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 PetscViewerFormat format; /* Format to write and read */ 14 PetscBool second_write_read; /* Write and read for the 2nd time */ 15 PetscBool use_low_level_functions; /* Use low level functions for viewing and loading */ 16 } AppCtx; 17 18 static PetscErrorCode ProcessOptions(MPI_Comm comm, AppCtx *options) 19 { 20 PetscErrorCode ierr; 21 22 PetscFunctionBeginUser; 23 options->compare = PETSC_FALSE; 24 options->compare_labels = PETSC_FALSE; 25 options->distribute = PETSC_TRUE; 26 options->interpolate = PETSC_FALSE; 27 options->filename[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 ierr = PetscOptionsBegin(comm, "", "Meshing Problem Options", "DMPLEX");CHKERRQ(ierr); 33 ierr = PetscOptionsBool("-compare", "Compare the meshes using DMPlexEqual()", "ex55.c", options->compare, &options->compare, NULL);CHKERRQ(ierr); 34 ierr = PetscOptionsBool("-compare_labels", "Compare labels in the meshes using DMCompareLabels()", "ex55.c", options->compare_labels, &options->compare_labels, NULL);CHKERRQ(ierr); 35 ierr = PetscOptionsBool("-distribute", "Distribute the mesh", "ex55.c", options->distribute, &options->distribute, NULL);CHKERRQ(ierr); 36 ierr = PetscOptionsBool("-interpolate", "Generate intermediate mesh elements", "ex55.c", options->interpolate, &options->interpolate, NULL);CHKERRQ(ierr); 37 ierr = PetscOptionsString("-filename", "The mesh file", "ex55.c", options->filename, options->filename, sizeof(options->filename), NULL);CHKERRQ(ierr); 38 ierr = PetscOptionsEnum("-format", "Format to write and read", "ex55.c", PetscViewerFormats, (PetscEnum)options->format, (PetscEnum*)&options->format, NULL);CHKERRQ(ierr); 39 ierr = PetscOptionsBool("-second_write_read", "Write and read for the 2nd time", "ex55.c", options->second_write_read, &options->second_write_read, NULL);CHKERRQ(ierr); 40 ierr = 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);CHKERRQ(ierr); 41 ierr = PetscOptionsEnd();CHKERRQ(ierr); 42 PetscFunctionReturn(0); 43 }; 44 45 static PetscErrorCode DMPlexWriteAndReadHDF5(DM dm, const char filename[], const char prefix[], AppCtx user, DM *dm_new) 46 { 47 DM dmnew; 48 const char exampleDMPlexName[] = "DMPlex Object"; 49 PetscViewer v; 50 PetscErrorCode ierr; 51 52 PetscFunctionBeginUser; 53 ierr = PetscViewerHDF5Open(PetscObjectComm((PetscObject) dm), filename, FILE_MODE_WRITE, &v);CHKERRQ(ierr); 54 ierr = PetscViewerPushFormat(v, user.format);CHKERRQ(ierr); 55 ierr = PetscObjectSetName((PetscObject) dm, exampleDMPlexName);CHKERRQ(ierr); 56 if (user.use_low_level_functions) { 57 ierr = DMPlexTopologyView(dm, v);CHKERRQ(ierr); 58 ierr = DMPlexCoordinatesView(dm, v);CHKERRQ(ierr); 59 ierr = DMPlexLabelsView(dm, v);CHKERRQ(ierr); 60 } else { 61 ierr = DMView(dm, v);CHKERRQ(ierr); 62 } 63 64 ierr = PetscViewerFileSetMode(v, FILE_MODE_READ);CHKERRQ(ierr); 65 ierr = DMCreate(PETSC_COMM_WORLD, &dmnew);CHKERRQ(ierr); 66 ierr = DMSetType(dmnew, DMPLEX);CHKERRQ(ierr); 67 ierr = PetscObjectSetName((PetscObject) dmnew, exampleDMPlexName);CHKERRQ(ierr); 68 ierr = DMSetOptionsPrefix(dmnew, prefix);CHKERRQ(ierr); 69 if (user.use_low_level_functions) { 70 PetscSF sfXC; 71 72 ierr = DMPlexTopologyLoad(dmnew, v, &sfXC);CHKERRQ(ierr); 73 ierr = DMPlexCoordinatesLoad(dmnew, v, sfXC);CHKERRQ(ierr); 74 ierr = PetscSFDestroy(&sfXC);CHKERRQ(ierr); 75 ierr = DMPlexLabelsLoad(dmnew, v);CHKERRQ(ierr); 76 } else { 77 ierr = DMLoad(dmnew, v);CHKERRQ(ierr); 78 } 79 ierr = PetscObjectSetName((PetscObject)dmnew,"Mesh_new");CHKERRQ(ierr); 80 81 ierr = PetscViewerPopFormat(v);CHKERRQ(ierr); 82 ierr = PetscViewerDestroy(&v);CHKERRQ(ierr); 83 *dm_new = dmnew; 84 PetscFunctionReturn(0); 85 } 86 87 int main(int argc, char **argv) 88 { 89 DM dm, dmnew; 90 PetscPartitioner part; 91 AppCtx user; 92 PetscBool flg; 93 PetscErrorCode ierr; 94 95 ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr; 96 ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr); 97 ierr = DMPlexCreateFromFile(PETSC_COMM_WORLD, user.filename, "ex55_plex", user.interpolate, &dm);CHKERRQ(ierr); 98 ierr = DMSetOptionsPrefix(dm,"orig_");CHKERRQ(ierr); 99 ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr); 100 101 if (user.distribute) { 102 DM dmdist; 103 104 ierr = DMPlexGetPartitioner(dm, &part);CHKERRQ(ierr); 105 ierr = PetscPartitionerSetFromOptions(part);CHKERRQ(ierr); 106 ierr = DMPlexDistribute(dm, 0, NULL, &dmdist);CHKERRQ(ierr); 107 if (dmdist) { 108 ierr = DMDestroy(&dm);CHKERRQ(ierr); 109 dm = dmdist; 110 } 111 } 112 113 ierr = DMSetOptionsPrefix(dm,NULL);CHKERRQ(ierr); 114 ierr = DMSetFromOptions(dm);CHKERRQ(ierr); 115 ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr); 116 117 ierr = DMPlexWriteAndReadHDF5(dm, "dmdist.h5", "new_", user, &dmnew);CHKERRQ(ierr); 118 119 if (user.second_write_read) { 120 ierr = DMDestroy(&dm);CHKERRQ(ierr); 121 dm = dmnew; 122 ierr = DMPlexWriteAndReadHDF5(dm, "dmdist.h5", "new_", user, &dmnew);CHKERRQ(ierr); 123 } 124 125 ierr = DMViewFromOptions(dmnew, NULL, "-dm_view");CHKERRQ(ierr); 126 /* TODO: Is it still true? */ 127 /* The NATIVE format for coordiante viewing is killing parallel output, since we have a local vector. Map it to global, and it will work. */ 128 129 /* This currently makes sense only for sequential meshes. */ 130 if (user.compare) { 131 ierr = DMPlexEqual(dmnew, dm, &flg);CHKERRQ(ierr); 132 if (!flg) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_INCOMP, "DMs are not equal"); 133 ierr = PetscPrintf(PETSC_COMM_WORLD,"DMs equal\n");CHKERRQ(ierr); 134 } 135 if (user.compare_labels) { 136 ierr = DMCompareLabels(dmnew, dm, NULL, NULL);CHKERRQ(ierr); 137 ierr = PetscPrintf(PETSC_COMM_WORLD,"DMLabels equal\n");CHKERRQ(ierr); 138 } 139 140 ierr = DMDestroy(&dm);CHKERRQ(ierr); 141 ierr = DMDestroy(&dmnew);CHKERRQ(ierr); 142 ierr = PetscFinalize(); 143 return ierr; 144 } 145 146 /*TEST 147 build: 148 requires: hdf5 149 # Idempotence of saving/loading 150 # Have to replace Exodus file, which is creating uninterpolated edges 151 test: 152 suffix: 0 153 TODO: broken 154 requires: exodusii 155 args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/Rect-tri3.exo -dm_view ascii::ascii_info_detail 156 args: -format hdf5_petsc -compare 157 test: 158 suffix: 1 159 TODO: broken 160 requires: exodusii parmetis !defined(PETSC_USE_64BIT_INDICES) 161 nsize: 2 162 args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/Rect-tri3.exo -dm_view ascii::ascii_info_detail 163 args: -petscpartitioner_type parmetis 164 args: -format hdf5_petsc -new_dm_view ascii::ascii_info_detail 165 testset: 166 requires: exodusii 167 args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/blockcylinder-50.exo 168 args: -petscpartitioner_type simple 169 args: -dm_view ascii::ascii_info_detail 170 args: -new_dm_view ascii::ascii_info_detail 171 test: 172 suffix: 2 173 nsize: {{1 2 4 8}separate output} 174 args: -format {{default hdf5_petsc}separate output} 175 args: -interpolate {{0 1}separate output} 176 test: 177 suffix: 2a 178 nsize: {{1 2 4 8}separate output} 179 args: -format {{hdf5_xdmf hdf5_viz}separate output} 180 test: 181 suffix: 3 182 requires: exodusii 183 args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/blockcylinder-50.exo -compare -compare_labels 184 185 # Load HDF5 file in XDMF format in parallel, write, read dm1, write, read dm2, and compare dm1 and dm2 186 testset: 187 suffix: 4 188 requires: !complex 189 args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/blockcylinder-50.h5 -dm_plex_create_from_hdf5_xdmf 190 args: -distribute 0 -second_write_read -compare 191 test: 192 suffix: hdf5_petsc 193 nsize: {{1 2}} 194 args: -format hdf5_petsc -compare_labels 195 test: 196 suffix: hdf5_xdmf 197 nsize: {{1 3 8}} 198 args: -format hdf5_xdmf 199 200 # Use low level functions, DMPlexTopologyView()/Load(), DMPlexCoordinatesView()/Load(), and DMPlexLabelsView()/Load() 201 # Output must be the same as ex55_2_nsize-2_format-hdf5_petsc_interpolate-0.out 202 test: 203 suffix: 5 204 requires: exodusii 205 nsize: 2 206 args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/blockcylinder-50.exo 207 args: -petscpartitioner_type simple 208 args: -dm_view ascii::ascii_info_detail 209 args: -new_dm_view ascii::ascii_info_detail 210 args: -format hdf5_petsc -use_low_level_functions 211 212 testset: 213 suffix: 6 214 requires: hdf5 !complex datafilespath 215 nsize: {{1 3}} 216 args: -dm_plex_check_symmetry -dm_plex_check_skeleton -dm_plex_check_geometry 217 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 218 args: -format hdf5_petsc -second_write_read -compare -compare_labels 219 args: -interpolate {{0 1}} -distribute {{0 1}} -petscpartitioner_type simple 220 221 testset: 222 # the same data and settings as dm_impls_plex_tests-ex18_9% 223 suffix: 9 224 requires: hdf5 !complex datafilespath 225 nsize: {{1 2 4}} 226 args: -dm_plex_check_symmetry -dm_plex_check_skeleton -dm_plex_check_geometry 227 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 228 args: -format hdf5_xdmf -second_write_read -compare 229 test: 230 suffix: hdf5_seqload 231 args: -distribute -petscpartitioner_type simple 232 args: -interpolate {{0 1}} 233 args: -dm_plex_hdf5_force_sequential 234 test: 235 suffix: hdf5_seqload_metis 236 requires: parmetis 237 args: -distribute -petscpartitioner_type parmetis 238 args: -interpolate 1 239 args: -dm_plex_hdf5_force_sequential 240 test: 241 suffix: hdf5 242 args: -interpolate 1 -petscpartitioner_type simple 243 test: 244 suffix: hdf5_repart 245 requires: parmetis 246 args: -distribute -petscpartitioner_type parmetis 247 args: -interpolate 1 248 test: 249 TODO: Parallel partitioning of uninterpolated meshes not supported 250 suffix: hdf5_repart_ppu 251 requires: parmetis 252 args: -distribute -petscpartitioner_type parmetis 253 args: -interpolate 0 254 255 # reproduce PetscSFView() crash - fixed, left as regression test 256 test: 257 suffix: new_dm_view 258 requires: exodusii 259 nsize: 2 260 args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/TwoQuads.exo -new_dm_view ascii:ex5_new_dm_view.log:ascii_info_detail 261 262 # test backward compatibility of petsc_hdf5 format 263 testset: 264 suffix: 10-v3.16.0-v1.0.0 265 requires: hdf5 !complex datafilespath 266 args: -dm_plex_check_all -compare 267 args: -dm_plex_view_hdf5_storage_version {{1.0.0 2.0.0}} -use_low_level_functions {{0 1}} 268 test: 269 suffix: a 270 args: -filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/annulus-20.h5 271 test: 272 suffix: b 273 TODO: broken 274 args: -filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/barycentricallyrefinedcube.h5 275 test: 276 suffix: c 277 args: -filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/blockcylinder-50.h5 278 test: 279 suffix: d 280 args: -filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/cube-hexahedra-refined.h5 281 test: 282 suffix: e 283 args: -filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/hybrid_hexwedge.h5 284 test: 285 suffix: f 286 args: -filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/square.h5 287 288 TEST*/ 289