1 static char help[] = "Load and save the mesh and fields to HDF5 and ExodusII\n\n"; 2 3 #include <petscdmplex.h> 4 #include <petscviewerhdf5.h> 5 #include <petscsf.h> 6 7 typedef struct { 8 PetscBool compare; /* Compare the meshes using DMPlexEqual() */ 9 PetscBool compare_labels; /* Compare labels in the meshes using DMCompareLabels() */ 10 PetscBool distribute; /* Distribute the mesh */ 11 PetscBool interpolate; /* Generate intermediate mesh elements */ 12 char filename[PETSC_MAX_PATH_LEN]; /* Mesh filename */ 13 char meshname[PETSC_MAX_PATH_LEN]; /* Mesh name */ 14 PetscViewerFormat format; /* Format to write and read */ 15 PetscBool second_write_read; /* Write and read for the 2nd time */ 16 PetscBool use_low_level_functions; /* Use low level functions for viewing and loading */ 17 } AppCtx; 18 19 static PetscErrorCode ProcessOptions(MPI_Comm comm, AppCtx *options) 20 { 21 PetscFunctionBeginUser; 22 options->compare = PETSC_FALSE; 23 options->compare_labels = PETSC_FALSE; 24 options->distribute = PETSC_TRUE; 25 options->interpolate = PETSC_FALSE; 26 options->filename[0] = '\0'; 27 options->meshname[0] = '\0'; 28 options->format = PETSC_VIEWER_DEFAULT; 29 options->second_write_read = PETSC_FALSE; 30 options->use_low_level_functions = PETSC_FALSE; 31 32 PetscOptionsBegin(comm, "", "Meshing Problem Options", "DMPLEX"); 33 PetscCall(PetscOptionsBool("-compare", "Compare the meshes using DMPlexEqual()", "ex55.c", options->compare, &options->compare, NULL)); 34 PetscCall(PetscOptionsBool("-compare_labels", "Compare labels in the meshes using DMCompareLabels()", "ex55.c", options->compare_labels, &options->compare_labels, NULL)); 35 PetscCall(PetscOptionsBool("-distribute", "Distribute the mesh", "ex55.c", options->distribute, &options->distribute, NULL)); 36 PetscCall(PetscOptionsBool("-interpolate", "Generate intermediate mesh elements", "ex55.c", options->interpolate, &options->interpolate, NULL)); 37 PetscCall(PetscOptionsString("-filename", "The mesh file", "ex55.c", options->filename, options->filename, sizeof(options->filename), NULL)); 38 PetscCall(PetscOptionsString("-meshname", "The mesh file", "ex55.c", options->meshname, options->meshname, sizeof(options->meshname), NULL)); 39 PetscCall(PetscOptionsEnum("-format", "Format to write and read", "ex55.c", PetscViewerFormats, (PetscEnum)options->format, (PetscEnum*)&options->format, NULL)); 40 PetscCall(PetscOptionsBool("-second_write_read", "Write and read for the 2nd time", "ex55.c", options->second_write_read, &options->second_write_read, NULL)); 41 PetscCall(PetscOptionsBool("-use_low_level_functions", "Use low level functions for viewing and loading", "ex55.c", options->use_low_level_functions, &options->use_low_level_functions, NULL)); 42 PetscOptionsEnd(); 43 PetscFunctionReturn(0); 44 }; 45 46 static PetscErrorCode DMPlexWriteAndReadHDF5(DM dm, const char filename[], const char prefix[], AppCtx user, DM *dm_new) 47 { 48 DM dmnew; 49 const char savedName[] = "Mesh"; 50 const char loadedName[] = "Mesh_new"; 51 PetscViewer v; 52 53 PetscFunctionBeginUser; 54 PetscCall(PetscViewerHDF5Open(PetscObjectComm((PetscObject) dm), filename, FILE_MODE_WRITE, &v)); 55 PetscCall(PetscViewerPushFormat(v, user.format)); 56 PetscCall(PetscObjectSetName((PetscObject) dm, savedName)); 57 if (user.use_low_level_functions) { 58 PetscCall(DMPlexTopologyView(dm, v)); 59 PetscCall(DMPlexCoordinatesView(dm, v)); 60 PetscCall(DMPlexLabelsView(dm, v)); 61 } else { 62 PetscCall(DMView(dm, v)); 63 } 64 65 PetscCall(PetscViewerFileSetMode(v, FILE_MODE_READ)); 66 PetscCall(DMCreate(PETSC_COMM_WORLD, &dmnew)); 67 PetscCall(DMSetType(dmnew, DMPLEX)); 68 PetscCall(PetscObjectSetName((PetscObject) dmnew, savedName)); 69 PetscCall(DMSetOptionsPrefix(dmnew, prefix)); 70 if (user.use_low_level_functions) { 71 PetscSF sfXC; 72 73 PetscCall(DMPlexTopologyLoad(dmnew, v, &sfXC)); 74 PetscCall(DMPlexCoordinatesLoad(dmnew, v, sfXC)); 75 PetscCall(DMPlexLabelsLoad(dmnew, v, sfXC)); 76 PetscCall(PetscSFDestroy(&sfXC)); 77 } else { 78 PetscCall(DMLoad(dmnew, v)); 79 } 80 PetscCall(PetscObjectSetName((PetscObject)dmnew,loadedName)); 81 82 PetscCall(PetscViewerPopFormat(v)); 83 PetscCall(PetscViewerDestroy(&v)); 84 *dm_new = dmnew; 85 PetscFunctionReturn(0); 86 } 87 88 int main(int argc, char **argv) 89 { 90 DM dm, dmnew; 91 PetscPartitioner part; 92 AppCtx user; 93 PetscBool flg; 94 95 PetscCall(PetscInitialize(&argc, &argv, NULL,help)); 96 PetscCall(ProcessOptions(PETSC_COMM_WORLD, &user)); 97 PetscCall(DMPlexCreateFromFile(PETSC_COMM_WORLD, user.filename, user.meshname, user.interpolate, &dm)); 98 PetscCall(DMSetOptionsPrefix(dm,"orig_")); 99 PetscCall(DMViewFromOptions(dm, NULL, "-dm_view")); 100 101 if (user.distribute) { 102 DM dmdist; 103 104 PetscCall(DMPlexGetPartitioner(dm, &part)); 105 PetscCall(PetscPartitionerSetFromOptions(part)); 106 PetscCall(DMPlexDistribute(dm, 0, NULL, &dmdist)); 107 if (dmdist) { 108 PetscCall(DMDestroy(&dm)); 109 dm = dmdist; 110 } 111 } 112 113 PetscCall(DMSetOptionsPrefix(dm,NULL)); 114 PetscCall(DMPlexDistributeSetDefault(dm, PETSC_FALSE)); 115 PetscCall(DMSetFromOptions(dm)); 116 PetscCall(DMViewFromOptions(dm, NULL, "-dm_view")); 117 118 PetscCall(DMPlexWriteAndReadHDF5(dm, "dmdist.h5", "new_", user, &dmnew)); 119 120 if (user.second_write_read) { 121 PetscCall(DMDestroy(&dm)); 122 dm = dmnew; 123 PetscCall(DMPlexWriteAndReadHDF5(dm, "dmdist.h5", "new_", user, &dmnew)); 124 } 125 126 PetscCall(DMViewFromOptions(dmnew, NULL, "-dm_view")); 127 /* TODO: Is it still true? */ 128 /* The NATIVE format for coordiante viewing is killing parallel output, since we have a local vector. Map it to global, and it will work. */ 129 130 /* This currently makes sense only for sequential meshes. */ 131 if (user.compare) { 132 PetscCall(DMPlexEqual(dmnew, dm, &flg)); 133 PetscCheck(flg,PETSC_COMM_WORLD, PETSC_ERR_ARG_INCOMP, "DMs are not equal"); 134 PetscCall(PetscPrintf(PETSC_COMM_WORLD,"DMs equal\n")); 135 } 136 if (user.compare_labels) { 137 PetscCall(DMCompareLabels(dmnew, dm, NULL, NULL)); 138 PetscCall(PetscPrintf(PETSC_COMM_WORLD,"DMLabels equal\n")); 139 } 140 141 PetscCall(DMDestroy(&dm)); 142 PetscCall(DMDestroy(&dmnew)); 143 PetscCall(PetscFinalize()); 144 return 0; 145 } 146 147 /*TEST 148 build: 149 requires: hdf5 150 # Idempotence of saving/loading 151 # Have to replace Exodus file, which is creating uninterpolated edges 152 test: 153 suffix: 0 154 TODO: broken 155 requires: exodusii 156 args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/Rect-tri3.exo -dm_view ascii::ascii_info_detail 157 args: -format hdf5_petsc -compare 158 test: 159 suffix: 1 160 TODO: broken 161 requires: exodusii parmetis !defined(PETSC_USE_64BIT_INDICES) 162 nsize: 2 163 args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/Rect-tri3.exo -dm_view ascii::ascii_info_detail 164 args: -petscpartitioner_type parmetis 165 args: -format hdf5_petsc -new_dm_view ascii::ascii_info_detail 166 testset: 167 requires: exodusii 168 args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/blockcylinder-50.exo 169 args: -petscpartitioner_type simple 170 args: -dm_view ascii::ascii_info_detail 171 args: -new_dm_view ascii::ascii_info_detail 172 test: 173 suffix: 2 174 nsize: {{1 2 4 8}separate output} 175 args: -format {{default hdf5_petsc}separate output} 176 args: -interpolate {{0 1}separate output} 177 test: 178 suffix: 2a 179 nsize: {{1 2 4 8}separate output} 180 args: -format {{hdf5_xdmf hdf5_viz}separate output} 181 test: 182 suffix: 3 183 requires: exodusii 184 args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/blockcylinder-50.exo -compare -compare_labels 185 186 # Load HDF5 file in XDMF format in parallel, write, read dm1, write, read dm2, and compare dm1 and dm2 187 testset: 188 suffix: 4 189 requires: !complex 190 args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/blockcylinder-50.h5 -dm_plex_create_from_hdf5_xdmf 191 args: -distribute 0 -second_write_read -compare 192 test: 193 suffix: hdf5_petsc 194 nsize: {{1 2}} 195 args: -format hdf5_petsc -compare_labels 196 test: 197 suffix: hdf5_xdmf 198 nsize: {{1 3 8}} 199 args: -format hdf5_xdmf 200 201 # Use low level functions, DMPlexTopologyView()/Load(), DMPlexCoordinatesView()/Load(), and DMPlexLabelsView()/Load() 202 # Output must be the same as ex55_2_nsize-2_format-hdf5_petsc_interpolate-0.out 203 test: 204 suffix: 5 205 requires: exodusii 206 nsize: 2 207 args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/blockcylinder-50.exo 208 args: -petscpartitioner_type simple 209 args: -dm_view ascii::ascii_info_detail 210 args: -new_dm_view ascii::ascii_info_detail 211 args: -format hdf5_petsc -use_low_level_functions 212 213 testset: 214 suffix: 6 215 requires: hdf5 !complex datafilespath 216 nsize: {{1 3}} 217 args: -dm_plex_check_symmetry -dm_plex_check_skeleton -dm_plex_check_geometry 218 args: -filename ${DATAFILESPATH}/meshes/cube-hexahedra-refined.h5 -dm_plex_create_from_hdf5_xdmf -dm_plex_hdf5_topology_path /cells -dm_plex_hdf5_geometry_path /coordinates 219 args: -format hdf5_petsc -second_write_read -compare -compare_labels 220 args: -interpolate {{0 1}} -distribute {{0 1}} -petscpartitioner_type simple 221 222 testset: 223 # the same data and settings as dm_impls_plex_tests-ex18_9% 224 suffix: 9 225 requires: hdf5 !complex datafilespath 226 nsize: {{1 2 4}} 227 args: -dm_plex_check_symmetry -dm_plex_check_skeleton -dm_plex_check_geometry 228 args: -filename ${DATAFILESPATH}/meshes/cube-hexahedra-refined.h5 -dm_plex_create_from_hdf5_xdmf -dm_plex_hdf5_topology_path /cells -dm_plex_hdf5_geometry_path /coordinates 229 args: -format hdf5_xdmf -second_write_read -compare 230 test: 231 suffix: hdf5_seqload 232 args: -distribute -petscpartitioner_type simple 233 args: -interpolate {{0 1}} 234 args: -dm_plex_hdf5_force_sequential 235 test: 236 suffix: hdf5_seqload_metis 237 requires: parmetis 238 args: -distribute -petscpartitioner_type parmetis 239 args: -interpolate 1 240 args: -dm_plex_hdf5_force_sequential 241 test: 242 suffix: hdf5 243 args: -interpolate 1 -petscpartitioner_type simple 244 test: 245 suffix: hdf5_repart 246 requires: parmetis 247 args: -distribute -petscpartitioner_type parmetis 248 args: -interpolate 1 249 test: 250 TODO: Parallel partitioning of uninterpolated meshes not supported 251 suffix: hdf5_repart_ppu 252 requires: parmetis 253 args: -distribute -petscpartitioner_type parmetis 254 args: -interpolate 0 255 256 # reproduce PetscSFView() crash - fixed, left as regression test 257 test: 258 suffix: new_dm_view 259 requires: exodusii 260 nsize: 2 261 args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/TwoQuads.exo -new_dm_view ascii:ex5_new_dm_view.log:ascii_info_detail 262 263 # test backward compatibility of petsc_hdf5 format 264 testset: 265 suffix: 10-v3.16.0-v1.0.0 266 requires: hdf5 !complex datafilespath 267 args: -dm_plex_check_all -compare -compare_labels 268 args: -dm_plex_view_hdf5_storage_version {{1.0.0 2.0.0}} -use_low_level_functions {{0 1}} 269 test: 270 suffix: a 271 args: -filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/annulus-20.h5 272 test: 273 suffix: b 274 TODO: broken 275 args: -filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/barycentricallyrefinedcube.h5 276 test: 277 suffix: c 278 args: -filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/blockcylinder-50.h5 279 test: 280 suffix: d 281 args: -filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/cube-hexahedra-refined.h5 282 test: 283 suffix: e 284 args: -filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/hybrid_hexwedge.h5 285 test: 286 suffix: f 287 args: -filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/square.h5 288 289 TEST*/ 290