Merge pull request #1836 from danielpeter/devel

updates scripts; code cleaning

Author: danielpeter

EXAMPLES/applications/Gmsh_simple_box_hex27/mesh_example_with_Gmsh.py

@@ -36,7 +36,7 @@
 import gmsh
 
 # from python file import
-sys.path.append('../../utils/Cubit_or_Gmsh/')
+sys.path.append('../../../utils/Cubit_or_Gmsh/')
 from Gmsh2specfem import export2SPECFEM3D
 
 
@@ -717,6 +717,24 @@ def mesh_3D():
     meshio.write(filename, mesh)
     print("VTK file written to : ",filename)
 
+    # cleans out unnecessary cell data
+    # to avoid issues when storing/reading mesh in older Gmsh format (legacy) 2.2
+    if pygmsh_major_version >= 7:
+        print("")
+        print("mesh items:")
+        keys_to_clean = []
+        for key, d in mesh.cell_data.items():
+            print("  key: ",key)
+            if key in ["gmsh:physical", "gmsh:geometrical", "cell_tags"]:
+                continue
+            else:
+                # delete key
+                print("        will be cleaned out...")
+                keys_to_clean.append(key)
+        # clean out element data
+        for key in keys_to_clean: del mesh.cell_data[key]
+        print("")
+
     # saves as Gmsh-file
     filename = "MESH/box.msh"
     if pygmsh_major_version >= 7:
@@ -761,12 +779,19 @@ def create_mesh():
     print("pygmsh version: ",version)
 
     # Gmsh version
+    # try to get Gmsh version also through pygmsh and compare against loaded gmsh module
     if pygmsh_major_version >= 7:
         # pygmsh version >= 7.x
-        version = pygmsh.__gmsh_version__
+        try:
+            version = pygmsh.__gmsh_version__
+        except:
+            version = gmsh.__version__
     else:
         # pygmsh version 6.x
-        version = pygmsh.get_gmsh_major_version()
+        try:
+            version = pygmsh.get_gmsh_major_version()
+        except:
+            version = gmsh.__version__
     print("Gmsh version  : ",version, " module version ",gmsh.__version__)
 
     # creates a simple 3D mesh

EXAMPLES/applications/Gmsh_simple_lddrk/mesh_example_with_Gmsh_simple.py

@@ -36,7 +36,7 @@
 import gmsh
 
 # from python file import
-sys.path.append('../../utils/Cubit_or_Gmsh/')
+sys.path.append('../../../utils/Cubit_or_Gmsh/')
 from Gmsh2specfem import export2SPECFEM3D
 
 
@@ -634,6 +634,24 @@ def mesh_3D():
     meshio.write(filename, mesh)
     print("VTK file written to : ",filename)
 
+    # cleans out unnecessary cell data
+    # to avoid issues when storing/reading mesh in older Gmsh format (legacy) 2.2
+    if pygmsh_major_version >= 7:
+        print("")
+        print("mesh items:")
+        keys_to_clean = []
+        for key, d in mesh.cell_data.items():
+            print("  key: ",key)
+            if key in ["gmsh:physical", "gmsh:geometrical", "cell_tags"]:
+                continue
+            else:
+                # delete key
+                print("        will be cleaned out...")
+                keys_to_clean.append(key)
+        # clean out element data
+        for key in keys_to_clean: del mesh.cell_data[key]
+        print("")
+
     # saves as Gmsh-file (msh mesh format)
     filename = "MESH/box.msh"
     if pygmsh_major_version >= 7:
@@ -678,12 +696,19 @@ def create_mesh():
     print("pygmsh version: ",version)
 
     # Gmsh version
+    # try to get Gmsh version also through pygmsh and compare against loaded gmsh module
     if pygmsh_major_version >= 7:
         # pygmsh version >= 7.x
-        version = pygmsh.__gmsh_version__
+        try:
+            version = pygmsh.__gmsh_version__
+        except:
+            version = gmsh.__version__
     else:
         # pygmsh version 6.x
-        version = pygmsh.get_gmsh_major_version()
+        try:
+            version = pygmsh.get_gmsh_major_version()
+        except:
+            version = gmsh.__version__
     print("Gmsh version  : ",version, " module version ",gmsh.__version__)
 
     # creates a simple 3D mesh

src/generate_databases/read_parameters.f90

@@ -196,16 +196,16 @@ subroutine read_parameters()
     ! else
     !    write(IMAIN,*) 'using a CMTSOLUTION source'
     ! endif
-    if(.not. USE_CMT_AND_FORCE_SOURCE) then 
+    if (.not. USE_CMT_AND_FORCE_SOURCE) then
       if (USE_FORCE_POINT_SOURCE) then
         write(IMAIN,*) 'using a FORCESOLUTION source instead of a CMTSOLUTION source'
       else
         write(IMAIN,*) 'using a CMTSOLUTION source'
       endif
-    else 
+    else
       write(IMAIN,*) 'using both a FORCESOLUTION and a CMTSOLUTION source'
     endif
-    
+
     if (USE_RICKER_TIME_FUNCTION) then
        write(IMAIN,*) '  with a Ricker source time function'
     else
@@ -215,13 +215,13 @@ subroutine read_parameters()
       !  else
       !     write(IMAIN,*) '  with a Gaussian source time function'
       !  endif
-      if(USE_CMT_AND_FORCE_SOURCE) then
+      if (USE_CMT_AND_FORCE_SOURCE) then
        write(IMAIN,*) ' CMTSOLUTION with a quasi-Heaviside source time function'
        write(IMAIN,*) ' FORCESOLUTION with a Gaussian source time function'
-      else 
+      else
         if (USE_FORCE_POINT_SOURCE) then
           write(IMAIN,*) ' with a quasi-Heaviside source time function'
-        else 
+        else
           write(IMAIN,*) ' with a Gaussian source time function'
         endif
       endif

src/gpu/initialize_gpu.cu

@@ -241,7 +241,16 @@ void initialize_cuda_device(int* myrank_f,int* ncuda_devices) {
       }else{
         fprintf(fp,"  canMapHostMemory: FALSE\n");
       }
+#if CUDA_VERSION < 13000 || (defined (__CUDACC_VER_MAJOR__) && (__CUDACC_VER_MAJOR__ < 13))
+      if (deviceProp.deviceOverlap){
+        fprintf(fp,"  deviceOverlap: TRUE\n");
+      }else{
+        fprintf(fp,"  deviceOverlap: FALSE\n");
+      }
+#else
+      // CUDA version >= 13, deviceOverlap deprecated, replaced by asyncEngineCount
       fprintf(fp,"  asyncEngineCount: %d\n", deviceProp.asyncEngineCount);
+#endif
       if (deviceProp.concurrentKernels){
         fprintf(fp,"  concurrentKernels: TRUE\n");
       }else{

src/gpu/smooth_pde_cuda.cu

@@ -17,7 +17,7 @@ void FC_FUNC_(prepare_smooth_pde_gpu,
   Mesh* mp = (Mesh*)(*Mesh_pointer);
   Smooth_pde_data* sp = (Smooth_pde_data*) malloc(sizeof(Smooth_pde_data));
   *Container_smooth_pde = (long)sp;
-  
+
   gpuCreateCopy_todevice_realw((void**)&sp->d_dat_smooth_glob, dat_smooth_glob, mp->NGLOB_AB);
   gpuMalloc_field((void**)&sp->d_ddat_smooth_glob, mp->NGLOB_AB);
   // initializes values to zero
@@ -70,8 +70,8 @@ void FC_FUNC_(compute_update_element_smooth_pde_gpu,
                                                                mp->xix_regular,mp->jacobian_regular,
                                                                mp->d_hprime_xx,
                                                                mp->d_hprimewgll_xx,
-                                                               mp->d_wgllwgll_xy, 
-                                                               mp->d_wgllwgll_xz, 
+                                                               mp->d_wgllwgll_xy,
+                                                               mp->d_wgllwgll_xz,
                                                                mp->d_wgllwgll_yz,
                                                                sp->cv, sp->ch
                                                                );
@@ -94,8 +94,8 @@ void FC_FUNC_(compute_update_element_smooth_pde_gpu,
                                                                mp->xix_regular,mp->jacobian_regular,
                                                                mp->d_hprime_xx,
                                                                mp->d_hprimewgll_xx,
-                                                               mp->d_wgllwgll_xy, 
-                                                               mp->d_wgllwgll_xz, 
+                                                               mp->d_wgllwgll_xy,
+                                                               mp->d_wgllwgll_xz,
                                                                mp->d_wgllwgll_yz,
                                                                sp->cv, sp->ch
                                                                );
@@ -114,7 +114,7 @@ void FC_FUNC_(transfer_boun_dat_smooth_pde_from_device,
   TRACE("transfer_boun_dat_smooth_pde_from_device");
   Mesh* mp = (Mesh*)(*Mesh_pointer);
   Smooth_pde_data* sp = (Smooth_pde_data*)(*Container_smooth_pde);
-  
+
   if (sp->size_mpi_buffer_smooth > 0) {
     int blocksize = BLOCKSIZE_TRANSFER;
     int size_padded = ((int)ceil(((double)(mp->max_nibool_interfaces_ext_mesh))/((double)blocksize)))*blocksize;
@@ -152,7 +152,7 @@ void FC_FUNC_(transfer_boun_dat_smooth_pde_from_device,
     // copies buffer to CPU
     gpuMemcpy_tohost_field(send_buffer_smooth,sp->d_send_buffer,sp->size_mpi_buffer_smooth);
   }
-  
+
   GPU_ERROR_CHECKING("transfer_boun_dat_smooth_pde_from_device");
 }
 
@@ -162,7 +162,7 @@ void FC_FUNC_(transfer_asmbl_dat_smooth_pde_from_device,
                                                          long * Container_smooth_pde,
                                                          field * recv_buffer_smooth){
   TRACE("transfer_asmbl_dat_smooth_pde_from_device");
-  
+
   Mesh* mp = (Mesh*)(*Mesh_pointer);
   Smooth_pde_data* sp = (Smooth_pde_data*)(*Container_smooth_pde);
 
@@ -244,7 +244,7 @@ void FC_FUNC_(kernel_3_smooth_pde_cuda,
                                                                               sp->d_rvol,
                                                                               size);
   }
-#endif  
+#endif
 
   GPU_ERROR_CHECKING("kernel_3_smooth_pde_cuda");
 }
@@ -295,7 +295,7 @@ void FC_FUNC_(zero_pml_smooth_pde_cuda,
               ZERO_PML_SMOOTH_PDE_CUDA)(long * Mesh_pointer,
                                         long * Container_smooth_pde) {
   TRACE("zero_pml_smooth_pde_cuda");
-  
+
   Mesh* mp = (Mesh*)(*Mesh_pointer);
   Smooth_pde_data* sp = (Smooth_pde_data*)(*Container_smooth_pde);
 
@@ -325,7 +325,7 @@ void FC_FUNC_(zero_pml_smooth_pde_cuda,
                                                                          mp->d_ibool,
                                                                          sp->d_CPML_to_spec);
   }
-#endif 
+#endif
 
   GPU_ERROR_CHECKING("zero_pml_smooth_pde_cuda");
 }
@@ -429,5 +429,5 @@ void FC_FUNC_(transfer_dat_smooth_pde_from_device,
   gpuMemcpy_tohost_realw(dat_smooth_glob, sp->d_dat_smooth_glob, mp->NGLOB_AB);
 
   GPU_ERROR_CHECKING("transfer_dat_smooth_pde_from_device");
-  
+
 }

src/shared/check_mesh_resolution.f90

@@ -440,7 +440,10 @@ subroutine check_mesh_resolution(NSPEC_AB,NGLOB_AB,ibool,xstore,ystore,zstore, &
     write(IMAIN,*) '*** Min element size = ',elemsize_min_glob
     write(IMAIN,*) '*** Max/min ratio = ',elemsize_max_glob/elemsize_min_glob
     write(IMAIN,*)
-    write(IMAIN,*) '*** Minimum period resolved = ',pmax_glob
+    write(IMAIN,*) '*** Minimum period resolved = ',pmax_glob,'(s)'
+    if (abs(pmax_glob) > TINYVAL) then
+      write(IMAIN,*) '***          (as frequency) = ',1.0_CUSTOM_REAL / pmax_glob,'(Hz)'
+    endif
     write(IMAIN,*) '*** Maximum suggested time step = ',dt_suggested_glob
     write(IMAIN,*)
     if (DT_PRESENT) then

src/shared/count_number_of_sources.f90

@@ -197,7 +197,7 @@ subroutine count_number_of_sources_by_type(NSOURCES,sources_filename,source_is_f
 
   ! get the number of lines describing the sources
   !if (USE_FORCE_POINT_SOURCE) then
-  if(source_is_force) then 
+  if (source_is_force) then
     ! FORCESOLUTION
     nlines_per_source = NLINES_PER_FORCESOLUTION_SOURCE
   else
@@ -233,7 +233,7 @@ subroutine count_number_of_sources_by_type(NSOURCES,sources_filename,source_is_f
   ! checks lines are a multiple
   if (mod(icounter,nlines_per_source) /= 0) then
     !if (USE_FORCE_POINT_SOURCE) then
-    if(source_is_force) then 
+    if (source_is_force) then
       print *,'Error: total number of lines in FORCESOLUTION file should be a multiple of ',nlines_per_source
       stop 'Error total number of lines in FORCESOLUTION file should be a multiple of NLINES_PER_FORCESOLUTION_SOURCE'
     else
@@ -261,15 +261,15 @@ end subroutine count_number_of_sources_by_type
 
   ! NQDU for binary source file
   subroutine count_number_of_sources_binary(ns_cmt,ns_force,sources_filename)
-    use constants, only : MAX_STRING_LEN
+    use constants, only: MAX_STRING_LEN
     implicit none
     integer,intent(inout) :: ns_cmt,ns_force
-    character(len=MAX_STRING_LEN),intent(in) :: sources_filename 
+    character(len=MAX_STRING_LEN),intent(in) :: sources_filename
 
     ! local
     integer,parameter :: IO_SOURCE = 12341
 
-    open(IO_SOURCE,file=trim(sources_filename),form='unformatted',&
+    open(IO_SOURCE,file=trim(sources_filename),form='unformatted', &
               action='read',access='stream')
     read(IO_SOURCE) ns_cmt
     read(IO_SOURCE) ns_force

src/shared/read_parameter_file.F90

@@ -426,14 +426,14 @@ subroutine read_parameter_file(BROADCAST_AFTER_READ)
     ! read two flags in CMT + FORCE simulation
     call read_value_logical(USE_CMT_AND_FORCE_SOURCE, 'USE_CMT_AND_FORCE_SOURCE', ier)
     ier = 0
-    if (USE_CMT_AND_FORCE_SOURCE) then 
+    if (USE_CMT_AND_FORCE_SOURCE) then
       ! write(*,'(a)') 'cmt + force simulation is enabled'
       USE_FORCE_POINT_SOURCE  = .true.
     endif
 
     call read_value_logical(USE_BINARY_SOURCE_FILE, 'USE_BINARY_SOURCE_FILE', ier)
     ier = 0
-    if(.not. USE_CMT_AND_FORCE_SOURCE) USE_BINARY_SOURCE_FILE = .false.  ! binary file is disabled 
+    if (.not. USE_CMT_AND_FORCE_SOURCE) USE_BINARY_SOURCE_FILE = .false.  ! binary file is disabled
 
     call read_value_logical(USE_RICKER_TIME_FUNCTION, 'USE_RICKER_TIME_FUNCTION', ier)
     if (ier /= 0) then
@@ -850,8 +850,8 @@ subroutine read_parameter_file(BROADCAST_AFTER_READ)
     endif
 
     ! inverse problem is enabled, disable USE_CMT_AND_FORCE/USE_BINARY_SOURCE_FILE
-    if(INVERSE_FWI_FULL_PROBLEM .and. (USE_CMT_AND_FORCE_SOURCE)) then
-      if(myrank == 0) then
+    if (INVERSE_FWI_FULL_PROBLEM .and. (USE_CMT_AND_FORCE_SOURCE)) then
+      if (myrank == 0) then
         write(*,'(a)') 'INVERSE_FWI_FULL_PROBLEM is enabled, disabling USE_CMT_AND_FORCE_SOURCE'
         write(*,*)
       endif
@@ -1258,8 +1258,8 @@ subroutine read_compute_parameters()
   else
     ! gets number of sources
     !NQDU call count_number_of_sources(NSOURCES,sources_filename)
-    if(USE_CMT_AND_FORCE_SOURCE) then 
-      if(.not. USE_BINARY_SOURCE_FILE) then
+    if (USE_CMT_AND_FORCE_SOURCE) then
+      if (.not. USE_BINARY_SOURCE_FILE) then
         ! Force
         sources_filename = path_to_add(1:len_trim(path_to_add)) // &
                            IN_DATA_FILES(1:len_trim(IN_DATA_FILES))//'FORCESOLUTION'
@@ -1269,17 +1269,17 @@ subroutine read_compute_parameters()
         sources_filename = path_to_add(1:len_trim(path_to_add)) // &
                            IN_DATA_FILES(1:len_trim(IN_DATA_FILES))//'CMTSOLUTION'
         call count_number_of_sources_by_type(NSOURCES_CMT,sources_filename,.false.)
-      else 
+      else
         sources_filename = path_to_add(1:len_trim(path_to_add)) // &
                           IN_DATA_FILES(1:len_trim(IN_DATA_FILES))//'SOLUTION.bin'
         call count_number_of_sources_binary(NSOURCES_CMT,NSOURCES_FORCE,sources_filename)
       endif
       NSOURCES = NSOURCES_CMT + NSOURCES_FORCE
-    else 
+    else
       NSOURCES_CMT = 0
       NSOURCES_FORCE = 0
       call count_number_of_sources_by_type(NSOURCES,sources_filename,USE_FORCE_POINT_SOURCE)
-      if(USE_FORCE_POINT_SOURCE) then 
+      if (USE_FORCE_POINT_SOURCE) then
         NSOURCES_FORCE = NSOURCES
       else
         NSOURCES_CMT = NSOURCES

src/shared/shared_par.F90

@@ -169,7 +169,7 @@ module shared_input_parameters
   logical :: HAS_FINITE_FAULT_SOURCE
 
   ! cmt + point force simulation
-  logical :: USE_CMT_AND_FORCE_SOURCE = .false. 
+  logical :: USE_CMT_AND_FORCE_SOURCE = .false.
   logical :: USE_BINARY_SOURCE_FILE = .false.
 
   ! external source time function
@@ -234,7 +234,7 @@ module shared_compute_parameters
   integer :: NSOURCES
 
   !number of sources in CMTSOLUTION/FORCESOLUTION
-  integer :: NSOURCES_CMT, NSOURCES_FORCE 
+  integer :: NSOURCES_CMT, NSOURCES_FORCE
 
   ! anchor points
   integer :: NGNOD2D