Actual source code: sectionhdf5.c

  1: #include <petsc/private/sectionimpl.h>
  2: #include <petscsf.h>
  3: #include <petscis.h>
  4: #include <petscviewerhdf5.h>
  5: #include <petsclayouthdf5.h>

  7: static PetscErrorCode PetscSectionView_HDF5_SingleField(PetscSection s, PetscViewer viewer)
  8: {
  9:   MPI_Comm  comm;
 10:   PetscInt  pStart, pEnd, p, n;
 11:   PetscBool hasConstraints, includesConstraints;
 12:   IS        dofIS, offIS, cdofIS, coffIS, cindIS;
 13:   PetscInt *dofs, *offs, *cdofs, *coffs, *cinds, dof, cdof, m, moff, i;

 15:   PetscFunctionBegin;
 16:   PetscCall(PetscObjectGetComm((PetscObject)s, &comm));
 17:   PetscCall(PetscSectionGetChart(s, &pStart, &pEnd));
 18:   hasConstraints = (s->bc) ? PETSC_TRUE : PETSC_FALSE;
 19:   PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, &hasConstraints, 1, MPIU_BOOL, MPI_LOR, comm));
 20:   for (p = pStart, n = 0, m = 0; p < pEnd; ++p) {
 21:     PetscCall(PetscSectionGetDof(s, p, &dof));
 22:     if (dof >= 0) {
 23:       if (hasConstraints) {
 24:         PetscCall(PetscSectionGetConstraintDof(s, p, &cdof));
 25:         m += cdof;
 26:       }
 27:       n++;
 28:     }
 29:   }
 30:   PetscCall(PetscMalloc1(n, &dofs));
 31:   PetscCall(PetscMalloc1(n, &offs));
 32:   if (hasConstraints) {
 33:     PetscCall(PetscMalloc1(n, &cdofs));
 34:     PetscCall(PetscMalloc1(n, &coffs));
 35:     PetscCall(PetscMalloc1(m, &cinds));
 36:   }
 37:   for (p = pStart, n = 0, m = 0; p < pEnd; ++p) {
 38:     PetscCall(PetscSectionGetDof(s, p, &dof));
 39:     if (dof >= 0) {
 40:       dofs[n] = dof;
 41:       PetscCall(PetscSectionGetOffset(s, p, &offs[n]));
 42:       if (hasConstraints) {
 43:         const PetscInt *cpinds;

 45:         PetscCall(PetscSectionGetConstraintDof(s, p, &cdof));
 46:         PetscCall(PetscSectionGetConstraintIndices(s, p, &cpinds));
 47:         cdofs[n] = cdof;
 48:         coffs[n] = m;
 49:         for (i = 0; i < cdof; ++i) cinds[m++] = cpinds[i];
 50:       }
 51:       n++;
 52:     }
 53:   }
 54:   if (hasConstraints) {
 55:     PetscCallMPI(MPI_Scan(&m, &moff, 1, MPIU_INT, MPI_SUM, comm));
 56:     moff -= m;
 57:     for (p = 0; p < n; ++p) coffs[p] += moff;
 58:   }
 59:   PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "hasConstraints", PETSC_BOOL, (void *)&hasConstraints));
 60:   PetscCall(PetscSectionGetIncludesConstraints(s, &includesConstraints));
 61:   PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "includesConstraints", PETSC_BOOL, (void *)&includesConstraints));
 62:   PetscCall(ISCreateGeneral(comm, n, dofs, PETSC_OWN_POINTER, &dofIS));
 63:   PetscCall(PetscObjectSetName((PetscObject)dofIS, "atlasDof"));
 64:   PetscCall(ISView(dofIS, viewer));
 65:   PetscCall(ISDestroy(&dofIS));
 66:   PetscCall(ISCreateGeneral(comm, n, offs, PETSC_OWN_POINTER, &offIS));
 67:   PetscCall(PetscObjectSetName((PetscObject)offIS, "atlasOff"));
 68:   PetscCall(ISView(offIS, viewer));
 69:   PetscCall(ISDestroy(&offIS));
 70:   if (hasConstraints) {
 71:     PetscCall(PetscViewerHDF5PushGroup(viewer, "bc"));
 72:     PetscCall(ISCreateGeneral(comm, n, cdofs, PETSC_OWN_POINTER, &cdofIS));
 73:     PetscCall(PetscObjectSetName((PetscObject)cdofIS, "atlasDof"));
 74:     PetscCall(ISView(cdofIS, viewer));
 75:     PetscCall(ISDestroy(&cdofIS));
 76:     PetscCall(ISCreateGeneral(comm, n, coffs, PETSC_OWN_POINTER, &coffIS));
 77:     PetscCall(PetscObjectSetName((PetscObject)coffIS, "atlasOff"));
 78:     PetscCall(ISView(coffIS, viewer));
 79:     PetscCall(ISDestroy(&coffIS));
 80:     PetscCall(PetscViewerHDF5PopGroup(viewer));
 81:     PetscCall(ISCreateGeneral(comm, m, cinds, PETSC_OWN_POINTER, &cindIS));
 82:     PetscCall(PetscObjectSetName((PetscObject)cindIS, "bcIndices"));
 83:     PetscCall(ISView(cindIS, viewer));
 84:     PetscCall(ISDestroy(&cindIS));
 85:   }
 86:   PetscFunctionReturn(PETSC_SUCCESS);
 87: }

 89: PetscErrorCode PetscSectionView_HDF5_Internal(PetscSection s, PetscViewer viewer)
 90: {
 91:   PetscInt numFields, f;

 93:   PetscFunctionBegin;
 94:   PetscCall(PetscViewerHDF5PushGroup(viewer, "section"));
 95:   PetscCall(PetscSectionGetNumFields(s, &numFields));
 96:   PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "numFields", PETSC_INT, (void *)&numFields));
 97:   PetscCall(PetscSectionView_HDF5_SingleField(s, viewer));
 98:   for (f = 0; f < numFields; ++f) {
 99:     char        fname[PETSC_MAX_PATH_LEN];
100:     const char *fieldName;
101:     PetscInt    fieldComponents, c;

103:     PetscCall(PetscSNPrintf(fname, sizeof(fname), "field%" PetscInt_FMT, f));
104:     PetscCall(PetscViewerHDF5PushGroup(viewer, fname));
105:     PetscCall(PetscSectionGetFieldName(s, f, &fieldName));
106:     PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "fieldName", PETSC_STRING, fieldName));
107:     PetscCall(PetscSectionGetFieldComponents(s, f, &fieldComponents));
108:     PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "fieldComponents", PETSC_INT, (void *)&fieldComponents));
109:     for (c = 0; c < fieldComponents; ++c) {
110:       char        cname[PETSC_MAX_PATH_LEN];
111:       const char *componentName;

113:       PetscCall(PetscSNPrintf(cname, sizeof(cname), "component%" PetscInt_FMT, c));
114:       PetscCall(PetscViewerHDF5PushGroup(viewer, cname));
115:       PetscCall(PetscSectionGetComponentName(s, f, c, &componentName));
116:       PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "componentName", PETSC_STRING, componentName));
117:       PetscCall(PetscViewerHDF5PopGroup(viewer));
118:     }
119:     PetscCall(PetscSectionView_HDF5_SingleField(s->field[f], viewer));
120:     PetscCall(PetscViewerHDF5PopGroup(viewer));
121:   }
122:   PetscCall(PetscViewerHDF5PopGroup(viewer));
123:   PetscFunctionReturn(PETSC_SUCCESS);
124: }

126: static PetscErrorCode PetscSectionLoad_HDF5_SingleField_SetConstraintIndices(PetscSection s, IS cindIS, IS coffIS)
127: {
128:   MPI_Comm        comm;
129:   PetscInt        pStart, pEnd, p, M, m, i, cdof;
130:   const PetscInt *data;
131:   PetscInt       *cinds;
132:   const PetscInt *coffs;
133:   PetscInt       *coffsets;
134:   PetscSF         sf;
135:   PetscLayout     layout;

137:   PetscFunctionBegin;
138:   PetscCall(PetscObjectGetComm((PetscObject)s, &comm));
139:   PetscCall(PetscSectionGetChart(s, &pStart, &pEnd));
140:   PetscCall(ISGetSize(cindIS, &M));
141:   PetscCall(ISGetLocalSize(cindIS, &m));
142:   PetscCall(PetscMalloc1(m, &coffsets));
143:   PetscCall(ISGetIndices(coffIS, &coffs));
144:   for (p = pStart, m = 0; p < pEnd; ++p) {
145:     PetscCall(PetscSectionGetConstraintDof(s, p, &cdof));
146:     for (i = 0; i < cdof; ++i) coffsets[m++] = coffs[p - pStart] + i;
147:   }
148:   PetscCall(ISRestoreIndices(coffIS, &coffs));
149:   PetscCall(PetscSFCreate(comm, &sf));
150:   PetscCall(PetscLayoutCreate(comm, &layout));
151:   PetscCall(PetscLayoutSetSize(layout, M));
152:   PetscCall(PetscLayoutSetLocalSize(layout, m));
153:   PetscCall(PetscLayoutSetBlockSize(layout, 1));
154:   PetscCall(PetscLayoutSetUp(layout));
155:   PetscCall(PetscSFSetGraphLayout(sf, layout, m, NULL, PETSC_OWN_POINTER, coffsets));
156:   PetscCall(PetscLayoutDestroy(&layout));
157:   PetscCall(PetscFree(coffsets));
158:   PetscCall(PetscMalloc1(m, &cinds));
159:   PetscCall(ISGetIndices(cindIS, &data));
160:   PetscCall(PetscSFBcastBegin(sf, MPIU_INT, data, cinds, MPI_REPLACE));
161:   PetscCall(PetscSFBcastEnd(sf, MPIU_INT, data, cinds, MPI_REPLACE));
162:   PetscCall(ISRestoreIndices(cindIS, &data));
163:   PetscCall(PetscSFDestroy(&sf));
164:   PetscCall(PetscSectionSetUpBC(s));
165:   for (p = pStart, m = 0; p < pEnd; ++p) {
166:     PetscCall(PetscSectionGetConstraintDof(s, p, &cdof));
167:     PetscCall(PetscSectionSetConstraintIndices(s, p, PetscSafePointerPlusOffset(cinds, m)));
168:     m += cdof;
169:   }
170:   PetscCall(PetscFree(cinds));
171:   PetscFunctionReturn(PETSC_SUCCESS);
172: }

174: static PetscErrorCode PetscSectionLoad_HDF5_SingleField(PetscSection s, PetscViewer viewer)
175: {
176:   MPI_Comm comm;
177:   PetscInt pStart, pEnd, p, N, n, M, m;
178: #if defined(PETSC_USE_DEBUG)
179:   PetscInt N1, M1;
180: #endif
181:   PetscBool       hasConstraints, includesConstraints;
182:   IS              dofIS, offIS, cdofIS, coffIS, cindIS;
183:   const PetscInt *dofs, *offs, *cdofs;
184:   PetscLayout     map;

186:   PetscFunctionBegin;
187:   PetscCall(PetscObjectGetComm((PetscObject)s, &comm));
188:   PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "includesConstraints", PETSC_BOOL, NULL, (void *)&includesConstraints));
189:   PetscCall(PetscSectionSetIncludesConstraints(s, includesConstraints));
190:   PetscCall(PetscSectionGetChart(s, &pStart, &pEnd));
191:   n = pEnd - pStart;
192: #if defined(PETSC_USE_DEBUG)
193:   PetscCallMPI(MPIU_Allreduce(&n, &N1, 1, MPIU_INT, MPI_SUM, comm));
194: #endif
195:   PetscCall(ISCreate(comm, &dofIS));
196:   PetscCall(PetscObjectSetName((PetscObject)dofIS, "atlasDof"));
197:   PetscCall(PetscViewerHDF5ReadSizes(viewer, "atlasDof", NULL, &N));
198: #if defined(PETSC_USE_DEBUG)
199:   PetscCheck(N1 == N, comm, PETSC_ERR_ARG_SIZ, "Unable to load s->atlasDof: sum of local sizes (%" PetscInt_FMT ") != global size (%" PetscInt_FMT "): local size on this process is %" PetscInt_FMT, N1, N, n);
200: #endif
201:   PetscCall(ISGetLayout(dofIS, &map));
202:   PetscCall(PetscLayoutSetSize(map, N));
203:   PetscCall(PetscLayoutSetLocalSize(map, n));
204:   PetscCall(ISLoad(dofIS, viewer));
205:   PetscCall(ISCreate(comm, &offIS));
206:   PetscCall(PetscObjectSetName((PetscObject)offIS, "atlasOff"));
207:   PetscCall(PetscViewerHDF5ReadSizes(viewer, "atlasOff", NULL, &N));
208: #if defined(PETSC_USE_DEBUG)
209:   PetscCheck(N1 == N, comm, PETSC_ERR_ARG_SIZ, "Unable to load s->atlasOff: sum of local sizes (%" PetscInt_FMT ") != global size (%" PetscInt_FMT "): local size on this process is %" PetscInt_FMT, N1, N, n);
210: #endif
211:   PetscCall(ISGetLayout(offIS, &map));
212:   PetscCall(PetscLayoutSetSize(map, N));
213:   PetscCall(PetscLayoutSetLocalSize(map, n));
214:   PetscCall(ISLoad(offIS, viewer));
215:   PetscCall(ISGetIndices(dofIS, &dofs));
216:   PetscCall(ISGetIndices(offIS, &offs));
217:   for (p = pStart, n = 0; p < pEnd; ++p, ++n) {
218:     PetscCall(PetscSectionSetDof(s, p, dofs[n]));
219:     PetscCall(PetscSectionSetOffset(s, p, offs[n]));
220:   }
221:   PetscCall(ISRestoreIndices(dofIS, &dofs));
222:   PetscCall(ISRestoreIndices(offIS, &offs));
223:   PetscCall(ISDestroy(&dofIS));
224:   PetscCall(ISDestroy(&offIS));
225:   PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "hasConstraints", PETSC_BOOL, NULL, (void *)&hasConstraints));
226:   if (hasConstraints) {
227:     PetscCall(PetscViewerHDF5PushGroup(viewer, "bc"));
228:     PetscCall(ISCreate(comm, &cdofIS));
229:     PetscCall(PetscObjectSetName((PetscObject)cdofIS, "atlasDof"));
230:     PetscCall(PetscViewerHDF5ReadSizes(viewer, "atlasDof", NULL, &N));
231: #if defined(PETSC_USE_DEBUG)
232:     PetscCheck(N1 == N, comm, PETSC_ERR_ARG_SIZ, "Unable to load s->bc->atlasDof: sum of local sizes (%" PetscInt_FMT ") != global size (%" PetscInt_FMT "): local size on this process is %" PetscInt_FMT, N1, N, n);
233: #endif
234:     PetscCall(ISGetLayout(cdofIS, &map));
235:     PetscCall(PetscLayoutSetSize(map, N));
236:     PetscCall(PetscLayoutSetLocalSize(map, n));
237:     PetscCall(ISLoad(cdofIS, viewer));
238:     PetscCall(ISGetIndices(cdofIS, &cdofs));
239:     for (p = pStart, n = 0; p < pEnd; ++p, ++n) PetscCall(PetscSectionSetConstraintDof(s, p, cdofs[n]));
240:     PetscCall(ISRestoreIndices(cdofIS, &cdofs));
241:     PetscCall(ISDestroy(&cdofIS));
242:     PetscCall(ISCreate(comm, &coffIS));
243:     PetscCall(PetscObjectSetName((PetscObject)coffIS, "atlasOff"));
244:     PetscCall(PetscViewerHDF5ReadSizes(viewer, "atlasOff", NULL, &N));
245: #if defined(PETSC_USE_DEBUG)
246:     PetscCheck(N1 == N, comm, PETSC_ERR_ARG_SIZ, "Unable to load s->bc->atlasOff: sum of local sizes (%" PetscInt_FMT ") != global size (%" PetscInt_FMT "): local size on this process is %" PetscInt_FMT, N1, N, n);
247: #endif
248:     PetscCall(ISGetLayout(coffIS, &map));
249:     PetscCall(PetscLayoutSetSize(map, N));
250:     PetscCall(PetscLayoutSetLocalSize(map, n));
251:     PetscCall(ISLoad(coffIS, viewer));
252:     PetscCall(PetscViewerHDF5PopGroup(viewer));
253:     PetscCall(ISCreate(comm, &cindIS));
254:     PetscCall(PetscObjectSetName((PetscObject)cindIS, "bcIndices"));
255:     PetscCall(PetscViewerHDF5ReadSizes(viewer, "bcIndices", NULL, &M));
256:     if (!s->bc) m = 0;
257:     else PetscCall(PetscSectionGetStorageSize(s->bc, &m));
258: #if defined(PETSC_USE_DEBUG)
259:     PetscCallMPI(MPIU_Allreduce(&m, &M1, 1, MPIU_INT, MPI_SUM, comm));
260:     PetscCheck(M1 == M, comm, PETSC_ERR_ARG_SIZ, "Unable to load s->bcIndices: sum of local sizes (%" PetscInt_FMT ") != global size (%" PetscInt_FMT "): local size on this process is %" PetscInt_FMT, M1, M, m);
261: #endif
262:     PetscCall(ISGetLayout(cindIS, &map));
263:     PetscCall(PetscLayoutSetSize(map, M));
264:     PetscCall(PetscLayoutSetLocalSize(map, m));
265:     PetscCall(ISLoad(cindIS, viewer));
266:     PetscCall(PetscSectionLoad_HDF5_SingleField_SetConstraintIndices(s, cindIS, coffIS));
267:     PetscCall(ISDestroy(&coffIS));
268:     PetscCall(ISDestroy(&cindIS));
269:   }
270:   PetscFunctionReturn(PETSC_SUCCESS);
271: }

273: PetscErrorCode PetscSectionLoad_HDF5_Internal(PetscSection s, PetscViewer viewer)
274: {
275:   MPI_Comm comm;
276:   PetscInt N, n, numFields, f;

278:   PetscFunctionBegin;
279:   PetscCall(PetscObjectGetComm((PetscObject)s, &comm));
280:   PetscCall(PetscViewerHDF5PushGroup(viewer, "section"));
281:   PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "numFields", PETSC_INT, NULL, (void *)&numFields));
282:   if (s->pStart < 0 && s->pEnd < 0) n = PETSC_DECIDE;
283:   else {
284:     PetscCheck(s->pStart == 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "s->pStart must be 0 (got %" PetscInt_FMT ")", s->pStart);
285:     PetscCheck(s->pEnd >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "s->pEnd must be >= 0, (got %" PetscInt_FMT ")", s->pEnd);
286:     n = s->pEnd;
287:   }
288:   if (numFields > 0) PetscCall(PetscSectionSetNumFields(s, numFields));
289:   PetscCall(PetscViewerHDF5ReadSizes(viewer, "atlasDof", NULL, &N));
290:   if (n == PETSC_DECIDE) PetscCall(PetscSplitOwnership(comm, &n, &N));
291:   PetscCall(PetscSectionSetChart(s, 0, n));
292:   PetscCall(PetscSectionLoad_HDF5_SingleField(s, viewer));
293:   for (f = 0; f < numFields; ++f) {
294:     char     fname[PETSC_MAX_PATH_LEN];
295:     char    *fieldName;
296:     PetscInt fieldComponents, c;

298:     PetscCall(PetscSNPrintf(fname, sizeof(fname), "field%" PetscInt_FMT, f));
299:     PetscCall(PetscViewerHDF5PushGroup(viewer, fname));
300:     PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "fieldName", PETSC_STRING, NULL, &fieldName));
301:     PetscCall(PetscSectionSetFieldName(s, f, fieldName));
302:     PetscCall(PetscFree(fieldName));
303:     PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "fieldComponents", PETSC_INT, NULL, (void *)&fieldComponents));
304:     PetscCall(PetscSectionSetFieldComponents(s, f, fieldComponents));
305:     for (c = 0; c < fieldComponents; ++c) {
306:       char  cname[PETSC_MAX_PATH_LEN];
307:       char *componentName;

309:       PetscCall(PetscSNPrintf(cname, sizeof(cname), "component%" PetscInt_FMT, c));
310:       PetscCall(PetscViewerHDF5PushGroup(viewer, cname));
311:       PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "componentName", PETSC_STRING, NULL, &componentName));
312:       PetscCall(PetscSectionSetComponentName(s, f, c, componentName));
313:       PetscCall(PetscFree(componentName));
314:       PetscCall(PetscViewerHDF5PopGroup(viewer));
315:     }
316:     PetscCall(PetscSectionLoad_HDF5_SingleField(s->field[f], viewer));
317:     PetscCall(PetscViewerHDF5PopGroup(viewer));
318:   }
319:   PetscCall(PetscViewerHDF5PopGroup(viewer));
320:   PetscFunctionReturn(PETSC_SUCCESS);
321: }