.github/workflows/CI.yml

@@ -552,3 +552,31 @@ jobs:
         RUN_KERNEL: true
       run: ./.github/scripts/run_tests.sh
       shell: bash
+
+  linuxTest_11:
+    name: Test run example 11 - regional_Greece_small hdf5 i/o
+    runs-on: ubuntu-latest
+    needs: [linuxCheck]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install packages
+      env:
+        HDF5: true
+      run: ./.github/scripts/run_install.sh
+      shell: bash
+
+    - name: Run build
+      env:
+        TESTFLAGS: # no extra flags
+        HDF5: true
+      run: ./.github/scripts/run_build.sh
+      shell: bash
+
+    - name: Run test
+      env:
+        TESTDIR: EXAMPLES/regional_Greece_small
+        HDF5: true
+      run: ./.github/scripts/run_tests.sh
+      shell: bash

EXAMPLES/regional_s40rts/DATA/Par_file

@@ -433,5 +433,5 @@ ADIOS_FOR_UNDO_ATTENUATION      = .true.
 
 # HDF5 Database I/O
 # (note the flags for HDF5 and ADIOS are mutually exclusive, only one can be used)
-HDF5_ENABLED                    = .true.
+HDF5_ENABLED                    = .false.
 

EXAMPLES/regional_small_adjoint/DATA/Par_file

@@ -433,5 +433,5 @@ ADIOS_FOR_UNDO_ATTENUATION      = .true.
 
 # HDF5 Database I/O
 # (note the flags for HDF5 and ADIOS are mutually exclusive, only one can be used)
-HDF5_ENABLED                    = .true.
+HDF5_ENABLED                    = .false.
 

src/meshfem3D/save_arrays_solver_hdf5.F90

@@ -1,3 +1,31 @@
+!=====================================================================
+!
+!                       S p e c f e m 3 D  G l o b e
+!                       ----------------------------
+!
+!     Main historical authors: Dimitri Komatitsch and Jeroen Tromp
+!                        Princeton University, USA
+!                and CNRS / University of Marseille, France
+!                 (there are currently many more authors!)
+! (c) Princeton University and CNRS / University of Marseille, April 2014
+!
+! This program is free software; you can redistribute it and/or modify
+! it under the terms of the GNU General Public License as published by
+! the Free Software Foundation; either version 3 of the License, or
+! (at your option) any later version.
+!
+! This program is distributed in the hope that it will be useful,
+! but WITHOUT ANY WARRANTY; without even the implied warranty of
+! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+! GNU General Public License for more details.
+!
+! You should have received a copy of the GNU General Public License along
+! with this program; if not, write to the Free Software Foundation, Inc.,
+! 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+!
+!=====================================================================
+
+
   subroutine save_arrays_solver_hdf5(idoubling,ibool,xstore,ystore,zstore, &
                                      NSPEC2D_TOP,NSPEC2D_BOTTOM)
 
@@ -37,8 +65,6 @@ subroutine save_arrays_solver_hdf5(idoubling,ibool,xstore,ystore,zstore, &
     tau_s_store,tau_e_store,Qmu_store, &
     nglob_oceans, nglob_xy
 
-
-
   use manager_hdf5
 #endif
 
@@ -125,7 +151,7 @@ subroutine save_arrays_solver_hdf5(idoubling,ibool,xstore,ystore,zstore, &
   !
   if (myrank == 0) then
     ! create and open solver_data.h5
-    name_database_hdf5 = LOCAL_PATH(1:len_trim(LOCAL_PATH))//'/'//'solver_data.h5'
+    name_database_hdf5 = LOCAL_PATH(1:len_trim(LOCAL_PATH)) // '/' // 'solver_data.h5'
     if (iregion_code == 1) then
       call h5_create_file(name_database_hdf5)
     else
@@ -608,6 +634,16 @@ subroutine save_arrays_solver_hdf5(idoubling,ibool,xstore,ystore,zstore, &
 #else
   ! no HDF5 compilation
 
+  ! to avoid compiler warnings
+  integer :: idummy
+
+  idummy = size(idoubling,kind=4)
+  idummy = size(ibool,kind=4)
+  idummy = size(xstore,kind=4)
+  idummy = size(ystore,kind=4)
+  idummy = size(zstore,kind=4)
+  idummy = max(NSPEC2D_TOP,NSPEC2D_BOTTOM)
+
   ! user output
   print *
   print *, "Error: HDF5 routine save_databases_hdf5() called without HDF5 Support."
@@ -617,7 +653,7 @@ subroutine save_arrays_solver_hdf5(idoubling,ibool,xstore,ystore,zstore, &
 
 #endif
 
-end subroutine save_arrays_solver_hdf5
+  end subroutine save_arrays_solver_hdf5
 
 !
 !-----------------------------------------------------------------------
@@ -672,9 +708,6 @@ subroutine save_arrays_boundary_hdf5()
   ! processor dependent group names
   character(len=64) :: gname_region
 
-  ! process rank
-  myrank = myrank
-
   ! first check the number of surface elements are the same for Moho, 400, 670
   if (.not. SUPPRESS_CRUSTAL_MESH .and. HONOR_1D_SPHERICAL_MOHO) then
     if (ispec2D_moho_top /= NSPEC2D_MOHO .or. ispec2D_moho_bot /= NSPEC2D_MOHO) &
@@ -794,7 +827,7 @@ subroutine save_arrays_boundary_hdf5()
   stop 'Error HDF5 save_databases_hdf5(): called without compilation support'
 #endif
 
-end subroutine save_arrays_boundary_hdf5
+  end subroutine save_arrays_boundary_hdf5
 
 !
 !-------------------------------------------------------------------------------------------------
@@ -853,8 +886,6 @@ subroutine save_MPI_arrays_hdf5(iregion_code,LOCAL_PATH, &
   integer, dimension(0:NPROCTOT-1) :: offset_num_colors_outer
   integer, dimension(0:NPROCTOT-1) :: offset_num_colors_inner
 
-  myrank = myrank
-
   ! gather the offsets
   call gather_all_all_singlei(num_interfaces, offset_num_interfaces, NPROCTOT)
   call gather_all_all_singlei(max_nibool_interfaces, offset_max_nibool_interfaces, NPROCTOT)
@@ -990,13 +1021,29 @@ subroutine save_MPI_arrays_hdf5(iregion_code,LOCAL_PATH, &
 
 #else
   ! no HDF5 compilation
-  print* , "Error: HDF5 routine save_MPI_arrays_hdf5() called without HDF5 Support."
-  print* , "To enable HDF5 support, reconfigure with --with-hdf5 flag."
+
+  ! to avoid compiler warnings
+  integer :: idummy
+
+  idummy = iregion_code
+  idummy = len_trim(LOCAL_PATH)
+  idummy = size(ibool_interfaces,kind=4)
+  idummy = size(my_neighbors,kind=4)
+  idummy = size(nibool_interfaces,kind=4)
+  idummy = max(nspec_inner,nspec_outer)
+  idummy = size(num_elem_colors)
+  idummy = size(phase_ispec_inner)
+
+  print * , "Error: HDF5 routine save_MPI_arrays_hdf5() called without HDF5 Support."
+  print * , "To enable HDF5 support, reconfigure with --with-hdf5 flag."
   stop 'Error HDF5 save_MPI_arrays_hdf5(): called without compilation support'
 #endif
 
   end subroutine save_MPI_arrays_hdf5
 
+!
+!-------------------------------------------------------------------------------------------------
+!
 
   subroutine get_absorb_stacey_boundary_hdf5(iregion, num_abs_boundary_faces, &
                                          abs_boundary_ispec,abs_boundary_npoin, &
@@ -1139,15 +1186,21 @@ subroutine get_absorb_stacey_boundary_hdf5(iregion, num_abs_boundary_faces, &
   call h5_close_file_p()
 
 #else
-    ! no HDF5 compilation
-    print* , "Error: HDF5 routine get_absorb_stacey_boundary_hdf5() called without HDF5 Support."
-    print* , "To enable HDF5 support, reconfigure with --with-hdf5 flag."
-    stop 'Error HDF5 get_absorb_stacey_boundary_hdf5(): called without compilation support'
-#endif
-
-
+  ! no HDF5 compilation
 
+  ! to avoid compiler warnings
+  integer :: idummy
 
+  idummy = iregion
+  idummy = size(abs_boundary_ispec,kind=4)
+  idummy = size(abs_boundary_npoin)
+  idummy = size(abs_boundary_ijk)
+  idummy = size(abs_boundary_normal,kind=4)
+  idummy = size(abs_boundary_jacobian2dw,kind=4)
 
+  print * , "Error: HDF5 routine get_absorb_stacey_boundary_hdf5() called without HDF5 Support."
+  print * , "To enable HDF5 support, reconfigure with --with-hdf5 flag."
+  stop 'Error HDF5 get_absorb_stacey_boundary_hdf5(): called without compilation support'
+#endif
 
-    end subroutine get_absorb_stacey_boundary_hdf5
+  end subroutine get_absorb_stacey_boundary_hdf5

src/meshfem3D/save_model_meshfiles_hdf5.F90

@@ -241,10 +241,10 @@ subroutine save_model_meshfiles_hdf5()
           do j = 1,NGLLY
             do i = 1,NGLLX
               temp_store(i,j,k,ispec) = Qmu_store(1,1,1,ispec)
-            end do
-          end do
-        end do
-      end do
+            enddo
+          enddo
+        enddo
+      enddo
     endif
 
     ! Qmu
@@ -273,5 +273,4 @@ subroutine save_model_meshfiles_hdf5()
 
 #endif
 
-
-end subroutine save_model_meshfiles_hdf5
+  end subroutine save_model_meshfiles_hdf5

src/shared/read_parameter_file.F90

@@ -437,5 +437,4 @@ subroutine read_parameter_file()
   endif
 #endif
 
-
   end subroutine read_parameter_file

src/shared/rules.mk

@@ -93,6 +93,7 @@ shared_OBJECTS = \
 shared_MODULES = \
 	$(FC_MODDIR)/constants.$(FC_MODEXT) \
 	$(FC_MODDIR)/manager_adios.$(FC_MODEXT) \
+	$(FC_MODDIR)/manager_hdf5.$(FC_MODEXT) \
 	$(FC_MODDIR)/model_prem_par.$(FC_MODEXT) \
 	$(FC_MODDIR)/model_sohl_par.$(FC_MODEXT) \
 	$(FC_MODDIR)/model_mars_1d_par.$(FC_MODEXT) \

src/specfem3D/locate_point.f90

@@ -509,13 +509,13 @@ subroutine find_local_coordinates(x_target,y_target,z_target,xi,eta,gamma,x,y,z,
     ! the polynomial solution is defined everywhere
     ! can be useful for convergence of iterative scheme with distorted elements
     !if (xi > 1.10d0) xi = 1.10d0
-    !if (xi < -1.10d0) xi = -1.10d0
+    !if (xi <-1.10d0) xi = -1.10d0
     if (abs(xi) > 1.10d0) xi = sign(1.10d0,xi)
     !if (eta > 1.10d0) eta = 1.10d0
-    !if (eta < -1.10d0) eta = -1.10d0
+    !if (eta <-1.10d0) eta = -1.10d0
     if (abs(eta) > 1.10d0) eta = sign(1.10d0,eta)
     !if (gamma > 1.10d0) gamma = 1.10d0
-    !if (gamma < -1.10d0) gamma = -1.10d0
+    !if (gamma <-1.10d0) gamma = -1.10d0
     if (abs(gamma) > 1.10d0) gamma = sign(1.10d0,gamma)
 
   ! end of non linear iterations

src/specfem3D/prepare_movie.f90

@@ -76,7 +76,7 @@ subroutine prepare_movie_surface()
       nmovie_points = NGLLX * NGLLY * NSPEC2D_TOP(IREGION_CRUST_MANTLE)
     else ! HDF5
       nmovie_points = 4 * (NGLLX-1) * (NGLLY-1) * NSPEC2D_TOP(IREGION_CRUST_MANTLE)
-    end if
+    endif
     NIT = 1
   endif