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 PetscFunctionBeginUser; 96 PetscCall(PetscInitialize(&argc, &argv, NULL,help)); 97 PetscCall(ProcessOptions(PETSC_COMM_WORLD, &user)); 98 PetscCall(DMPlexCreateFromFile(PETSC_COMM_WORLD, user.filename, user.meshname, user.interpolate, &dm)); 99 PetscCall(DMSetOptionsPrefix(dm,"orig_")); 100 PetscCall(DMViewFromOptions(dm, NULL, "-dm_view")); 101 102 if (user.distribute) { 103 DM dmdist; 104 105 PetscCall(DMPlexGetPartitioner(dm, &part)); 106 PetscCall(PetscPartitionerSetFromOptions(part)); 107 PetscCall(DMPlexDistribute(dm, 0, NULL, &dmdist)); 108 if (dmdist) { 109 PetscCall(DMDestroy(&dm)); 110 dm = dmdist; 111 } 112 } 113 114 PetscCall(DMSetOptionsPrefix(dm,NULL)); 115 PetscCall(DMPlexDistributeSetDefault(dm, PETSC_FALSE)); 116 PetscCall(DMSetFromOptions(dm)); 117 PetscCall(DMViewFromOptions(dm, NULL, "-dm_view")); 118 119 PetscCall(DMPlexWriteAndReadHDF5(dm, "dmdist.h5", "new_", user, &dmnew)); 120 121 if (user.second_write_read) { 122 PetscCall(DMDestroy(&dm)); 123 dm = dmnew; 124 PetscCall(DMPlexWriteAndReadHDF5(dm, "dmdist.h5", "new_", user, &dmnew)); 125 } 126 127 PetscCall(DMViewFromOptions(dmnew, NULL, "-dm_view")); 128 /* TODO: Is it still true? */ 129 /* The NATIVE format for coordiante viewing is killing parallel output, since we have a local vector. Map it to global, and it will work. */ 130 131 /* This currently makes sense only for sequential meshes. */ 132 if (user.compare) { 133 PetscCall(DMPlexEqual(dmnew, dm, &flg)); 134 PetscCheck(flg,PETSC_COMM_WORLD, PETSC_ERR_ARG_INCOMP, "DMs are not equal"); 135 PetscCall(PetscPrintf(PETSC_COMM_WORLD,"DMs equal\n")); 136 } 137 if (user.compare_labels) { 138 PetscCall(DMCompareLabels(dmnew, dm, NULL, NULL)); 139 PetscCall(PetscPrintf(PETSC_COMM_WORLD,"DMLabels equal\n")); 140 } 141 142 PetscCall(DMDestroy(&dm)); 143 PetscCall(DMDestroy(&dmnew)); 144 PetscCall(PetscFinalize()); 145 return 0; 146 } 147 148 /*TEST 149 build: 150 requires: hdf5 151 # Idempotence of saving/loading 152 # Have to replace Exodus file, which is creating uninterpolated edges 153 test: 154 suffix: 0 155 TODO: broken 156 requires: exodusii 157 args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/Rect-tri3.exo -dm_view ascii::ascii_info_detail 158 args: -format hdf5_petsc -compare 159 test: 160 suffix: 1 161 TODO: broken 162 requires: exodusii parmetis !defined(PETSC_USE_64BIT_INDICES) 163 nsize: 2 164 args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/Rect-tri3.exo -dm_view ascii::ascii_info_detail 165 args: -petscpartitioner_type parmetis 166 args: -format hdf5_petsc -new_dm_view ascii::ascii_info_detail 167 testset: 168 requires: exodusii 169 args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/blockcylinder-50.exo 170 args: -petscpartitioner_type simple 171 args: -dm_view ascii::ascii_info_detail 172 args: -new_dm_view ascii::ascii_info_detail 173 test: 174 suffix: 2 175 nsize: {{1 2 4 8}separate output} 176 args: -format {{default hdf5_petsc}separate output} 177 args: -interpolate {{0 1}separate output} 178 test: 179 suffix: 2a 180 nsize: {{1 2 4 8}separate output} 181 args: -format {{hdf5_xdmf hdf5_viz}separate output} 182 test: 183 suffix: 3 184 requires: exodusii 185 args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/blockcylinder-50.exo -compare -compare_labels 186 187 # Load HDF5 file in XDMF format in parallel, write, read dm1, write, read dm2, and compare dm1 and dm2 188 testset: 189 suffix: 4 190 requires: !complex 191 args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/blockcylinder-50.h5 -dm_plex_create_from_hdf5_xdmf 192 args: -distribute 0 -second_write_read -compare 193 test: 194 suffix: hdf5_petsc 195 nsize: {{1 2}} 196 args: -format hdf5_petsc -compare_labels 197 test: 198 suffix: hdf5_xdmf 199 nsize: {{1 3 8}} 200 args: -format hdf5_xdmf 201 202 # Use low level functions, DMPlexTopologyView()/Load(), DMPlexCoordinatesView()/Load(), and DMPlexLabelsView()/Load() 203 # Output must be the same as ex55_2_nsize-2_format-hdf5_petsc_interpolate-0.out 204 test: 205 suffix: 5 206 requires: exodusii 207 nsize: 2 208 args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/blockcylinder-50.exo 209 args: -petscpartitioner_type simple 210 args: -dm_view ascii::ascii_info_detail 211 args: -new_dm_view ascii::ascii_info_detail 212 args: -format hdf5_petsc -use_low_level_functions 213 214 testset: 215 suffix: 6 216 requires: hdf5 !complex datafilespath 217 nsize: {{1 3}} 218 args: -dm_plex_check_symmetry -dm_plex_check_skeleton -dm_plex_check_geometry 219 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 220 args: -format hdf5_petsc -second_write_read -compare -compare_labels 221 args: -interpolate {{0 1}} -distribute {{0 1}} -petscpartitioner_type simple 222 223 testset: 224 # the same data and settings as dm_impls_plex_tests-ex18_9% 225 suffix: 9 226 requires: hdf5 !complex datafilespath 227 nsize: {{1 2 4}} 228 args: -dm_plex_check_symmetry -dm_plex_check_skeleton -dm_plex_check_geometry 229 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 230 args: -format hdf5_xdmf -second_write_read -compare 231 test: 232 suffix: hdf5_seqload 233 args: -distribute -petscpartitioner_type simple 234 args: -interpolate {{0 1}} 235 args: -dm_plex_hdf5_force_sequential 236 test: 237 suffix: hdf5_seqload_metis 238 requires: parmetis 239 args: -distribute -petscpartitioner_type parmetis 240 args: -interpolate 1 241 args: -dm_plex_hdf5_force_sequential 242 test: 243 suffix: hdf5 244 args: -interpolate 1 -petscpartitioner_type simple 245 test: 246 suffix: hdf5_repart 247 requires: parmetis 248 args: -distribute -petscpartitioner_type parmetis 249 args: -interpolate 1 250 test: 251 TODO: Parallel partitioning of uninterpolated meshes not supported 252 suffix: hdf5_repart_ppu 253 requires: parmetis 254 args: -distribute -petscpartitioner_type parmetis 255 args: -interpolate 0 256 257 # reproduce PetscSFView() crash - fixed, left as regression test 258 test: 259 suffix: new_dm_view 260 requires: exodusii 261 nsize: 2 262 args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/TwoQuads.exo -new_dm_view ascii:ex5_new_dm_view.log:ascii_info_detail 263 264 # test backward compatibility of petsc_hdf5 format 265 testset: 266 suffix: 10-v3.16.0-v1.0.0 267 requires: hdf5 !complex datafilespath 268 args: -dm_plex_check_all -compare -compare_labels 269 args: -dm_plex_view_hdf5_storage_version {{1.0.0 2.0.0}} -use_low_level_functions {{0 1}} 270 test: 271 suffix: a 272 args: -filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/annulus-20.h5 273 test: 274 suffix: b 275 TODO: broken 276 args: -filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/barycentricallyrefinedcube.h5 277 test: 278 suffix: c 279 args: -filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/blockcylinder-50.h5 280 test: 281 suffix: d 282 args: -filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/cube-hexahedra-refined.h5 283 test: 284 suffix: e 285 args: -filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/hybrid_hexwedge.h5 286 test: 287 suffix: f 288 args: -filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/square.h5 289 290 TEST*/ 291