Actual source code: plexhdf5.c
1: #include <petsc/private/dmpleximpl.h>
2: #include <petsc/private/isimpl.h>
3: #include <petsc/private/vecimpl.h>
4: #include <petsc/private/viewerhdf5impl.h>
5: #include <petsclayouthdf5.h>
7: /* Logging support */
8: PetscLogEvent DMPLEX_DistributionView, DMPLEX_DistributionLoad;
10: #if defined(PETSC_HAVE_HDF5)
11: static PetscErrorCode PetscViewerParseVersion_Private(PetscViewer, const char[], DMPlexStorageVersion *);
12: static PetscErrorCode PetscViewerCheckVersion_Private(PetscViewer, DMPlexStorageVersion);
13: static PetscErrorCode PetscViewerAttachVersion_Private(PetscViewer, const char[], DMPlexStorageVersion);
14: static PetscErrorCode PetscViewerGetAttachedVersion_Private(PetscViewer, const char[], DMPlexStorageVersion *);
16: PETSC_EXTERN PetscErrorCode VecView_MPI(Vec, PetscViewer);
18: static PetscErrorCode PetscViewerParseVersion_Private(PetscViewer viewer, const char str[], DMPlexStorageVersion *version)
19: {
20: PetscToken t;
21: char *ts;
22: PetscInt i;
23: PetscInt ti[3];
24: DMPlexStorageVersion v;
26: PetscFunctionBegin;
27: PetscCall(PetscTokenCreate(str, '.', &t));
28: for (i = 0; i < 3; i++) {
29: PetscCall(PetscTokenFind(t, &ts));
30: PetscCheck(ts, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONG, "Malformed version string %s", str);
31: PetscCall(PetscOptionsStringToInt(ts, &ti[i]));
32: }
33: PetscCall(PetscTokenFind(t, &ts));
34: PetscCheck(!ts, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONG, "Malformed version string %s", str);
35: PetscCall(PetscTokenDestroy(&t));
36: PetscCall(PetscNew(&v));
37: v->major = ti[0];
38: v->minor = ti[1];
39: v->subminor = ti[2];
40: PetscCall(PetscViewerCheckVersion_Private(viewer, v));
41: *version = v;
42: PetscFunctionReturn(PETSC_SUCCESS);
43: }
45: static PetscErrorCode PetscViewerAttachVersion_Private(PetscViewer viewer, const char key[], DMPlexStorageVersion v)
46: {
47: PetscContainer cont;
49: PetscFunctionBegin;
50: PetscCall(PetscContainerCreate(PetscObjectComm((PetscObject)viewer), &cont));
51: PetscCall(PetscContainerSetPointer(cont, v));
52: PetscCall(PetscContainerSetUserDestroy(cont, PetscContainerUserDestroyDefault));
53: PetscCall(PetscObjectCompose((PetscObject)viewer, key, (PetscObject)cont));
54: PetscCall(PetscContainerDestroy(&cont));
55: PetscFunctionReturn(PETSC_SUCCESS);
56: }
58: static PetscErrorCode PetscViewerGetAttachedVersion_Private(PetscViewer viewer, const char key[], DMPlexStorageVersion *v)
59: {
60: PetscContainer cont;
62: PetscFunctionBegin;
63: PetscCall(PetscObjectQuery((PetscObject)viewer, key, (PetscObject *)&cont));
64: *v = NULL;
65: if (cont) PetscCall(PetscContainerGetPointer(cont, (void **)v));
66: PetscFunctionReturn(PETSC_SUCCESS);
67: }
69: /*
70: Version log:
71: 1.0.0 legacy version (default if no "dmplex_storage_version" attribute found in file)
72: 2.0.0 introduce versioning and multiple topologies
73: 2.1.0 introduce distributions
74: */
75: static PetscErrorCode PetscViewerCheckVersion_Private(PetscViewer viewer, DMPlexStorageVersion version)
76: {
77: PetscBool valid = PETSC_FALSE;
79: PetscFunctionBegin;
80: switch (version->major) {
81: case 1:
82: switch (version->minor) {
83: case 0:
84: switch (version->subminor) {
85: case 0:
86: valid = PETSC_TRUE;
87: break;
88: };
89: break;
90: };
91: break;
92: case 2:
93: switch (version->minor) {
94: case 0:
95: switch (version->subminor) {
96: case 0:
97: valid = PETSC_TRUE;
98: break;
99: };
100: break;
101: case 1:
102: switch (version->subminor) {
103: case 0:
104: valid = PETSC_TRUE;
105: break;
106: };
107: break;
108: };
109: break;
110: case 3:
111: switch (version->minor) {
112: case 0:
113: switch (version->subminor) {
114: case 0:
115: valid = PETSC_TRUE;
116: break;
117: };
118: break;
119: };
120: break;
121: }
122: PetscCheck(valid, PetscObjectComm((PetscObject)viewer), PETSC_ERR_SUP, "DMPlexStorageVersion %d.%d.%d not supported", version->major, version->minor, version->subminor);
123: PetscFunctionReturn(PETSC_SUCCESS);
124: }
126: static inline PetscBool DMPlexStorageVersionGE(DMPlexStorageVersion version, int major, int minor, int subminor)
127: {
128: return (PetscBool)((version->major == major && version->minor == minor && version->subminor >= subminor) || (version->major == major && version->minor > minor) || (version->major > major));
129: }
131: PetscErrorCode PetscViewerHDF5GetDMPlexStorageVersionWriting(PetscViewer viewer, DMPlexStorageVersion *version)
132: {
133: const char ATTR_NAME[] = "dmplex_storage_version";
134: PetscBool fileHasVersion;
135: char optVersion[16], fileVersion[16];
137: PetscFunctionBegin;
140: PetscCall(PetscViewerGetAttachedVersion_Private(viewer, DMPLEX_STORAGE_VERSION_WRITING_KEY, version));
141: if (*version) PetscFunctionReturn(PETSC_SUCCESS);
143: PetscCall(PetscStrncpy(fileVersion, DMPLEX_STORAGE_VERSION_STABLE, sizeof(fileVersion)));
144: PetscCall(PetscViewerHDF5HasAttribute(viewer, NULL, ATTR_NAME, &fileHasVersion));
145: if (fileHasVersion) {
146: char *tmp;
148: PetscCall(PetscViewerHDF5ReadAttribute(viewer, "/", ATTR_NAME, PETSC_STRING, NULL, &tmp));
149: PetscCall(PetscStrncpy(fileVersion, tmp, sizeof(fileVersion)));
150: PetscCall(PetscFree(tmp));
151: }
152: PetscCall(PetscStrncpy(optVersion, fileVersion, sizeof(optVersion)));
153: PetscObjectOptionsBegin((PetscObject)viewer);
154: PetscCall(PetscOptionsString("-dm_plex_view_hdf5_storage_version", "DMPlex HDF5 viewer storage version", NULL, optVersion, optVersion, sizeof(optVersion), NULL));
155: PetscOptionsEnd();
156: if (!fileHasVersion) {
157: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, ATTR_NAME, PETSC_STRING, optVersion));
158: } else {
159: PetscBool flg;
161: PetscCall(PetscStrcmp(fileVersion, optVersion, &flg));
162: PetscCheck(flg, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "User requested DMPlex storage version %s but file already has version %s - cannot mix versions", optVersion, fileVersion);
163: }
164: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "petsc_version_git", PETSC_STRING, PETSC_VERSION_GIT));
165: PetscCall(PetscViewerParseVersion_Private(viewer, optVersion, version));
166: PetscCall(PetscViewerAttachVersion_Private(viewer, DMPLEX_STORAGE_VERSION_WRITING_KEY, *version));
167: PetscFunctionReturn(PETSC_SUCCESS);
168: }
170: PetscErrorCode PetscViewerHDF5GetDMPlexStorageVersionReading(PetscViewer viewer, DMPlexStorageVersion *version)
171: {
172: const char ATTR_NAME[] = "dmplex_storage_version";
173: char *defaultVersion;
174: char *versionString;
176: PetscFunctionBegin;
179: PetscCall(PetscViewerGetAttachedVersion_Private(viewer, DMPLEX_STORAGE_VERSION_READING_KEY, version));
180: if (*version) PetscFunctionReturn(PETSC_SUCCESS);
182: //TODO string HDF5 attribute handling is terrible and should be redesigned
183: PetscCall(PetscStrallocpy(DMPLEX_STORAGE_VERSION_FIRST, &defaultVersion));
184: PetscCall(PetscViewerHDF5ReadAttribute(viewer, "/", ATTR_NAME, PETSC_STRING, &defaultVersion, &versionString));
185: PetscCall(PetscViewerParseVersion_Private(viewer, versionString, version));
186: PetscCall(PetscViewerAttachVersion_Private(viewer, DMPLEX_STORAGE_VERSION_READING_KEY, *version));
187: PetscCall(PetscFree(versionString));
188: PetscCall(PetscFree(defaultVersion));
189: PetscFunctionReturn(PETSC_SUCCESS);
190: }
192: static PetscErrorCode DMPlexGetHDF5Name_Private(DM dm, const char *name[])
193: {
194: PetscFunctionBegin;
195: if (((PetscObject)dm)->name) {
196: PetscCall(PetscObjectGetName((PetscObject)dm, name));
197: } else {
198: *name = "plex";
199: }
200: PetscFunctionReturn(PETSC_SUCCESS);
201: }
203: static PetscErrorCode DMSequenceView_HDF5(DM dm, const char *seqname, PetscInt seqnum, PetscScalar value, PetscViewer viewer)
204: {
205: Vec stamp;
206: PetscMPIInt rank;
208: PetscFunctionBegin;
209: if (seqnum < 0) PetscFunctionReturn(PETSC_SUCCESS);
210: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)viewer), &rank));
211: PetscCall(VecCreateMPI(PetscObjectComm((PetscObject)viewer), rank ? 0 : 1, 1, &stamp));
212: PetscCall(VecSetBlockSize(stamp, 1));
213: PetscCall(PetscObjectSetName((PetscObject)stamp, seqname));
214: if (rank == 0) {
215: PetscReal timeScale;
216: PetscBool istime;
218: PetscCall(PetscStrncmp(seqname, "time", 5, &istime));
219: if (istime) {
220: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_TIME, &timeScale));
221: value *= timeScale;
222: }
223: PetscCall(VecSetValue(stamp, 0, value, INSERT_VALUES));
224: }
225: PetscCall(VecAssemblyBegin(stamp));
226: PetscCall(VecAssemblyEnd(stamp));
227: PetscCall(PetscViewerHDF5PushGroup(viewer, "/"));
228: PetscCall(PetscViewerHDF5PushTimestepping(viewer));
229: PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum)); /* seqnum < 0 jumps out above */
230: PetscCall(VecView(stamp, viewer));
231: PetscCall(PetscViewerHDF5PopTimestepping(viewer));
232: PetscCall(PetscViewerHDF5PopGroup(viewer));
233: PetscCall(VecDestroy(&stamp));
234: PetscFunctionReturn(PETSC_SUCCESS);
235: }
237: PetscErrorCode DMSequenceLoad_HDF5_Internal(DM dm, const char *seqname, PetscInt seqnum, PetscScalar *value, PetscViewer viewer)
238: {
239: Vec stamp;
240: PetscMPIInt rank;
242: PetscFunctionBegin;
243: if (seqnum < 0) PetscFunctionReturn(PETSC_SUCCESS);
244: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)viewer), &rank));
245: PetscCall(VecCreateMPI(PetscObjectComm((PetscObject)viewer), rank ? 0 : 1, 1, &stamp));
246: PetscCall(VecSetBlockSize(stamp, 1));
247: PetscCall(PetscObjectSetName((PetscObject)stamp, seqname));
248: PetscCall(PetscViewerHDF5PushGroup(viewer, "/"));
249: PetscCall(PetscViewerHDF5PushTimestepping(viewer));
250: PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum)); /* seqnum < 0 jumps out above */
251: PetscCall(VecLoad(stamp, viewer));
252: PetscCall(PetscViewerHDF5PopTimestepping(viewer));
253: PetscCall(PetscViewerHDF5PopGroup(viewer));
254: if (rank == 0) {
255: const PetscScalar *a;
256: PetscReal timeScale;
257: PetscBool istime;
259: PetscCall(VecGetArrayRead(stamp, &a));
260: *value = a[0];
261: PetscCall(VecRestoreArrayRead(stamp, &a));
262: PetscCall(PetscStrncmp(seqname, "time", 5, &istime));
263: if (istime) {
264: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_TIME, &timeScale));
265: *value /= timeScale;
266: }
267: }
268: PetscCall(VecDestroy(&stamp));
269: PetscFunctionReturn(PETSC_SUCCESS);
270: }
272: static PetscErrorCode DMPlexCreateCutVertexLabel_Private(DM dm, DMLabel cutLabel, DMLabel *cutVertexLabel)
273: {
274: IS cutcells = NULL;
275: const PetscInt *cutc;
276: PetscInt cellHeight, vStart, vEnd, cStart, cEnd, c;
278: PetscFunctionBegin;
279: if (!cutLabel) PetscFunctionReturn(PETSC_SUCCESS);
280: PetscCall(DMPlexGetVTKCellHeight(dm, &cellHeight));
281: PetscCall(DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd));
282: PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
283: /* Label vertices that should be duplicated */
284: PetscCall(DMLabelCreate(PETSC_COMM_SELF, "Cut Vertices", cutVertexLabel));
285: PetscCall(DMLabelGetStratumIS(cutLabel, 2, &cutcells));
286: if (cutcells) {
287: PetscInt n;
289: PetscCall(ISGetIndices(cutcells, &cutc));
290: PetscCall(ISGetLocalSize(cutcells, &n));
291: for (c = 0; c < n; ++c) {
292: if ((cutc[c] >= cStart) && (cutc[c] < cEnd)) {
293: PetscInt *closure = NULL;
294: PetscInt closureSize, cl, value;
296: PetscCall(DMPlexGetTransitiveClosure(dm, cutc[c], PETSC_TRUE, &closureSize, &closure));
297: for (cl = 0; cl < closureSize * 2; cl += 2) {
298: if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) {
299: PetscCall(DMLabelGetValue(cutLabel, closure[cl], &value));
300: if (value == 1) PetscCall(DMLabelSetValue(*cutVertexLabel, closure[cl], 1));
301: }
302: }
303: PetscCall(DMPlexRestoreTransitiveClosure(dm, cutc[c], PETSC_TRUE, &closureSize, &closure));
304: }
305: }
306: PetscCall(ISRestoreIndices(cutcells, &cutc));
307: }
308: PetscCall(ISDestroy(&cutcells));
309: PetscFunctionReturn(PETSC_SUCCESS);
310: }
312: PetscErrorCode VecView_Plex_Local_HDF5_Internal(Vec v, PetscViewer viewer)
313: {
314: DM dm;
315: DM dmBC;
316: PetscSection section, sectionGlobal;
317: Vec gv;
318: const char *name;
319: PetscViewerVTKFieldType ft;
320: PetscViewerFormat format;
321: PetscInt seqnum;
322: PetscReal seqval;
323: PetscBool isseq;
325: PetscFunctionBegin;
326: PetscCall(PetscObjectTypeCompare((PetscObject)v, VECSEQ, &isseq));
327: PetscCall(VecGetDM(v, &dm));
328: PetscCall(DMGetLocalSection(dm, §ion));
329: PetscCall(DMGetOutputSequenceNumber(dm, &seqnum, &seqval));
330: PetscCall(DMSequenceView_HDF5(dm, "time", seqnum, (PetscScalar)seqval, viewer));
331: if (seqnum >= 0) {
332: PetscCall(PetscViewerHDF5PushTimestepping(viewer));
333: PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum));
334: }
335: PetscCall(PetscViewerGetFormat(viewer, &format));
336: PetscCall(DMGetOutputDM(dm, &dmBC));
337: PetscCall(DMGetGlobalSection(dmBC, §ionGlobal));
338: PetscCall(DMGetGlobalVector(dmBC, &gv));
339: PetscCall(PetscObjectGetName((PetscObject)v, &name));
340: PetscCall(PetscObjectSetName((PetscObject)gv, name));
341: PetscCall(DMLocalToGlobalBegin(dmBC, v, INSERT_VALUES, gv));
342: PetscCall(DMLocalToGlobalEnd(dmBC, v, INSERT_VALUES, gv));
343: PetscCall(PetscObjectTypeCompare((PetscObject)gv, VECSEQ, &isseq));
344: if (isseq) PetscCall(VecView_Seq(gv, viewer));
345: else PetscCall(VecView_MPI(gv, viewer));
346: if (format == PETSC_VIEWER_HDF5_VIZ) {
347: /* Output visualization representation */
348: PetscInt numFields, f;
349: DMLabel cutLabel, cutVertexLabel = NULL;
351: PetscCall(PetscSectionGetNumFields(section, &numFields));
352: PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel));
353: for (f = 0; f < numFields; ++f) {
354: Vec subv;
355: IS is;
356: const char *fname, *fgroup, *componentName;
357: char subname[PETSC_MAX_PATH_LEN];
358: PetscInt pStart, pEnd, Nc, c;
360: PetscCall(DMPlexGetFieldType_Internal(dm, section, f, &pStart, &pEnd, &ft));
361: fgroup = (ft == PETSC_VTK_POINT_VECTOR_FIELD) || (ft == PETSC_VTK_POINT_FIELD) ? "/vertex_fields" : "/cell_fields";
362: PetscCall(PetscSectionGetFieldName(section, f, &fname));
363: if (!fname || ft == PETSC_VTK_INVALID) continue;
364: PetscCall(PetscViewerHDF5PushGroup(viewer, fgroup));
365: if (cutLabel) {
366: const PetscScalar *ga;
367: PetscScalar *suba;
368: PetscInt gstart, subSize = 0, extSize = 0, subOff = 0, newOff = 0, p;
370: PetscCall(DMPlexCreateCutVertexLabel_Private(dm, cutLabel, &cutVertexLabel));
371: PetscCall(PetscSectionGetFieldComponents(section, f, &Nc));
372: for (p = pStart; p < pEnd; ++p) {
373: PetscInt gdof, fdof = 0, val;
375: PetscCall(PetscSectionGetDof(sectionGlobal, p, &gdof));
376: if (gdof > 0) PetscCall(PetscSectionGetFieldDof(section, p, f, &fdof));
377: subSize += fdof;
378: PetscCall(DMLabelGetValue(cutVertexLabel, p, &val));
379: if (val == 1) extSize += fdof;
380: }
381: PetscCall(VecCreate(PetscObjectComm((PetscObject)gv), &subv));
382: PetscCall(VecSetSizes(subv, subSize + extSize, PETSC_DETERMINE));
383: PetscCall(VecSetBlockSize(subv, Nc));
384: PetscCall(VecSetType(subv, VECSTANDARD));
385: PetscCall(VecGetOwnershipRange(gv, &gstart, NULL));
386: PetscCall(VecGetArrayRead(gv, &ga));
387: PetscCall(VecGetArray(subv, &suba));
388: for (p = pStart; p < pEnd; ++p) {
389: PetscInt gdof, goff, val;
391: PetscCall(PetscSectionGetDof(sectionGlobal, p, &gdof));
392: if (gdof > 0) {
393: PetscInt fdof, fc, f2, poff = 0;
395: PetscCall(PetscSectionGetOffset(sectionGlobal, p, &goff));
396: /* Can get rid of this loop by storing field information in the global section */
397: for (f2 = 0; f2 < f; ++f2) {
398: PetscCall(PetscSectionGetFieldDof(section, p, f2, &fdof));
399: poff += fdof;
400: }
401: PetscCall(PetscSectionGetFieldDof(section, p, f, &fdof));
402: for (fc = 0; fc < fdof; ++fc, ++subOff) suba[subOff] = ga[goff + poff + fc - gstart];
403: PetscCall(DMLabelGetValue(cutVertexLabel, p, &val));
404: if (val == 1) {
405: for (fc = 0; fc < fdof; ++fc, ++newOff) suba[subSize + newOff] = ga[goff + poff + fc - gstart];
406: }
407: }
408: }
409: PetscCall(VecRestoreArrayRead(gv, &ga));
410: PetscCall(VecRestoreArray(subv, &suba));
411: PetscCall(DMLabelDestroy(&cutVertexLabel));
412: } else {
413: PetscCall(PetscSectionGetField_Internal(section, sectionGlobal, gv, f, pStart, pEnd, &is, &subv));
414: }
415: PetscCall(PetscStrncpy(subname, name, sizeof(subname)));
416: PetscCall(PetscStrlcat(subname, "_", sizeof(subname)));
417: PetscCall(PetscStrlcat(subname, fname, sizeof(subname)));
418: PetscCall(PetscObjectSetName((PetscObject)subv, subname));
419: if (isseq) PetscCall(VecView_Seq(subv, viewer));
420: else PetscCall(VecView_MPI(subv, viewer));
421: if ((ft == PETSC_VTK_POINT_VECTOR_FIELD) || (ft == PETSC_VTK_CELL_VECTOR_FIELD)) {
422: PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)subv, "vector_field_type", PETSC_STRING, "vector"));
423: } else {
424: PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)subv, "vector_field_type", PETSC_STRING, "scalar"));
425: }
427: /* Output the component names in the field if available */
428: PetscCall(PetscSectionGetFieldComponents(section, f, &Nc));
429: for (c = 0; c < Nc; ++c) {
430: char componentNameLabel[PETSC_MAX_PATH_LEN];
431: PetscCall(PetscSectionGetComponentName(section, f, c, &componentName));
432: PetscCall(PetscSNPrintf(componentNameLabel, sizeof(componentNameLabel), "componentName%" PetscInt_FMT, c));
433: PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)subv, componentNameLabel, PETSC_STRING, componentName));
434: }
436: if (cutLabel) PetscCall(VecDestroy(&subv));
437: else PetscCall(PetscSectionRestoreField_Internal(section, sectionGlobal, gv, f, pStart, pEnd, &is, &subv));
438: PetscCall(PetscViewerHDF5PopGroup(viewer));
439: }
440: }
441: if (seqnum >= 0) PetscCall(PetscViewerHDF5PopTimestepping(viewer));
442: PetscCall(DMRestoreGlobalVector(dmBC, &gv));
443: PetscFunctionReturn(PETSC_SUCCESS);
444: }
446: PetscErrorCode VecView_Plex_HDF5_Internal(Vec v, PetscViewer viewer)
447: {
448: DM dm;
449: Vec locv;
450: PetscObject isZero;
451: const char *name;
452: PetscReal time;
454: PetscFunctionBegin;
455: PetscCall(VecGetDM(v, &dm));
456: PetscCall(DMGetLocalVector(dm, &locv));
457: PetscCall(PetscObjectGetName((PetscObject)v, &name));
458: PetscCall(PetscObjectSetName((PetscObject)locv, name));
459: PetscCall(PetscObjectQuery((PetscObject)v, "__Vec_bc_zero__", &isZero));
460: PetscCall(PetscObjectCompose((PetscObject)locv, "__Vec_bc_zero__", isZero));
461: PetscCall(DMGlobalToLocalBegin(dm, v, INSERT_VALUES, locv));
462: PetscCall(DMGlobalToLocalEnd(dm, v, INSERT_VALUES, locv));
463: PetscCall(DMGetOutputSequenceNumber(dm, NULL, &time));
464: PetscCall(DMPlexInsertBoundaryValues(dm, PETSC_TRUE, locv, time, NULL, NULL, NULL));
465: PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
466: PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_VIZ));
467: PetscCall(VecView_Plex_Local_HDF5_Internal(locv, viewer));
468: PetscCall(PetscViewerPopFormat(viewer));
469: PetscCall(PetscViewerHDF5PopGroup(viewer));
470: PetscCall(PetscObjectCompose((PetscObject)locv, "__Vec_bc_zero__", NULL));
471: PetscCall(DMRestoreLocalVector(dm, &locv));
472: PetscFunctionReturn(PETSC_SUCCESS);
473: }
475: PetscErrorCode VecView_Plex_HDF5_Native_Internal(Vec v, PetscViewer viewer)
476: {
477: PetscBool isseq;
479: PetscFunctionBegin;
480: PetscCall(PetscObjectTypeCompare((PetscObject)v, VECSEQ, &isseq));
481: PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
482: if (isseq) PetscCall(VecView_Seq(v, viewer));
483: else PetscCall(VecView_MPI(v, viewer));
484: PetscCall(PetscViewerHDF5PopGroup(viewer));
485: PetscFunctionReturn(PETSC_SUCCESS);
486: }
488: PetscErrorCode VecLoad_Plex_HDF5_Internal(Vec v, PetscViewer viewer)
489: {
490: DM dm;
491: Vec locv;
492: const char *name;
493: PetscInt seqnum;
495: PetscFunctionBegin;
496: PetscCall(VecGetDM(v, &dm));
497: PetscCall(DMGetLocalVector(dm, &locv));
498: PetscCall(PetscObjectGetName((PetscObject)v, &name));
499: PetscCall(PetscObjectSetName((PetscObject)locv, name));
500: PetscCall(DMGetOutputSequenceNumber(dm, &seqnum, NULL));
501: PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
502: if (seqnum >= 0) {
503: PetscCall(PetscViewerHDF5PushTimestepping(viewer));
504: PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum));
505: }
506: PetscCall(VecLoad_Plex_Local(locv, viewer));
507: if (seqnum >= 0) PetscCall(PetscViewerHDF5PopTimestepping(viewer));
508: PetscCall(PetscViewerHDF5PopGroup(viewer));
509: PetscCall(DMLocalToGlobalBegin(dm, locv, INSERT_VALUES, v));
510: PetscCall(DMLocalToGlobalEnd(dm, locv, INSERT_VALUES, v));
511: PetscCall(DMRestoreLocalVector(dm, &locv));
512: PetscFunctionReturn(PETSC_SUCCESS);
513: }
515: PetscErrorCode VecLoad_Plex_HDF5_Native_Internal(Vec v, PetscViewer viewer)
516: {
517: DM dm;
518: PetscInt seqnum;
520: PetscFunctionBegin;
521: PetscCall(VecGetDM(v, &dm));
522: PetscCall(DMGetOutputSequenceNumber(dm, &seqnum, NULL));
523: PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
524: if (seqnum >= 0) {
525: PetscCall(PetscViewerHDF5PushTimestepping(viewer));
526: PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum));
527: }
528: PetscCall(VecLoad_Default(v, viewer));
529: if (seqnum >= 0) PetscCall(PetscViewerHDF5PopTimestepping(viewer));
530: PetscCall(PetscViewerHDF5PopGroup(viewer));
531: PetscFunctionReturn(PETSC_SUCCESS);
532: }
534: static PetscErrorCode DMPlexDistributionView_HDF5_Private(DM dm, IS globalPointNumbers, PetscViewer viewer)
535: {
536: MPI_Comm comm;
537: PetscMPIInt size, rank;
538: PetscInt size_petsc_int;
539: const char *topologydm_name, *distribution_name;
540: const PetscInt *gpoint;
541: PetscInt pStart, pEnd, p;
542: PetscSF pointSF;
543: PetscInt nroots, nleaves;
544: const PetscInt *ilocal;
545: const PetscSFNode *iremote;
546: IS chartSizesIS, ownersIS, gpointsIS;
547: PetscInt *chartSize, *owners, *gpoints;
549: PetscFunctionBegin;
550: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
551: PetscCallMPI(MPI_Comm_size(comm, &size));
552: PetscCallMPI(MPI_Comm_rank(comm, &rank));
553: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
554: PetscCall(DMPlexDistributionGetName(dm, &distribution_name));
555: if (!distribution_name) PetscFunctionReturn(PETSC_SUCCESS);
556: PetscCall(PetscLogEventBegin(DMPLEX_DistributionView, viewer, 0, 0, 0));
557: size_petsc_int = (PetscInt)size;
558: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "comm_size", PETSC_INT, (void *)&size_petsc_int));
559: PetscCall(ISGetIndices(globalPointNumbers, &gpoint));
560: PetscCall(DMPlexGetChart(dm, &pStart, &pEnd));
561: PetscCall(PetscMalloc1(1, &chartSize));
562: *chartSize = pEnd - pStart;
563: PetscCall(PetscMalloc1(*chartSize, &owners));
564: PetscCall(PetscMalloc1(*chartSize, &gpoints));
565: PetscCall(DMGetPointSF(dm, &pointSF));
566: PetscCall(PetscSFGetGraph(pointSF, &nroots, &nleaves, &ilocal, &iremote));
567: for (p = pStart; p < pEnd; ++p) {
568: PetscInt gp = gpoint[p - pStart];
570: owners[p - pStart] = rank;
571: gpoints[p - pStart] = (gp < 0 ? -(gp + 1) : gp);
572: }
573: for (p = 0; p < nleaves; ++p) {
574: PetscInt ilocalp = (ilocal ? ilocal[p] : p);
576: owners[ilocalp] = iremote[p].rank;
577: }
578: PetscCall(ISCreateGeneral(comm, 1, chartSize, PETSC_OWN_POINTER, &chartSizesIS));
579: PetscCall(ISCreateGeneral(comm, *chartSize, owners, PETSC_OWN_POINTER, &ownersIS));
580: PetscCall(ISCreateGeneral(comm, *chartSize, gpoints, PETSC_OWN_POINTER, &gpointsIS));
581: PetscCall(PetscObjectSetName((PetscObject)chartSizesIS, "chart_sizes"));
582: PetscCall(PetscObjectSetName((PetscObject)ownersIS, "owners"));
583: PetscCall(PetscObjectSetName((PetscObject)gpointsIS, "global_point_numbers"));
584: PetscCall(ISView(chartSizesIS, viewer));
585: PetscCall(ISView(ownersIS, viewer));
586: PetscCall(ISView(gpointsIS, viewer));
587: PetscCall(ISDestroy(&chartSizesIS));
588: PetscCall(ISDestroy(&ownersIS));
589: PetscCall(ISDestroy(&gpointsIS));
590: PetscCall(ISRestoreIndices(globalPointNumbers, &gpoint));
591: PetscCall(PetscLogEventEnd(DMPLEX_DistributionView, viewer, 0, 0, 0));
592: PetscFunctionReturn(PETSC_SUCCESS);
593: }
595: static PetscErrorCode DMPlexTopologyView_HDF5_Inner_Private(DM dm, IS globalPointNumbers, PetscViewer viewer, PetscInt pStart, PetscInt pEnd, const char pointsName[], const char coneSizesName[], const char conesName[], const char orientationsName[])
596: {
597: IS coneSizesIS, conesIS, orientationsIS;
598: PetscInt *coneSizes, *cones, *orientations;
599: const PetscInt *gpoint;
600: PetscInt nPoints = 0, conesSize = 0;
601: PetscInt p, c, s;
602: MPI_Comm comm;
604: PetscFunctionBegin;
605: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
606: PetscCall(ISGetIndices(globalPointNumbers, &gpoint));
607: for (p = pStart; p < pEnd; ++p) {
608: if (gpoint[p] >= 0) {
609: PetscInt coneSize;
611: PetscCall(DMPlexGetConeSize(dm, p, &coneSize));
612: nPoints += 1;
613: conesSize += coneSize;
614: }
615: }
616: PetscCall(PetscMalloc1(nPoints, &coneSizes));
617: PetscCall(PetscMalloc1(conesSize, &cones));
618: PetscCall(PetscMalloc1(conesSize, &orientations));
619: for (p = pStart, c = 0, s = 0; p < pEnd; ++p) {
620: if (gpoint[p] >= 0) {
621: const PetscInt *cone, *ornt;
622: PetscInt coneSize, cp;
624: PetscCall(DMPlexGetConeSize(dm, p, &coneSize));
625: PetscCall(DMPlexGetCone(dm, p, &cone));
626: PetscCall(DMPlexGetConeOrientation(dm, p, &ornt));
627: coneSizes[s] = coneSize;
628: for (cp = 0; cp < coneSize; ++cp, ++c) {
629: cones[c] = gpoint[cone[cp]] < 0 ? -(gpoint[cone[cp]] + 1) : gpoint[cone[cp]];
630: orientations[c] = ornt[cp];
631: }
632: ++s;
633: }
634: }
635: PetscCheck(s == nPoints, PETSC_COMM_SELF, PETSC_ERR_LIB, "Total number of points %" PetscInt_FMT " != %" PetscInt_FMT, s, nPoints);
636: PetscCheck(c == conesSize, PETSC_COMM_SELF, PETSC_ERR_LIB, "Total number of cone points %" PetscInt_FMT " != %" PetscInt_FMT, c, conesSize);
637: PetscCall(ISCreateGeneral(comm, nPoints, coneSizes, PETSC_OWN_POINTER, &coneSizesIS));
638: PetscCall(ISCreateGeneral(comm, conesSize, cones, PETSC_OWN_POINTER, &conesIS));
639: PetscCall(ISCreateGeneral(comm, conesSize, orientations, PETSC_OWN_POINTER, &orientationsIS));
640: PetscCall(PetscObjectSetName((PetscObject)coneSizesIS, coneSizesName));
641: PetscCall(PetscObjectSetName((PetscObject)conesIS, conesName));
642: PetscCall(PetscObjectSetName((PetscObject)orientationsIS, orientationsName));
643: PetscCall(ISView(coneSizesIS, viewer));
644: PetscCall(ISView(conesIS, viewer));
645: PetscCall(ISView(orientationsIS, viewer));
646: PetscCall(ISDestroy(&coneSizesIS));
647: PetscCall(ISDestroy(&conesIS));
648: PetscCall(ISDestroy(&orientationsIS));
649: if (pointsName) {
650: IS pointsIS;
651: PetscInt *points;
653: PetscCall(PetscMalloc1(nPoints, &points));
654: for (p = pStart, c = 0, s = 0; p < pEnd; ++p) {
655: if (gpoint[p] >= 0) {
656: points[s] = gpoint[p];
657: ++s;
658: }
659: }
660: PetscCall(ISCreateGeneral(comm, nPoints, points, PETSC_OWN_POINTER, &pointsIS));
661: PetscCall(PetscObjectSetName((PetscObject)pointsIS, pointsName));
662: PetscCall(ISView(pointsIS, viewer));
663: PetscCall(ISDestroy(&pointsIS));
664: }
665: PetscCall(ISRestoreIndices(globalPointNumbers, &gpoint));
666: PetscFunctionReturn(PETSC_SUCCESS);
667: }
669: static PetscErrorCode DMPlexTopologyView_HDF5_Legacy_Private(DM dm, IS globalPointNumbers, PetscViewer viewer)
670: {
671: const char *pointsName, *coneSizesName, *conesName, *orientationsName;
672: PetscInt pStart, pEnd, dim;
674: PetscFunctionBegin;
675: pointsName = "order";
676: coneSizesName = "cones";
677: conesName = "cells";
678: orientationsName = "orientation";
679: PetscCall(DMPlexGetChart(dm, &pStart, &pEnd));
680: PetscCall(DMPlexTopologyView_HDF5_Inner_Private(dm, globalPointNumbers, viewer, pStart, pEnd, pointsName, coneSizesName, conesName, orientationsName));
681: PetscCall(DMGetDimension(dm, &dim));
682: PetscCall(PetscViewerHDF5WriteAttribute(viewer, conesName, "cell_dim", PETSC_INT, (void *)&dim));
683: PetscFunctionReturn(PETSC_SUCCESS);
684: }
686: //TODO get this numbering right away without needing this function
687: /* Renumber global point numbers so that they are 0-based per stratum */
688: static PetscErrorCode RenumberGlobalPointNumbersPerStratum_Private(DM dm, IS globalPointNumbers, IS *newGlobalPointNumbers, IS *strataPermutation)
689: {
690: PetscInt d, depth, p, n;
691: PetscInt *offsets;
692: const PetscInt *gpn;
693: PetscInt *ngpn;
694: MPI_Comm comm;
696: PetscFunctionBegin;
697: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
698: PetscCall(ISGetLocalSize(globalPointNumbers, &n));
699: PetscCall(ISGetIndices(globalPointNumbers, &gpn));
700: PetscCall(PetscMalloc1(n, &ngpn));
701: PetscCall(DMPlexGetDepth(dm, &depth));
702: PetscCall(PetscMalloc1(depth + 1, &offsets));
703: for (d = 0; d <= depth; d++) {
704: PetscInt pStart, pEnd;
706: PetscCall(DMPlexGetDepthStratum(dm, d, &pStart, &pEnd));
707: offsets[d] = PETSC_MAX_INT;
708: for (p = pStart; p < pEnd; p++) {
709: if (gpn[p] >= 0 && gpn[p] < offsets[d]) offsets[d] = gpn[p];
710: }
711: }
712: PetscCall(MPIU_Allreduce(MPI_IN_PLACE, offsets, depth + 1, MPIU_INT, MPI_MIN, comm));
713: for (d = 0; d <= depth; d++) {
714: PetscInt pStart, pEnd;
716: PetscCall(DMPlexGetDepthStratum(dm, d, &pStart, &pEnd));
717: for (p = pStart; p < pEnd; p++) ngpn[p] = gpn[p] - PetscSign(gpn[p]) * offsets[d];
718: }
719: PetscCall(ISRestoreIndices(globalPointNumbers, &gpn));
720: PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)globalPointNumbers), n, ngpn, PETSC_OWN_POINTER, newGlobalPointNumbers));
721: {
722: PetscInt *perm;
724: PetscCall(PetscMalloc1(depth + 1, &perm));
725: for (d = 0; d <= depth; d++) perm[d] = d;
726: PetscCall(PetscSortIntWithPermutation(depth + 1, offsets, perm));
727: PetscCall(ISCreateGeneral(PETSC_COMM_SELF, depth + 1, perm, PETSC_OWN_POINTER, strataPermutation));
728: }
729: PetscCall(PetscFree(offsets));
730: PetscFunctionReturn(PETSC_SUCCESS);
731: }
733: static PetscErrorCode DMPlexTopologyView_HDF5_Private(DM dm, IS globalPointNumbers, PetscViewer viewer)
734: {
735: IS globalPointNumbers0, strataPermutation;
736: const char *coneSizesName, *conesName, *orientationsName;
737: PetscInt depth, d;
738: MPI_Comm comm;
740: PetscFunctionBegin;
741: coneSizesName = "cone_sizes";
742: conesName = "cones";
743: orientationsName = "orientations";
744: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
745: PetscCall(DMPlexGetDepth(dm, &depth));
746: {
747: PetscInt dim;
749: PetscCall(DMGetDimension(dm, &dim));
750: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "cell_dim", PETSC_INT, &dim));
751: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "depth", PETSC_INT, &depth));
752: }
754: PetscCall(RenumberGlobalPointNumbersPerStratum_Private(dm, globalPointNumbers, &globalPointNumbers0, &strataPermutation));
755: /* TODO dirty trick to save serial IS using the same parallel viewer */
756: {
757: IS spOnComm;
758: PetscInt n = 0, N;
759: const PetscInt *idx = NULL;
760: const PetscInt *old;
761: PetscMPIInt rank;
763: PetscCallMPI(MPI_Comm_rank(comm, &rank));
764: PetscCall(ISGetLocalSize(strataPermutation, &N));
765: PetscCall(ISGetIndices(strataPermutation, &old));
766: if (!rank) {
767: n = N;
768: idx = old;
769: }
770: PetscCall(ISCreateGeneral(comm, n, idx, PETSC_COPY_VALUES, &spOnComm));
771: PetscCall(ISRestoreIndices(strataPermutation, &old));
772: PetscCall(ISDestroy(&strataPermutation));
773: strataPermutation = spOnComm;
774: }
775: PetscCall(PetscObjectSetName((PetscObject)strataPermutation, "permutation"));
776: PetscCall(ISView(strataPermutation, viewer));
777: PetscCall(PetscViewerHDF5PushGroup(viewer, "strata"));
778: for (d = 0; d <= depth; d++) {
779: PetscInt pStart, pEnd;
780: char group[128];
782: PetscCall(PetscSNPrintf(group, sizeof(group), "%" PetscInt_FMT, d));
783: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
784: PetscCall(DMPlexGetDepthStratum(dm, d, &pStart, &pEnd));
785: PetscCall(DMPlexTopologyView_HDF5_Inner_Private(dm, globalPointNumbers0, viewer, pStart, pEnd, NULL, coneSizesName, conesName, orientationsName));
786: PetscCall(PetscViewerHDF5PopGroup(viewer));
787: }
788: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* strata */
789: PetscCall(ISDestroy(&globalPointNumbers0));
790: PetscCall(ISDestroy(&strataPermutation));
791: PetscFunctionReturn(PETSC_SUCCESS);
792: }
794: PetscErrorCode DMPlexTopologyView_HDF5_Internal(DM dm, IS globalPointNumbers, PetscViewer viewer)
795: {
796: DMPlexStorageVersion version;
797: const char *topologydm_name;
798: char group[PETSC_MAX_PATH_LEN];
800: PetscFunctionBegin;
801: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
802: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
803: if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
804: PetscCall(PetscSNPrintf(group, sizeof(group), "topologies/%s", topologydm_name));
805: } else {
806: PetscCall(PetscStrncpy(group, "/", sizeof(group)));
807: }
808: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
810: PetscCall(PetscViewerHDF5PushGroup(viewer, "topology"));
811: if (version->major < 3) {
812: PetscCall(DMPlexTopologyView_HDF5_Legacy_Private(dm, globalPointNumbers, viewer));
813: } else {
814: /* since DMPlexStorageVersion 3.0.0 */
815: PetscCall(DMPlexTopologyView_HDF5_Private(dm, globalPointNumbers, viewer));
816: }
817: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* "topology" */
819: if (DMPlexStorageVersionGE(version, 2, 1, 0)) {
820: const char *distribution_name;
822: PetscCall(DMPlexDistributionGetName(dm, &distribution_name));
823: PetscCall(PetscViewerHDF5PushGroup(viewer, "distributions"));
824: PetscCall(PetscViewerHDF5WriteGroup(viewer, NULL));
825: PetscCall(PetscViewerHDF5PushGroup(viewer, distribution_name));
826: PetscCall(DMPlexDistributionView_HDF5_Private(dm, globalPointNumbers, viewer));
827: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* distribution_name */
828: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* "distributions" */
829: }
831: PetscCall(PetscViewerHDF5PopGroup(viewer));
832: PetscFunctionReturn(PETSC_SUCCESS);
833: }
835: static PetscErrorCode CreateConesIS_Private(DM dm, PetscInt cStart, PetscInt cEnd, IS globalCellNumbers, PetscInt *numCorners, IS *cellIS)
836: {
837: PetscSF sfPoint;
838: DMLabel cutLabel, cutVertexLabel = NULL;
839: IS globalVertexNumbers, cutvertices = NULL;
840: const PetscInt *gcell, *gvertex, *cutverts = NULL;
841: PetscInt *vertices;
842: PetscInt conesSize = 0;
843: PetscInt dim, numCornersLocal = 0, cell, vStart, vEnd, vExtra = 0, v;
845: PetscFunctionBegin;
846: *numCorners = 0;
847: PetscCall(DMGetDimension(dm, &dim));
848: PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
849: PetscCall(ISGetIndices(globalCellNumbers, &gcell));
851: for (cell = cStart; cell < cEnd; ++cell) {
852: PetscInt *closure = NULL;
853: PetscInt closureSize, v, Nc = 0;
855: if (gcell[cell] < 0) continue;
856: PetscCall(DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure));
857: for (v = 0; v < closureSize * 2; v += 2) {
858: if ((closure[v] >= vStart) && (closure[v] < vEnd)) ++Nc;
859: }
860: PetscCall(DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure));
861: conesSize += Nc;
862: if (!numCornersLocal) numCornersLocal = Nc;
863: else if (numCornersLocal != Nc) numCornersLocal = 1;
864: }
865: PetscCall(MPIU_Allreduce(&numCornersLocal, numCorners, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)dm)));
866: PetscCheck(!numCornersLocal || !(numCornersLocal != *numCorners || *numCorners == 0), PETSC_COMM_SELF, PETSC_ERR_SUP, "Visualization topology currently only supports identical cell shapes");
867: /* Handle periodic cuts by identifying vertices which should be duplicated */
868: PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel));
869: PetscCall(DMPlexCreateCutVertexLabel_Private(dm, cutLabel, &cutVertexLabel));
870: if (cutVertexLabel) PetscCall(DMLabelGetStratumIS(cutVertexLabel, 1, &cutvertices));
871: if (cutvertices) {
872: PetscCall(ISGetIndices(cutvertices, &cutverts));
873: PetscCall(ISGetLocalSize(cutvertices, &vExtra));
874: }
875: PetscCall(DMGetPointSF(dm, &sfPoint));
876: if (cutLabel) {
877: const PetscInt *ilocal;
878: const PetscSFNode *iremote;
879: PetscInt nroots, nleaves;
881: PetscCall(PetscSFGetGraph(sfPoint, &nroots, &nleaves, &ilocal, &iremote));
882: if (nleaves < 0) {
883: PetscCall(PetscObjectReference((PetscObject)sfPoint));
884: } else {
885: PetscCall(PetscSFCreate(PetscObjectComm((PetscObject)sfPoint), &sfPoint));
886: PetscCall(PetscSFSetGraph(sfPoint, nroots + vExtra, nleaves, (PetscInt *)ilocal, PETSC_COPY_VALUES, (PetscSFNode *)iremote, PETSC_COPY_VALUES));
887: }
888: } else {
889: PetscCall(PetscObjectReference((PetscObject)sfPoint));
890: }
891: /* Number all vertices */
892: PetscCall(DMPlexCreateNumbering_Plex(dm, vStart, vEnd + vExtra, 0, NULL, sfPoint, &globalVertexNumbers));
893: PetscCall(PetscSFDestroy(&sfPoint));
894: /* Create cones */
895: PetscCall(ISGetIndices(globalVertexNumbers, &gvertex));
896: PetscCall(PetscMalloc1(conesSize, &vertices));
897: for (cell = cStart, v = 0; cell < cEnd; ++cell) {
898: PetscInt *closure = NULL;
899: PetscInt closureSize, Nc = 0, p, value = -1;
900: PetscBool replace;
902: if (gcell[cell] < 0) continue;
903: if (cutLabel) PetscCall(DMLabelGetValue(cutLabel, cell, &value));
904: replace = (value == 2) ? PETSC_TRUE : PETSC_FALSE;
905: PetscCall(DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure));
906: for (p = 0; p < closureSize * 2; p += 2) {
907: if ((closure[p] >= vStart) && (closure[p] < vEnd)) closure[Nc++] = closure[p];
908: }
909: PetscCall(DMPlexReorderCell(dm, cell, closure));
910: for (p = 0; p < Nc; ++p) {
911: PetscInt nv, gv = gvertex[closure[p] - vStart];
913: if (replace) {
914: PetscCall(PetscFindInt(closure[p], vExtra, cutverts, &nv));
915: if (nv >= 0) gv = gvertex[vEnd - vStart + nv];
916: }
917: vertices[v++] = gv < 0 ? -(gv + 1) : gv;
918: }
919: PetscCall(DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure));
920: }
921: PetscCall(ISRestoreIndices(globalVertexNumbers, &gvertex));
922: PetscCall(ISDestroy(&globalVertexNumbers));
923: PetscCall(ISRestoreIndices(globalCellNumbers, &gcell));
924: if (cutvertices) PetscCall(ISRestoreIndices(cutvertices, &cutverts));
925: PetscCall(ISDestroy(&cutvertices));
926: PetscCall(DMLabelDestroy(&cutVertexLabel));
927: PetscCheck(v == conesSize, PETSC_COMM_SELF, PETSC_ERR_LIB, "Total number of cell vertices %" PetscInt_FMT " != %" PetscInt_FMT, v, conesSize);
928: PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)dm), conesSize, vertices, PETSC_OWN_POINTER, cellIS));
929: PetscCall(PetscLayoutSetBlockSize((*cellIS)->map, *numCorners));
930: PetscCall(PetscObjectSetName((PetscObject)*cellIS, "cells"));
931: PetscFunctionReturn(PETSC_SUCCESS);
932: }
934: static PetscErrorCode DMPlexTopologyView_HDF5_XDMF_Private(DM dm, IS globalCellNumbers, PetscViewer viewer)
935: {
936: DM cdm;
937: DMLabel depthLabel, ctLabel;
938: IS cellIS;
939: PetscInt dim, depth, cellHeight, c, n = 0;
941: PetscFunctionBegin;
942: PetscCall(PetscViewerHDF5PushGroup(viewer, "/viz"));
943: PetscCall(PetscViewerHDF5WriteGroup(viewer, NULL));
945: PetscCall(PetscViewerHDF5PopGroup(viewer));
946: PetscCall(DMGetDimension(dm, &dim));
947: PetscCall(DMPlexGetDepth(dm, &depth));
948: PetscCall(DMGetCoordinateDM(dm, &cdm));
949: PetscCall(DMPlexGetVTKCellHeight(dm, &cellHeight));
950: PetscCall(DMPlexGetDepthLabel(dm, &depthLabel));
951: PetscCall(DMPlexGetCellTypeLabel(dm, &ctLabel));
952: for (c = 0; c < DM_NUM_POLYTOPES; ++c) {
953: const DMPolytopeType ict = (DMPolytopeType)c;
954: PetscInt pStart, pEnd, dep, numCorners;
955: PetscBool output = PETSC_FALSE, doOutput;
957: if (ict == DM_POLYTOPE_FV_GHOST) continue;
958: PetscCall(DMLabelGetStratumBounds(ctLabel, ict, &pStart, &pEnd));
959: if (pStart >= 0) {
960: PetscCall(DMLabelGetValue(depthLabel, pStart, &dep));
961: if (dep == depth - cellHeight) output = PETSC_TRUE;
962: }
963: PetscCall(MPIU_Allreduce(&output, &doOutput, 1, MPIU_BOOL, MPI_LOR, PetscObjectComm((PetscObject)dm)));
964: if (!doOutput) continue;
965: PetscCall(CreateConesIS_Private(dm, pStart, pEnd, globalCellNumbers, &numCorners, &cellIS));
966: if (!n) {
967: PetscCall(PetscViewerHDF5PushGroup(viewer, "/viz/topology"));
968: } else {
969: char group[PETSC_MAX_PATH_LEN];
971: PetscCall(PetscSNPrintf(group, PETSC_MAX_PATH_LEN, "/viz/topology_%" PetscInt_FMT, n));
972: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
973: }
974: PetscCall(ISView(cellIS, viewer));
975: PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)cellIS, "cell_corners", PETSC_INT, (void *)&numCorners));
976: PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)cellIS, "cell_dim", PETSC_INT, (void *)&dim));
977: PetscCall(ISDestroy(&cellIS));
978: PetscCall(PetscViewerHDF5PopGroup(viewer));
979: ++n;
980: }
981: PetscFunctionReturn(PETSC_SUCCESS);
982: }
984: static PetscErrorCode DMPlexCoordinatesView_HDF5_Legacy_Private(DM dm, PetscViewer viewer)
985: {
986: DM cdm;
987: Vec coordinates, newcoords;
988: PetscReal lengthScale;
989: PetscInt m, M, bs;
991: PetscFunctionBegin;
992: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
993: PetscCall(DMGetCoordinateDM(dm, &cdm));
994: PetscCall(DMGetCoordinates(dm, &coordinates));
995: PetscCall(VecCreate(PetscObjectComm((PetscObject)coordinates), &newcoords));
996: PetscCall(PetscObjectSetName((PetscObject)newcoords, "vertices"));
997: PetscCall(VecGetSize(coordinates, &M));
998: PetscCall(VecGetLocalSize(coordinates, &m));
999: PetscCall(VecSetSizes(newcoords, m, M));
1000: PetscCall(VecGetBlockSize(coordinates, &bs));
1001: PetscCall(VecSetBlockSize(newcoords, bs));
1002: PetscCall(VecSetType(newcoords, VECSTANDARD));
1003: PetscCall(VecCopy(coordinates, newcoords));
1004: PetscCall(VecScale(newcoords, lengthScale));
1005: /* Did not use DMGetGlobalVector() in order to bypass default group assignment */
1006: PetscCall(PetscViewerHDF5PushGroup(viewer, "/geometry"));
1007: PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_NATIVE));
1008: PetscCall(VecView(newcoords, viewer));
1009: PetscCall(PetscViewerPopFormat(viewer));
1010: PetscCall(PetscViewerHDF5PopGroup(viewer));
1011: PetscCall(VecDestroy(&newcoords));
1012: PetscFunctionReturn(PETSC_SUCCESS);
1013: }
1015: PetscErrorCode DMPlexCoordinatesView_HDF5_Internal(DM dm, PetscViewer viewer)
1016: {
1017: DM cdm;
1018: Vec coords, newcoords;
1019: PetscInt m, M, bs;
1020: PetscReal lengthScale;
1021: const char *topologydm_name, *coordinatedm_name, *coordinates_name;
1023: PetscFunctionBegin;
1024: {
1025: PetscViewerFormat format;
1026: DMPlexStorageVersion version;
1028: PetscCall(PetscViewerGetFormat(viewer, &format));
1029: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
1030: if (!DMPlexStorageVersionGE(version, 2, 0, 0) || format == PETSC_VIEWER_HDF5_XDMF || format == PETSC_VIEWER_HDF5_VIZ) {
1031: PetscCall(DMPlexCoordinatesView_HDF5_Legacy_Private(dm, viewer));
1032: PetscFunctionReturn(PETSC_SUCCESS);
1033: }
1034: }
1035: /* since 2.0.0 */
1036: PetscCall(DMGetCoordinateDM(dm, &cdm));
1037: PetscCall(DMGetCoordinates(dm, &coords));
1038: PetscCall(PetscObjectGetName((PetscObject)cdm, &coordinatedm_name));
1039: PetscCall(PetscObjectGetName((PetscObject)coords, &coordinates_name));
1040: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
1041: PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
1042: PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
1043: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "coordinateDMName", PETSC_STRING, coordinatedm_name));
1044: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "coordinatesName", PETSC_STRING, coordinates_name));
1045: PetscCall(PetscViewerHDF5PopGroup(viewer));
1046: PetscCall(PetscViewerHDF5PopGroup(viewer));
1047: PetscCall(DMPlexSectionView(dm, viewer, cdm));
1048: PetscCall(VecCreate(PetscObjectComm((PetscObject)coords), &newcoords));
1049: PetscCall(PetscObjectSetName((PetscObject)newcoords, coordinates_name));
1050: PetscCall(VecGetSize(coords, &M));
1051: PetscCall(VecGetLocalSize(coords, &m));
1052: PetscCall(VecSetSizes(newcoords, m, M));
1053: PetscCall(VecGetBlockSize(coords, &bs));
1054: PetscCall(VecSetBlockSize(newcoords, bs));
1055: PetscCall(VecSetType(newcoords, VECSTANDARD));
1056: PetscCall(VecCopy(coords, newcoords));
1057: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
1058: PetscCall(VecScale(newcoords, lengthScale));
1059: PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_NATIVE));
1060: PetscCall(DMPlexGlobalVectorView(dm, viewer, cdm, newcoords));
1061: PetscCall(PetscViewerPopFormat(viewer));
1062: PetscCall(VecDestroy(&newcoords));
1063: PetscFunctionReturn(PETSC_SUCCESS);
1064: }
1066: static PetscErrorCode DMPlexCoordinatesView_HDF5_XDMF_Private(DM dm, PetscViewer viewer)
1067: {
1068: DM cdm;
1069: Vec coordinatesLocal, newcoords;
1070: PetscSection cSection, cGlobalSection;
1071: PetscScalar *coords, *ncoords;
1072: DMLabel cutLabel, cutVertexLabel = NULL;
1073: const PetscReal *L;
1074: PetscReal lengthScale;
1075: PetscInt vStart, vEnd, v, bs, N, coordSize, dof, off, d;
1076: PetscBool localized, embedded;
1078: PetscFunctionBegin;
1079: PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
1080: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
1081: PetscCall(DMGetCoordinatesLocal(dm, &coordinatesLocal));
1082: PetscCall(VecGetBlockSize(coordinatesLocal, &bs));
1083: PetscCall(DMGetCoordinatesLocalized(dm, &localized));
1084: if (localized == PETSC_FALSE) PetscFunctionReturn(PETSC_SUCCESS);
1085: PetscCall(DMGetPeriodicity(dm, NULL, NULL, &L));
1086: PetscCall(DMGetCoordinateDM(dm, &cdm));
1087: PetscCall(DMGetLocalSection(cdm, &cSection));
1088: PetscCall(DMGetGlobalSection(cdm, &cGlobalSection));
1089: PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel));
1090: N = 0;
1092: PetscCall(DMPlexCreateCutVertexLabel_Private(dm, cutLabel, &cutVertexLabel));
1093: PetscCall(VecCreate(PetscObjectComm((PetscObject)dm), &newcoords));
1094: PetscCall(PetscSectionGetDof(cSection, vStart, &dof));
1095: PetscCall(PetscPrintf(PETSC_COMM_SELF, "DOF: %" PetscInt_FMT "\n", dof));
1096: embedded = (PetscBool)(L && dof == 2 && !cutLabel);
1097: if (cutVertexLabel) {
1098: PetscCall(DMLabelGetStratumSize(cutVertexLabel, 1, &v));
1099: N += dof * v;
1100: }
1101: for (v = vStart; v < vEnd; ++v) {
1102: PetscCall(PetscSectionGetDof(cGlobalSection, v, &dof));
1103: if (dof < 0) continue;
1104: if (embedded) N += dof + 1;
1105: else N += dof;
1106: }
1107: if (embedded) PetscCall(VecSetBlockSize(newcoords, bs + 1));
1108: else PetscCall(VecSetBlockSize(newcoords, bs));
1109: PetscCall(VecSetSizes(newcoords, N, PETSC_DETERMINE));
1110: PetscCall(VecSetType(newcoords, VECSTANDARD));
1111: PetscCall(VecGetArray(coordinatesLocal, &coords));
1112: PetscCall(VecGetArray(newcoords, &ncoords));
1113: coordSize = 0;
1114: for (v = vStart; v < vEnd; ++v) {
1115: PetscCall(PetscSectionGetDof(cGlobalSection, v, &dof));
1116: PetscCall(PetscSectionGetOffset(cSection, v, &off));
1117: if (dof < 0) continue;
1118: if (embedded) {
1119: if (L && (L[0] > 0.0) && (L[1] > 0.0)) {
1120: PetscReal theta, phi, r, R;
1121: /* XY-periodic */
1122: /* Suppose its an y-z circle, then
1123: \hat r = (0, cos(th), sin(th)) \hat x = (1, 0, 0)
1124: and the circle in that plane is
1125: \hat r cos(phi) + \hat x sin(phi) */
1126: theta = 2.0 * PETSC_PI * PetscRealPart(coords[off + 1]) / L[1];
1127: phi = 2.0 * PETSC_PI * PetscRealPart(coords[off + 0]) / L[0];
1128: r = L[0] / (2.0 * PETSC_PI * 2.0 * L[1]);
1129: R = L[1] / (2.0 * PETSC_PI);
1130: ncoords[coordSize++] = PetscSinReal(phi) * r;
1131: ncoords[coordSize++] = -PetscCosReal(theta) * (R + r * PetscCosReal(phi));
1132: ncoords[coordSize++] = PetscSinReal(theta) * (R + r * PetscCosReal(phi));
1133: } else if (L && (L[0] > 0.0)) {
1134: /* X-periodic */
1135: ncoords[coordSize++] = -PetscCosReal(2.0 * PETSC_PI * PetscRealPart(coords[off + 0]) / L[0]) * (L[0] / (2.0 * PETSC_PI));
1136: ncoords[coordSize++] = coords[off + 1];
1137: ncoords[coordSize++] = PetscSinReal(2.0 * PETSC_PI * PetscRealPart(coords[off + 0]) / L[0]) * (L[0] / (2.0 * PETSC_PI));
1138: } else if (L && (L[1] > 0.0)) {
1139: /* Y-periodic */
1140: ncoords[coordSize++] = coords[off + 0];
1141: ncoords[coordSize++] = PetscSinReal(2.0 * PETSC_PI * PetscRealPart(coords[off + 1]) / L[1]) * (L[1] / (2.0 * PETSC_PI));
1142: ncoords[coordSize++] = -PetscCosReal(2.0 * PETSC_PI * PetscRealPart(coords[off + 1]) / L[1]) * (L[1] / (2.0 * PETSC_PI));
1143: #if 0
1144: } else if ((bd[0] == DM_BOUNDARY_TWIST)) {
1145: PetscReal phi, r, R;
1146: /* Mobius strip */
1147: /* Suppose its an x-z circle, then
1148: \hat r = (-cos(phi), 0, sin(phi)) \hat y = (0, 1, 0)
1149: and in that plane we rotate by pi as we go around the circle
1150: \hat r cos(phi/2) + \hat y sin(phi/2) */
1151: phi = 2.0*PETSC_PI*PetscRealPart(coords[off+0])/L[0];
1152: R = L[0];
1153: r = PetscRealPart(coords[off+1]) - L[1]/2.0;
1154: ncoords[coordSize++] = -PetscCosReal(phi) * (R + r * PetscCosReal(phi/2.0));
1155: ncoords[coordSize++] = PetscSinReal(phi/2.0) * r;
1156: ncoords[coordSize++] = PetscSinReal(phi) * (R + r * PetscCosReal(phi/2.0));
1157: #endif
1158: } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Cannot handle periodicity in this domain");
1159: } else {
1160: for (d = 0; d < dof; ++d, ++coordSize) ncoords[coordSize] = coords[off + d];
1161: }
1162: }
1163: if (cutVertexLabel) {
1164: IS vertices;
1165: const PetscInt *verts;
1166: PetscInt n;
1168: PetscCall(DMLabelGetStratumIS(cutVertexLabel, 1, &vertices));
1169: if (vertices) {
1170: PetscCall(ISGetIndices(vertices, &verts));
1171: PetscCall(ISGetLocalSize(vertices, &n));
1172: for (v = 0; v < n; ++v) {
1173: PetscCall(PetscSectionGetDof(cSection, verts[v], &dof));
1174: PetscCall(PetscSectionGetOffset(cSection, verts[v], &off));
1175: for (d = 0; d < dof; ++d) ncoords[coordSize++] = coords[off + d] + ((L[d] > 0.) ? L[d] : 0.0);
1176: }
1177: PetscCall(ISRestoreIndices(vertices, &verts));
1178: PetscCall(ISDestroy(&vertices));
1179: }
1180: }
1181: PetscCheck(coordSize == N, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatched sizes: %" PetscInt_FMT " != %" PetscInt_FMT, coordSize, N);
1182: PetscCall(DMLabelDestroy(&cutVertexLabel));
1183: PetscCall(VecRestoreArray(coordinatesLocal, &coords));
1184: PetscCall(VecRestoreArray(newcoords, &ncoords));
1185: PetscCall(PetscObjectSetName((PetscObject)newcoords, "vertices"));
1186: PetscCall(VecScale(newcoords, lengthScale));
1187: PetscCall(PetscViewerHDF5PushGroup(viewer, "/viz"));
1188: PetscCall(PetscViewerHDF5WriteGroup(viewer, NULL));
1189: PetscCall(PetscViewerHDF5PopGroup(viewer));
1190: PetscCall(PetscViewerHDF5PushGroup(viewer, "/viz/geometry"));
1191: PetscCall(VecView(newcoords, viewer));
1192: PetscCall(PetscViewerHDF5PopGroup(viewer));
1193: PetscCall(VecDestroy(&newcoords));
1194: PetscFunctionReturn(PETSC_SUCCESS);
1195: }
1197: PetscErrorCode DMPlexLabelsView_HDF5_Internal(DM dm, IS globalPointNumbers, PetscViewer viewer)
1198: {
1199: const char *topologydm_name;
1200: const PetscInt *gpoint;
1201: PetscInt numLabels, l;
1202: DMPlexStorageVersion version;
1203: char group[PETSC_MAX_PATH_LEN];
1205: PetscFunctionBegin;
1206: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
1207: PetscCall(ISGetIndices(globalPointNumbers, &gpoint));
1208: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
1209: if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
1210: PetscCall(PetscSNPrintf(group, sizeof(group), "topologies/%s/labels", topologydm_name));
1211: } else {
1212: PetscCall(PetscStrncpy(group, "/labels", sizeof(group)));
1213: }
1214: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
1215: PetscCall(DMGetNumLabels(dm, &numLabels));
1216: for (l = 0; l < numLabels; ++l) {
1217: DMLabel label;
1218: const char *name;
1219: IS valueIS, pvalueIS, globalValueIS;
1220: const PetscInt *values;
1221: PetscInt numValues, v;
1222: PetscBool isDepth, output;
1224: PetscCall(DMGetLabelByNum(dm, l, &label));
1225: PetscCall(PetscObjectGetName((PetscObject)label, &name));
1226: PetscCall(DMGetLabelOutput(dm, name, &output));
1227: PetscCall(PetscStrncmp(name, "depth", 10, &isDepth));
1228: if (isDepth || !output) continue;
1229: PetscCall(PetscViewerHDF5PushGroup(viewer, name));
1230: PetscCall(DMLabelGetValueIS(label, &valueIS));
1231: /* Must copy to a new IS on the global comm */
1232: PetscCall(ISGetLocalSize(valueIS, &numValues));
1233: PetscCall(ISGetIndices(valueIS, &values));
1234: PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)dm), numValues, values, PETSC_COPY_VALUES, &pvalueIS));
1235: PetscCall(ISRestoreIndices(valueIS, &values));
1236: PetscCall(ISAllGather(pvalueIS, &globalValueIS));
1237: PetscCall(ISDestroy(&pvalueIS));
1238: PetscCall(ISSortRemoveDups(globalValueIS));
1239: PetscCall(ISGetLocalSize(globalValueIS, &numValues));
1240: PetscCall(ISGetIndices(globalValueIS, &values));
1241: for (v = 0; v < numValues; ++v) {
1242: IS stratumIS, globalStratumIS;
1243: const PetscInt *spoints = NULL;
1244: PetscInt *gspoints, n = 0, gn, p;
1245: const char *iname = "indices";
1246: char group[PETSC_MAX_PATH_LEN];
1248: PetscCall(PetscSNPrintf(group, sizeof(group), "%" PetscInt_FMT, values[v]));
1249: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
1250: PetscCall(DMLabelGetStratumIS(label, values[v], &stratumIS));
1252: if (stratumIS) PetscCall(ISGetLocalSize(stratumIS, &n));
1253: if (stratumIS) PetscCall(ISGetIndices(stratumIS, &spoints));
1254: for (gn = 0, p = 0; p < n; ++p)
1255: if (gpoint[spoints[p]] >= 0) ++gn;
1256: PetscCall(PetscMalloc1(gn, &gspoints));
1257: for (gn = 0, p = 0; p < n; ++p)
1258: if (gpoint[spoints[p]] >= 0) gspoints[gn++] = gpoint[spoints[p]];
1259: if (stratumIS) PetscCall(ISRestoreIndices(stratumIS, &spoints));
1260: PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)dm), gn, gspoints, PETSC_OWN_POINTER, &globalStratumIS));
1261: PetscCall(PetscObjectSetName((PetscObject)globalStratumIS, iname));
1263: PetscCall(ISView(globalStratumIS, viewer));
1264: PetscCall(ISDestroy(&globalStratumIS));
1265: PetscCall(ISDestroy(&stratumIS));
1266: PetscCall(PetscViewerHDF5PopGroup(viewer));
1267: }
1268: PetscCall(ISRestoreIndices(globalValueIS, &values));
1269: PetscCall(ISDestroy(&globalValueIS));
1270: PetscCall(ISDestroy(&valueIS));
1271: PetscCall(PetscViewerHDF5PopGroup(viewer));
1272: }
1273: PetscCall(ISRestoreIndices(globalPointNumbers, &gpoint));
1274: PetscCall(PetscViewerHDF5PopGroup(viewer));
1275: PetscFunctionReturn(PETSC_SUCCESS);
1276: }
1278: /* We only write cells and vertices. Does this screw up parallel reading? */
1279: PetscErrorCode DMPlexView_HDF5_Internal(DM dm, PetscViewer viewer)
1280: {
1281: IS globalPointNumbers;
1282: PetscViewerFormat format;
1283: PetscBool viz_geom = PETSC_FALSE, xdmf_topo = PETSC_FALSE, petsc_topo = PETSC_FALSE;
1285: PetscFunctionBegin;
1286: PetscCall(DMPlexCreatePointNumbering(dm, &globalPointNumbers));
1287: PetscCall(DMPlexCoordinatesView_HDF5_Internal(dm, viewer));
1289: PetscCall(PetscViewerGetFormat(viewer, &format));
1290: switch (format) {
1291: case PETSC_VIEWER_HDF5_VIZ:
1292: viz_geom = PETSC_TRUE;
1293: xdmf_topo = PETSC_TRUE;
1294: break;
1295: case PETSC_VIEWER_HDF5_XDMF:
1296: xdmf_topo = PETSC_TRUE;
1297: break;
1298: case PETSC_VIEWER_HDF5_PETSC:
1299: petsc_topo = PETSC_TRUE;
1300: break;
1301: case PETSC_VIEWER_DEFAULT:
1302: case PETSC_VIEWER_NATIVE:
1303: viz_geom = PETSC_TRUE;
1304: xdmf_topo = PETSC_TRUE;
1305: petsc_topo = PETSC_TRUE;
1306: break;
1307: default:
1308: SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 output.", PetscViewerFormats[format]);
1309: }
1311: if (viz_geom) PetscCall(DMPlexCoordinatesView_HDF5_XDMF_Private(dm, viewer));
1312: if (xdmf_topo) PetscCall(DMPlexTopologyView_HDF5_XDMF_Private(dm, globalPointNumbers, viewer));
1313: if (petsc_topo) {
1314: PetscCall(DMPlexTopologyView_HDF5_Internal(dm, globalPointNumbers, viewer));
1315: PetscCall(DMPlexLabelsView_HDF5_Internal(dm, globalPointNumbers, viewer));
1316: }
1318: PetscCall(ISDestroy(&globalPointNumbers));
1319: PetscFunctionReturn(PETSC_SUCCESS);
1320: }
1322: PetscErrorCode DMPlexSectionView_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm)
1323: {
1324: MPI_Comm comm;
1325: const char *topologydm_name;
1326: const char *sectiondm_name;
1327: PetscSection gsection;
1329: PetscFunctionBegin;
1330: PetscCall(PetscObjectGetComm((PetscObject)sectiondm, &comm));
1331: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
1332: PetscCall(PetscObjectGetName((PetscObject)sectiondm, §iondm_name));
1333: PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
1334: PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
1335: PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
1336: PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
1337: PetscCall(DMGetGlobalSection(sectiondm, &gsection));
1338: /* Save raw section */
1339: PetscCall(PetscSectionView(gsection, viewer));
1340: /* Save plex wrapper */
1341: {
1342: PetscInt pStart, pEnd, p, n;
1343: IS globalPointNumbers;
1344: const PetscInt *gpoints;
1345: IS orderIS;
1346: PetscInt *order;
1348: PetscCall(PetscSectionGetChart(gsection, &pStart, &pEnd));
1349: PetscCall(DMPlexCreatePointNumbering(dm, &globalPointNumbers));
1350: PetscCall(ISGetIndices(globalPointNumbers, &gpoints));
1351: for (p = pStart, n = 0; p < pEnd; ++p)
1352: if (gpoints[p] >= 0) n++;
1353: /* "order" is an array of global point numbers.
1354: When loading, it is used with topology/order array
1355: to match section points with plex topology points. */
1356: PetscCall(PetscMalloc1(n, &order));
1357: for (p = pStart, n = 0; p < pEnd; ++p)
1358: if (gpoints[p] >= 0) order[n++] = gpoints[p];
1359: PetscCall(ISRestoreIndices(globalPointNumbers, &gpoints));
1360: PetscCall(ISDestroy(&globalPointNumbers));
1361: PetscCall(ISCreateGeneral(comm, n, order, PETSC_OWN_POINTER, &orderIS));
1362: PetscCall(PetscObjectSetName((PetscObject)orderIS, "order"));
1363: PetscCall(ISView(orderIS, viewer));
1364: PetscCall(ISDestroy(&orderIS));
1365: }
1366: PetscCall(PetscViewerHDF5PopGroup(viewer));
1367: PetscCall(PetscViewerHDF5PopGroup(viewer));
1368: PetscCall(PetscViewerHDF5PopGroup(viewer));
1369: PetscCall(PetscViewerHDF5PopGroup(viewer));
1370: PetscFunctionReturn(PETSC_SUCCESS);
1371: }
1373: PetscErrorCode DMPlexGlobalVectorView_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm, Vec vec)
1374: {
1375: const char *topologydm_name;
1376: const char *sectiondm_name;
1377: const char *vec_name;
1378: PetscInt bs;
1380: PetscFunctionBegin;
1381: /* Check consistency */
1382: {
1383: PetscSF pointsf, pointsf1;
1385: PetscCall(DMGetPointSF(dm, &pointsf));
1386: PetscCall(DMGetPointSF(sectiondm, &pointsf1));
1387: PetscCheck(pointsf1 == pointsf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatching point SFs for dm and sectiondm");
1388: }
1389: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
1390: PetscCall(PetscObjectGetName((PetscObject)sectiondm, §iondm_name));
1391: PetscCall(PetscObjectGetName((PetscObject)vec, &vec_name));
1392: PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
1393: PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
1394: PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
1395: PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
1396: PetscCall(PetscViewerHDF5PushGroup(viewer, "vecs"));
1397: PetscCall(PetscViewerHDF5PushGroup(viewer, vec_name));
1398: PetscCall(VecGetBlockSize(vec, &bs));
1399: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "blockSize", PETSC_INT, (void *)&bs));
1400: PetscCall(VecSetBlockSize(vec, 1));
1401: /* VecView(vec, viewer) would call (*vec->opt->view)(vec, viewer), but, */
1402: /* if vec was created with DMGet{Global, Local}Vector(), vec->opt->view */
1403: /* is set to VecView_Plex, which would save vec in a predefined location. */
1404: /* To save vec in where we want, we create a new Vec (temp) with */
1405: /* VecCreate(), wrap the vec data in temp, and call VecView(temp, viewer). */
1406: {
1407: Vec temp;
1408: const PetscScalar *array;
1409: PetscLayout map;
1411: PetscCall(VecCreate(PetscObjectComm((PetscObject)vec), &temp));
1412: PetscCall(PetscObjectSetName((PetscObject)temp, vec_name));
1413: PetscCall(VecGetLayout(vec, &map));
1414: PetscCall(VecSetLayout(temp, map));
1415: PetscCall(VecSetUp(temp));
1416: PetscCall(VecGetArrayRead(vec, &array));
1417: PetscCall(VecPlaceArray(temp, array));
1418: PetscCall(VecView(temp, viewer));
1419: PetscCall(VecResetArray(temp));
1420: PetscCall(VecRestoreArrayRead(vec, &array));
1421: PetscCall(VecDestroy(&temp));
1422: }
1423: PetscCall(VecSetBlockSize(vec, bs));
1424: PetscCall(PetscViewerHDF5PopGroup(viewer));
1425: PetscCall(PetscViewerHDF5PopGroup(viewer));
1426: PetscCall(PetscViewerHDF5PopGroup(viewer));
1427: PetscCall(PetscViewerHDF5PopGroup(viewer));
1428: PetscCall(PetscViewerHDF5PopGroup(viewer));
1429: PetscCall(PetscViewerHDF5PopGroup(viewer));
1430: PetscFunctionReturn(PETSC_SUCCESS);
1431: }
1433: PetscErrorCode DMPlexLocalVectorView_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm, Vec vec)
1434: {
1435: MPI_Comm comm;
1436: const char *topologydm_name;
1437: const char *sectiondm_name;
1438: const char *vec_name;
1439: PetscSection section;
1440: PetscBool includesConstraints;
1441: Vec gvec;
1442: PetscInt m, bs;
1444: PetscFunctionBegin;
1445: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
1446: /* Check consistency */
1447: {
1448: PetscSF pointsf, pointsf1;
1450: PetscCall(DMGetPointSF(dm, &pointsf));
1451: PetscCall(DMGetPointSF(sectiondm, &pointsf1));
1452: PetscCheck(pointsf1 == pointsf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatching point SFs for dm and sectiondm");
1453: }
1454: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
1455: PetscCall(PetscObjectGetName((PetscObject)sectiondm, §iondm_name));
1456: PetscCall(PetscObjectGetName((PetscObject)vec, &vec_name));
1457: PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
1458: PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
1459: PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
1460: PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
1461: PetscCall(PetscViewerHDF5PushGroup(viewer, "vecs"));
1462: PetscCall(PetscViewerHDF5PushGroup(viewer, vec_name));
1463: PetscCall(VecGetBlockSize(vec, &bs));
1464: PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "blockSize", PETSC_INT, (void *)&bs));
1465: PetscCall(VecCreate(comm, &gvec));
1466: PetscCall(PetscObjectSetName((PetscObject)gvec, vec_name));
1467: PetscCall(DMGetGlobalSection(sectiondm, §ion));
1468: PetscCall(PetscSectionGetIncludesConstraints(section, &includesConstraints));
1469: if (includesConstraints) PetscCall(PetscSectionGetStorageSize(section, &m));
1470: else PetscCall(PetscSectionGetConstrainedStorageSize(section, &m));
1471: PetscCall(VecSetSizes(gvec, m, PETSC_DECIDE));
1472: PetscCall(VecSetUp(gvec));
1473: PetscCall(DMLocalToGlobalBegin(sectiondm, vec, INSERT_VALUES, gvec));
1474: PetscCall(DMLocalToGlobalEnd(sectiondm, vec, INSERT_VALUES, gvec));
1475: PetscCall(VecView(gvec, viewer));
1476: PetscCall(VecDestroy(&gvec));
1477: PetscCall(PetscViewerHDF5PopGroup(viewer));
1478: PetscCall(PetscViewerHDF5PopGroup(viewer));
1479: PetscCall(PetscViewerHDF5PopGroup(viewer));
1480: PetscCall(PetscViewerHDF5PopGroup(viewer));
1481: PetscCall(PetscViewerHDF5PopGroup(viewer));
1482: PetscCall(PetscViewerHDF5PopGroup(viewer));
1483: PetscFunctionReturn(PETSC_SUCCESS);
1484: }
1486: struct _n_LoadLabelsCtx {
1487: MPI_Comm comm;
1488: PetscMPIInt rank;
1489: DM dm;
1490: PetscViewer viewer;
1491: DMLabel label;
1492: PetscSF sfXC;
1493: PetscLayout layoutX;
1494: };
1495: typedef struct _n_LoadLabelsCtx *LoadLabelsCtx;
1497: static PetscErrorCode LoadLabelsCtxCreate(DM dm, PetscViewer viewer, PetscSF sfXC, LoadLabelsCtx *ctx)
1498: {
1499: PetscFunctionBegin;
1500: PetscCall(PetscNew(ctx));
1501: PetscCall(PetscObjectReference((PetscObject)((*ctx)->dm = dm)));
1502: PetscCall(PetscObjectReference((PetscObject)((*ctx)->viewer = viewer)));
1503: PetscCall(PetscObjectGetComm((PetscObject)dm, &(*ctx)->comm));
1504: PetscCallMPI(MPI_Comm_rank((*ctx)->comm, &(*ctx)->rank));
1505: (*ctx)->sfXC = sfXC;
1506: if (sfXC) {
1507: PetscInt nX;
1509: PetscCall(PetscObjectReference((PetscObject)sfXC));
1510: PetscCall(PetscSFGetGraph(sfXC, &nX, NULL, NULL, NULL));
1511: PetscCall(PetscLayoutCreateFromSizes((*ctx)->comm, nX, PETSC_DECIDE, 1, &(*ctx)->layoutX));
1512: }
1513: PetscFunctionReturn(PETSC_SUCCESS);
1514: }
1516: static PetscErrorCode LoadLabelsCtxDestroy(LoadLabelsCtx *ctx)
1517: {
1518: PetscFunctionBegin;
1519: if (!*ctx) PetscFunctionReturn(PETSC_SUCCESS);
1520: PetscCall(DMDestroy(&(*ctx)->dm));
1521: PetscCall(PetscViewerDestroy(&(*ctx)->viewer));
1522: PetscCall(PetscSFDestroy(&(*ctx)->sfXC));
1523: PetscCall(PetscLayoutDestroy(&(*ctx)->layoutX));
1524: PetscCall(PetscFree(*ctx));
1525: PetscFunctionReturn(PETSC_SUCCESS);
1526: }
1528: /*
1529: A: on-disk points
1530: X: global points [0, NX)
1531: C: distributed plex points
1532: */
1533: static herr_t ReadLabelStratumHDF5_Distribute_Private(IS stratumIS, LoadLabelsCtx ctx, IS *newStratumIS)
1534: {
1535: MPI_Comm comm = ctx->comm;
1536: PetscSF sfXC = ctx->sfXC;
1537: PetscLayout layoutX = ctx->layoutX;
1538: PetscSF sfXA;
1539: const PetscInt *A_points;
1540: PetscInt nX, nC;
1541: PetscInt n;
1543: PetscFunctionBegin;
1544: PetscCall(PetscSFGetGraph(sfXC, &nX, &nC, NULL, NULL));
1545: PetscCall(ISGetLocalSize(stratumIS, &n));
1546: PetscCall(ISGetIndices(stratumIS, &A_points));
1547: PetscCall(PetscSFCreate(comm, &sfXA));
1548: PetscCall(PetscSFSetGraphLayout(sfXA, layoutX, n, NULL, PETSC_USE_POINTER, A_points));
1549: PetscCall(ISCreate(comm, newStratumIS));
1550: PetscCall(ISSetType(*newStratumIS, ISGENERAL));
1551: {
1552: PetscInt i;
1553: PetscBool *A_mask, *X_mask, *C_mask;
1555: PetscCall(PetscCalloc3(n, &A_mask, nX, &X_mask, nC, &C_mask));
1556: for (i = 0; i < n; i++) A_mask[i] = PETSC_TRUE;
1557: PetscCall(PetscSFReduceBegin(sfXA, MPIU_BOOL, A_mask, X_mask, MPI_REPLACE));
1558: PetscCall(PetscSFReduceEnd(sfXA, MPIU_BOOL, A_mask, X_mask, MPI_REPLACE));
1559: PetscCall(PetscSFBcastBegin(sfXC, MPIU_BOOL, X_mask, C_mask, MPI_LOR));
1560: PetscCall(PetscSFBcastEnd(sfXC, MPIU_BOOL, X_mask, C_mask, MPI_LOR));
1561: PetscCall(ISGeneralSetIndicesFromMask(*newStratumIS, 0, nC, C_mask));
1562: PetscCall(PetscFree3(A_mask, X_mask, C_mask));
1563: }
1564: PetscCall(PetscSFDestroy(&sfXA));
1565: PetscCall(ISRestoreIndices(stratumIS, &A_points));
1566: PetscFunctionReturn(PETSC_SUCCESS);
1567: }
1569: static herr_t ReadLabelStratumHDF5_Static(hid_t g_id, const char *vname, const H5L_info_t *info, void *op_data)
1570: {
1571: LoadLabelsCtx ctx = (LoadLabelsCtx)op_data;
1572: PetscViewer viewer = ctx->viewer;
1573: DMLabel label = ctx->label;
1574: MPI_Comm comm = ctx->comm;
1575: IS stratumIS;
1576: const PetscInt *ind;
1577: PetscInt value, N, i;
1579: PetscCall(PetscOptionsStringToInt(vname, &value));
1580: PetscCall(ISCreate(comm, &stratumIS));
1581: PetscCall(PetscObjectSetName((PetscObject)stratumIS, "indices"));
1582: PetscCall(PetscViewerHDF5PushGroup(viewer, vname)); /* labels/<lname>/<vname> */
1584: if (!ctx->sfXC) {
1585: /* Force serial load */
1586: PetscCall(PetscViewerHDF5ReadSizes(viewer, "indices", NULL, &N));
1587: PetscCall(PetscLayoutSetLocalSize(stratumIS->map, !ctx->rank ? N : 0));
1588: PetscCall(PetscLayoutSetSize(stratumIS->map, N));
1589: }
1590: PetscCall(ISLoad(stratumIS, viewer));
1592: if (ctx->sfXC) {
1593: IS newStratumIS;
1595: PetscCallHDF5(ReadLabelStratumHDF5_Distribute_Private, (stratumIS, ctx, &newStratumIS));
1596: PetscCall(ISDestroy(&stratumIS));
1597: stratumIS = newStratumIS;
1598: }
1600: PetscCall(PetscViewerHDF5PopGroup(viewer));
1601: PetscCall(ISGetLocalSize(stratumIS, &N));
1602: PetscCall(ISGetIndices(stratumIS, &ind));
1603: for (i = 0; i < N; ++i) PetscCall(DMLabelSetValue(label, ind[i], value));
1604: PetscCall(ISRestoreIndices(stratumIS, &ind));
1605: PetscCall(ISDestroy(&stratumIS));
1606: return 0;
1607: }
1609: /* TODO: Fix this code, it is returning PETSc error codes when it should be translating them to herr_t codes */
1610: static herr_t ReadLabelHDF5_Static(hid_t g_id, const char *lname, const H5L_info_t *info, void *op_data)
1611: {
1612: LoadLabelsCtx ctx = (LoadLabelsCtx)op_data;
1613: DM dm = ctx->dm;
1614: hsize_t idx = 0;
1615: PetscErrorCode ierr;
1616: PetscBool flg;
1617: herr_t err;
1619: PetscCall(DMHasLabel(dm, lname, &flg));
1620: if (flg) PetscCall(DMRemoveLabel(dm, lname, NULL));
1621: ierr = DMCreateLabel(dm, lname);
1622: if (ierr) return (herr_t)ierr;
1623: ierr = DMGetLabel(dm, lname, &ctx->label);
1624: if (ierr) return (herr_t)ierr;
1625: ierr = PetscViewerHDF5PushGroup(ctx->viewer, lname);
1626: if (ierr) return (herr_t)ierr;
1627: /* Iterate over the label's strata */
1628: PetscCallHDF5Return(err, H5Literate_by_name, (g_id, lname, H5_INDEX_NAME, H5_ITER_NATIVE, &idx, ReadLabelStratumHDF5_Static, op_data, 0));
1629: ierr = PetscViewerHDF5PopGroup(ctx->viewer);
1630: if (ierr) return (herr_t)ierr;
1631: return err;
1632: }
1634: PetscErrorCode DMPlexLabelsLoad_HDF5_Internal(DM dm, PetscViewer viewer, PetscSF sfXC)
1635: {
1636: const char *topologydm_name;
1637: LoadLabelsCtx ctx;
1638: hsize_t idx = 0;
1639: char group[PETSC_MAX_PATH_LEN];
1640: DMPlexStorageVersion version;
1641: PetscBool distributed, hasGroup;
1643: PetscFunctionBegin;
1644: PetscCall(DMPlexIsDistributed(dm, &distributed));
1645: if (distributed) PetscCheck(sfXC, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_NULL, "PetscSF must be given for parallel load");
1646: PetscCall(LoadLabelsCtxCreate(dm, viewer, sfXC, &ctx));
1647: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
1648: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionReading(viewer, &version));
1649: if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
1650: PetscCall(PetscSNPrintf(group, sizeof(group), "topologies/%s/labels", topologydm_name));
1651: } else {
1652: PetscCall(PetscStrncpy(group, "labels", sizeof(group)));
1653: }
1654: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
1655: PetscCall(PetscViewerHDF5HasGroup(viewer, NULL, &hasGroup));
1656: if (hasGroup) {
1657: hid_t fileId, groupId;
1659: PetscCall(PetscViewerHDF5OpenGroup(viewer, NULL, &fileId, &groupId));
1660: /* Iterate over labels */
1661: PetscCallHDF5(H5Literate, (groupId, H5_INDEX_NAME, H5_ITER_NATIVE, &idx, ReadLabelHDF5_Static, ctx));
1662: PetscCallHDF5(H5Gclose, (groupId));
1663: }
1664: PetscCall(PetscViewerHDF5PopGroup(viewer));
1665: PetscCall(LoadLabelsCtxDestroy(&ctx));
1666: PetscFunctionReturn(PETSC_SUCCESS);
1667: }
1669: static PetscErrorCode DMPlexDistributionLoad_HDF5_Private(DM dm, PetscViewer viewer, PetscSF sf, PetscSF *distsf, DM *distdm)
1670: {
1671: MPI_Comm comm;
1672: PetscMPIInt size, rank;
1673: PetscInt dist_size;
1674: const char *distribution_name;
1675: PetscInt p, lsize;
1676: IS chartSizesIS, ownersIS, gpointsIS;
1677: const PetscInt *chartSize, *owners, *gpoints;
1678: PetscLayout layout;
1679: PetscBool has;
1681: PetscFunctionBegin;
1682: *distsf = NULL;
1683: *distdm = NULL;
1684: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
1685: PetscCallMPI(MPI_Comm_size(comm, &size));
1686: PetscCallMPI(MPI_Comm_rank(comm, &rank));
1687: PetscCall(DMPlexDistributionGetName(dm, &distribution_name));
1688: if (!distribution_name) PetscFunctionReturn(PETSC_SUCCESS);
1689: PetscCall(PetscLogEventBegin(DMPLEX_DistributionLoad, viewer, 0, 0, 0));
1690: PetscCall(PetscViewerHDF5HasGroup(viewer, NULL, &has));
1691: if (!has) {
1692: char *full_group;
1694: PetscCall(PetscViewerHDF5GetGroup(viewer, NULL, &full_group));
1695: PetscCheck(has, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Distribution %s cannot be found: HDF5 group %s not found in file", distribution_name, full_group);
1696: }
1697: PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "comm_size", PETSC_INT, NULL, (void *)&dist_size));
1698: PetscCheck(dist_size == (PetscInt)size, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Mismatching comm sizes: comm size of this session (%d) != comm size used for %s (%" PetscInt_FMT ")", size, distribution_name, dist_size);
1699: PetscCall(ISCreate(comm, &chartSizesIS));
1700: PetscCall(PetscObjectSetName((PetscObject)chartSizesIS, "chart_sizes"));
1701: PetscCall(ISCreate(comm, &ownersIS));
1702: PetscCall(PetscObjectSetName((PetscObject)ownersIS, "owners"));
1703: PetscCall(ISCreate(comm, &gpointsIS));
1704: PetscCall(PetscObjectSetName((PetscObject)gpointsIS, "global_point_numbers"));
1705: PetscCall(PetscLayoutSetLocalSize(chartSizesIS->map, 1));
1706: PetscCall(ISLoad(chartSizesIS, viewer));
1707: PetscCall(ISGetIndices(chartSizesIS, &chartSize));
1708: PetscCall(PetscLayoutSetLocalSize(ownersIS->map, *chartSize));
1709: PetscCall(PetscLayoutSetLocalSize(gpointsIS->map, *chartSize));
1710: PetscCall(ISLoad(ownersIS, viewer));
1711: PetscCall(ISLoad(gpointsIS, viewer));
1712: PetscCall(ISGetIndices(ownersIS, &owners));
1713: PetscCall(ISGetIndices(gpointsIS, &gpoints));
1714: PetscCall(PetscSFCreate(comm, distsf));
1715: PetscCall(PetscSFSetFromOptions(*distsf));
1716: PetscCall(PetscLayoutCreate(comm, &layout));
1717: PetscCall(PetscSFGetGraph(sf, &lsize, NULL, NULL, NULL));
1718: PetscCall(PetscLayoutSetLocalSize(layout, lsize));
1719: PetscCall(PetscLayoutSetBlockSize(layout, 1));
1720: PetscCall(PetscLayoutSetUp(layout));
1721: PetscCall(PetscSFSetGraphLayout(*distsf, layout, *chartSize, NULL, PETSC_OWN_POINTER, gpoints));
1722: PetscCall(PetscLayoutDestroy(&layout));
1723: /* Migrate DM */
1724: {
1725: PetscInt pStart, pEnd;
1726: PetscSFNode *buffer0, *buffer1, *buffer2;
1728: PetscCall(DMPlexGetChart(dm, &pStart, &pEnd));
1729: PetscCall(PetscMalloc2(pEnd - pStart, &buffer0, lsize, &buffer1));
1730: PetscCall(PetscMalloc1(*chartSize, &buffer2));
1731: {
1732: PetscSF workPointSF;
1733: PetscInt workNroots, workNleaves;
1734: const PetscInt *workIlocal;
1735: const PetscSFNode *workIremote;
1737: for (p = pStart; p < pEnd; ++p) {
1738: buffer0[p - pStart].rank = rank;
1739: buffer0[p - pStart].index = p - pStart;
1740: }
1741: PetscCall(DMGetPointSF(dm, &workPointSF));
1742: PetscCall(PetscSFGetGraph(workPointSF, &workNroots, &workNleaves, &workIlocal, &workIremote));
1743: for (p = 0; p < workNleaves; ++p) {
1744: PetscInt workIlocalp = (workIlocal ? workIlocal[p] : p);
1746: buffer0[workIlocalp].rank = -1;
1747: }
1748: }
1749: for (p = 0; p < lsize; ++p) buffer1[p].rank = -1;
1750: for (p = 0; p < *chartSize; ++p) buffer2[p].rank = -1;
1751: PetscCall(PetscSFReduceBegin(sf, MPIU_2INT, buffer0, buffer1, MPI_MAXLOC));
1752: PetscCall(PetscSFReduceEnd(sf, MPIU_2INT, buffer0, buffer1, MPI_MAXLOC));
1753: PetscCall(PetscSFBcastBegin(*distsf, MPIU_2INT, buffer1, buffer2, MPI_REPLACE));
1754: PetscCall(PetscSFBcastEnd(*distsf, MPIU_2INT, buffer1, buffer2, MPI_REPLACE));
1755: if (PetscDefined(USE_DEBUG)) {
1756: for (p = 0; p < *chartSize; ++p) {
1757: PetscCheck(buffer2[p].rank >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Found negative root rank %" PetscInt_FMT " at local point %" PetscInt_FMT " on rank %d when making migrationSF", buffer2[p].rank, p, rank);
1758: }
1759: }
1760: PetscCall(PetscFree2(buffer0, buffer1));
1761: PetscCall(DMCreate(comm, distdm));
1762: PetscCall(DMSetType(*distdm, DMPLEX));
1763: PetscCall(PetscObjectSetName((PetscObject)(*distdm), ((PetscObject)dm)->name));
1764: PetscCall(DMPlexDistributionSetName(*distdm, distribution_name));
1765: {
1766: PetscSF migrationSF;
1768: PetscCall(PetscSFCreate(comm, &migrationSF));
1769: PetscCall(PetscSFSetFromOptions(migrationSF));
1770: PetscCall(PetscSFSetGraph(migrationSF, pEnd - pStart, *chartSize, NULL, PETSC_OWN_POINTER, buffer2, PETSC_OWN_POINTER));
1771: PetscCall(PetscSFSetUp(migrationSF));
1772: PetscCall(DMPlexMigrate(dm, migrationSF, *distdm));
1773: PetscCall(PetscSFDestroy(&migrationSF));
1774: }
1775: }
1776: /* Set pointSF */
1777: {
1778: PetscSF pointSF;
1779: PetscInt *ilocal, nleaves, q;
1780: PetscSFNode *iremote, *buffer0, *buffer1;
1782: PetscCall(PetscMalloc2(*chartSize, &buffer0, lsize, &buffer1));
1783: for (p = 0, nleaves = 0; p < *chartSize; ++p) {
1784: if (owners[p] == rank) {
1785: buffer0[p].rank = rank;
1786: } else {
1787: buffer0[p].rank = -1;
1788: nleaves++;
1789: }
1790: buffer0[p].index = p;
1791: }
1792: for (p = 0; p < lsize; ++p) buffer1[p].rank = -1;
1793: PetscCall(PetscSFReduceBegin(*distsf, MPIU_2INT, buffer0, buffer1, MPI_MAXLOC));
1794: PetscCall(PetscSFReduceEnd(*distsf, MPIU_2INT, buffer0, buffer1, MPI_MAXLOC));
1795: for (p = 0; p < *chartSize; ++p) buffer0[p].rank = -1;
1796: PetscCall(PetscSFBcastBegin(*distsf, MPIU_2INT, buffer1, buffer0, MPI_REPLACE));
1797: PetscCall(PetscSFBcastEnd(*distsf, MPIU_2INT, buffer1, buffer0, MPI_REPLACE));
1798: if (PetscDefined(USE_DEBUG)) {
1799: for (p = 0; p < *chartSize; ++p) PetscCheck(buffer0[p].rank >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Found negative root rank %" PetscInt_FMT " at local point %" PetscInt_FMT " on rank %d when making pointSF", buffer0[p].rank, p, rank);
1800: }
1801: PetscCall(PetscMalloc1(nleaves, &ilocal));
1802: PetscCall(PetscMalloc1(nleaves, &iremote));
1803: for (p = 0, q = 0; p < *chartSize; ++p) {
1804: if (buffer0[p].rank != rank) {
1805: ilocal[q] = p;
1806: iremote[q].rank = buffer0[p].rank;
1807: iremote[q].index = buffer0[p].index;
1808: q++;
1809: }
1810: }
1811: PetscCheck(q == nleaves, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatching leaf sizes: %" PetscInt_FMT " != %" PetscInt_FMT, q, nleaves);
1812: PetscCall(PetscFree2(buffer0, buffer1));
1813: PetscCall(PetscSFCreate(comm, &pointSF));
1814: PetscCall(PetscSFSetFromOptions(pointSF));
1815: PetscCall(PetscSFSetGraph(pointSF, *chartSize, nleaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER));
1816: PetscCall(DMSetPointSF(*distdm, pointSF));
1817: {
1818: DM cdm;
1820: PetscCall(DMGetCoordinateDM(*distdm, &cdm));
1821: PetscCall(DMSetPointSF(cdm, pointSF));
1822: }
1823: PetscCall(PetscSFDestroy(&pointSF));
1824: }
1825: PetscCall(ISRestoreIndices(chartSizesIS, &chartSize));
1826: PetscCall(ISRestoreIndices(ownersIS, &owners));
1827: PetscCall(ISRestoreIndices(gpointsIS, &gpoints));
1828: PetscCall(ISDestroy(&chartSizesIS));
1829: PetscCall(ISDestroy(&ownersIS));
1830: PetscCall(ISDestroy(&gpointsIS));
1831: /* Record that overlap has been manually created. */
1832: /* This is to pass `DMPlexCheckPointSF()`, which checks that */
1833: /* pointSF does not contain cells in the leaves if overlap = 0. */
1834: PetscCall(DMPlexSetOverlap_Plex(*distdm, NULL, DMPLEX_OVERLAP_MANUAL));
1835: PetscCall(DMPlexDistributeSetDefault(*distdm, PETSC_FALSE));
1836: PetscCall(DMPlexReorderSetDefault(*distdm, DMPLEX_REORDER_DEFAULT_FALSE));
1837: PetscCall(PetscLogEventEnd(DMPLEX_DistributionLoad, viewer, 0, 0, 0));
1838: PetscFunctionReturn(PETSC_SUCCESS);
1839: }
1841: static PetscErrorCode DMPlexTopologyLoad_HDF5_Legacy_Private(DM dm, PetscViewer viewer, PetscSF *sf)
1842: {
1843: MPI_Comm comm;
1844: const char *pointsName, *coneSizesName, *conesName, *orientationsName;
1845: IS pointsIS, coneSizesIS, conesIS, orientationsIS;
1846: const PetscInt *points, *coneSizes, *cones, *orientations;
1847: PetscInt *cone, *ornt;
1848: PetscInt dim, N, Np, pEnd, p, q, maxConeSize = 0, c;
1849: PetscMPIInt size, rank;
1851: PetscFunctionBegin;
1852: pointsName = "order";
1853: coneSizesName = "cones";
1854: conesName = "cells";
1855: orientationsName = "orientation";
1856: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
1857: PetscCallMPI(MPI_Comm_size(comm, &size));
1858: PetscCallMPI(MPI_Comm_rank(comm, &rank));
1859: PetscCall(ISCreate(comm, &pointsIS));
1860: PetscCall(PetscObjectSetName((PetscObject)pointsIS, pointsName));
1861: PetscCall(ISCreate(comm, &coneSizesIS));
1862: PetscCall(PetscObjectSetName((PetscObject)coneSizesIS, coneSizesName));
1863: PetscCall(ISCreate(comm, &conesIS));
1864: PetscCall(PetscObjectSetName((PetscObject)conesIS, conesName));
1865: PetscCall(ISCreate(comm, &orientationsIS));
1866: PetscCall(PetscObjectSetName((PetscObject)orientationsIS, orientationsName));
1867: PetscCall(PetscViewerHDF5ReadObjectAttribute(viewer, (PetscObject)conesIS, "cell_dim", PETSC_INT, NULL, &dim));
1868: PetscCall(DMSetDimension(dm, dim));
1869: {
1870: /* Force serial load */
1871: PetscCall(PetscViewerHDF5ReadSizes(viewer, pointsName, NULL, &Np));
1872: PetscCall(PetscLayoutSetLocalSize(pointsIS->map, rank == 0 ? Np : 0));
1873: PetscCall(PetscLayoutSetSize(pointsIS->map, Np));
1874: pEnd = rank == 0 ? Np : 0;
1875: PetscCall(PetscViewerHDF5ReadSizes(viewer, coneSizesName, NULL, &Np));
1876: PetscCall(PetscLayoutSetLocalSize(coneSizesIS->map, rank == 0 ? Np : 0));
1877: PetscCall(PetscLayoutSetSize(coneSizesIS->map, Np));
1878: PetscCall(PetscViewerHDF5ReadSizes(viewer, conesName, NULL, &N));
1879: PetscCall(PetscLayoutSetLocalSize(conesIS->map, rank == 0 ? N : 0));
1880: PetscCall(PetscLayoutSetSize(conesIS->map, N));
1881: PetscCall(PetscViewerHDF5ReadSizes(viewer, orientationsName, NULL, &N));
1882: PetscCall(PetscLayoutSetLocalSize(orientationsIS->map, rank == 0 ? N : 0));
1883: PetscCall(PetscLayoutSetSize(orientationsIS->map, N));
1884: }
1885: PetscCall(ISLoad(pointsIS, viewer));
1886: PetscCall(ISLoad(coneSizesIS, viewer));
1887: PetscCall(ISLoad(conesIS, viewer));
1888: PetscCall(ISLoad(orientationsIS, viewer));
1889: /* Create Plex */
1890: PetscCall(DMPlexSetChart(dm, 0, pEnd));
1891: PetscCall(ISGetIndices(pointsIS, &points));
1892: PetscCall(ISGetIndices(coneSizesIS, &coneSizes));
1893: for (p = 0; p < pEnd; ++p) {
1894: PetscCall(DMPlexSetConeSize(dm, points[p], coneSizes[p]));
1895: maxConeSize = PetscMax(maxConeSize, coneSizes[p]);
1896: }
1897: PetscCall(DMSetUp(dm));
1898: PetscCall(ISGetIndices(conesIS, &cones));
1899: PetscCall(ISGetIndices(orientationsIS, &orientations));
1900: PetscCall(PetscMalloc2(maxConeSize, &cone, maxConeSize, &ornt));
1901: for (p = 0, q = 0; p < pEnd; ++p) {
1902: for (c = 0; c < coneSizes[p]; ++c, ++q) {
1903: cone[c] = cones[q];
1904: ornt[c] = orientations[q];
1905: }
1906: PetscCall(DMPlexSetCone(dm, points[p], cone));
1907: PetscCall(DMPlexSetConeOrientation(dm, points[p], ornt));
1908: }
1909: PetscCall(PetscFree2(cone, ornt));
1910: /* Create global section migration SF */
1911: if (sf) {
1912: PetscLayout layout;
1913: PetscInt *globalIndices;
1915: PetscCall(PetscMalloc1(pEnd, &globalIndices));
1916: /* plex point == globalPointNumber in this case */
1917: for (p = 0; p < pEnd; ++p) globalIndices[p] = p;
1918: PetscCall(PetscLayoutCreate(comm, &layout));
1919: PetscCall(PetscLayoutSetSize(layout, Np));
1920: PetscCall(PetscLayoutSetBlockSize(layout, 1));
1921: PetscCall(PetscLayoutSetUp(layout));
1922: PetscCall(PetscSFCreate(comm, sf));
1923: PetscCall(PetscSFSetFromOptions(*sf));
1924: PetscCall(PetscSFSetGraphLayout(*sf, layout, pEnd, NULL, PETSC_OWN_POINTER, globalIndices));
1925: PetscCall(PetscLayoutDestroy(&layout));
1926: PetscCall(PetscFree(globalIndices));
1927: }
1928: /* Clean-up */
1929: PetscCall(ISRestoreIndices(pointsIS, &points));
1930: PetscCall(ISRestoreIndices(coneSizesIS, &coneSizes));
1931: PetscCall(ISRestoreIndices(conesIS, &cones));
1932: PetscCall(ISRestoreIndices(orientationsIS, &orientations));
1933: PetscCall(ISDestroy(&pointsIS));
1934: PetscCall(ISDestroy(&coneSizesIS));
1935: PetscCall(ISDestroy(&conesIS));
1936: PetscCall(ISDestroy(&orientationsIS));
1937: /* Fill in the rest of the topology structure */
1938: PetscCall(DMPlexSymmetrize(dm));
1939: PetscCall(DMPlexStratify(dm));
1940: PetscFunctionReturn(PETSC_SUCCESS);
1941: }
1943: /* Representation of two DMPlex strata in 0-based global numbering */
1944: struct _n_PlexLayer {
1945: PetscInt d;
1946: IS conesIS, orientationsIS;
1947: PetscSection coneSizesSection;
1948: PetscLayout vertexLayout;
1949: PetscSF overlapSF, l2gSF; //TODO maybe confusing names (in DMPlex in general)
1950: PetscInt offset, conesOffset, leafOffset;
1951: };
1952: typedef struct _n_PlexLayer *PlexLayer;
1954: static PetscErrorCode PlexLayerDestroy(PlexLayer *layer)
1955: {
1956: PetscFunctionBegin;
1957: if (!*layer) PetscFunctionReturn(PETSC_SUCCESS);
1958: PetscCall(PetscSectionDestroy(&(*layer)->coneSizesSection));
1959: PetscCall(ISDestroy(&(*layer)->conesIS));
1960: PetscCall(ISDestroy(&(*layer)->orientationsIS));
1961: PetscCall(PetscSFDestroy(&(*layer)->overlapSF));
1962: PetscCall(PetscSFDestroy(&(*layer)->l2gSF));
1963: PetscCall(PetscLayoutDestroy(&(*layer)->vertexLayout));
1964: PetscCall(PetscFree(*layer));
1965: PetscFunctionReturn(PETSC_SUCCESS);
1966: }
1968: static PetscErrorCode PlexLayerCreate_Private(PlexLayer *layer)
1969: {
1970: PetscFunctionBegin;
1971: PetscCall(PetscNew(layer));
1972: (*layer)->d = -1;
1973: (*layer)->offset = -1;
1974: (*layer)->conesOffset = -1;
1975: (*layer)->leafOffset = -1;
1976: PetscFunctionReturn(PETSC_SUCCESS);
1977: }
1979: static PetscErrorCode PlexLayerLoad_Private(PlexLayer layer, PetscViewer viewer, PetscInt d, PetscLayout pointsLayout)
1980: {
1981: char path[128];
1982: MPI_Comm comm;
1983: const char *coneSizesName, *conesName, *orientationsName;
1984: IS coneSizesIS, conesIS, orientationsIS;
1985: PetscSection coneSizesSection;
1986: PetscLayout vertexLayout = NULL;
1987: PetscInt s;
1989: PetscFunctionBegin;
1990: coneSizesName = "cone_sizes";
1991: conesName = "cones";
1992: orientationsName = "orientations";
1993: PetscCall(PetscObjectGetComm((PetscObject)viewer, &comm));
1995: /* query size of next lower depth stratum (next lower dimension) */
1996: if (d > 0) {
1997: PetscInt NVertices;
1999: PetscCall(PetscSNPrintf(path, sizeof(path), "%" PetscInt_FMT "/%s", d - 1, coneSizesName));
2000: PetscCall(PetscViewerHDF5ReadSizes(viewer, path, NULL, &NVertices));
2001: PetscCall(PetscLayoutCreate(comm, &vertexLayout));
2002: PetscCall(PetscLayoutSetSize(vertexLayout, NVertices));
2003: PetscCall(PetscLayoutSetUp(vertexLayout));
2004: }
2006: PetscCall(PetscSNPrintf(path, sizeof(path), "%" PetscInt_FMT, d));
2007: PetscCall(PetscViewerHDF5PushGroup(viewer, path));
2009: /* create coneSizesSection from stored IS coneSizes */
2010: {
2011: const PetscInt *coneSizes;
2013: PetscCall(ISCreate(comm, &coneSizesIS));
2014: PetscCall(PetscObjectSetName((PetscObject)coneSizesIS, coneSizesName));
2015: if (pointsLayout) PetscCall(ISSetLayout(coneSizesIS, pointsLayout));
2016: PetscCall(ISLoad(coneSizesIS, viewer));
2017: if (!pointsLayout) PetscCall(ISGetLayout(coneSizesIS, &pointsLayout));
2018: PetscCall(ISGetIndices(coneSizesIS, &coneSizes));
2019: PetscCall(PetscSectionCreate(comm, &coneSizesSection));
2020: //TODO different start ?
2021: PetscCall(PetscSectionSetChart(coneSizesSection, 0, pointsLayout->n));
2022: for (s = 0; s < pointsLayout->n; ++s) PetscCall(PetscSectionSetDof(coneSizesSection, s, coneSizes[s]));
2023: PetscCall(PetscSectionSetUp(coneSizesSection));
2024: PetscCall(ISRestoreIndices(coneSizesIS, &coneSizes));
2025: {
2026: PetscLayout tmp = NULL;
2028: /* We need to keep the layout until the end of function */
2029: PetscCall(PetscLayoutReference((PetscLayout)pointsLayout, &tmp));
2030: }
2031: PetscCall(ISDestroy(&coneSizesIS));
2032: }
2034: /* use value layout of coneSizesSection as layout of cones and orientations */
2035: {
2036: PetscLayout conesLayout;
2038: PetscCall(PetscSectionGetValueLayout(comm, coneSizesSection, &conesLayout));
2039: PetscCall(ISCreate(comm, &conesIS));
2040: PetscCall(ISCreate(comm, &orientationsIS));
2041: PetscCall(PetscObjectSetName((PetscObject)conesIS, conesName));
2042: PetscCall(PetscObjectSetName((PetscObject)orientationsIS, orientationsName));
2043: PetscCall(PetscLayoutDuplicate(conesLayout, &conesIS->map));
2044: PetscCall(PetscLayoutDuplicate(conesLayout, &orientationsIS->map));
2045: PetscCall(ISLoad(conesIS, viewer));
2046: PetscCall(ISLoad(orientationsIS, viewer));
2047: PetscCall(PetscLayoutDestroy(&conesLayout));
2048: }
2050: /* check assertion that layout of points is the same as point layout of coneSizesSection */
2051: {
2052: PetscLayout pointsLayout0;
2053: PetscBool flg;
2055: PetscCall(PetscSectionGetPointLayout(comm, coneSizesSection, &pointsLayout0));
2056: PetscCall(PetscLayoutCompare(pointsLayout, pointsLayout0, &flg));
2057: PetscCheck(flg, comm, PETSC_ERR_PLIB, "points layout != coneSizesSection point layout");
2058: PetscCall(PetscLayoutDestroy(&pointsLayout0));
2059: }
2060: PetscCall(PetscViewerHDF5PopGroup(viewer));
2061: PetscCall(PetscLayoutDestroy(&pointsLayout));
2063: layer->d = d;
2064: layer->conesIS = conesIS;
2065: layer->coneSizesSection = coneSizesSection;
2066: layer->orientationsIS = orientationsIS;
2067: layer->vertexLayout = vertexLayout;
2068: PetscFunctionReturn(PETSC_SUCCESS);
2069: }
2071: static PetscErrorCode PlexLayerDistribute_Private(PlexLayer layer, PetscSF cellLocalToGlobalSF)
2072: {
2073: IS newConesIS, newOrientationsIS;
2074: PetscSection newConeSizesSection;
2075: MPI_Comm comm;
2077: PetscFunctionBegin;
2078: PetscCall(PetscObjectGetComm((PetscObject)cellLocalToGlobalSF, &comm));
2079: PetscCall(PetscSectionCreate(comm, &newConeSizesSection));
2080: //TODO rename to something like ISDistribute() with optional PetscSection argument
2081: PetscCall(DMPlexDistributeFieldIS(NULL, cellLocalToGlobalSF, layer->coneSizesSection, layer->conesIS, newConeSizesSection, &newConesIS));
2082: PetscCall(DMPlexDistributeFieldIS(NULL, cellLocalToGlobalSF, layer->coneSizesSection, layer->orientationsIS, newConeSizesSection, &newOrientationsIS));
2084: PetscCall(PetscObjectSetName((PetscObject)newConeSizesSection, ((PetscObject)layer->coneSizesSection)->name));
2085: PetscCall(PetscObjectSetName((PetscObject)newConesIS, ((PetscObject)layer->conesIS)->name));
2086: PetscCall(PetscObjectSetName((PetscObject)newOrientationsIS, ((PetscObject)layer->orientationsIS)->name));
2087: PetscCall(PetscSectionDestroy(&layer->coneSizesSection));
2088: PetscCall(ISDestroy(&layer->conesIS));
2089: PetscCall(ISDestroy(&layer->orientationsIS));
2090: layer->coneSizesSection = newConeSizesSection;
2091: layer->conesIS = newConesIS;
2092: layer->orientationsIS = newOrientationsIS;
2093: PetscFunctionReturn(PETSC_SUCCESS);
2094: }
2096: //TODO share code with DMPlexBuildFromCellListParallel()
2097: #include <petsc/private/hashseti.h>
2098: static PetscErrorCode PlexLayerCreateSFs_Private(PlexLayer layer, PetscSF *vertexOverlapSF, PetscSF *sfXC)
2099: {
2100: PetscLayout vertexLayout = layer->vertexLayout;
2101: PetscSection coneSection = layer->coneSizesSection;
2102: IS cellVertexData = layer->conesIS;
2103: IS coneOrientations = layer->orientationsIS;
2104: PetscSF vl2gSF, vOverlapSF;
2105: PetscInt *verticesAdj;
2106: PetscInt i, n, numVerticesAdj;
2107: const PetscInt *cvd, *co = NULL;
2108: MPI_Comm comm;
2110: PetscFunctionBegin;
2111: PetscCall(PetscObjectGetComm((PetscObject)coneSection, &comm));
2112: PetscCall(PetscSectionGetStorageSize(coneSection, &n));
2113: {
2114: PetscInt n0;
2116: PetscCall(ISGetLocalSize(cellVertexData, &n0));
2117: PetscCheck(n == n0, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Local size of IS cellVertexData = %" PetscInt_FMT " != %" PetscInt_FMT " = storage size of PetscSection coneSection", n0, n);
2118: PetscCall(ISGetIndices(cellVertexData, &cvd));
2119: }
2120: if (coneOrientations) {
2121: PetscInt n0;
2123: PetscCall(ISGetLocalSize(coneOrientations, &n0));
2124: PetscCheck(n == n0, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Local size of IS coneOrientations = %" PetscInt_FMT " != %" PetscInt_FMT " = storage size of PetscSection coneSection", n0, n);
2125: PetscCall(ISGetIndices(coneOrientations, &co));
2126: }
2127: /* Get/check global number of vertices */
2128: {
2129: PetscInt NVerticesInCells = PETSC_MIN_INT;
2131: /* NVerticesInCells = max(cellVertexData) + 1 */
2132: for (i = 0; i < n; i++)
2133: if (cvd[i] > NVerticesInCells) NVerticesInCells = cvd[i];
2134: ++NVerticesInCells;
2135: PetscCall(MPIU_Allreduce(MPI_IN_PLACE, &NVerticesInCells, 1, MPIU_INT, MPI_MAX, comm));
2137: if (vertexLayout->n == PETSC_DECIDE && vertexLayout->N == PETSC_DECIDE) vertexLayout->N = NVerticesInCells;
2138: else
2139: PetscCheck(vertexLayout->N == PETSC_DECIDE || vertexLayout->N >= NVerticesInCells, comm, PETSC_ERR_ARG_SIZ, "Specified global number of vertices %" PetscInt_FMT " must be greater than or equal to the number of unique vertices in the cell-vertex dataset %" PetscInt_FMT,
2140: vertexLayout->N, NVerticesInCells);
2141: PetscCall(PetscLayoutSetUp(vertexLayout));
2142: }
2143: /* Find locally unique vertices in cellVertexData */
2144: {
2145: PetscHSetI vhash;
2146: PetscInt off = 0;
2148: PetscCall(PetscHSetICreate(&vhash));
2149: for (i = 0; i < n; ++i) PetscCall(PetscHSetIAdd(vhash, cvd[i]));
2150: PetscCall(PetscHSetIGetSize(vhash, &numVerticesAdj));
2151: PetscCall(PetscMalloc1(numVerticesAdj, &verticesAdj));
2152: PetscCall(PetscHSetIGetElems(vhash, &off, verticesAdj));
2153: PetscAssert(off == numVerticesAdj, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Assertion failed: off == numVerticesAdj (%" PetscInt_FMT " != %" PetscInt_FMT ")", off, numVerticesAdj);
2154: PetscCall(PetscHSetIDestroy(&vhash));
2155: }
2156: /* We must sort vertices to preserve numbering */
2157: PetscCall(PetscSortInt(numVerticesAdj, verticesAdj));
2158: /* Connect locally unique vertices with star forest */
2159: PetscCall(PetscSFCreateByMatchingIndices(vertexLayout, numVerticesAdj, verticesAdj, NULL, 0, numVerticesAdj, verticesAdj, NULL, 0, &vl2gSF, &vOverlapSF));
2160: PetscCall(PetscObjectSetName((PetscObject)vOverlapSF, "overlapSF"));
2161: PetscCall(PetscObjectSetName((PetscObject)vl2gSF, "localToGlobalSF"));
2163: PetscCall(PetscFree(verticesAdj));
2164: *vertexOverlapSF = vOverlapSF;
2165: *sfXC = vl2gSF;
2166: PetscFunctionReturn(PETSC_SUCCESS);
2167: }
2169: static PetscErrorCode PlexLayerCreateCellSFs_Private(PlexLayer layer, PetscSF *cellOverlapSF, PetscSF *cellLocalToGlobalSF)
2170: {
2171: PetscSection coneSection = layer->coneSizesSection;
2172: PetscInt nCells;
2173: MPI_Comm comm;
2175: PetscFunctionBegin;
2176: PetscCall(PetscObjectGetComm((PetscObject)coneSection, &comm));
2177: {
2178: PetscInt cStart;
2180: PetscCall(PetscSectionGetChart(coneSection, &cStart, &nCells));
2181: PetscCheck(cStart == 0, comm, PETSC_ERR_ARG_OUTOFRANGE, "coneSection must start at 0");
2182: }
2183: /* Create overlapSF as empty SF with the right number of roots */
2184: PetscCall(PetscSFCreate(comm, cellOverlapSF));
2185: PetscCall(PetscSFSetGraph(*cellOverlapSF, nCells, 0, NULL, PETSC_USE_POINTER, NULL, PETSC_USE_POINTER));
2186: PetscCall(PetscSFSetUp(*cellOverlapSF));
2187: /* Create localToGlobalSF as identity mapping */
2188: {
2189: PetscLayout map;
2191: PetscCall(PetscLayoutCreateFromSizes(comm, nCells, PETSC_DECIDE, 1, &map));
2192: PetscCall(PetscSFCreateFromLayouts(map, map, cellLocalToGlobalSF));
2193: PetscCall(PetscSFSetUp(*cellLocalToGlobalSF));
2194: PetscCall(PetscLayoutDestroy(&map));
2195: }
2196: PetscFunctionReturn(PETSC_SUCCESS);
2197: }
2199: static PetscErrorCode DMPlexTopologyBuildFromLayers_Private(DM dm, PetscInt depth, PlexLayer *layers, IS strataPermutation)
2200: {
2201: const PetscInt *permArr;
2202: PetscInt d, nPoints;
2203: MPI_Comm comm;
2205: PetscFunctionBegin;
2206: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
2207: PetscCall(ISGetIndices(strataPermutation, &permArr));
2209: /* Count points, strata offsets and cones offsets (taking strataPermutation into account) */
2210: {
2211: PetscInt stratumOffset = 0;
2212: PetscInt conesOffset = 0;
2214: for (d = 0; d <= depth; d++) {
2215: const PetscInt e = permArr[d];
2216: const PlexLayer l = layers[e];
2217: PetscInt lo, n, size;
2219: PetscCall(PetscSectionGetChart(l->coneSizesSection, &lo, &n));
2220: PetscCall(PetscSectionGetStorageSize(l->coneSizesSection, &size));
2221: PetscCheck(lo == 0, comm, PETSC_ERR_PLIB, "starting point should be 0 in coneSizesSection %" PetscInt_FMT, d);
2222: l->offset = stratumOffset;
2223: l->conesOffset = conesOffset;
2224: stratumOffset += n;
2225: conesOffset += size;
2226: }
2227: nPoints = stratumOffset;
2228: }
2230: /* Set interval for all plex points */
2231: //TODO we should store starting point of plex
2232: PetscCall(DMPlexSetChart(dm, 0, nPoints));
2234: /* Set up plex coneSection from layer coneSections */
2235: {
2236: PetscSection coneSection;
2238: PetscCall(DMPlexGetConeSection(dm, &coneSection));
2239: for (d = 0; d <= depth; d++) {
2240: const PlexLayer l = layers[d];
2241: PetscInt n, q;
2243: PetscCall(PetscSectionGetChart(l->coneSizesSection, NULL, &n));
2244: for (q = 0; q < n; q++) {
2245: const PetscInt p = l->offset + q;
2246: PetscInt coneSize;
2248: PetscCall(PetscSectionGetDof(l->coneSizesSection, q, &coneSize));
2249: PetscCall(PetscSectionSetDof(coneSection, p, coneSize));
2250: }
2251: }
2252: }
2253: //TODO this is terrible, DMSetUp_Plex() should be DMPlexSetUpSections() or so
2254: PetscCall(DMSetUp(dm));
2256: /* Renumber cones points from layer-global numbering to plex-local numbering */
2257: {
2258: PetscInt *cones, *ornts;
2260: PetscCall(DMPlexGetCones(dm, &cones));
2261: PetscCall(DMPlexGetConeOrientations(dm, &ornts));
2262: for (d = 1; d <= depth; d++) {
2263: const PlexLayer l = layers[d];
2264: PetscInt i, lConesSize;
2265: PetscInt *lCones;
2266: const PetscInt *lOrnts;
2267: PetscInt *pCones = &cones[l->conesOffset];
2268: PetscInt *pOrnts = &ornts[l->conesOffset];
2270: PetscCall(PetscSectionGetStorageSize(l->coneSizesSection, &lConesSize));
2271: /* Get cones in local plex numbering */
2272: {
2273: ISLocalToGlobalMapping l2g;
2274: PetscLayout vertexLayout = l->vertexLayout;
2275: PetscSF vertexSF = layers[d - 1]->l2gSF; /* vertices of this layer are cells of previous layer */
2276: const PetscInt *gCones;
2277: PetscInt lConesSize0;
2279: PetscCall(ISGetLocalSize(l->conesIS, &lConesSize0));
2280: PetscCheck(lConesSize0 == lConesSize, comm, PETSC_ERR_PLIB, "layer %" PetscInt_FMT " size(conesIS) = %" PetscInt_FMT " != %" PetscInt_FMT " = storageSize(coneSizesSection)", d, lConesSize0, lConesSize);
2281: PetscCall(ISGetLocalSize(l->orientationsIS, &lConesSize0));
2282: PetscCheck(lConesSize0 == lConesSize, comm, PETSC_ERR_PLIB, "layer %" PetscInt_FMT " size(orientationsIS) = %" PetscInt_FMT " != %" PetscInt_FMT " = storageSize(coneSizesSection)", d, lConesSize0, lConesSize);
2284: PetscCall(PetscMalloc1(lConesSize, &lCones));
2285: PetscCall(ISGetIndices(l->conesIS, &gCones));
2286: PetscCall(ISLocalToGlobalMappingCreateSF(vertexSF, vertexLayout->rstart, &l2g));
2287: PetscCall(ISGlobalToLocalMappingApply(l2g, IS_GTOLM_MASK, lConesSize, gCones, &lConesSize0, lCones));
2288: PetscCheck(lConesSize0 == lConesSize, comm, PETSC_ERR_PLIB, "global to local does not cover all indices (%" PetscInt_FMT " of %" PetscInt_FMT ")", lConesSize0, lConesSize);
2289: PetscCall(ISLocalToGlobalMappingDestroy(&l2g));
2290: PetscCall(ISRestoreIndices(l->conesIS, &gCones));
2291: }
2292: PetscCall(ISGetIndices(l->orientationsIS, &lOrnts));
2293: /* Set cones, need to add stratum offset */
2294: for (i = 0; i < lConesSize; i++) {
2295: pCones[i] = lCones[i] + layers[d - 1]->offset; /* cone points of current layer are points of previous layer */
2296: pOrnts[i] = lOrnts[i];
2297: }
2298: PetscCall(PetscFree(lCones));
2299: PetscCall(ISRestoreIndices(l->orientationsIS, &lOrnts));
2300: }
2301: }
2302: PetscCall(DMPlexSymmetrize(dm));
2303: PetscCall(DMPlexStratify(dm));
2304: PetscCall(ISRestoreIndices(strataPermutation, &permArr));
2305: PetscFunctionReturn(PETSC_SUCCESS);
2306: }
2308: static PetscErrorCode PlexLayerConcatenateSFs_Private(MPI_Comm comm, PetscInt depth, PlexLayer layers[], IS strataPermutation, PetscSF *overlapSF, PetscSF *l2gSF)
2309: {
2310: PetscInt d;
2311: PetscSF *osfs, *lsfs;
2312: PetscInt *leafOffsets;
2313: const PetscInt *permArr;
2315: PetscFunctionBegin;
2316: PetscCall(ISGetIndices(strataPermutation, &permArr));
2317: PetscCall(PetscCalloc3(depth + 1, &osfs, depth + 1, &lsfs, depth + 1, &leafOffsets));
2318: for (d = 0; d <= depth; d++) {
2319: const PetscInt e = permArr[d];
2321: PetscAssert(e == layers[e]->d, PETSC_COMM_SELF, PETSC_ERR_PLIB, "assertion: e == layers[e]->d");
2322: osfs[d] = layers[e]->overlapSF;
2323: lsfs[d] = layers[e]->l2gSF;
2324: leafOffsets[d] = layers[e]->offset;
2325: }
2326: PetscCall(PetscSFConcatenate(comm, depth + 1, osfs, PETSCSF_CONCATENATE_../../../..MODE_LOCAL, leafOffsets, overlapSF));
2327: PetscCall(PetscSFConcatenate(comm, depth + 1, lsfs, PETSCSF_CONCATENATE_../../../..MODE_GLOBAL, leafOffsets, l2gSF));
2328: PetscCall(PetscFree3(osfs, lsfs, leafOffsets));
2329: PetscCall(ISRestoreIndices(strataPermutation, &permArr));
2330: PetscFunctionReturn(PETSC_SUCCESS);
2331: }
2333: static PetscErrorCode DMPlexTopologyLoad_HDF5_Private(DM dm, PetscViewer viewer, PetscSF *sfXC)
2334: {
2335: PlexLayer *layers;
2336: IS strataPermutation;
2337: PetscLayout pointsLayout;
2338: PetscInt depth;
2339: PetscInt d;
2340: MPI_Comm comm;
2342: PetscFunctionBegin;
2343: {
2344: PetscInt dim;
2346: PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "depth", PETSC_INT, NULL, &depth));
2347: PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "cell_dim", PETSC_INT, NULL, &dim));
2348: PetscCall(DMSetDimension(dm, dim));
2349: }
2350: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
2352: {
2353: IS spOnComm;
2355: PetscCall(ISCreate(comm, &spOnComm));
2356: PetscCall(PetscObjectSetName((PetscObject)spOnComm, "permutation"));
2357: PetscCall(ISLoad(spOnComm, viewer));
2358: /* have the same serial IS on every rank */
2359: PetscCall(ISAllGather(spOnComm, &strataPermutation));
2360: PetscCall(PetscObjectSetName((PetscObject)strataPermutation, ((PetscObject)spOnComm)->name));
2361: PetscCall(ISDestroy(&spOnComm));
2362: }
2364: /* Create layers, load raw data for each layer */
2365: PetscCall(PetscViewerHDF5PushGroup(viewer, "strata"));
2366: PetscCall(PetscMalloc1(depth + 1, &layers));
2367: for (d = depth, pointsLayout = NULL; d >= 0; pointsLayout = layers[d]->vertexLayout, d--) {
2368: PetscCall(PlexLayerCreate_Private(&layers[d]));
2369: PetscCall(PlexLayerLoad_Private(layers[d], viewer, d, pointsLayout));
2370: }
2371: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* strata */
2373: for (d = depth; d >= 0; d--) {
2374: /* Redistribute cells and vertices for each applicable layer */
2375: if (d < depth) PetscCall(PlexLayerDistribute_Private(layers[d], layers[d]->l2gSF));
2376: /* Create vertex overlap SF and vertex localToGlobal SF for each applicable layer */
2377: if (d > 0) PetscCall(PlexLayerCreateSFs_Private(layers[d], &layers[d - 1]->overlapSF, &layers[d - 1]->l2gSF));
2378: }
2379: /* Build trivial SFs for the cell layer as well */
2380: PetscCall(PlexLayerCreateCellSFs_Private(layers[depth], &layers[depth]->overlapSF, &layers[depth]->l2gSF));
2382: /* Build DMPlex topology from the layers */
2383: PetscCall(DMPlexTopologyBuildFromLayers_Private(dm, depth, layers, strataPermutation));
2385: /* Build overall point SF alias overlap SF */
2386: {
2387: PetscSF overlapSF;
2389: PetscCall(PlexLayerConcatenateSFs_Private(comm, depth, layers, strataPermutation, &overlapSF, sfXC));
2390: PetscCall(DMSetPointSF(dm, overlapSF));
2391: PetscCall(PetscSFDestroy(&overlapSF));
2392: }
2394: for (d = depth; d >= 0; d--) PetscCall(PlexLayerDestroy(&layers[d]));
2395: PetscCall(PetscFree(layers));
2396: PetscCall(ISDestroy(&strataPermutation));
2397: PetscFunctionReturn(PETSC_SUCCESS);
2398: }
2400: PetscErrorCode DMPlexTopologyLoad_HDF5_Internal(DM dm, PetscViewer viewer, PetscSF *sfXC)
2401: {
2402: DMPlexStorageVersion version;
2403: const char *topologydm_name;
2404: char group[PETSC_MAX_PATH_LEN];
2405: PetscSF sfwork = NULL;
2407: PetscFunctionBegin;
2408: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
2409: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionReading(viewer, &version));
2410: if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
2411: PetscCall(PetscSNPrintf(group, sizeof(group), "topologies/%s", topologydm_name));
2412: } else {
2413: PetscCall(PetscStrncpy(group, "/", sizeof(group)));
2414: }
2415: PetscCall(PetscViewerHDF5PushGroup(viewer, group));
2417: PetscCall(PetscViewerHDF5PushGroup(viewer, "topology"));
2418: if (version->major < 3) {
2419: PetscCall(DMPlexTopologyLoad_HDF5_Legacy_Private(dm, viewer, &sfwork));
2420: } else {
2421: /* since DMPlexStorageVersion 3.0.0 */
2422: PetscCall(DMPlexTopologyLoad_HDF5_Private(dm, viewer, &sfwork));
2423: }
2424: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* "topology" */
2426: if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
2427: DM distdm;
2428: PetscSF distsf;
2429: const char *distribution_name;
2430: PetscBool exists;
2432: PetscCall(DMPlexDistributionGetName(dm, &distribution_name));
2433: /* this group is guaranteed to be present since DMPlexStorageVersion 2.1.0 */
2434: PetscCall(PetscViewerHDF5PushGroup(viewer, "distributions"));
2435: PetscCall(PetscViewerHDF5HasGroup(viewer, NULL, &exists));
2436: if (exists) {
2437: PetscCall(PetscViewerHDF5PushGroup(viewer, distribution_name));
2438: PetscCall(DMPlexDistributionLoad_HDF5_Private(dm, viewer, sfwork, &distsf, &distdm));
2439: if (distdm) {
2440: PetscCall(DMPlexReplace_Internal(dm, &distdm));
2441: PetscCall(PetscSFDestroy(&sfwork));
2442: sfwork = distsf;
2443: }
2444: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* distribution_name */
2445: }
2446: PetscCall(PetscViewerHDF5PopGroup(viewer)); /* "distributions" */
2447: }
2448: if (sfXC) {
2449: *sfXC = sfwork;
2450: } else {
2451: PetscCall(PetscSFDestroy(&sfwork));
2452: }
2454: PetscCall(PetscViewerHDF5PopGroup(viewer));
2455: PetscFunctionReturn(PETSC_SUCCESS);
2456: }
2458: /* If the file is old, it not only has different path to the coordinates, but */
2459: /* does not contain coordinateDMs, so must fall back to the old implementation. */
2460: static PetscErrorCode DMPlexCoordinatesLoad_HDF5_Legacy_Private(DM dm, PetscViewer viewer)
2461: {
2462: PetscSection coordSection;
2463: Vec coordinates;
2464: PetscReal lengthScale;
2465: PetscInt spatialDim, N, numVertices, vStart, vEnd, v;
2466: PetscMPIInt rank;
2468: PetscFunctionBegin;
2469: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank));
2470: /* Read geometry */
2471: PetscCall(PetscViewerHDF5PushGroup(viewer, "/geometry"));
2472: PetscCall(VecCreate(PetscObjectComm((PetscObject)dm), &coordinates));
2473: PetscCall(PetscObjectSetName((PetscObject)coordinates, "vertices"));
2474: {
2475: /* Force serial load */
2476: PetscCall(PetscViewerHDF5ReadSizes(viewer, "vertices", &spatialDim, &N));
2477: PetscCall(VecSetSizes(coordinates, rank == 0 ? N : 0, N));
2478: PetscCall(VecSetBlockSize(coordinates, spatialDim));
2479: }
2480: PetscCall(VecLoad(coordinates, viewer));
2481: PetscCall(PetscViewerHDF5PopGroup(viewer));
2482: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
2483: PetscCall(VecScale(coordinates, 1.0 / lengthScale));
2484: PetscCall(VecGetLocalSize(coordinates, &numVertices));
2485: PetscCall(VecGetBlockSize(coordinates, &spatialDim));
2486: numVertices /= spatialDim;
2487: /* Create coordinates */
2488: PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
2489: PetscCheck(numVertices == vEnd - vStart, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of coordinates loaded %" PetscInt_FMT " does not match number of vertices %" PetscInt_FMT, numVertices, vEnd - vStart);
2490: PetscCall(DMGetCoordinateSection(dm, &coordSection));
2491: PetscCall(PetscSectionSetNumFields(coordSection, 1));
2492: PetscCall(PetscSectionSetFieldComponents(coordSection, 0, spatialDim));
2493: PetscCall(PetscSectionSetChart(coordSection, vStart, vEnd));
2494: for (v = vStart; v < vEnd; ++v) {
2495: PetscCall(PetscSectionSetDof(coordSection, v, spatialDim));
2496: PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, spatialDim));
2497: }
2498: PetscCall(PetscSectionSetUp(coordSection));
2499: PetscCall(DMSetCoordinates(dm, coordinates));
2500: PetscCall(VecDestroy(&coordinates));
2501: PetscFunctionReturn(PETSC_SUCCESS);
2502: }
2504: PetscErrorCode DMPlexCoordinatesLoad_HDF5_Internal(DM dm, PetscViewer viewer, PetscSF sfXC)
2505: {
2506: DMPlexStorageVersion version;
2507: DM cdm;
2508: Vec coords;
2509: PetscInt blockSize;
2510: PetscReal lengthScale;
2511: PetscSF lsf;
2512: const char *topologydm_name;
2513: char *coordinatedm_name, *coordinates_name;
2515: PetscFunctionBegin;
2516: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionReading(viewer, &version));
2517: if (!DMPlexStorageVersionGE(version, 2, 0, 0)) {
2518: PetscCall(DMPlexCoordinatesLoad_HDF5_Legacy_Private(dm, viewer));
2519: PetscFunctionReturn(PETSC_SUCCESS);
2520: }
2521: /* else: since DMPlexStorageVersion 2.0.0 */
2522: PetscCheck(sfXC, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_NULL, "PetscSF must be given for parallel load");
2523: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
2524: PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
2525: PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
2526: PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "coordinateDMName", PETSC_STRING, NULL, &coordinatedm_name));
2527: PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "coordinatesName", PETSC_STRING, NULL, &coordinates_name));
2528: PetscCall(PetscViewerHDF5PopGroup(viewer));
2529: PetscCall(PetscViewerHDF5PopGroup(viewer));
2530: PetscCall(DMGetCoordinateDM(dm, &cdm));
2531: PetscCall(PetscObjectSetName((PetscObject)cdm, coordinatedm_name));
2532: PetscCall(PetscFree(coordinatedm_name));
2533: /* lsf: on-disk data -> in-memory local vector associated with cdm's local section */
2534: PetscCall(DMPlexSectionLoad(dm, viewer, cdm, sfXC, NULL, &lsf));
2535: PetscCall(DMCreateLocalVector(cdm, &coords));
2536: PetscCall(PetscObjectSetName((PetscObject)coords, coordinates_name));
2537: PetscCall(PetscFree(coordinates_name));
2538: PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_NATIVE));
2539: PetscCall(DMPlexLocalVectorLoad(dm, viewer, cdm, lsf, coords));
2540: PetscCall(PetscViewerPopFormat(viewer));
2541: PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
2542: PetscCall(VecScale(coords, 1.0 / lengthScale));
2543: PetscCall(DMSetCoordinatesLocal(dm, coords));
2544: PetscCall(VecGetBlockSize(coords, &blockSize));
2545: PetscCall(DMSetCoordinateDim(dm, blockSize));
2546: PetscCall(VecDestroy(&coords));
2547: PetscCall(PetscSFDestroy(&lsf));
2548: PetscFunctionReturn(PETSC_SUCCESS);
2549: }
2551: PetscErrorCode DMPlexLoad_HDF5_Internal(DM dm, PetscViewer viewer)
2552: {
2553: DMPlexStorageVersion version;
2555: PetscFunctionBegin;
2556: PetscCall(PetscViewerHDF5GetDMPlexStorageVersionReading(viewer, &version));
2557: if (!DMPlexStorageVersionGE(version, 2, 0, 0)) {
2558: PetscCall(DMPlexTopologyLoad_HDF5_Internal(dm, viewer, NULL));
2559: PetscCall(DMPlexLabelsLoad_HDF5_Internal(dm, viewer, NULL));
2560: PetscCall(DMPlexCoordinatesLoad_HDF5_Legacy_Private(dm, viewer));
2561: } else {
2562: PetscSF sfXC;
2564: /* since DMPlexStorageVersion 2.0.0 */
2565: PetscCall(DMPlexTopologyLoad_HDF5_Internal(dm, viewer, &sfXC));
2566: PetscCall(DMPlexLabelsLoad_HDF5_Internal(dm, viewer, sfXC));
2567: PetscCall(DMPlexCoordinatesLoad_HDF5_Internal(dm, viewer, sfXC));
2568: PetscCall(PetscSFDestroy(&sfXC));
2569: }
2570: PetscFunctionReturn(PETSC_SUCCESS);
2571: }
2573: static PetscErrorCode DMPlexSectionLoad_HDF5_Internal_CreateDataSF(PetscSection rootSection, PetscLayout layout, PetscInt globalOffsets[], PetscSection leafSection, PetscSF *sectionSF)
2574: {
2575: MPI_Comm comm;
2576: PetscInt pStart, pEnd, p, m;
2577: PetscInt *goffs, *ilocal;
2578: PetscBool rootIncludeConstraints, leafIncludeConstraints;
2580: PetscFunctionBegin;
2581: PetscCall(PetscObjectGetComm((PetscObject)leafSection, &comm));
2582: PetscCall(PetscSectionGetChart(leafSection, &pStart, &pEnd));
2583: PetscCall(PetscSectionGetIncludesConstraints(rootSection, &rootIncludeConstraints));
2584: PetscCall(PetscSectionGetIncludesConstraints(leafSection, &leafIncludeConstraints));
2585: if (rootIncludeConstraints && leafIncludeConstraints) PetscCall(PetscSectionGetStorageSize(leafSection, &m));
2586: else PetscCall(PetscSectionGetConstrainedStorageSize(leafSection, &m));
2587: PetscCall(PetscMalloc1(m, &ilocal));
2588: PetscCall(PetscMalloc1(m, &goffs));
2589: /* Currently, PetscSFDistributeSection() returns globalOffsets[] only */
2590: /* for the top-level section (not for each field), so one must have */
2591: /* rootSection->pointMajor == PETSC_TRUE. */
2592: PetscCheck(rootSection->pointMajor, PETSC_COMM_SELF, PETSC_ERR_SUP, "No support for field major ordering");
2593: /* Currently, we also assume that leafSection->pointMajor == PETSC_TRUE. */
2594: PetscCheck(leafSection->pointMajor, PETSC_COMM_SELF, PETSC_ERR_SUP, "No support for field major ordering");
2595: for (p = pStart, m = 0; p < pEnd; ++p) {
2596: PetscInt dof, cdof, i, j, off, goff;
2597: const PetscInt *cinds;
2599: PetscCall(PetscSectionGetDof(leafSection, p, &dof));
2600: if (dof < 0) continue;
2601: goff = globalOffsets[p - pStart];
2602: PetscCall(PetscSectionGetOffset(leafSection, p, &off));
2603: PetscCall(PetscSectionGetConstraintDof(leafSection, p, &cdof));
2604: PetscCall(PetscSectionGetConstraintIndices(leafSection, p, &cinds));
2605: for (i = 0, j = 0; i < dof; ++i) {
2606: PetscBool constrained = (PetscBool)(j < cdof && i == cinds[j]);
2608: if (!constrained || (leafIncludeConstraints && rootIncludeConstraints)) {
2609: ilocal[m] = off++;
2610: goffs[m++] = goff++;
2611: } else if (leafIncludeConstraints && !rootIncludeConstraints) ++off;
2612: else if (!leafIncludeConstraints && rootIncludeConstraints) ++goff;
2613: if (constrained) ++j;
2614: }
2615: }
2616: PetscCall(PetscSFCreate(comm, sectionSF));
2617: PetscCall(PetscSFSetFromOptions(*sectionSF));
2618: PetscCall(PetscSFSetGraphLayout(*sectionSF, layout, m, ilocal, PETSC_OWN_POINTER, goffs));
2619: PetscCall(PetscFree(goffs));
2620: PetscFunctionReturn(PETSC_SUCCESS);
2621: }
2623: PetscErrorCode DMPlexSectionLoad_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm, PetscSF sfXB, PetscSF *gsf, PetscSF *lsf)
2624: {
2625: MPI_Comm comm;
2626: PetscMPIInt size, rank;
2627: const char *topologydm_name;
2628: const char *sectiondm_name;
2629: PetscSection sectionA, sectionB;
2630: PetscInt nX, n, i;
2631: PetscSF sfAB;
2633: PetscFunctionBegin;
2634: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
2635: PetscCallMPI(MPI_Comm_size(comm, &size));
2636: PetscCallMPI(MPI_Comm_rank(comm, &rank));
2637: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
2638: PetscCall(PetscObjectGetName((PetscObject)sectiondm, §iondm_name));
2639: PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
2640: PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
2641: PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
2642: PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
2643: /* A: on-disk points */
2644: /* X: list of global point numbers, [0, NX) */
2645: /* B: plex points */
2646: /* Load raw section (sectionA) */
2647: PetscCall(PetscSectionCreate(comm, §ionA));
2648: PetscCall(PetscSectionLoad(sectionA, viewer));
2649: PetscCall(PetscSectionGetChart(sectionA, NULL, &n));
2650: /* Create sfAB: A -> B */
2651: #if defined(PETSC_USE_DEBUG)
2652: {
2653: PetscInt N, N1;
2655: PetscCall(PetscViewerHDF5ReadSizes(viewer, "order", NULL, &N1));
2656: PetscCall(MPIU_Allreduce(&n, &N, 1, MPIU_INT, MPI_SUM, comm));
2657: PetscCheck(N1 == N, comm, PETSC_ERR_ARG_SIZ, "Mismatching sizes: on-disk order array size (%" PetscInt_FMT ") != number of loaded section points (%" PetscInt_FMT ")", N1, N);
2658: }
2659: #endif
2660: {
2661: IS orderIS;
2662: const PetscInt *gpoints;
2663: PetscSF sfXA, sfAX;
2664: PetscLayout layout;
2665: PetscSFNode *owners, *buffer;
2666: PetscInt nleaves;
2667: PetscInt *ilocal;
2668: PetscSFNode *iremote;
2670: /* Create sfAX: A -> X */
2671: PetscCall(ISCreate(comm, &orderIS));
2672: PetscCall(PetscObjectSetName((PetscObject)orderIS, "order"));
2673: PetscCall(PetscLayoutSetLocalSize(orderIS->map, n));
2674: PetscCall(ISLoad(orderIS, viewer));
2675: PetscCall(PetscLayoutCreate(comm, &layout));
2676: PetscCall(PetscSFGetGraph(sfXB, &nX, NULL, NULL, NULL));
2677: PetscCall(PetscLayoutSetLocalSize(layout, nX));
2678: PetscCall(PetscLayoutSetBlockSize(layout, 1));
2679: PetscCall(PetscLayoutSetUp(layout));
2680: PetscCall(PetscSFCreate(comm, &sfXA));
2681: PetscCall(ISGetIndices(orderIS, &gpoints));
2682: PetscCall(PetscSFSetGraphLayout(sfXA, layout, n, NULL, PETSC_OWN_POINTER, gpoints));
2683: PetscCall(ISRestoreIndices(orderIS, &gpoints));
2684: PetscCall(ISDestroy(&orderIS));
2685: PetscCall(PetscLayoutDestroy(&layout));
2686: PetscCall(PetscMalloc1(n, &owners));
2687: PetscCall(PetscMalloc1(nX, &buffer));
2688: for (i = 0; i < n; ++i) {
2689: owners[i].rank = rank;
2690: owners[i].index = i;
2691: }
2692: for (i = 0; i < nX; ++i) {
2693: buffer[i].rank = -1;
2694: buffer[i].index = -1;
2695: }
2696: PetscCall(PetscSFReduceBegin(sfXA, MPIU_2INT, owners, buffer, MPI_MAXLOC));
2697: PetscCall(PetscSFReduceEnd(sfXA, MPIU_2INT, owners, buffer, MPI_MAXLOC));
2698: PetscCall(PetscSFDestroy(&sfXA));
2699: PetscCall(PetscFree(owners));
2700: for (i = 0, nleaves = 0; i < nX; ++i)
2701: if (buffer[i].rank >= 0) nleaves++;
2702: PetscCall(PetscMalloc1(nleaves, &ilocal));
2703: PetscCall(PetscMalloc1(nleaves, &iremote));
2704: for (i = 0, nleaves = 0; i < nX; ++i) {
2705: if (buffer[i].rank >= 0) {
2706: ilocal[nleaves] = i;
2707: iremote[nleaves].rank = buffer[i].rank;
2708: iremote[nleaves].index = buffer[i].index;
2709: nleaves++;
2710: }
2711: }
2712: PetscCall(PetscFree(buffer));
2713: PetscCall(PetscSFCreate(comm, &sfAX));
2714: PetscCall(PetscSFSetFromOptions(sfAX));
2715: PetscCall(PetscSFSetGraph(sfAX, n, nleaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER));
2716: PetscCall(PetscSFCompose(sfAX, sfXB, &sfAB));
2717: PetscCall(PetscSFDestroy(&sfAX));
2718: }
2719: PetscCall(PetscViewerHDF5PopGroup(viewer));
2720: PetscCall(PetscViewerHDF5PopGroup(viewer));
2721: PetscCall(PetscViewerHDF5PopGroup(viewer));
2722: PetscCall(PetscViewerHDF5PopGroup(viewer));
2723: /* Create plex section (sectionB) */
2724: PetscCall(DMGetLocalSection(sectiondm, §ionB));
2725: if (lsf || gsf) {
2726: PetscLayout layout;
2727: PetscInt M, m;
2728: PetscInt *offsetsA;
2729: PetscBool includesConstraintsA;
2731: PetscCall(PetscSFDistributeSection(sfAB, sectionA, &offsetsA, sectionB));
2732: PetscCall(PetscSectionGetIncludesConstraints(sectionA, &includesConstraintsA));
2733: if (includesConstraintsA) PetscCall(PetscSectionGetStorageSize(sectionA, &m));
2734: else PetscCall(PetscSectionGetConstrainedStorageSize(sectionA, &m));
2735: PetscCall(MPIU_Allreduce(&m, &M, 1, MPIU_INT, MPI_SUM, comm));
2736: PetscCall(PetscLayoutCreate(comm, &layout));
2737: PetscCall(PetscLayoutSetSize(layout, M));
2738: PetscCall(PetscLayoutSetUp(layout));
2739: if (lsf) {
2740: PetscSF lsfABdata;
2742: PetscCall(DMPlexSectionLoad_HDF5_Internal_CreateDataSF(sectionA, layout, offsetsA, sectionB, &lsfABdata));
2743: *lsf = lsfABdata;
2744: }
2745: if (gsf) {
2746: PetscSection gsectionB, gsectionB1;
2747: PetscBool includesConstraintsB;
2748: PetscSF gsfABdata, pointsf;
2750: PetscCall(DMGetGlobalSection(sectiondm, &gsectionB1));
2751: PetscCall(PetscSectionGetIncludesConstraints(gsectionB1, &includesConstraintsB));
2752: PetscCall(DMGetPointSF(sectiondm, &pointsf));
2753: PetscCall(PetscSectionCreateGlobalSection(sectionB, pointsf, includesConstraintsB, PETSC_TRUE, &gsectionB));
2754: PetscCall(DMPlexSectionLoad_HDF5_Internal_CreateDataSF(sectionA, layout, offsetsA, gsectionB, &gsfABdata));
2755: PetscCall(PetscSectionDestroy(&gsectionB));
2756: *gsf = gsfABdata;
2757: }
2758: PetscCall(PetscLayoutDestroy(&layout));
2759: PetscCall(PetscFree(offsetsA));
2760: } else {
2761: PetscCall(PetscSFDistributeSection(sfAB, sectionA, NULL, sectionB));
2762: }
2763: PetscCall(PetscSFDestroy(&sfAB));
2764: PetscCall(PetscSectionDestroy(§ionA));
2765: PetscFunctionReturn(PETSC_SUCCESS);
2766: }
2768: PetscErrorCode DMPlexVecLoad_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm, PetscSF sf, Vec vec)
2769: {
2770: MPI_Comm comm;
2771: const char *topologydm_name;
2772: const char *sectiondm_name;
2773: const char *vec_name;
2774: Vec vecA;
2775: PetscInt mA, m, bs;
2776: const PetscInt *ilocal;
2777: const PetscScalar *src;
2778: PetscScalar *dest;
2780: PetscFunctionBegin;
2781: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
2782: PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
2783: PetscCall(PetscObjectGetName((PetscObject)sectiondm, §iondm_name));
2784: PetscCall(PetscObjectGetName((PetscObject)vec, &vec_name));
2785: PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
2786: PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
2787: PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
2788: PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
2789: PetscCall(PetscViewerHDF5PushGroup(viewer, "vecs"));
2790: PetscCall(PetscViewerHDF5PushGroup(viewer, vec_name));
2791: PetscCall(VecCreate(comm, &vecA));
2792: PetscCall(PetscObjectSetName((PetscObject)vecA, vec_name));
2793: PetscCall(PetscSFGetGraph(sf, &mA, &m, &ilocal, NULL));
2794: /* Check consistency */
2795: {
2796: PetscSF pointsf, pointsf1;
2797: PetscInt m1, i, j;
2799: PetscCall(DMGetPointSF(dm, &pointsf));
2800: PetscCall(DMGetPointSF(sectiondm, &pointsf1));
2801: PetscCheck(pointsf1 == pointsf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatching point SFs for dm and sectiondm");
2802: #if defined(PETSC_USE_DEBUG)
2803: {
2804: PetscInt MA, MA1;
2806: PetscCall(MPIU_Allreduce(&mA, &MA, 1, MPIU_INT, MPI_SUM, comm));
2807: PetscCall(PetscViewerHDF5ReadSizes(viewer, vec_name, NULL, &MA1));
2808: PetscCheck(MA1 == MA, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Total SF root size (%" PetscInt_FMT ") != On-disk vector data size (%" PetscInt_FMT ")", MA, MA1);
2809: }
2810: #endif
2811: PetscCall(VecGetLocalSize(vec, &m1));
2812: PetscCheck(m1 >= m, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Target vector size (%" PetscInt_FMT ") < SF leaf size (%" PetscInt_FMT ")", m1, m);
2813: for (i = 0; i < m; ++i) {
2814: j = ilocal ? ilocal[i] : i;
2815: PetscCheck(j >= 0 && j < m1, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Leaf's %" PetscInt_FMT "-th index, %" PetscInt_FMT ", not in [%" PetscInt_FMT ", %" PetscInt_FMT ")", i, j, (PetscInt)0, m1);
2816: }
2817: }
2818: PetscCall(VecSetSizes(vecA, mA, PETSC_DECIDE));
2819: PetscCall(VecLoad(vecA, viewer));
2820: PetscCall(VecGetArrayRead(vecA, &src));
2821: PetscCall(VecGetArray(vec, &dest));
2822: PetscCall(PetscSFBcastBegin(sf, MPIU_SCALAR, src, dest, MPI_REPLACE));
2823: PetscCall(PetscSFBcastEnd(sf, MPIU_SCALAR, src, dest, MPI_REPLACE));
2824: PetscCall(VecRestoreArray(vec, &dest));
2825: PetscCall(VecRestoreArrayRead(vecA, &src));
2826: PetscCall(VecDestroy(&vecA));
2827: PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "blockSize", PETSC_INT, NULL, (void *)&bs));
2828: PetscCall(VecSetBlockSize(vec, bs));
2829: PetscCall(PetscViewerHDF5PopGroup(viewer));
2830: PetscCall(PetscViewerHDF5PopGroup(viewer));
2831: PetscCall(PetscViewerHDF5PopGroup(viewer));
2832: PetscCall(PetscViewerHDF5PopGroup(viewer));
2833: PetscCall(PetscViewerHDF5PopGroup(viewer));
2834: PetscCall(PetscViewerHDF5PopGroup(viewer));
2835: PetscFunctionReturn(PETSC_SUCCESS);
2836: }
2837: #endif