Actual source code: ex55.c
1: static char help[] = "Load and save the mesh and fields to HDF5 and ExodusII\n\n";
3: #include <petsc/private/dmpleximpl.h>
4: #include <petscviewerhdf5.h>
5: #include <petscsf.h>
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 field; /* Layout a field over the mesh */
12: PetscBool reorder; /* Reorder the points in the section */
13: char ofname[PETSC_MAX_PATH_LEN]; /* Output mesh filename */
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;
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->field = PETSC_FALSE;
26: options->reorder = PETSC_FALSE;
27: options->format = PETSC_VIEWER_DEFAULT;
28: options->second_write_read = PETSC_FALSE;
29: options->use_low_level_functions = PETSC_FALSE;
30: PetscCall(PetscStrncpy(options->ofname, "ex55.h5", sizeof(options->ofname)));
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("-field", "Layout a field over the mesh", "ex55.c", options->field, &options->field, NULL));
37: PetscCall(PetscOptionsBool("-reorder", "Reorder the points in the section", "ex55.c", options->reorder, &options->reorder, NULL));
38: PetscCall(PetscOptionsString("-ofilename", "The output mesh file", "ex55.c", options->ofname, options->ofname, sizeof(options->ofname), 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(PETSC_SUCCESS);
44: }
46: static PetscErrorCode CreateMesh(MPI_Comm comm, DM *dm)
47: {
48: PetscFunctionBeginUser;
49: PetscCall(DMCreate(comm, dm));
50: PetscCall(DMSetType(*dm, DMPLEX));
51: PetscCall(DMSetOptionsPrefix(*dm, "orig_"));
52: PetscCall(DMSetFromOptions(*dm));
53: PetscCall(DMViewFromOptions(*dm, NULL, "-dm_view"));
54: PetscFunctionReturn(PETSC_SUCCESS);
55: }
57: static PetscErrorCode CreateDiscretization(DM dm)
58: {
59: PetscFE fe;
60: DMPolytopeType ct;
61: PetscInt dim, cStart;
63: PetscFunctionBeginUser;
64: PetscCall(DMGetDimension(dm, &dim));
65: PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, NULL));
66: PetscCall(DMPlexGetCellType(dm, cStart, &ct));
67: PetscCall(PetscFECreateLagrangeByCell(PETSC_COMM_SELF, dim, 1, ct, 1, PETSC_DETERMINE, &fe));
68: PetscCall(DMSetField(dm, 0, NULL, (PetscObject)fe));
69: PetscCall(PetscFEDestroy(&fe));
70: PetscCall(DMCreateDS(dm));
71: PetscFunctionReturn(PETSC_SUCCESS);
72: }
74: static PetscErrorCode CheckDistributed(DM dm, PetscBool expectedDistributed)
75: {
76: PetscMPIInt size;
77: PetscBool distributed;
78: const char YES[] = "DISTRIBUTED";
79: const char NO[] = "NOT DISTRIBUTED";
81: PetscFunctionBeginUser;
82: PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)dm), &size));
83: if (size < 2) PetscFunctionReturn(PETSC_SUCCESS);
84: PetscCall(DMPlexIsDistributed(dm, &distributed));
85: PetscCheck(distributed == expectedDistributed, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Expected DM being %s but actually is %s", expectedDistributed ? YES : NO, distributed ? YES : NO);
86: PetscFunctionReturn(PETSC_SUCCESS);
87: }
89: static PetscErrorCode CheckInterpolated(DM dm, PetscBool expectedInterpolated)
90: {
91: DMPlexInterpolatedFlag iflg;
92: PetscBool interpolated;
93: const char YES[] = "INTERPOLATED";
94: const char NO[] = "NOT INTERPOLATED";
96: PetscFunctionBeginUser;
97: PetscCall(DMPlexIsInterpolatedCollective(dm, &iflg));
98: interpolated = (PetscBool)(iflg == DMPLEX_INTERPOLATED_FULL);
99: PetscCheck(interpolated == expectedInterpolated, PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Expected DM being %s but actually is %s", expectedInterpolated ? YES : NO, interpolated ? YES : NO);
100: PetscFunctionReturn(PETSC_SUCCESS);
101: }
103: static PetscErrorCode CheckDistributedInterpolated(DM dm, PetscBool expectedInterpolated, PetscViewer v, AppCtx *user)
104: {
105: PetscViewerFormat format;
106: PetscBool distributed, interpolated = expectedInterpolated;
108: PetscFunctionBeginUser;
109: PetscCall(PetscViewerGetFormat(v, &format));
110: switch (format) {
111: case PETSC_VIEWER_HDF5_XDMF:
112: case PETSC_VIEWER_HDF5_VIZ: {
113: distributed = PETSC_TRUE;
114: interpolated = PETSC_FALSE;
115: }; break;
116: case PETSC_VIEWER_HDF5_PETSC:
117: case PETSC_VIEWER_DEFAULT:
118: case PETSC_VIEWER_NATIVE: {
119: DMPlexStorageVersion version;
121: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionReading(v, &version));
122: distributed = (PetscBool)(version->major >= 3);
123: }; break;
124: default:
125: distributed = PETSC_FALSE;
126: }
127: PetscCall(CheckDistributed(dm, distributed));
128: PetscCall(CheckInterpolated(dm, interpolated));
129: PetscFunctionReturn(PETSC_SUCCESS);
130: }
132: static PetscErrorCode DMPlexWriteAndReadHDF5(DM dm, Vec vec, const char filename[], const char prefix[], PetscBool expectedInterpolated, AppCtx *user, DM *dm_new, Vec *v_new)
133: {
134: DM dmnew;
135: Vec vnew = NULL;
136: const char savedName[] = "Mesh";
137: const char loadedName[] = "Mesh_new";
138: PetscViewer v;
140: PetscFunctionBeginUser;
141: PetscCall(PetscViewerHDF5Open(PetscObjectComm((PetscObject)dm), filename, FILE_MODE_WRITE, &v));
142: PetscCall(PetscViewerPushFormat(v, user->format));
143: PetscCall(PetscObjectSetName((PetscObject)dm, savedName));
144: if (user->use_low_level_functions) {
145: PetscCall(DMPlexTopologyView(dm, v));
146: PetscCall(DMPlexCoordinatesView(dm, v));
147: PetscCall(DMPlexLabelsView(dm, v));
148: } else {
149: PetscCall(DMView(dm, v));
150: if (vec) PetscCall(VecView(vec, v));
151: }
152: PetscCall(PetscViewerFileSetMode(v, FILE_MODE_READ));
153: PetscCall(DMCreate(PETSC_COMM_WORLD, &dmnew));
154: PetscCall(DMSetType(dmnew, DMPLEX));
155: PetscCall(DMPlexDistributeSetDefault(dmnew, PETSC_FALSE));
156: PetscCall(PetscObjectSetName((PetscObject)dmnew, savedName));
157: PetscCall(DMSetOptionsPrefix(dmnew, prefix));
158: if (user->use_low_level_functions) {
159: PetscSF sfXC;
161: PetscCall(DMPlexTopologyLoad(dmnew, v, &sfXC));
162: PetscCall(DMPlexCoordinatesLoad(dmnew, v, sfXC));
163: PetscCall(DMPlexLabelsLoad(dmnew, v, sfXC));
164: PetscCall(PetscSFDestroy(&sfXC));
165: } else {
166: PetscCall(DMLoad(dmnew, v));
167: if (vec) {
168: PetscCall(CreateDiscretization(dmnew));
169: PetscCall(DMCreateGlobalVector(dmnew, &vnew));
170: PetscCall(PetscObjectSetName((PetscObject)vnew, "solution"));
171: PetscCall(VecLoad(vnew, v));
172: }
173: }
174: PetscCall(CheckDistributedInterpolated(dmnew, expectedInterpolated, v, user));
175: PetscCall(PetscObjectSetName((PetscObject)dmnew, loadedName));
176: PetscCall(PetscViewerPopFormat(v));
177: PetscCall(PetscViewerDestroy(&v));
178: *dm_new = dmnew;
179: *v_new = vnew;
180: PetscFunctionReturn(PETSC_SUCCESS);
181: }
183: int main(int argc, char **argv)
184: {
185: DM dm, dmnew;
186: Vec v = NULL, vnew = NULL;
187: PetscPartitioner part;
188: AppCtx user;
189: PetscBool interpolated = PETSC_TRUE, flg;
191: PetscFunctionBeginUser;
192: PetscCall(PetscInitialize(&argc, &argv, NULL, help));
193: PetscCall(ProcessOptions(PETSC_COMM_WORLD, &user));
194: PetscCall(CreateMesh(PETSC_COMM_WORLD, &dm));
195: PetscCall(PetscOptionsGetBool(NULL, "orig_", "-dm_plex_interpolate", &interpolated, NULL));
196: PetscCall(CheckInterpolated(dm, interpolated));
198: if (user.distribute) {
199: DM dmdist;
201: PetscCall(DMPlexGetPartitioner(dm, &part));
202: PetscCall(PetscPartitionerSetType(part, PETSCPARTITIONERSIMPLE));
203: PetscCall(PetscPartitionerSetFromOptions(part));
204: PetscCall(DMPlexDistribute(dm, 0, NULL, &dmdist));
205: if (dmdist) {
206: PetscCall(DMDestroy(&dm));
207: dm = dmdist;
208: PetscCall(CheckDistributed(dm, PETSC_TRUE));
209: PetscCall(CheckInterpolated(dm, interpolated));
210: }
211: }
212: if (user.field) {
213: PetscSection gs;
214: PetscScalar *a;
215: PetscInt pStart, pEnd, rStart;
217: PetscCall(CreateDiscretization(dm));
219: PetscCall(DMCreateGlobalVector(dm, &v));
220: PetscCall(PetscObjectSetName((PetscObject)v, "solution"));
221: PetscCall(DMGetGlobalSection(dm, &gs));
222: PetscCall(PetscSectionGetChart(gs, &pStart, &pEnd));
223: PetscCall(VecGetOwnershipRange(v, &rStart, NULL));
224: PetscCall(VecGetArrayWrite(v, &a));
225: for (PetscInt p = pStart; p < pEnd; ++p) {
226: PetscInt dof, off;
228: PetscCall(PetscSectionGetDof(gs, p, &dof));
229: PetscCall(PetscSectionGetOffset(gs, p, &off));
230: if (off < 0) continue;
231: for (PetscInt d = 0; d < dof; ++d) a[off + d] = p;
232: }
233: PetscCall(VecRestoreArrayWrite(v, &a));
234: }
236: PetscCall(DMSetOptionsPrefix(dm, NULL));
237: PetscCall(DMPlexDistributeSetDefault(dm, PETSC_FALSE));
238: PetscCall(DMSetFromOptions(dm));
239: PetscCall(DMViewFromOptions(dm, NULL, "-dm_view"));
241: PetscCall(DMPlexWriteAndReadHDF5(dm, v, user.ofname, "new_", interpolated, &user, &dmnew, &vnew));
243: if (user.second_write_read) {
244: PetscCall(DMDestroy(&dm));
245: dm = dmnew;
246: PetscCall(DMPlexWriteAndReadHDF5(dm, v, user.ofname, "new_", interpolated, &user, &dmnew, &vnew));
247: }
249: PetscCall(DMViewFromOptions(dmnew, NULL, "-dm_view"));
251: /* This currently makes sense only for sequential meshes. */
252: if (user.compare) {
253: PetscCall(DMPlexEqual(dmnew, dm, &flg));
254: PetscCheck(flg, PETSC_COMM_WORLD, PETSC_ERR_ARG_INCOMP, "DMs are not equal");
255: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "DMs equal\n"));
256: if (v) {
257: PetscCall(VecEqual(vnew, v, &flg));
258: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "Vecs %s\n", flg ? "equal" : "are not equal"));
259: PetscCall(VecViewFromOptions(v, NULL, "-old_vec_view"));
260: PetscCall(VecViewFromOptions(vnew, NULL, "-new_vec_view"));
261: }
262: }
263: if (user.compare_labels) {
264: PetscCall(DMCompareLabels(dmnew, dm, NULL, NULL));
265: PetscCall(PetscPrintf(PETSC_COMM_WORLD, "DMLabels equal\n"));
266: }
268: PetscCall(VecDestroy(&v));
269: PetscCall(DMDestroy(&dm));
270: PetscCall(VecDestroy(&vnew));
271: PetscCall(DMDestroy(&dmnew));
272: PetscCall(PetscFinalize());
273: return 0;
274: }
276: /*TEST
277: build:
278: requires: hdf5
279: # Idempotence of saving/loading
280: # Have to replace Exodus file, which is creating uninterpolated edges
281: test:
282: suffix: 0
283: TODO: broken
284: requires: exodusii
285: args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/Rect-tri3.exo -dm_view ascii::ascii_info_detail
286: args: -format hdf5_petsc -compare
287: test:
288: suffix: 1
289: TODO: broken
290: requires: exodusii parmetis !defined(PETSC_USE_64BIT_INDICES)
291: nsize: 2
292: args: -filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/Rect-tri3.exo -dm_view ascii::ascii_info_detail
293: args: -petscpartitioner_type parmetis
294: args: -format hdf5_petsc -new_dm_view ascii::ascii_info_detail
296: testset:
297: requires: exodusii
298: args: -orig_dm_plex_filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/blockcylinder-50.exo
299: test:
300: suffix: 2
301: nsize: {{1 2 4 8}separate output}
302: args: -format {{default hdf5_petsc}separate output}
303: args: -dm_plex_view_hdf5_storage_version {{1.0.0 2.0.0 3.0.0}}
304: args: -orig_dm_plex_interpolate {{0 1}separate output}
305: test:
306: suffix: 2a
307: nsize: {{1 2 4 8}separate output}
308: args: -format {{hdf5_xdmf hdf5_viz}separate output}
310: test:
311: suffix: 3
312: requires: exodusii
313: args: -orig_dm_plex_filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/blockcylinder-50.exo -compare -compare_labels
314: args: -dm_plex_view_hdf5_storage_version {{1.0.0 2.0.0 3.0.0}}
316: # Load HDF5 file in XDMF format in parallel, write, read dm1, write, read dm2, and compare dm1 and dm2
317: testset:
318: suffix: 4
319: requires: !complex
320: args: -orig_dm_plex_filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/blockcylinder-50.h5 -dm_plex_create_from_hdf5_xdmf
321: args: -distribute 0 -second_write_read -compare
322: test:
323: suffix: hdf5_petsc
324: nsize: {{1 2}}
325: args: -format hdf5_petsc -compare_labels
326: args: -dm_plex_view_hdf5_storage_version {{1.0.0 2.0.0 3.0.0}}
327: test:
328: suffix: hdf5_xdmf
329: nsize: {{1 3 8}}
330: args: -format hdf5_xdmf
332: # Use low level functions, DMPlexTopologyView()/Load(), DMPlexCoordinatesView()/Load(), and DMPlexLabelsView()/Load()
333: # TODO: The output is very long so keeping just 1.0.0 version. This test should be redesigned or removed.
334: test:
335: suffix: 5
336: requires: exodusii
337: nsize: 2
338: args: -orig_dm_plex_filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/blockcylinder-50.exo
339: args: -orig_dm_plex_interpolate 0 -orig_dm_distribute 0
340: args: -dm_view ascii::ascii_info_detail
341: args: -new_dm_view ascii::ascii_info_detail
342: args: -format hdf5_petsc -use_low_level_functions {{0 1}}
343: args: -dm_plex_view_hdf5_storage_version 1.0.0
345: testset:
346: suffix: 6
347: requires: hdf5 !complex datafilespath
348: nsize: {{1 3}}
349: args: -dm_plex_check_symmetry -dm_plex_check_skeleton -dm_plex_check_geometry
350: args: -orig_dm_plex_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
351: args: -orig_dm_distribute 0
352: args: -format hdf5_petsc -second_write_read -compare -compare_labels
353: args: -orig_dm_plex_interpolate {{0 1}} -distribute {{0 1}}
354: args: -dm_plex_view_hdf5_storage_version {{1.0.0 2.0.0 3.0.0}}
356: testset:
357: # the same data and settings as dm_impls_plex_tests-ex18_9%
358: suffix: 9
359: requires: hdf5 !complex datafilespath
360: nsize: {{1 2 4}}
361: args: -dm_plex_check_symmetry -dm_plex_check_skeleton -dm_plex_check_geometry
362: args: -orig_dm_plex_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
363: args: -orig_dm_distribute 0
364: args: -format {{hdf5_petsc hdf5_xdmf}} -second_write_read -compare
365: args: -dm_plex_view_hdf5_storage_version 3.0.0
366: test:
367: suffix: hdf5_seqload
368: args: -distribute
369: args: -orig_dm_plex_interpolate {{0 1}}
370: args: -dm_plex_hdf5_force_sequential
371: test:
372: suffix: hdf5_seqload_metis
373: requires: parmetis
374: args: -distribute -petscpartitioner_type parmetis
375: args: -orig_dm_plex_interpolate 1
376: args: -dm_plex_hdf5_force_sequential
377: test:
378: suffix: hdf5
379: args: -orig_dm_plex_interpolate 1
380: test:
381: suffix: hdf5_repart
382: requires: parmetis
383: args: -distribute -petscpartitioner_type parmetis
384: args: -orig_dm_plex_interpolate 1
385: test:
386: TODO: Parallel partitioning of uninterpolated meshes not supported
387: suffix: hdf5_repart_ppu
388: requires: parmetis
389: args: -distribute -petscpartitioner_type parmetis
390: args: -orig_dm_plex_interpolate 0
392: # reproduce PetscSFView() crash - fixed, left as regression test
393: test:
394: suffix: new_dm_view
395: requires: exodusii
396: nsize: 2
397: args: -orig_dm_plex_filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/TwoQuads.exo -new_dm_view ascii:ex5_new_dm_view.log:ascii_info_detail
398: args: -dm_plex_view_hdf5_storage_version {{1.0.0 2.0.0 3.0.0}}
400: # test backward compatibility with petsc_hdf5 format version 1.0.0, serial idempotence
401: testset:
402: suffix: 10-v3.16.0-v1.0.0
403: requires: hdf5 !complex datafilespath
404: args: -dm_plex_check_all -compare -compare_labels
405: args: -dm_plex_view_hdf5_storage_version {{1.0.0 2.0.0 3.0.0}} -use_low_level_functions {{0 1}}
406: test:
407: suffix: a
408: args: -orig_dm_plex_filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/annulus-20.h5
409: test:
410: suffix: b
411: TODO: broken
412: args: -orig_dm_plex_filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/barycentricallyrefinedcube.h5
413: test:
414: suffix: c
415: args: -orig_dm_plex_filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/blockcylinder-50.h5
416: test:
417: suffix: d
418: args: -orig_dm_plex_filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/cube-hexahedra-refined.h5
419: test:
420: suffix: e
421: args: -orig_dm_plex_filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/hybrid_hexwedge.h5
422: test:
423: suffix: f
424: args: -orig_dm_plex_filename ${DATAFILESPATH}/meshes/hdf5-petsc/petsc-v3.16.0/v1.0.0/square.h5
426: # test permuted sections with petsc_hdf5 format version 1.0.0
427: testset:
428: suffix: 11
429: requires: hdf5 triangle
430: args: -field
431: args: -dm_plex_check_all -compare -compare_labels
432: args: -orig_dm_plex_box_faces 3,3 -dm_plex_view_hdf5_storage_version 1.0.0
433: args: -orig_dm_reorder_section -orig_dm_reorder_section_type reverse
435: test:
436: suffix: serial
437: test:
438: suffix: serial_no_perm
439: args: -orig_dm_ignore_perm_output
441: TEST*/