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: static PetscErrorCode PetscViewerParseVersion_Private(PetscViewer, const char[], DMPlexStorageVersion *);
     11: static PetscErrorCode PetscViewerCheckVersion_Private(PetscViewer, DMPlexStorageVersion);
     12: static PetscErrorCode PetscViewerAttachVersion_Private(PetscViewer, const char[], DMPlexStorageVersion);
     13: static PetscErrorCode PetscViewerGetAttachedVersion_Private(PetscViewer, const char[], DMPlexStorageVersion *);

     15: PETSC_EXTERN PetscErrorCode VecView_MPI(Vec, PetscViewer);

     17: static PetscErrorCode PetscViewerPrintVersion_Private(PetscViewer viewer, DMPlexStorageVersion version, char str[], size_t len)
     18: {
     19:   PetscFunctionBegin;
     20:   PetscCall(PetscViewerCheckVersion_Private(viewer, version));
     21:   PetscCall(PetscSNPrintf(str, len, "%d.%d.%d", version->major, version->minor, version->subminor));
     22:   PetscFunctionReturn(PETSC_SUCCESS);
     23: }

     25: static PetscErrorCode PetscViewerParseVersion_Private(PetscViewer viewer, const char str[], DMPlexStorageVersion *version)
     26: {
     27:   PetscToken           t;
     28:   char                *ts;
     29:   PetscInt             i;
     30:   PetscInt             ti[3];
     31:   DMPlexStorageVersion v;

     33:   PetscFunctionBegin;
     34:   PetscCall(PetscTokenCreate(str, '.', &t));
     35:   for (i = 0; i < 3; i++) {
     36:     PetscCall(PetscTokenFind(t, &ts));
     37:     PetscCheck(ts, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONG, "Malformed version string %s", str);
     38:     PetscCall(PetscOptionsStringToInt(ts, &ti[i]));
     39:   }
     40:   PetscCall(PetscTokenFind(t, &ts));
     41:   PetscCheck(!ts, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONG, "Malformed version string %s", str);
     42:   PetscCall(PetscTokenDestroy(&t));
     43:   PetscCall(PetscNew(&v));
     44:   v->major    = (int)ti[0];
     45:   v->minor    = (int)ti[1];
     46:   v->subminor = (int)ti[2];
     47:   PetscCall(PetscViewerCheckVersion_Private(viewer, v));
     48:   *version = v;
     49:   PetscFunctionReturn(PETSC_SUCCESS);
     50: }

     52: static PetscErrorCode PetscViewerAttachVersion_Private(PetscViewer viewer, const char key[], DMPlexStorageVersion v)
     53: {
     54:   PetscFunctionBegin;
     55:   PetscCall(PetscObjectContainerCompose((PetscObject)viewer, key, v, PetscContainerUserDestroyDefault));
     56:   PetscFunctionReturn(PETSC_SUCCESS);
     57: }

     59: static PetscErrorCode PetscViewerGetAttachedVersion_Private(PetscViewer viewer, const char key[], DMPlexStorageVersion *v)
     60: {
     61:   PetscContainer cont;

     63:   PetscFunctionBegin;
     64:   PetscCall(PetscObjectQuery((PetscObject)viewer, key, (PetscObject *)&cont));
     65:   *v = NULL;
     66:   if (cont) PetscCall(PetscContainerGetPointer(cont, (void **)v));
     67:   PetscFunctionReturn(PETSC_SUCCESS);
     68: }

     70: /*
     71:   Version log:
     72:   1.0.0 legacy version (default if no "dmplex_storage_version" attribute found in file)
     73:   1.1.0 legacy version, but output VIZ by default
     74:   2.0.0 introduce versioning and multiple topologies
     75:   2.1.0 introduce distributions
     76:   3.0.0 new checkpointing format in Firedrake paper
     77:   3.1.0 new format with IS compression
     78: */
     79: static PetscErrorCode PetscViewerCheckVersion_Private(PetscViewer viewer, DMPlexStorageVersion version)
     80: {
     81:   PetscBool valid = PETSC_FALSE;

     83:   PetscFunctionBegin;
     84:   switch (version->major) {
     85:   case 1:
     86:     switch (version->minor) {
     87:     case 0:
     88:       switch (version->subminor) {
     89:       case 0:
     90:         valid = PETSC_TRUE;
     91:         break;
     92:       }
     93:       break;
     94:     case 1:
     95:       switch (version->subminor) {
     96:       case 0:
     97:         valid = PETSC_TRUE;
     98:         break;
     99:       }
    100:       break;
    101:     }
    102:     break;
    103:   case 2:
    104:     switch (version->minor) {
    105:     case 0:
    106:       switch (version->subminor) {
    107:       case 0:
    108:         valid = PETSC_TRUE;
    109:         break;
    110:       }
    111:       break;
    112:     case 1:
    113:       switch (version->subminor) {
    114:       case 0:
    115:         valid = PETSC_TRUE;
    116:         break;
    117:       }
    118:       break;
    119:     }
    120:     break;
    121:   case 3:
    122:     switch (version->minor) {
    123:     case 0:
    124:       switch (version->subminor) {
    125:       case 0:
    126:         valid = PETSC_TRUE;
    127:         break;
    128:       }
    129:       break;
    130:     case 1:
    131:       switch (version->subminor) {
    132:       case 0:
    133:         valid = PETSC_TRUE;
    134:         break;
    135:       }
    136:       break;
    137:     }
    138:     break;
    139:   }
    140:   PetscCheck(valid, PetscObjectComm((PetscObject)viewer), PETSC_ERR_SUP, "DMPlexStorageVersion %d.%d.%d not supported", version->major, version->minor, version->subminor);
    141:   PetscFunctionReturn(PETSC_SUCCESS);
    142: }

    144: static inline PetscBool DMPlexStorageVersionEQ(DMPlexStorageVersion version, int major, int minor, int subminor)
    145: {
    146:   return (PetscBool)(version->major == major && version->minor == minor && version->subminor == subminor);
    147: }

    149: static inline PetscBool DMPlexStorageVersionGE(DMPlexStorageVersion version, int major, int minor, int subminor)
    150: {
    151:   return (PetscBool)((version->major == major && version->minor == minor && version->subminor >= subminor) || (version->major == major && version->minor > minor) || (version->major > major));
    152: }

    154: /*@C
    155:   PetscViewerHDF5SetDMPlexStorageVersionWriting - Set the storage version for writing

    157:   Logically collective

    159:   Input Parameters:
    160: + viewer  - The `PetscViewer`
    161: - version - The storage format version

    163:   Level: advanced

    165:   Note:
    166:   The version has major, minor, and subminor integers. Parallel operations are only available for version 3.0.0.

    168: .seealso: [](ch_dmbase), `DM`, `PetscViewerHDF5GetDMPlexStorageVersionWriting()`, `PetscViewerHDF5GetDMPlexStorageVersionReading()`, `PetscViewerHDF5SetDMPlexStorageVersionReading()`
    169: @*/
    170: PetscErrorCode PetscViewerHDF5SetDMPlexStorageVersionWriting(PetscViewer viewer, DMPlexStorageVersion version)
    171: {
    172:   const char           ATTR_NAME[] = "dmplex_storage_version";
    173:   DMPlexStorageVersion viewerVersion;
    174:   PetscBool            fileHasVersion;
    175:   char                 fileVersion[16], versionStr[16], viewerVersionStr[16];

    177:   PetscFunctionBegin;
    179:   PetscAssertPointer(version, 2);
    180:   PetscCall(PetscViewerPrintVersion_Private(viewer, version, versionStr, 16));
    181:   PetscCall(PetscViewerGetAttachedVersion_Private(viewer, DMPLEX_STORAGE_VERSION_WRITING_KEY, &viewerVersion));
    182:   if (viewerVersion) {
    183:     PetscBool flg;

    185:     PetscCall(PetscViewerPrintVersion_Private(viewer, viewerVersion, viewerVersionStr, 16));
    186:     PetscCall(PetscStrcmp(versionStr, viewerVersionStr, &flg));
    187:     PetscCheck(flg, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "User requested DMPlex storage version %s but viewer already has version %s - cannot mix versions", versionStr, viewerVersionStr);
    188:   }

    190:   PetscCall(PetscViewerHDF5HasAttribute(viewer, NULL, ATTR_NAME, &fileHasVersion));
    191:   if (fileHasVersion) {
    192:     PetscBool flg;
    193:     char     *tmp;

    195:     PetscCall(PetscViewerHDF5ReadAttribute(viewer, "/", ATTR_NAME, PETSC_STRING, NULL, &tmp));
    196:     PetscCall(PetscStrncpy(fileVersion, tmp, sizeof(fileVersion)));
    197:     PetscCall(PetscFree(tmp));
    198:     PetscCall(PetscStrcmp(fileVersion, versionStr, &flg));
    199:     PetscCheck(flg, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "User requested DMPlex storage version %s but file already has version %s - cannot mix versions", versionStr, fileVersion);
    200:   } else {
    201:     PetscCall(PetscViewerHDF5WriteAttribute(viewer, "/", ATTR_NAME, PETSC_STRING, versionStr));
    202:   }
    203:   PetscCall(PetscNew(&viewerVersion));
    204:   viewerVersion->major    = version->major;
    205:   viewerVersion->minor    = version->minor;
    206:   viewerVersion->subminor = version->subminor;
    207:   PetscCall(PetscViewerAttachVersion_Private(viewer, DMPLEX_STORAGE_VERSION_WRITING_KEY, viewerVersion));
    208:   PetscFunctionReturn(PETSC_SUCCESS);
    209: }

    211: /*@C
    212:   PetscViewerHDF5GetDMPlexStorageVersionWriting - Get the storage version for writing

    214:   Logically collective

    216:   Input Parameter:
    217: . viewer - The `PetscViewer`

    219:   Output Parameter:
    220: . version - The storage format version

    222:   Options Database Keys:
    223: . -dm_plex_view_hdf5_storage_version <num> - Overrides the storage format version

    225:   Level: advanced

    227:   Note:
    228:   The version has major, minor, and subminor integers. Parallel operations are only available for version 3.0.0.

    230: .seealso: [](ch_dmbase), `DM`, `PetscViewerHDF5SetDMPlexStorageVersionWriting()`, `PetscViewerHDF5GetDMPlexStorageVersionReading()`, `PetscViewerHDF5SetDMPlexStorageVersionReading()`
    231: @*/
    232: PetscErrorCode PetscViewerHDF5GetDMPlexStorageVersionWriting(PetscViewer viewer, DMPlexStorageVersion *version)
    233: {
    234:   const char ATTR_NAME[] = "dmplex_storage_version";
    235:   PetscBool  fileHasVersion;
    236:   char       optVersion[16], fileVersion[16];

    238:   PetscFunctionBegin;
    240:   PetscAssertPointer(version, 2);
    241:   PetscCall(PetscViewerGetAttachedVersion_Private(viewer, DMPLEX_STORAGE_VERSION_WRITING_KEY, version));
    242:   if (*version) PetscFunctionReturn(PETSC_SUCCESS);

    244:   PetscCall(PetscStrncpy(fileVersion, DMPLEX_STORAGE_VERSION_STABLE, sizeof(fileVersion)));
    245:   PetscCall(PetscViewerHDF5HasAttribute(viewer, NULL, ATTR_NAME, &fileHasVersion));
    246:   if (fileHasVersion) {
    247:     char *tmp;

    249:     PetscCall(PetscViewerHDF5ReadAttribute(viewer, "/", ATTR_NAME, PETSC_STRING, NULL, &tmp));
    250:     PetscCall(PetscStrncpy(fileVersion, tmp, sizeof(fileVersion)));
    251:     PetscCall(PetscFree(tmp));
    252:   }
    253:   PetscCall(PetscStrncpy(optVersion, fileVersion, sizeof(optVersion)));
    254:   PetscObjectOptionsBegin((PetscObject)viewer);
    255:   PetscCall(PetscOptionsString("-dm_plex_view_hdf5_storage_version", "DMPlex HDF5 viewer storage version", NULL, optVersion, optVersion, sizeof(optVersion), NULL));
    256:   PetscOptionsEnd();
    257:   if (!fileHasVersion) {
    258:     PetscCall(PetscViewerHDF5WriteAttribute(viewer, "/", ATTR_NAME, PETSC_STRING, optVersion));
    259:   } else {
    260:     PetscBool flg;

    262:     PetscCall(PetscStrcmp(fileVersion, optVersion, &flg));
    263:     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);
    264:   }
    265:   PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "petsc_version_git", PETSC_STRING, PETSC_VERSION_GIT));
    266:   PetscCall(PetscViewerParseVersion_Private(viewer, optVersion, version));
    267:   PetscCall(PetscViewerAttachVersion_Private(viewer, DMPLEX_STORAGE_VERSION_WRITING_KEY, *version));
    268:   PetscFunctionReturn(PETSC_SUCCESS);
    269: }

    271: /*@C
    272:   PetscViewerHDF5SetDMPlexStorageVersionReading - Set the storage version for reading

    274:   Logically collective

    276:   Input Parameters:
    277: + viewer  - The `PetscViewer`
    278: - version - The storage format version

    280:   Level: advanced

    282:   Note:
    283:   The version has major, minor, and subminor integers. Parallel operations are only available for version 3.0.0.

    285: .seealso: [](ch_dmbase), `DM`, `PetscViewerHDF5GetDMPlexStorageVersionReading()`, `PetscViewerHDF5GetDMPlexStorageVersionWriting()`, `PetscViewerHDF5SetDMPlexStorageVersionWriting()`
    286: @*/
    287: PetscErrorCode PetscViewerHDF5SetDMPlexStorageVersionReading(PetscViewer viewer, DMPlexStorageVersion version)
    288: {
    289:   const char           ATTR_NAME[] = "dmplex_storage_version";
    290:   DMPlexStorageVersion viewerVersion;
    291:   PetscBool            fileHasVersion;
    292:   char                 versionStr[16], viewerVersionStr[16];

    294:   PetscFunctionBegin;
    296:   PetscAssertPointer(version, 2);
    297:   PetscCall(PetscViewerPrintVersion_Private(viewer, version, versionStr, 16));
    298:   PetscCall(PetscViewerGetAttachedVersion_Private(viewer, DMPLEX_STORAGE_VERSION_READING_KEY, &viewerVersion));
    299:   if (viewerVersion) {
    300:     PetscBool flg;

    302:     PetscCall(PetscViewerPrintVersion_Private(viewer, viewerVersion, viewerVersionStr, 16));
    303:     PetscCall(PetscStrcmp(versionStr, viewerVersionStr, &flg));
    304:     PetscCheck(flg, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "User requested DMPlex storage version %s but viewer already has version %s - cannot mix versions", versionStr, viewerVersionStr);
    305:   }

    307:   PetscCall(PetscViewerHDF5HasAttribute(viewer, NULL, ATTR_NAME, &fileHasVersion));
    308:   if (fileHasVersion) {
    309:     char     *fileVersion;
    310:     PetscBool flg;

    312:     PetscCall(PetscViewerHDF5ReadAttribute(viewer, "/", ATTR_NAME, PETSC_STRING, NULL, &fileVersion));
    313:     PetscCall(PetscStrcmp(fileVersion, versionStr, &flg));
    314:     PetscCheck(flg, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "User requested DMPlex storage version %s but file already has version %s - cannot mix versions", versionStr, fileVersion);
    315:     PetscCall(PetscFree(fileVersion));
    316:   }
    317:   PetscCall(PetscNew(&viewerVersion));
    318:   viewerVersion->major    = version->major;
    319:   viewerVersion->minor    = version->minor;
    320:   viewerVersion->subminor = version->subminor;
    321:   PetscCall(PetscViewerAttachVersion_Private(viewer, DMPLEX_STORAGE_VERSION_READING_KEY, viewerVersion));
    322:   PetscFunctionReturn(PETSC_SUCCESS);
    323: }

    325: /*@C
    326:   PetscViewerHDF5GetDMPlexStorageVersionReading - Get the storage version for reading

    328:   Logically collective

    330:   Input Parameter:
    331: . viewer - The `PetscViewer`

    333:   Output Parameter:
    334: . version - The storage format version

    336:   Options Database Keys:
    337: . -dm_plex_view_hdf5_storage_version <num> - Overrides the storage format version

    339:   Level: advanced

    341:   Note:
    342:   The version has major, minor, and subminor integers. Parallel operations are only available for version 3.0.0.

    344: .seealso: [](ch_dmbase), `DM`, `PetscViewerHDF5SetDMPlexStorageVersionReading()`, `PetscViewerHDF5GetDMPlexStorageVersionWriting()`, `PetscViewerHDF5SetDMPlexStorageVersionWriting()`
    345: @*/
    346: PetscErrorCode PetscViewerHDF5GetDMPlexStorageVersionReading(PetscViewer viewer, DMPlexStorageVersion *version)
    347: {
    348:   const char ATTR_NAME[] = "dmplex_storage_version";
    349:   char      *defaultVersion;
    350:   char      *versionString;

    352:   PetscFunctionBegin;
    354:   PetscAssertPointer(version, 2);
    355:   PetscCall(PetscViewerGetAttachedVersion_Private(viewer, DMPLEX_STORAGE_VERSION_READING_KEY, version));
    356:   if (*version) PetscFunctionReturn(PETSC_SUCCESS);

    358:   //TODO string HDF5 attribute handling is terrible and should be redesigned
    359:   PetscCall(PetscStrallocpy(DMPLEX_STORAGE_VERSION_FIRST, &defaultVersion));
    360:   PetscCall(PetscViewerHDF5ReadAttribute(viewer, "/", ATTR_NAME, PETSC_STRING, &defaultVersion, &versionString));
    361:   PetscCall(PetscViewerParseVersion_Private(viewer, versionString, version));
    362:   PetscCall(PetscViewerAttachVersion_Private(viewer, DMPLEX_STORAGE_VERSION_READING_KEY, *version));
    363:   PetscCall(PetscFree(versionString));
    364:   PetscCall(PetscFree(defaultVersion));
    365:   PetscFunctionReturn(PETSC_SUCCESS);
    366: }

    368: static PetscErrorCode DMPlexGetHDF5Name_Private(DM dm, const char *name[])
    369: {
    370:   PetscFunctionBegin;
    371:   if (((PetscObject)dm)->name) {
    372:     PetscCall(PetscObjectGetName((PetscObject)dm, name));
    373:   } else {
    374:     *name = "plex";
    375:   }
    376:   PetscFunctionReturn(PETSC_SUCCESS);
    377: }

    379: PetscErrorCode DMSequenceGetLength_HDF5_Internal(DM dm, const char seqname[], PetscInt *seqlen, PetscViewer viewer)
    380: {
    381:   hid_t     file, group, dset, dspace;
    382:   hsize_t   rdim, *dims;
    383:   char     *groupname;
    384:   PetscBool has;

    386:   PetscFunctionBegin;
    387:   PetscCall(PetscViewerHDF5GetGroup(viewer, NULL, &groupname));
    388:   PetscCall(PetscViewerHDF5HasDataset(viewer, seqname, &has));
    389:   PetscCheck(has, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Object (dataset) \"%s\" not stored in group %s", seqname, groupname);

    391:   PetscCall(PetscViewerHDF5OpenGroup(viewer, NULL, &file, &group));
    392:   PetscCallHDF5Return(dset, H5Dopen2, (group, seqname, H5P_DEFAULT));
    393:   PetscCallHDF5Return(dspace, H5Dget_space, (dset));
    394:   PetscCallHDF5ReturnNoCheck(rdim, H5Sget_simple_extent_dims, (dspace, NULL, NULL));
    395:   PetscCall(PetscMalloc1(rdim, &dims));
    396:   PetscCallHDF5ReturnNoCheck(rdim, H5Sget_simple_extent_dims, (dspace, dims, NULL));
    397:   *seqlen = (PetscInt)dims[0];
    398:   PetscCall(PetscFree(dims));
    399:   PetscCallHDF5(H5Dclose, (dset));
    400:   PetscCallHDF5(H5Gclose, (group));
    401:   PetscFunctionReturn(PETSC_SUCCESS);
    402: }

    404: static PetscErrorCode DMSequenceView_HDF5(DM dm, const char seqname[], PetscInt seqnum, PetscScalar value, PetscViewer viewer)
    405: {
    406:   Vec         stamp;
    407:   PetscMPIInt rank;

    409:   PetscFunctionBegin;
    410:   if (seqnum < 0) PetscFunctionReturn(PETSC_SUCCESS);
    411:   PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)viewer), &rank));
    412:   PetscCall(VecCreateMPI(PetscObjectComm((PetscObject)viewer), rank ? 0 : 1, 1, &stamp));
    413:   PetscCall(VecSetBlockSize(stamp, 1));
    414:   PetscCall(PetscObjectSetName((PetscObject)stamp, seqname));
    415:   if (rank == 0) {
    416:     PetscReal timeScale;
    417:     PetscBool istime;

    419:     PetscCall(PetscStrncmp(seqname, "time", 5, &istime));
    420:     if (istime) {
    421:       PetscCall(DMPlexGetScale(dm, PETSC_UNIT_TIME, &timeScale));
    422:       value *= timeScale;
    423:     }
    424:     PetscCall(VecSetValue(stamp, 0, value, INSERT_VALUES));
    425:   }
    426:   PetscCall(VecAssemblyBegin(stamp));
    427:   PetscCall(VecAssemblyEnd(stamp));
    428:   PetscCall(PetscViewerHDF5PushGroup(viewer, "/"));
    429:   PetscCall(PetscViewerHDF5PushTimestepping(viewer));
    430:   PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum)); /* seqnum < 0 jumps out above */
    431:   PetscCall(VecView(stamp, viewer));
    432:   PetscCall(PetscViewerHDF5PopTimestepping(viewer));
    433:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    434:   PetscCall(VecDestroy(&stamp));
    435:   PetscFunctionReturn(PETSC_SUCCESS);
    436: }

    438: PetscErrorCode DMSequenceLoad_HDF5_Internal(DM dm, const char seqname[], PetscInt seqnum, PetscScalar *value, PetscViewer viewer)
    439: {
    440:   Vec         stamp;
    441:   PetscMPIInt rank;

    443:   PetscFunctionBegin;
    444:   if (seqnum < 0) PetscFunctionReturn(PETSC_SUCCESS);
    445:   PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)viewer), &rank));
    446:   PetscCall(VecCreateMPI(PetscObjectComm((PetscObject)viewer), rank ? 0 : 1, 1, &stamp));
    447:   PetscCall(VecSetBlockSize(stamp, 1));
    448:   PetscCall(PetscObjectSetName((PetscObject)stamp, seqname));
    449:   PetscCall(PetscViewerHDF5PushGroup(viewer, "/"));
    450:   PetscCall(PetscViewerHDF5PushTimestepping(viewer));
    451:   PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum)); /* seqnum < 0 jumps out above */
    452:   PetscCall(VecLoad(stamp, viewer));
    453:   PetscCall(PetscViewerHDF5PopTimestepping(viewer));
    454:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    455:   if (rank == 0) {
    456:     const PetscScalar *a;
    457:     PetscReal          timeScale;
    458:     PetscBool          istime;

    460:     PetscCall(VecGetArrayRead(stamp, &a));
    461:     *value = a[0];
    462:     PetscCall(VecRestoreArrayRead(stamp, &a));
    463:     PetscCall(PetscStrncmp(seqname, "time", 5, &istime));
    464:     if (istime) {
    465:       PetscCall(DMPlexGetScale(dm, PETSC_UNIT_TIME, &timeScale));
    466:       *value /= timeScale;
    467:     }
    468:   }
    469:   PetscCall(VecDestroy(&stamp));
    470:   PetscFunctionReturn(PETSC_SUCCESS);
    471: }

    473: static PetscErrorCode DMPlexCreateCutVertexLabel_Private(DM dm, DMLabel cutLabel, DMLabel *cutVertexLabel)
    474: {
    475:   IS              cutcells = NULL;
    476:   const PetscInt *cutc;
    477:   PetscInt        cellHeight, vStart, vEnd, cStart, cEnd, c;

    479:   PetscFunctionBegin;
    480:   if (!cutLabel) PetscFunctionReturn(PETSC_SUCCESS);
    481:   PetscCall(DMPlexGetVTKCellHeight(dm, &cellHeight));
    482:   PetscCall(DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd));
    483:   PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
    484:   /* Label vertices that should be duplicated */
    485:   PetscCall(DMLabelCreate(PETSC_COMM_SELF, "Cut Vertices", cutVertexLabel));
    486:   PetscCall(DMLabelGetStratumIS(cutLabel, 2, &cutcells));
    487:   if (cutcells) {
    488:     PetscInt n;

    490:     PetscCall(ISGetIndices(cutcells, &cutc));
    491:     PetscCall(ISGetLocalSize(cutcells, &n));
    492:     for (c = 0; c < n; ++c) {
    493:       if ((cutc[c] >= cStart) && (cutc[c] < cEnd)) {
    494:         PetscInt *closure = NULL;
    495:         PetscInt  closureSize, cl, value;

    497:         PetscCall(DMPlexGetTransitiveClosure(dm, cutc[c], PETSC_TRUE, &closureSize, &closure));
    498:         for (cl = 0; cl < closureSize * 2; cl += 2) {
    499:           if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) {
    500:             PetscCall(DMLabelGetValue(cutLabel, closure[cl], &value));
    501:             if (value == 1) PetscCall(DMLabelSetValue(*cutVertexLabel, closure[cl], 1));
    502:           }
    503:         }
    504:         PetscCall(DMPlexRestoreTransitiveClosure(dm, cutc[c], PETSC_TRUE, &closureSize, &closure));
    505:       }
    506:     }
    507:     PetscCall(ISRestoreIndices(cutcells, &cutc));
    508:   }
    509:   PetscCall(ISDestroy(&cutcells));
    510:   PetscFunctionReturn(PETSC_SUCCESS);
    511: }

    513: PetscErrorCode VecView_Plex_Local_HDF5_Internal(Vec v, PetscViewer viewer)
    514: {
    515:   DM                dm;
    516:   DM                dmBC;
    517:   PetscSection      section, sectionGlobal;
    518:   Vec               gv;
    519:   const char       *name;
    520:   PetscViewerFormat format;
    521:   PetscInt          seqnum;
    522:   PetscReal         seqval;
    523:   PetscBool         isseq;

    525:   PetscFunctionBegin;
    526:   PetscCall(PetscObjectTypeCompare((PetscObject)v, VECSEQ, &isseq));
    527:   PetscCall(VecGetDM(v, &dm));
    528:   PetscCall(DMGetLocalSection(dm, &section));
    529:   PetscCall(DMGetOutputSequenceNumber(dm, &seqnum, &seqval));
    530:   PetscCall(DMSequenceView_HDF5(dm, "time", seqnum, (PetscScalar)seqval, viewer));
    531:   if (seqnum >= 0) {
    532:     PetscCall(PetscViewerHDF5PushTimestepping(viewer));
    533:     PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum));
    534:   }
    535:   PetscCall(PetscViewerGetFormat(viewer, &format));
    536:   PetscCall(DMGetOutputDM(dm, &dmBC));
    537:   PetscCall(DMGetGlobalSection(dmBC, &sectionGlobal));
    538:   PetscCall(DMGetGlobalVector(dmBC, &gv));
    539:   PetscCall(PetscObjectGetName((PetscObject)v, &name));
    540:   PetscCall(PetscObjectSetName((PetscObject)gv, name));
    541:   PetscCall(DMLocalToGlobalBegin(dmBC, v, INSERT_VALUES, gv));
    542:   PetscCall(DMLocalToGlobalEnd(dmBC, v, INSERT_VALUES, gv));
    543:   PetscCall(PetscObjectTypeCompare((PetscObject)gv, VECSEQ, &isseq));
    544:   if (format == PETSC_VIEWER_HDF5_VIZ) {
    545:     /* Output visualization representation */
    546:     PetscInt numFields, f;
    547:     DMLabel  cutLabel, cutVertexLabel = NULL;

    549:     PetscCall(PetscSectionGetNumFields(section, &numFields));
    550:     PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel));
    551:     for (f = 0; f < numFields; ++f) {
    552:       Vec                     subv;
    553:       IS                      is;
    554:       const char             *fname, *fgroup, *componentName, *fname_def = "unnamed";
    555:       char                    subname[PETSC_MAX_PATH_LEN];
    556:       PetscInt                Nc, c;
    557:       PetscInt                pStart, pEnd;
    558:       PetscViewerVTKFieldType ft;

    560:       PetscCall(DMPlexGetFieldType_Internal(dm, section, f, &pStart, &pEnd, &ft));
    561:       if (ft == PETSC_VTK_INVALID) continue;
    562:       fgroup = (ft == PETSC_VTK_POINT_VECTOR_FIELD) || (ft == PETSC_VTK_POINT_FIELD) ? "/vertex_fields" : "/cell_fields";
    563:       PetscCall(PetscSectionGetFieldName(section, f, &fname));
    564:       if (!fname) fname = fname_def;

    566:       PetscCall(PetscViewerHDF5PushGroup(viewer, fgroup));

    568:       if (cutLabel) {
    569:         const PetscScalar *ga;
    570:         PetscScalar       *suba;
    571:         PetscInt           gstart, subSize = 0, extSize = 0, subOff = 0, newOff = 0, p;

    573:         PetscCall(DMPlexCreateCutVertexLabel_Private(dm, cutLabel, &cutVertexLabel));
    574:         PetscCall(PetscSectionGetFieldComponents(section, f, &Nc));
    575:         for (p = pStart; p < pEnd; ++p) {
    576:           PetscInt gdof, fdof = 0, val;

    578:           PetscCall(PetscSectionGetDof(sectionGlobal, p, &gdof));
    579:           if (gdof > 0) PetscCall(PetscSectionGetFieldDof(section, p, f, &fdof));
    580:           subSize += fdof;
    581:           PetscCall(DMLabelGetValue(cutVertexLabel, p, &val));
    582:           if (val == 1) extSize += fdof;
    583:         }
    584:         PetscCall(VecCreate(PetscObjectComm((PetscObject)gv), &subv));
    585:         PetscCall(VecSetSizes(subv, subSize + extSize, PETSC_DETERMINE));
    586:         PetscCall(VecSetBlockSize(subv, Nc));
    587:         PetscCall(VecSetType(subv, VECSTANDARD));
    588:         PetscCall(VecGetOwnershipRange(gv, &gstart, NULL));
    589:         PetscCall(VecGetArrayRead(gv, &ga));
    590:         PetscCall(VecGetArray(subv, &suba));
    591:         for (p = pStart; p < pEnd; ++p) {
    592:           PetscInt gdof, goff, val;

    594:           PetscCall(PetscSectionGetDof(sectionGlobal, p, &gdof));
    595:           if (gdof > 0) {
    596:             PetscInt fdof, fc, f2, poff = 0;

    598:             PetscCall(PetscSectionGetOffset(sectionGlobal, p, &goff));
    599:             /* Can get rid of this loop by storing field information in the global section */
    600:             for (f2 = 0; f2 < f; ++f2) {
    601:               PetscCall(PetscSectionGetFieldDof(section, p, f2, &fdof));
    602:               poff += fdof;
    603:             }
    604:             PetscCall(PetscSectionGetFieldDof(section, p, f, &fdof));
    605:             for (fc = 0; fc < fdof; ++fc, ++subOff) suba[subOff] = ga[goff + poff + fc - gstart];
    606:             PetscCall(DMLabelGetValue(cutVertexLabel, p, &val));
    607:             if (val == 1) {
    608:               for (fc = 0; fc < fdof; ++fc, ++newOff) suba[subSize + newOff] = ga[goff + poff + fc - gstart];
    609:             }
    610:           }
    611:         }
    612:         PetscCall(VecRestoreArrayRead(gv, &ga));
    613:         PetscCall(VecRestoreArray(subv, &suba));
    614:         PetscCall(DMLabelDestroy(&cutVertexLabel));
    615:       } else {
    616:         PetscCall(PetscSectionGetField_Internal(section, sectionGlobal, gv, f, pStart, pEnd, &is, &subv));
    617:       }
    618:       PetscCall(PetscStrncpy(subname, name, sizeof(subname)));
    619:       PetscCall(PetscStrlcat(subname, "_", sizeof(subname)));
    620:       PetscCall(PetscStrlcat(subname, fname, sizeof(subname)));
    621:       PetscCall(PetscObjectSetName((PetscObject)subv, subname));
    622:       if (isseq) PetscCall(VecView_Seq(subv, viewer));
    623:       else PetscCall(VecView_MPI(subv, viewer));
    624:       if (ft == PETSC_VTK_POINT_VECTOR_FIELD || ft == PETSC_VTK_CELL_VECTOR_FIELD) {
    625:         PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)subv, "vector_field_type", PETSC_STRING, "vector"));
    626:       } else {
    627:         PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)subv, "vector_field_type", PETSC_STRING, "scalar"));
    628:       }

    630:       /* Output the component names in the field if available */
    631:       PetscCall(PetscSectionGetFieldComponents(section, f, &Nc));
    632:       for (c = 0; c < Nc; ++c) {
    633:         char componentNameLabel[PETSC_MAX_PATH_LEN];
    634:         PetscCall(PetscSectionGetComponentName(section, f, c, &componentName));
    635:         PetscCall(PetscSNPrintf(componentNameLabel, sizeof(componentNameLabel), "componentName%" PetscInt_FMT, c));
    636:         PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)subv, componentNameLabel, PETSC_STRING, componentName));
    637:       }

    639:       if (cutLabel) PetscCall(VecDestroy(&subv));
    640:       else PetscCall(PetscSectionRestoreField_Internal(section, sectionGlobal, gv, f, pStart, pEnd, &is, &subv));
    641:       PetscCall(PetscViewerHDF5PopGroup(viewer));
    642:     }
    643:   } else {
    644:     /* Output full vector */
    645:     PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
    646:     if (isseq) PetscCall(VecView_Seq(gv, viewer));
    647:     else PetscCall(VecView_MPI(gv, viewer));
    648:     PetscCall(PetscViewerHDF5PopGroup(viewer));
    649:   }
    650:   if (seqnum >= 0) PetscCall(PetscViewerHDF5PopTimestepping(viewer));
    651:   PetscCall(DMRestoreGlobalVector(dmBC, &gv));
    652:   PetscFunctionReturn(PETSC_SUCCESS);
    653: }

    655: PetscErrorCode VecView_Plex_HDF5_Internal(Vec v, PetscViewer viewer)
    656: {
    657:   DMPlexStorageVersion version;
    658:   DM                   dm;
    659:   Vec                  locv;
    660:   PetscObject          isZero;
    661:   const char          *name;
    662:   PetscReal            time;

    664:   PetscFunctionBegin;
    665:   PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
    666:   PetscCall(PetscInfo(v, "Writing Vec %s storage version %d.%d.%d\n", v->hdr.name, version->major, version->minor, version->subminor));

    668:   PetscCall(VecGetDM(v, &dm));
    669:   PetscCall(DMGetLocalVector(dm, &locv));
    670:   PetscCall(PetscObjectGetName((PetscObject)v, &name));
    671:   PetscCall(PetscObjectSetName((PetscObject)locv, name));
    672:   PetscCall(PetscObjectQuery((PetscObject)v, "__Vec_bc_zero__", &isZero));
    673:   PetscCall(PetscObjectCompose((PetscObject)locv, "__Vec_bc_zero__", isZero));
    674:   PetscCall(DMGlobalToLocalBegin(dm, v, INSERT_VALUES, locv));
    675:   PetscCall(DMGlobalToLocalEnd(dm, v, INSERT_VALUES, locv));
    676:   PetscCall(DMGetOutputSequenceNumber(dm, NULL, &time));
    677:   PetscCall(DMPlexInsertBoundaryValues(dm, PETSC_TRUE, locv, time, NULL, NULL, NULL));
    678:   PetscCall(VecView_Plex_Local_HDF5_Internal(locv, viewer));
    679:   if (DMPlexStorageVersionEQ(version, 1, 1, 0)) {
    680:     PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
    681:     PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_VIZ));
    682:     PetscCall(VecView_Plex_Local_HDF5_Internal(locv, viewer));
    683:     PetscCall(PetscViewerPopFormat(viewer));
    684:     PetscCall(PetscViewerHDF5PopGroup(viewer));
    685:   }
    686:   PetscCall(PetscObjectCompose((PetscObject)locv, "__Vec_bc_zero__", NULL));
    687:   PetscCall(DMRestoreLocalVector(dm, &locv));
    688:   PetscFunctionReturn(PETSC_SUCCESS);
    689: }

    691: PetscErrorCode VecView_Plex_HDF5_Native_Internal(Vec v, PetscViewer viewer)
    692: {
    693:   PetscBool isseq;

    695:   PetscFunctionBegin;
    696:   PetscCall(PetscObjectTypeCompare((PetscObject)v, VECSEQ, &isseq));
    697:   PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
    698:   if (isseq) PetscCall(VecView_Seq(v, viewer));
    699:   else PetscCall(VecView_MPI(v, viewer));
    700:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    701:   PetscFunctionReturn(PETSC_SUCCESS);
    702: }

    704: PetscErrorCode VecLoad_Plex_HDF5_Internal(Vec v, PetscViewer viewer)
    705: {
    706:   DM          dm;
    707:   Vec         locv;
    708:   const char *name;
    709:   PetscInt    seqnum;

    711:   PetscFunctionBegin;
    712:   PetscCall(VecGetDM(v, &dm));
    713:   PetscCall(DMGetLocalVector(dm, &locv));
    714:   PetscCall(PetscObjectGetName((PetscObject)v, &name));
    715:   PetscCall(PetscObjectSetName((PetscObject)locv, name));
    716:   PetscCall(DMGetOutputSequenceNumber(dm, &seqnum, NULL));
    717:   PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
    718:   if (seqnum >= 0) {
    719:     PetscCall(PetscViewerHDF5PushTimestepping(viewer));
    720:     PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum));
    721:   }
    722:   PetscCall(VecLoad_Plex_Local(locv, viewer));
    723:   if (seqnum >= 0) PetscCall(PetscViewerHDF5PopTimestepping(viewer));
    724:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    725:   PetscCall(DMLocalToGlobalBegin(dm, locv, INSERT_VALUES, v));
    726:   PetscCall(DMLocalToGlobalEnd(dm, locv, INSERT_VALUES, v));
    727:   PetscCall(DMRestoreLocalVector(dm, &locv));
    728:   PetscFunctionReturn(PETSC_SUCCESS);
    729: }

    731: PetscErrorCode VecLoad_Plex_HDF5_Native_Internal(Vec v, PetscViewer viewer)
    732: {
    733:   DM       dm;
    734:   PetscInt seqnum;

    736:   PetscFunctionBegin;
    737:   PetscCall(VecGetDM(v, &dm));
    738:   PetscCall(DMGetOutputSequenceNumber(dm, &seqnum, NULL));
    739:   PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
    740:   if (seqnum >= 0) {
    741:     PetscCall(PetscViewerHDF5PushTimestepping(viewer));
    742:     PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum));
    743:   }
    744:   PetscCall(VecLoad_Default(v, viewer));
    745:   if (seqnum >= 0) PetscCall(PetscViewerHDF5PopTimestepping(viewer));
    746:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    747:   PetscFunctionReturn(PETSC_SUCCESS);
    748: }

    750: static PetscErrorCode DMPlexDistributionView_HDF5_Private(DM dm, IS globalPointNumbers, PetscViewer viewer)
    751: {
    752:   MPI_Comm           comm;
    753:   PetscMPIInt        size, rank;
    754:   PetscInt           size_petsc_int;
    755:   const char        *topologydm_name, *distribution_name;
    756:   const PetscInt    *gpoint;
    757:   PetscInt           pStart, pEnd, p;
    758:   PetscSF            pointSF;
    759:   PetscInt           nroots, nleaves;
    760:   const PetscInt    *ilocal;
    761:   const PetscSFNode *iremote;
    762:   IS                 chartSizesIS, ownersIS, gpointsIS;
    763:   PetscInt          *chartSize, *owners, *gpoints;

    765:   PetscFunctionBegin;
    766:   PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
    767:   PetscCallMPI(MPI_Comm_size(comm, &size));
    768:   PetscCallMPI(MPI_Comm_rank(comm, &rank));
    769:   PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
    770:   PetscCall(DMPlexDistributionGetName(dm, &distribution_name));
    771:   if (!distribution_name) PetscFunctionReturn(PETSC_SUCCESS);
    772:   PetscCall(PetscLogEventBegin(DMPLEX_DistributionView, viewer, 0, 0, 0));
    773:   size_petsc_int = (PetscInt)size;
    774:   PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "comm_size", PETSC_INT, (void *)&size_petsc_int));
    775:   PetscCall(ISGetIndices(globalPointNumbers, &gpoint));
    776:   PetscCall(DMPlexGetChart(dm, &pStart, &pEnd));
    777:   PetscCall(PetscMalloc1(1, &chartSize));
    778:   *chartSize = pEnd - pStart;
    779:   PetscCall(PetscMalloc1(*chartSize, &owners));
    780:   PetscCall(PetscMalloc1(*chartSize, &gpoints));
    781:   PetscCall(DMGetPointSF(dm, &pointSF));
    782:   PetscCall(PetscSFGetGraph(pointSF, &nroots, &nleaves, &ilocal, &iremote));
    783:   for (p = pStart; p < pEnd; ++p) {
    784:     PetscInt gp = gpoint[p - pStart];

    786:     owners[p - pStart]  = rank;
    787:     gpoints[p - pStart] = (gp < 0 ? -(gp + 1) : gp);
    788:   }
    789:   for (p = 0; p < nleaves; ++p) {
    790:     PetscInt ilocalp = (ilocal ? ilocal[p] : p);

    792:     owners[ilocalp] = iremote[p].rank;
    793:   }
    794:   PetscCall(ISCreateGeneral(comm, 1, chartSize, PETSC_OWN_POINTER, &chartSizesIS));
    795:   PetscCall(ISCreateGeneral(comm, *chartSize, owners, PETSC_OWN_POINTER, &ownersIS));
    796:   PetscCall(ISCreateGeneral(comm, *chartSize, gpoints, PETSC_OWN_POINTER, &gpointsIS));
    797:   PetscCall(PetscObjectSetName((PetscObject)chartSizesIS, "chart_sizes"));
    798:   PetscCall(PetscObjectSetName((PetscObject)ownersIS, "owners"));
    799:   PetscCall(PetscObjectSetName((PetscObject)gpointsIS, "global_point_numbers"));
    800:   PetscCall(ISView(chartSizesIS, viewer));
    801:   PetscCall(ISView(ownersIS, viewer));
    802:   PetscCall(ISView(gpointsIS, viewer));
    803:   PetscCall(ISDestroy(&chartSizesIS));
    804:   PetscCall(ISDestroy(&ownersIS));
    805:   PetscCall(ISDestroy(&gpointsIS));
    806:   PetscCall(ISRestoreIndices(globalPointNumbers, &gpoint));
    807:   PetscCall(PetscLogEventEnd(DMPLEX_DistributionView, viewer, 0, 0, 0));
    808:   PetscFunctionReturn(PETSC_SUCCESS);
    809: }

    811: 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[])
    812: {
    813:   IS              coneSizesIS, conesIS, orientationsIS;
    814:   PetscInt       *coneSizes, *cones, *orientations;
    815:   const PetscInt *gpoint;
    816:   PetscInt        nPoints = 0, conesSize = 0;
    817:   PetscInt        p, c, s;
    818:   MPI_Comm        comm;

    820:   PetscFunctionBegin;
    821:   PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
    822:   PetscCall(ISGetIndices(globalPointNumbers, &gpoint));
    823:   for (p = pStart; p < pEnd; ++p) {
    824:     if (gpoint[p] >= 0) {
    825:       PetscInt coneSize;

    827:       PetscCall(DMPlexGetConeSize(dm, p, &coneSize));
    828:       nPoints += 1;
    829:       conesSize += coneSize;
    830:     }
    831:   }
    832:   PetscCall(PetscMalloc1(nPoints, &coneSizes));
    833:   PetscCall(PetscMalloc1(conesSize, &cones));
    834:   PetscCall(PetscMalloc1(conesSize, &orientations));
    835:   for (p = pStart, c = 0, s = 0; p < pEnd; ++p) {
    836:     if (gpoint[p] >= 0) {
    837:       const PetscInt *cone, *ornt;
    838:       PetscInt        coneSize, cp;

    840:       PetscCall(DMPlexGetConeSize(dm, p, &coneSize));
    841:       PetscCall(DMPlexGetCone(dm, p, &cone));
    842:       PetscCall(DMPlexGetConeOrientation(dm, p, &ornt));
    843:       coneSizes[s] = coneSize;
    844:       for (cp = 0; cp < coneSize; ++cp, ++c) {
    845:         cones[c]        = gpoint[cone[cp]] < 0 ? -(gpoint[cone[cp]] + 1) : gpoint[cone[cp]];
    846:         orientations[c] = ornt[cp];
    847:       }
    848:       ++s;
    849:     }
    850:   }
    851:   PetscCheck(s == nPoints, PETSC_COMM_SELF, PETSC_ERR_LIB, "Total number of points %" PetscInt_FMT " != %" PetscInt_FMT, s, nPoints);
    852:   PetscCheck(c == conesSize, PETSC_COMM_SELF, PETSC_ERR_LIB, "Total number of cone points %" PetscInt_FMT " != %" PetscInt_FMT, c, conesSize);
    853:   PetscCall(ISCreateGeneral(comm, nPoints, coneSizes, PETSC_OWN_POINTER, &coneSizesIS));
    854:   PetscCall(ISCreateGeneral(comm, conesSize, cones, PETSC_OWN_POINTER, &conesIS));
    855:   PetscCall(ISCreateGeneral(comm, conesSize, orientations, PETSC_OWN_POINTER, &orientationsIS));
    856:   PetscCall(PetscObjectSetName((PetscObject)coneSizesIS, coneSizesName));
    857:   PetscCall(PetscObjectSetName((PetscObject)conesIS, conesName));
    858:   PetscCall(PetscObjectSetName((PetscObject)orientationsIS, orientationsName));
    859:   PetscCall(ISView(coneSizesIS, viewer));
    860:   PetscCall(ISView(conesIS, viewer));
    861:   PetscCall(ISView(orientationsIS, viewer));
    862:   PetscCall(ISDestroy(&coneSizesIS));
    863:   PetscCall(ISDestroy(&conesIS));
    864:   PetscCall(ISDestroy(&orientationsIS));
    865:   if (pointsName) {
    866:     IS        pointsIS;
    867:     PetscInt *points;

    869:     PetscCall(PetscMalloc1(nPoints, &points));
    870:     for (p = pStart, c = 0, s = 0; p < pEnd; ++p) {
    871:       if (gpoint[p] >= 0) {
    872:         points[s] = gpoint[p];
    873:         ++s;
    874:       }
    875:     }
    876:     PetscCall(ISCreateGeneral(comm, nPoints, points, PETSC_OWN_POINTER, &pointsIS));
    877:     PetscCall(PetscObjectSetName((PetscObject)pointsIS, pointsName));
    878:     PetscCall(ISView(pointsIS, viewer));
    879:     PetscCall(ISDestroy(&pointsIS));
    880:   }
    881:   PetscCall(ISRestoreIndices(globalPointNumbers, &gpoint));
    882:   PetscFunctionReturn(PETSC_SUCCESS);
    883: }

    885: static PetscErrorCode DMPlexTopologyView_HDF5_Legacy_Private(DM dm, IS globalPointNumbers, PetscViewer viewer)
    886: {
    887:   const char *pointsName, *coneSizesName, *conesName, *orientationsName;
    888:   PetscInt    pStart, pEnd, dim;

    890:   PetscFunctionBegin;
    891:   pointsName       = "order";
    892:   coneSizesName    = "cones";
    893:   conesName        = "cells";
    894:   orientationsName = "orientation";
    895:   PetscCall(DMPlexGetChart(dm, &pStart, &pEnd));
    896:   PetscCall(DMPlexTopologyView_HDF5_Inner_Private(dm, globalPointNumbers, viewer, pStart, pEnd, pointsName, coneSizesName, conesName, orientationsName));
    897:   PetscCall(DMGetDimension(dm, &dim));
    898:   PetscCall(PetscViewerHDF5WriteAttribute(viewer, conesName, "cell_dim", PETSC_INT, (void *)&dim));
    899:   PetscFunctionReturn(PETSC_SUCCESS);
    900: }

    902: //TODO get this numbering right away without needing this function
    903: /* Renumber global point numbers so that they are 0-based per stratum */
    904: static PetscErrorCode RenumberGlobalPointNumbersPerStratum_Private(DM dm, IS globalPointNumbers, IS *newGlobalPointNumbers, IS *strataPermutation)
    905: {
    906:   PetscInt        d, depth, p, n;
    907:   PetscInt       *offsets;
    908:   const PetscInt *gpn;
    909:   PetscInt       *ngpn;
    910:   MPI_Comm        comm;

    912:   PetscFunctionBegin;
    913:   PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
    914:   PetscCall(ISGetLocalSize(globalPointNumbers, &n));
    915:   PetscCall(ISGetIndices(globalPointNumbers, &gpn));
    916:   PetscCall(PetscMalloc1(n, &ngpn));
    917:   PetscCall(DMPlexGetDepth(dm, &depth));
    918:   PetscCall(PetscMalloc1(depth + 1, &offsets));
    919:   for (d = 0; d <= depth; d++) {
    920:     PetscInt pStart, pEnd;

    922:     PetscCall(DMPlexGetDepthStratum(dm, d, &pStart, &pEnd));
    923:     offsets[d] = PETSC_INT_MAX;
    924:     for (p = pStart; p < pEnd; p++) {
    925:       if (gpn[p] >= 0 && gpn[p] < offsets[d]) offsets[d] = gpn[p];
    926:     }
    927:   }
    928:   PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, offsets, depth + 1, MPIU_INT, MPI_MIN, comm));
    929:   for (d = 0; d <= depth; d++) {
    930:     PetscInt pStart, pEnd;

    932:     PetscCall(DMPlexGetDepthStratum(dm, d, &pStart, &pEnd));
    933:     for (p = pStart; p < pEnd; p++) ngpn[p] = gpn[p] - PetscSign(gpn[p]) * offsets[d];
    934:   }
    935:   PetscCall(ISRestoreIndices(globalPointNumbers, &gpn));
    936:   PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)globalPointNumbers), n, ngpn, PETSC_OWN_POINTER, newGlobalPointNumbers));
    937:   {
    938:     PetscInt *perm;

    940:     PetscCall(PetscMalloc1(depth + 1, &perm));
    941:     for (d = 0; d <= depth; d++) perm[d] = d;
    942:     PetscCall(PetscSortIntWithPermutation(depth + 1, offsets, perm));
    943:     PetscCall(ISCreateGeneral(PETSC_COMM_SELF, depth + 1, perm, PETSC_OWN_POINTER, strataPermutation));
    944:   }
    945:   PetscCall(PetscFree(offsets));
    946:   PetscFunctionReturn(PETSC_SUCCESS);
    947: }

    949: static PetscErrorCode DMPlexTopologyView_HDF5_Private(DM dm, IS globalPointNumbers, PetscViewer viewer)
    950: {
    951:   IS          globalPointNumbers0, strataPermutation;
    952:   const char *coneSizesName, *conesName, *orientationsName;
    953:   PetscInt    depth, d;
    954:   MPI_Comm    comm;

    956:   PetscFunctionBegin;
    957:   coneSizesName    = "cone_sizes";
    958:   conesName        = "cones";
    959:   orientationsName = "orientations";
    960:   PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
    961:   PetscCall(DMPlexGetDepth(dm, &depth));
    962:   {
    963:     PetscInt dim;

    965:     PetscCall(DMGetDimension(dm, &dim));
    966:     PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "cell_dim", PETSC_INT, &dim));
    967:     PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "depth", PETSC_INT, &depth));
    968:   }

    970:   PetscCall(RenumberGlobalPointNumbersPerStratum_Private(dm, globalPointNumbers, &globalPointNumbers0, &strataPermutation));
    971:   /* TODO dirty trick to save serial IS using the same parallel viewer */
    972:   {
    973:     IS              spOnComm;
    974:     PetscInt        n   = 0, N;
    975:     const PetscInt *idx = NULL;
    976:     const PetscInt *old;
    977:     PetscMPIInt     rank;

    979:     PetscCallMPI(MPI_Comm_rank(comm, &rank));
    980:     PetscCall(ISGetLocalSize(strataPermutation, &N));
    981:     PetscCall(ISGetIndices(strataPermutation, &old));
    982:     if (!rank) {
    983:       n   = N;
    984:       idx = old;
    985:     }
    986:     PetscCall(ISCreateGeneral(comm, n, idx, PETSC_COPY_VALUES, &spOnComm));
    987:     PetscCall(ISRestoreIndices(strataPermutation, &old));
    988:     PetscCall(ISDestroy(&strataPermutation));
    989:     strataPermutation = spOnComm;
    990:   }
    991:   PetscCall(PetscObjectSetName((PetscObject)strataPermutation, "permutation"));
    992:   PetscCall(ISView(strataPermutation, viewer));
    993:   PetscCall(PetscViewerHDF5PushGroup(viewer, "strata"));
    994:   for (d = 0; d <= depth; d++) {
    995:     PetscInt pStart, pEnd;
    996:     char     group[128];

    998:     PetscCall(PetscSNPrintf(group, sizeof(group), "%" PetscInt_FMT, d));
    999:     PetscCall(PetscViewerHDF5PushGroup(viewer, group));
    1000:     PetscCall(DMPlexGetDepthStratum(dm, d, &pStart, &pEnd));
    1001:     PetscCall(DMPlexTopologyView_HDF5_Inner_Private(dm, globalPointNumbers0, viewer, pStart, pEnd, NULL, coneSizesName, conesName, orientationsName));
    1002:     PetscCall(PetscViewerHDF5PopGroup(viewer));
    1003:   }
    1004:   PetscCall(PetscViewerHDF5PopGroup(viewer)); /* strata */
    1005:   PetscCall(ISDestroy(&globalPointNumbers0));
    1006:   PetscCall(ISDestroy(&strataPermutation));
    1007:   PetscFunctionReturn(PETSC_SUCCESS);
    1008: }

    1010: PetscErrorCode DMPlexTopologyView_HDF5_Internal(DM dm, IS globalPointNumbers, PetscViewer viewer)
    1011: {
    1012:   DMPlexStorageVersion version;
    1013:   const char          *topologydm_name;
    1014:   char                 group[PETSC_MAX_PATH_LEN];

    1016:   PetscFunctionBegin;
    1017:   PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
    1018:   PetscCall(PetscInfo(dm, "Writing DM %s storage version %d.%d.%d\n", dm->hdr.name, version->major, version->minor, version->subminor));
    1019:   PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
    1020:   if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
    1021:     PetscCall(PetscSNPrintf(group, sizeof(group), "topologies/%s", topologydm_name));
    1022:   } else {
    1023:     PetscCall(PetscStrncpy(group, "/", sizeof(group)));
    1024:   }
    1025:   PetscCall(PetscViewerHDF5PushGroup(viewer, group));

    1027:   PetscCall(PetscViewerHDF5PushGroup(viewer, "topology"));
    1028:   if (version->major < 3) {
    1029:     PetscCall(DMPlexTopologyView_HDF5_Legacy_Private(dm, globalPointNumbers, viewer));
    1030:   } else {
    1031:     /* since DMPlexStorageVersion 3.0.0 */
    1032:     PetscCall(DMPlexTopologyView_HDF5_Private(dm, globalPointNumbers, viewer));
    1033:   }
    1034:   PetscCall(PetscViewerHDF5PopGroup(viewer)); /* "topology" */

    1036:   if (DMPlexStorageVersionGE(version, 2, 1, 0)) {
    1037:     const char *distribution_name;

    1039:     PetscCall(DMPlexDistributionGetName(dm, &distribution_name));
    1040:     PetscCall(PetscViewerHDF5PushGroup(viewer, "distributions"));
    1041:     PetscCall(PetscViewerHDF5WriteGroup(viewer, NULL));
    1042:     PetscCall(PetscViewerHDF5PushGroup(viewer, distribution_name));
    1043:     PetscCall(DMPlexDistributionView_HDF5_Private(dm, globalPointNumbers, viewer));
    1044:     PetscCall(PetscViewerHDF5PopGroup(viewer)); /* distribution_name */
    1045:     PetscCall(PetscViewerHDF5PopGroup(viewer)); /* "distributions" */
    1046:   }

    1048:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1049:   PetscFunctionReturn(PETSC_SUCCESS);
    1050: }

    1052: static PetscErrorCode CreateConesIS_Private(DM dm, PetscInt cStart, PetscInt cEnd, IS globalCellNumbers, PetscInt *numCorners, IS *cellIS)
    1053: {
    1054:   PetscSF         sfPoint;
    1055:   DMLabel         cutLabel, cutVertexLabel         = NULL;
    1056:   IS              globalVertexNumbers, cutvertices = NULL;
    1057:   const PetscInt *gcell, *gvertex, *cutverts = NULL;
    1058:   PetscInt       *vertices;
    1059:   PetscInt        conesSize = 0;
    1060:   PetscInt        dim, numCornersLocal = 0, cell, vStart, vEnd, vExtra = 0, v;

    1062:   PetscFunctionBegin;
    1063:   *numCorners = 0;
    1064:   PetscCall(DMGetDimension(dm, &dim));
    1065:   PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
    1066:   PetscCall(ISGetIndices(globalCellNumbers, &gcell));

    1068:   for (cell = cStart; cell < cEnd; ++cell) {
    1069:     PetscInt *closure = NULL;
    1070:     PetscInt  closureSize, v, Nc = 0;

    1072:     if (gcell[cell] < 0) continue;
    1073:     PetscCall(DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure));
    1074:     for (v = 0; v < closureSize * 2; v += 2) {
    1075:       if ((closure[v] >= vStart) && (closure[v] < vEnd)) ++Nc;
    1076:     }
    1077:     PetscCall(DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure));
    1078:     conesSize += Nc;
    1079:     if (!numCornersLocal) numCornersLocal = Nc;
    1080:     else if (numCornersLocal != Nc) numCornersLocal = 1;
    1081:   }
    1082:   PetscCallMPI(MPIU_Allreduce(&numCornersLocal, numCorners, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)dm)));
    1083:   PetscCheck(!numCornersLocal || !(numCornersLocal != *numCorners || *numCorners == 0), PETSC_COMM_SELF, PETSC_ERR_SUP, "Visualization topology currently only supports identical cell shapes");
    1084:   /* Handle periodic cuts by identifying vertices which should be duplicated */
    1085:   PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel));
    1086:   PetscCall(DMPlexCreateCutVertexLabel_Private(dm, cutLabel, &cutVertexLabel));
    1087:   if (cutVertexLabel) PetscCall(DMLabelGetStratumIS(cutVertexLabel, 1, &cutvertices));
    1088:   if (cutvertices) {
    1089:     PetscCall(ISGetIndices(cutvertices, &cutverts));
    1090:     PetscCall(ISGetLocalSize(cutvertices, &vExtra));
    1091:   }
    1092:   PetscCall(DMGetPointSF(dm, &sfPoint));
    1093:   if (cutLabel) {
    1094:     const PetscInt    *ilocal;
    1095:     const PetscSFNode *iremote;
    1096:     PetscInt           nroots, nleaves;

    1098:     PetscCall(PetscSFGetGraph(sfPoint, &nroots, &nleaves, &ilocal, &iremote));
    1099:     if (nleaves < 0) {
    1100:       PetscCall(PetscObjectReference((PetscObject)sfPoint));
    1101:     } else {
    1102:       PetscCall(PetscSFCreate(PetscObjectComm((PetscObject)sfPoint), &sfPoint));
    1103:       PetscCall(PetscSFSetGraph(sfPoint, nroots + vExtra, nleaves, (PetscInt *)ilocal, PETSC_COPY_VALUES, (PetscSFNode *)iremote, PETSC_COPY_VALUES));
    1104:     }
    1105:   } else {
    1106:     PetscCall(PetscObjectReference((PetscObject)sfPoint));
    1107:   }
    1108:   /* Number all vertices */
    1109:   PetscCall(DMPlexCreateNumbering_Plex(dm, vStart, vEnd + vExtra, 0, NULL, sfPoint, &globalVertexNumbers));
    1110:   PetscCall(PetscSFDestroy(&sfPoint));
    1111:   /* Create cones */
    1112:   PetscCall(ISGetIndices(globalVertexNumbers, &gvertex));
    1113:   PetscCall(PetscMalloc1(conesSize, &vertices));
    1114:   for (cell = cStart, v = 0; cell < cEnd; ++cell) {
    1115:     PetscInt *closure = NULL;
    1116:     PetscInt  closureSize, Nc = 0, p, value = -1;
    1117:     PetscBool replace;

    1119:     if (gcell[cell] < 0) continue;
    1120:     if (cutLabel) PetscCall(DMLabelGetValue(cutLabel, cell, &value));
    1121:     replace = (value == 2) ? PETSC_TRUE : PETSC_FALSE;
    1122:     PetscCall(DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure));
    1123:     for (p = 0; p < closureSize * 2; p += 2) {
    1124:       if ((closure[p] >= vStart) && (closure[p] < vEnd)) closure[Nc++] = closure[p];
    1125:     }
    1126:     PetscCall(DMPlexReorderCell(dm, cell, closure));
    1127:     for (p = 0; p < Nc; ++p) {
    1128:       PetscInt nv, gv = gvertex[closure[p] - vStart];

    1130:       if (replace) {
    1131:         PetscCall(PetscFindInt(closure[p], vExtra, cutverts, &nv));
    1132:         if (nv >= 0) gv = gvertex[vEnd - vStart + nv];
    1133:       }
    1134:       vertices[v++] = gv < 0 ? -(gv + 1) : gv;
    1135:     }
    1136:     PetscCall(DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure));
    1137:   }
    1138:   PetscCall(ISRestoreIndices(globalVertexNumbers, &gvertex));
    1139:   PetscCall(ISDestroy(&globalVertexNumbers));
    1140:   PetscCall(ISRestoreIndices(globalCellNumbers, &gcell));
    1141:   if (cutvertices) PetscCall(ISRestoreIndices(cutvertices, &cutverts));
    1142:   PetscCall(ISDestroy(&cutvertices));
    1143:   PetscCall(DMLabelDestroy(&cutVertexLabel));
    1144:   PetscCheck(v == conesSize, PETSC_COMM_SELF, PETSC_ERR_LIB, "Total number of cell vertices %" PetscInt_FMT " != %" PetscInt_FMT, v, conesSize);
    1145:   PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)dm), conesSize, vertices, PETSC_OWN_POINTER, cellIS));
    1146:   PetscCall(PetscLayoutSetBlockSize((*cellIS)->map, *numCorners));
    1147:   PetscCall(PetscObjectSetName((PetscObject)*cellIS, "cells"));
    1148:   PetscFunctionReturn(PETSC_SUCCESS);
    1149: }

    1151: static PetscErrorCode DMPlexTopologyView_HDF5_XDMF_Private(DM dm, IS globalCellNumbers, PetscViewer viewer)
    1152: {
    1153:   DM       cdm;
    1154:   DMLabel  depthLabel, ctLabel;
    1155:   IS       cellIS;
    1156:   PetscInt dim, depth, cellHeight, c, n = 0;

    1158:   PetscFunctionBegin;
    1159:   PetscCall(PetscViewerHDF5PushGroup(viewer, "/viz"));
    1160:   PetscCall(PetscViewerHDF5WriteGroup(viewer, NULL));

    1162:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1163:   PetscCall(DMGetDimension(dm, &dim));
    1164:   PetscCall(DMPlexGetDepth(dm, &depth));
    1165:   PetscCall(DMGetCoordinateDM(dm, &cdm));
    1166:   PetscCall(DMPlexGetVTKCellHeight(dm, &cellHeight));
    1167:   PetscCall(DMPlexGetDepthLabel(dm, &depthLabel));
    1168:   PetscCall(DMPlexGetCellTypeLabel(dm, &ctLabel));
    1169:   for (c = 0; c < DM_NUM_POLYTOPES; ++c) {
    1170:     const DMPolytopeType ict = (DMPolytopeType)c;
    1171:     PetscInt             pStart, pEnd, dep, numCorners;
    1172:     PetscBool            output = PETSC_FALSE, doOutput;

    1174:     if (ict == DM_POLYTOPE_FV_GHOST) continue;
    1175:     PetscCall(DMLabelGetStratumBounds(ctLabel, ict, &pStart, &pEnd));
    1176:     if (pStart >= 0) {
    1177:       PetscCall(DMLabelGetValue(depthLabel, pStart, &dep));
    1178:       if (dep == depth - cellHeight) output = PETSC_TRUE;
    1179:     }
    1180:     PetscCallMPI(MPIU_Allreduce(&output, &doOutput, 1, MPIU_BOOL, MPI_LOR, PetscObjectComm((PetscObject)dm)));
    1181:     if (!doOutput) continue;
    1182:     PetscCall(CreateConesIS_Private(dm, pStart, pEnd, globalCellNumbers, &numCorners, &cellIS));
    1183:     if (!n) {
    1184:       PetscCall(PetscViewerHDF5PushGroup(viewer, "/viz/topology"));
    1185:     } else {
    1186:       char group[PETSC_MAX_PATH_LEN];

    1188:       PetscCall(PetscSNPrintf(group, PETSC_MAX_PATH_LEN, "/viz/topology_%" PetscInt_FMT, n));
    1189:       PetscCall(PetscViewerHDF5PushGroup(viewer, group));
    1190:     }
    1191:     PetscCall(ISView(cellIS, viewer));
    1192:     PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)cellIS, "cell_corners", PETSC_INT, (void *)&numCorners));
    1193:     PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)cellIS, "cell_dim", PETSC_INT, (void *)&dim));
    1194:     PetscCall(ISDestroy(&cellIS));
    1195:     PetscCall(PetscViewerHDF5PopGroup(viewer));
    1196:     ++n;
    1197:   }
    1198:   PetscFunctionReturn(PETSC_SUCCESS);
    1199: }

    1201: static PetscErrorCode DMPlexCoordinatesView_HDF5_Legacy_Private(DM dm, PetscViewer viewer)
    1202: {
    1203:   DM        cdm;
    1204:   Vec       coordinates, newcoords;
    1205:   PetscReal lengthScale;
    1206:   PetscInt  m, M, bs;

    1208:   PetscFunctionBegin;
    1209:   PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
    1210:   PetscCall(DMGetCoordinateDM(dm, &cdm));
    1211:   PetscCall(DMGetCoordinates(dm, &coordinates));
    1212:   PetscCall(VecCreate(PetscObjectComm((PetscObject)coordinates), &newcoords));
    1213:   PetscCall(PetscObjectSetName((PetscObject)newcoords, "vertices"));
    1214:   PetscCall(VecGetSize(coordinates, &M));
    1215:   PetscCall(VecGetLocalSize(coordinates, &m));
    1216:   PetscCall(VecSetSizes(newcoords, m, M));
    1217:   PetscCall(VecGetBlockSize(coordinates, &bs));
    1218:   PetscCall(VecSetBlockSize(newcoords, bs));
    1219:   PetscCall(VecSetType(newcoords, VECSTANDARD));
    1220:   PetscCall(VecCopy(coordinates, newcoords));
    1221:   PetscCall(VecScale(newcoords, lengthScale));
    1222:   /* Did not use DMGetGlobalVector() in order to bypass default group assignment */
    1223:   PetscCall(PetscViewerHDF5PushGroup(viewer, "/geometry"));
    1224:   PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_NATIVE));
    1225:   PetscCall(VecView(newcoords, viewer));
    1226:   PetscCall(PetscViewerPopFormat(viewer));
    1227:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1228:   PetscCall(VecDestroy(&newcoords));
    1229:   PetscFunctionReturn(PETSC_SUCCESS);
    1230: }

    1232: PetscErrorCode DMPlexCoordinatesView_HDF5_Internal(DM dm, PetscViewer viewer)
    1233: {
    1234:   DM          cdm;
    1235:   Vec         coords, newcoords;
    1236:   PetscInt    m, M, bs;
    1237:   PetscReal   lengthScale;
    1238:   PetscBool   viewSection = PETSC_TRUE;
    1239:   const char *topologydm_name, *coordinatedm_name, *coordinates_name;

    1241:   PetscFunctionBegin;
    1242:   {
    1243:     PetscViewerFormat    format;
    1244:     DMPlexStorageVersion version;

    1246:     PetscCall(PetscViewerGetFormat(viewer, &format));
    1247:     PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
    1248:     if (!DMPlexStorageVersionGE(version, 2, 0, 0) || format == PETSC_VIEWER_HDF5_XDMF || format == PETSC_VIEWER_HDF5_VIZ) {
    1249:       PetscCall(DMPlexCoordinatesView_HDF5_Legacy_Private(dm, viewer));
    1250:       PetscFunctionReturn(PETSC_SUCCESS);
    1251:     }
    1252:   }
    1253:   /* since 2.0.0 */
    1254:   PetscCall(PetscOptionsGetBool(NULL, dm->hdr.prefix, "-dm_plex_view_coordinate_section", &viewSection, NULL));
    1255:   PetscCall(DMGetCoordinateDM(dm, &cdm));
    1256:   PetscCall(DMGetCoordinates(dm, &coords));
    1257:   PetscCall(PetscObjectGetName((PetscObject)cdm, &coordinatedm_name));
    1258:   PetscCall(PetscObjectGetName((PetscObject)coords, &coordinates_name));
    1259:   PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
    1260:   PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
    1261:   PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
    1262:   PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "coordinateDMName", PETSC_STRING, coordinatedm_name));
    1263:   PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "coordinatesName", PETSC_STRING, coordinates_name));
    1264:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1265:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1266:   if (viewSection) PetscCall(DMPlexSectionView(dm, viewer, cdm));
    1267:   PetscCall(VecCreate(PetscObjectComm((PetscObject)coords), &newcoords));
    1268:   PetscCall(PetscObjectSetName((PetscObject)newcoords, coordinates_name));
    1269:   PetscCall(VecGetSize(coords, &M));
    1270:   PetscCall(VecGetLocalSize(coords, &m));
    1271:   PetscCall(VecSetSizes(newcoords, m, M));
    1272:   PetscCall(VecGetBlockSize(coords, &bs));
    1273:   PetscCall(VecSetBlockSize(newcoords, bs));
    1274:   PetscCall(VecSetType(newcoords, VECSTANDARD));
    1275:   PetscCall(VecCopy(coords, newcoords));
    1276:   PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
    1277:   PetscCall(VecScale(newcoords, lengthScale));
    1278:   PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_NATIVE));
    1279:   PetscCall(DMPlexGlobalVectorView(dm, viewer, cdm, newcoords));
    1280:   PetscCall(PetscViewerPopFormat(viewer));
    1281:   PetscCall(VecDestroy(&newcoords));
    1282:   PetscFunctionReturn(PETSC_SUCCESS);
    1283: }

    1285: static PetscErrorCode DMPlexCoordinatesView_HDF5_XDMF_Private(DM dm, PetscViewer viewer)
    1286: {
    1287:   DM               cdm;
    1288:   Vec              coordinatesLocal, newcoords;
    1289:   PetscSection     cSection, cGlobalSection;
    1290:   PetscScalar     *coords, *ncoords;
    1291:   DMLabel          cutLabel, cutVertexLabel = NULL;
    1292:   const PetscReal *L;
    1293:   PetscReal        lengthScale;
    1294:   PetscInt         vStart, vEnd, v, bs, N, coordSize, dof, off, d;
    1295:   PetscBool        localized, embedded;

    1297:   PetscFunctionBegin;
    1298:   PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
    1299:   PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
    1300:   PetscCall(DMGetCoordinatesLocal(dm, &coordinatesLocal));
    1301:   PetscCall(VecGetBlockSize(coordinatesLocal, &bs));
    1302:   PetscCall(DMGetCoordinatesLocalized(dm, &localized));
    1303:   if (localized == PETSC_FALSE) PetscFunctionReturn(PETSC_SUCCESS);
    1304:   PetscCall(DMGetPeriodicity(dm, NULL, NULL, &L));
    1305:   PetscCall(DMGetCoordinateDM(dm, &cdm));
    1306:   PetscCall(DMGetLocalSection(cdm, &cSection));
    1307:   PetscCall(DMGetGlobalSection(cdm, &cGlobalSection));
    1308:   PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel));
    1309:   N = 0;

    1311:   PetscCall(DMPlexCreateCutVertexLabel_Private(dm, cutLabel, &cutVertexLabel));
    1312:   PetscCall(VecCreate(PetscObjectComm((PetscObject)dm), &newcoords));
    1313:   PetscCall(PetscSectionGetDof(cSection, vStart, &dof));
    1314:   PetscCall(PetscPrintf(PETSC_COMM_SELF, "DOF: %" PetscInt_FMT "\n", dof));
    1315:   embedded = (PetscBool)(L && dof == 2 && !cutLabel);
    1316:   if (cutVertexLabel) {
    1317:     PetscCall(DMLabelGetStratumSize(cutVertexLabel, 1, &v));
    1318:     N += dof * v;
    1319:   }
    1320:   for (v = vStart; v < vEnd; ++v) {
    1321:     PetscCall(PetscSectionGetDof(cGlobalSection, v, &dof));
    1322:     if (dof < 0) continue;
    1323:     if (embedded) N += dof + 1;
    1324:     else N += dof;
    1325:   }
    1326:   if (embedded) PetscCall(VecSetBlockSize(newcoords, bs + 1));
    1327:   else PetscCall(VecSetBlockSize(newcoords, bs));
    1328:   PetscCall(VecSetSizes(newcoords, N, PETSC_DETERMINE));
    1329:   PetscCall(VecSetType(newcoords, VECSTANDARD));
    1330:   PetscCall(VecGetArray(coordinatesLocal, &coords));
    1331:   PetscCall(VecGetArray(newcoords, &ncoords));
    1332:   coordSize = 0;
    1333:   for (v = vStart; v < vEnd; ++v) {
    1334:     PetscCall(PetscSectionGetDof(cGlobalSection, v, &dof));
    1335:     PetscCall(PetscSectionGetOffset(cSection, v, &off));
    1336:     if (dof < 0) continue;
    1337:     if (embedded) {
    1338:       if (L && (L[0] > 0.0) && (L[1] > 0.0)) {
    1339:         PetscReal theta, phi, r, R;
    1340:         /* XY-periodic */
    1341:         /* Suppose its an y-z circle, then
    1342:              \hat r = (0, cos(th), sin(th)) \hat x = (1, 0, 0)
    1343:            and the circle in that plane is
    1344:              \hat r cos(phi) + \hat x sin(phi) */
    1345:         theta                = 2.0 * PETSC_PI * PetscRealPart(coords[off + 1]) / L[1];
    1346:         phi                  = 2.0 * PETSC_PI * PetscRealPart(coords[off + 0]) / L[0];
    1347:         r                    = L[0] / (2.0 * PETSC_PI * 2.0 * L[1]);
    1348:         R                    = L[1] / (2.0 * PETSC_PI);
    1349:         ncoords[coordSize++] = PetscSinReal(phi) * r;
    1350:         ncoords[coordSize++] = -PetscCosReal(theta) * (R + r * PetscCosReal(phi));
    1351:         ncoords[coordSize++] = PetscSinReal(theta) * (R + r * PetscCosReal(phi));
    1352:       } else if (L && (L[0] > 0.0)) {
    1353:         /* X-periodic */
    1354:         ncoords[coordSize++] = -PetscCosReal(2.0 * PETSC_PI * PetscRealPart(coords[off + 0]) / L[0]) * (L[0] / (2.0 * PETSC_PI));
    1355:         ncoords[coordSize++] = coords[off + 1];
    1356:         ncoords[coordSize++] = PetscSinReal(2.0 * PETSC_PI * PetscRealPart(coords[off + 0]) / L[0]) * (L[0] / (2.0 * PETSC_PI));
    1357:       } else if (L && (L[1] > 0.0)) {
    1358:         /* Y-periodic */
    1359:         ncoords[coordSize++] = coords[off + 0];
    1360:         ncoords[coordSize++] = PetscSinReal(2.0 * PETSC_PI * PetscRealPart(coords[off + 1]) / L[1]) * (L[1] / (2.0 * PETSC_PI));
    1361:         ncoords[coordSize++] = -PetscCosReal(2.0 * PETSC_PI * PetscRealPart(coords[off + 1]) / L[1]) * (L[1] / (2.0 * PETSC_PI));
    1362: #if 0
    1363:       } else if ((bd[0] == DM_BOUNDARY_TWIST)) {
    1364:         PetscReal phi, r, R;
    1365:         /* Mobius strip */
    1366:         /* Suppose its an x-z circle, then
    1367:              \hat r = (-cos(phi), 0, sin(phi)) \hat y = (0, 1, 0)
    1368:            and in that plane we rotate by pi as we go around the circle
    1369:              \hat r cos(phi/2) + \hat y sin(phi/2) */
    1370:         phi   = 2.0*PETSC_PI*PetscRealPart(coords[off+0])/L[0];
    1371:         R     = L[0];
    1372:         r     = PetscRealPart(coords[off+1]) - L[1]/2.0;
    1373:         ncoords[coordSize++] = -PetscCosReal(phi) * (R + r * PetscCosReal(phi/2.0));
    1374:         ncoords[coordSize++] =  PetscSinReal(phi/2.0) * r;
    1375:         ncoords[coordSize++] =  PetscSinReal(phi) * (R + r * PetscCosReal(phi/2.0));
    1376: #endif
    1377:       } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Cannot handle periodicity in this domain");
    1378:     } else {
    1379:       for (d = 0; d < dof; ++d, ++coordSize) ncoords[coordSize] = coords[off + d];
    1380:     }
    1381:   }
    1382:   if (cutVertexLabel) {
    1383:     IS              vertices;
    1384:     const PetscInt *verts;
    1385:     PetscInt        n;

    1387:     PetscCall(DMLabelGetStratumIS(cutVertexLabel, 1, &vertices));
    1388:     if (vertices) {
    1389:       PetscCall(ISGetIndices(vertices, &verts));
    1390:       PetscCall(ISGetLocalSize(vertices, &n));
    1391:       for (v = 0; v < n; ++v) {
    1392:         PetscCall(PetscSectionGetDof(cSection, verts[v], &dof));
    1393:         PetscCall(PetscSectionGetOffset(cSection, verts[v], &off));
    1394:         for (d = 0; d < dof; ++d) ncoords[coordSize++] = coords[off + d] + ((L[d] > 0.) ? L[d] : 0.0);
    1395:       }
    1396:       PetscCall(ISRestoreIndices(vertices, &verts));
    1397:       PetscCall(ISDestroy(&vertices));
    1398:     }
    1399:   }
    1400:   PetscCheck(coordSize == N, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatched sizes: %" PetscInt_FMT " != %" PetscInt_FMT, coordSize, N);
    1401:   PetscCall(DMLabelDestroy(&cutVertexLabel));
    1402:   PetscCall(VecRestoreArray(coordinatesLocal, &coords));
    1403:   PetscCall(VecRestoreArray(newcoords, &ncoords));
    1404:   PetscCall(PetscObjectSetName((PetscObject)newcoords, "vertices"));
    1405:   PetscCall(VecScale(newcoords, lengthScale));
    1406:   PetscCall(PetscViewerHDF5PushGroup(viewer, "/viz"));
    1407:   PetscCall(PetscViewerHDF5WriteGroup(viewer, NULL));
    1408:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1409:   PetscCall(PetscViewerHDF5PushGroup(viewer, "/viz/geometry"));
    1410:   PetscCall(VecView(newcoords, viewer));
    1411:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1412:   PetscCall(VecDestroy(&newcoords));
    1413:   PetscFunctionReturn(PETSC_SUCCESS);
    1414: }

    1416: PetscErrorCode DMPlexLabelsView_HDF5_Internal(DM dm, IS globalPointNumbers, PetscViewer viewer)
    1417: {
    1418:   const char          *topologydm_name;
    1419:   const PetscInt      *gpoint;
    1420:   PetscInt             numLabels;
    1421:   PetscBool            omitCelltypes = PETSC_FALSE;
    1422:   DMPlexStorageVersion version;
    1423:   char                 group[PETSC_MAX_PATH_LEN];

    1425:   PetscFunctionBegin;
    1426:   PetscCall(PetscOptionsGetBool(NULL, dm->hdr.prefix, "-dm_plex_omit_celltypes", &omitCelltypes, NULL));
    1427:   PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
    1428:   PetscCall(ISGetIndices(globalPointNumbers, &gpoint));
    1429:   PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
    1430:   if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
    1431:     PetscCall(PetscSNPrintf(group, sizeof(group), "topologies/%s/labels", topologydm_name));
    1432:   } else {
    1433:     PetscCall(PetscStrncpy(group, "/labels", sizeof(group)));
    1434:   }
    1435:   PetscCall(PetscViewerHDF5PushGroup(viewer, group));
    1436:   PetscCall(DMGetNumLabels(dm, &numLabels));
    1437:   for (PetscInt l = 0; l < numLabels; ++l) {
    1438:     DMLabel         label;
    1439:     const char     *name;
    1440:     IS              valueIS, pvalueIS, globalValueIS;
    1441:     const PetscInt *values;
    1442:     PetscInt        numValues, v;
    1443:     PetscBool       isDepth, isCelltype, output;

    1445:     PetscCall(DMGetLabelByNum(dm, l, &label));
    1446:     PetscCall(PetscObjectGetName((PetscObject)label, &name));
    1447:     PetscCall(DMGetLabelOutput(dm, name, &output));
    1448:     PetscCall(PetscStrncmp(name, "depth", 10, &isDepth));
    1449:     PetscCall(PetscStrncmp(name, "celltype", 10, &isCelltype));
    1450:     // TODO Should only filter out celltype if it can be calculated
    1451:     if (isDepth || (isCelltype && omitCelltypes) || !output) continue;
    1452:     PetscCall(PetscViewerHDF5PushGroup(viewer, name));
    1453:     PetscCall(DMLabelGetValueIS(label, &valueIS));
    1454:     /* Must copy to a new IS on the global comm */
    1455:     PetscCall(ISGetLocalSize(valueIS, &numValues));
    1456:     PetscCall(ISGetIndices(valueIS, &values));
    1457:     PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)dm), numValues, values, PETSC_COPY_VALUES, &pvalueIS));
    1458:     PetscCall(ISRestoreIndices(valueIS, &values));
    1459:     PetscCall(ISAllGather(pvalueIS, &globalValueIS));
    1460:     PetscCall(ISDestroy(&pvalueIS));
    1461:     PetscCall(ISSortRemoveDups(globalValueIS));
    1462:     PetscCall(ISGetLocalSize(globalValueIS, &numValues));
    1463:     PetscCall(ISGetIndices(globalValueIS, &values));
    1464:     for (v = 0; v < numValues; ++v) {
    1465:       IS              stratumIS, globalStratumIS;
    1466:       const PetscInt *spoints = NULL;
    1467:       PetscInt       *gspoints, n = 0, gn, p;
    1468:       const char     *iname = "indices";
    1469:       char            group[PETSC_MAX_PATH_LEN];

    1471:       PetscCall(PetscSNPrintf(group, sizeof(group), "%" PetscInt_FMT, values[v]));
    1472:       PetscCall(PetscViewerHDF5PushGroup(viewer, group));
    1473:       PetscCall(DMLabelGetStratumIS(label, values[v], &stratumIS));

    1475:       if (stratumIS) PetscCall(ISGetLocalSize(stratumIS, &n));
    1476:       if (stratumIS) PetscCall(ISGetIndices(stratumIS, &spoints));
    1477:       for (gn = 0, p = 0; p < n; ++p)
    1478:         if (gpoint[spoints[p]] >= 0) ++gn;
    1479:       PetscCall(PetscMalloc1(gn, &gspoints));
    1480:       for (gn = 0, p = 0; p < n; ++p)
    1481:         if (gpoint[spoints[p]] >= 0) gspoints[gn++] = gpoint[spoints[p]];
    1482:       if (stratumIS) PetscCall(ISRestoreIndices(stratumIS, &spoints));
    1483:       PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)dm), gn, gspoints, PETSC_OWN_POINTER, &globalStratumIS));
    1484:       PetscCall(PetscObjectSetName((PetscObject)globalStratumIS, iname));

    1486:       PetscCall(ISView(globalStratumIS, viewer));
    1487:       PetscCall(ISDestroy(&globalStratumIS));
    1488:       PetscCall(ISDestroy(&stratumIS));
    1489:       PetscCall(PetscViewerHDF5PopGroup(viewer));
    1490:     }
    1491:     PetscCall(ISRestoreIndices(globalValueIS, &values));
    1492:     PetscCall(ISDestroy(&globalValueIS));
    1493:     PetscCall(ISDestroy(&valueIS));
    1494:     PetscCall(PetscViewerHDF5PopGroup(viewer));
    1495:   }
    1496:   PetscCall(ISRestoreIndices(globalPointNumbers, &gpoint));
    1497:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1498:   PetscFunctionReturn(PETSC_SUCCESS);
    1499: }

    1501: /* We only write cells and vertices. Does this screw up parallel reading? */
    1502: PetscErrorCode DMPlexView_HDF5_Internal(DM dm, PetscViewer viewer)
    1503: {
    1504:   IS                globalPointNumbers;
    1505:   PetscViewerFormat format;
    1506:   PetscBool         viz_geom = PETSC_FALSE, xdmf_topo = PETSC_FALSE, petsc_topo = PETSC_FALSE;

    1508:   PetscFunctionBegin;
    1509:   PetscCall(DMPlexCreatePointNumbering(dm, &globalPointNumbers));
    1510:   PetscCall(DMPlexCoordinatesView_HDF5_Internal(dm, viewer));

    1512:   PetscCall(PetscViewerGetFormat(viewer, &format));
    1513:   switch (format) {
    1514:   case PETSC_VIEWER_HDF5_VIZ:
    1515:     viz_geom  = PETSC_TRUE;
    1516:     xdmf_topo = PETSC_TRUE;
    1517:     break;
    1518:   case PETSC_VIEWER_HDF5_XDMF:
    1519:     xdmf_topo = PETSC_TRUE;
    1520:     break;
    1521:   case PETSC_VIEWER_HDF5_PETSC:
    1522:     petsc_topo = PETSC_TRUE;
    1523:     break;
    1524:   case PETSC_VIEWER_DEFAULT:
    1525:   case PETSC_VIEWER_NATIVE:
    1526:     viz_geom   = PETSC_TRUE;
    1527:     xdmf_topo  = PETSC_TRUE;
    1528:     petsc_topo = PETSC_TRUE;
    1529:     break;
    1530:   default:
    1531:     SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 output.", PetscViewerFormats[format]);
    1532:   }

    1534:   if (viz_geom) PetscCall(DMPlexCoordinatesView_HDF5_XDMF_Private(dm, viewer));
    1535:   if (xdmf_topo) PetscCall(DMPlexTopologyView_HDF5_XDMF_Private(dm, globalPointNumbers, viewer));
    1536:   if (petsc_topo) {
    1537:     PetscBool viewLabels = PETSC_TRUE;

    1539:     PetscCall(DMPlexTopologyView_HDF5_Internal(dm, globalPointNumbers, viewer));
    1540:     PetscCall(PetscOptionsGetBool(NULL, dm->hdr.prefix, "-dm_plex_view_labels", &viewLabels, NULL));
    1541:     if (viewLabels) PetscCall(DMPlexLabelsView_HDF5_Internal(dm, globalPointNumbers, viewer));
    1542:   }

    1544:   PetscCall(ISDestroy(&globalPointNumbers));
    1545:   PetscFunctionReturn(PETSC_SUCCESS);
    1546: }

    1548: PetscErrorCode DMPlexSectionView_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm)
    1549: {
    1550:   MPI_Comm     comm;
    1551:   const char  *topologydm_name;
    1552:   const char  *sectiondm_name;
    1553:   PetscSection gsection;

    1555:   PetscFunctionBegin;
    1556:   PetscCall(PetscObjectGetComm((PetscObject)sectiondm, &comm));
    1557:   PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
    1558:   PetscCall(PetscObjectGetName((PetscObject)sectiondm, &sectiondm_name));
    1559:   PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
    1560:   PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
    1561:   PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
    1562:   PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
    1563:   PetscCall(DMGetGlobalSection(sectiondm, &gsection));
    1564:   /* Save raw section */
    1565:   PetscCall(PetscSectionView(gsection, viewer));
    1566:   /* Save plex wrapper */
    1567:   {
    1568:     PetscInt        pStart, pEnd, p, n;
    1569:     IS              globalPointNumbers;
    1570:     const PetscInt *gpoints;
    1571:     IS              orderIS;
    1572:     PetscInt       *order;

    1574:     PetscCall(PetscSectionGetChart(gsection, &pStart, &pEnd));
    1575:     PetscCall(DMPlexCreatePointNumbering(dm, &globalPointNumbers));
    1576:     PetscCall(ISGetIndices(globalPointNumbers, &gpoints));
    1577:     for (p = pStart, n = 0; p < pEnd; ++p)
    1578:       if (gpoints[p] >= 0) n++;
    1579:     /* "order" is an array of global point numbers.
    1580:        When loading, it is used with topology/order array
    1581:        to match section points with plex topology points. */
    1582:     PetscCall(PetscMalloc1(n, &order));
    1583:     for (p = pStart, n = 0; p < pEnd; ++p)
    1584:       if (gpoints[p] >= 0) order[n++] = gpoints[p];
    1585:     PetscCall(ISRestoreIndices(globalPointNumbers, &gpoints));
    1586:     PetscCall(ISDestroy(&globalPointNumbers));
    1587:     PetscCall(ISCreateGeneral(comm, n, order, PETSC_OWN_POINTER, &orderIS));
    1588:     PetscCall(PetscObjectSetName((PetscObject)orderIS, "order"));
    1589:     PetscCall(ISView(orderIS, viewer));
    1590:     PetscCall(ISDestroy(&orderIS));
    1591:   }
    1592:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1593:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1594:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1595:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1596:   PetscFunctionReturn(PETSC_SUCCESS);
    1597: }

    1599: PetscErrorCode DMPlexGlobalVectorView_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm, Vec vec)
    1600: {
    1601:   const char *topologydm_name;
    1602:   const char *sectiondm_name;
    1603:   const char *vec_name;
    1604:   PetscInt    bs;

    1606:   PetscFunctionBegin;
    1607:   /* Check consistency */
    1608:   {
    1609:     PetscSF pointsf, pointsf1;

    1611:     PetscCall(DMGetPointSF(dm, &pointsf));
    1612:     PetscCall(DMGetPointSF(sectiondm, &pointsf1));
    1613:     PetscCheck(pointsf1 == pointsf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatching point SFs for dm and sectiondm");
    1614:   }
    1615:   PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
    1616:   PetscCall(PetscObjectGetName((PetscObject)sectiondm, &sectiondm_name));
    1617:   PetscCall(PetscObjectGetName((PetscObject)vec, &vec_name));
    1618:   PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
    1619:   PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
    1620:   PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
    1621:   PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
    1622:   PetscCall(PetscViewerHDF5PushGroup(viewer, "vecs"));
    1623:   PetscCall(PetscViewerHDF5PushGroup(viewer, vec_name));
    1624:   PetscCall(VecGetBlockSize(vec, &bs));
    1625:   PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "blockSize", PETSC_INT, (void *)&bs));
    1626:   PetscCall(VecSetBlockSize(vec, 1));
    1627:   /* VecView(vec, viewer) would call (*vec->opt->view)(vec, viewer), but,    */
    1628:   /* if vec was created with DMGet{Global, Local}Vector(), vec->opt->view    */
    1629:   /* is set to VecView_Plex, which would save vec in a predefined location.  */
    1630:   /* To save vec in where we want, we create a new Vec (temp) with           */
    1631:   /* VecCreate(), wrap the vec data in temp, and call VecView(temp, viewer). */
    1632:   {
    1633:     Vec                temp;
    1634:     const PetscScalar *array;
    1635:     PetscLayout        map;

    1637:     PetscCall(VecCreate(PetscObjectComm((PetscObject)vec), &temp));
    1638:     PetscCall(PetscObjectSetName((PetscObject)temp, vec_name));
    1639:     PetscCall(VecGetLayout(vec, &map));
    1640:     PetscCall(VecSetLayout(temp, map));
    1641:     PetscCall(VecSetUp(temp));
    1642:     PetscCall(VecGetArrayRead(vec, &array));
    1643:     PetscCall(VecPlaceArray(temp, array));
    1644:     PetscCall(VecView(temp, viewer));
    1645:     PetscCall(VecResetArray(temp));
    1646:     PetscCall(VecRestoreArrayRead(vec, &array));
    1647:     PetscCall(VecDestroy(&temp));
    1648:   }
    1649:   PetscCall(VecSetBlockSize(vec, bs));
    1650:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1651:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1652:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1653:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1654:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1655:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1656:   PetscFunctionReturn(PETSC_SUCCESS);
    1657: }

    1659: PetscErrorCode DMPlexLocalVectorView_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm, Vec vec)
    1660: {
    1661:   MPI_Comm     comm;
    1662:   const char  *topologydm_name;
    1663:   const char  *sectiondm_name;
    1664:   const char  *vec_name;
    1665:   PetscSection section;
    1666:   PetscBool    includesConstraints;
    1667:   Vec          gvec;
    1668:   PetscInt     m, bs;

    1670:   PetscFunctionBegin;
    1671:   PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
    1672:   /* Check consistency */
    1673:   {
    1674:     PetscSF pointsf, pointsf1;

    1676:     PetscCall(DMGetPointSF(dm, &pointsf));
    1677:     PetscCall(DMGetPointSF(sectiondm, &pointsf1));
    1678:     PetscCheck(pointsf1 == pointsf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatching point SFs for dm and sectiondm");
    1679:   }
    1680:   PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
    1681:   PetscCall(PetscObjectGetName((PetscObject)sectiondm, &sectiondm_name));
    1682:   PetscCall(PetscObjectGetName((PetscObject)vec, &vec_name));
    1683:   PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
    1684:   PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
    1685:   PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
    1686:   PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
    1687:   PetscCall(PetscViewerHDF5PushGroup(viewer, "vecs"));
    1688:   PetscCall(PetscViewerHDF5PushGroup(viewer, vec_name));
    1689:   PetscCall(VecGetBlockSize(vec, &bs));
    1690:   PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "blockSize", PETSC_INT, (void *)&bs));
    1691:   PetscCall(VecCreate(comm, &gvec));
    1692:   PetscCall(PetscObjectSetName((PetscObject)gvec, vec_name));
    1693:   PetscCall(DMGetGlobalSection(sectiondm, &section));
    1694:   PetscCall(PetscSectionGetIncludesConstraints(section, &includesConstraints));
    1695:   if (includesConstraints) PetscCall(PetscSectionGetStorageSize(section, &m));
    1696:   else PetscCall(PetscSectionGetConstrainedStorageSize(section, &m));
    1697:   PetscCall(VecSetSizes(gvec, m, PETSC_DECIDE));
    1698:   PetscCall(VecSetUp(gvec));
    1699:   PetscCall(DMLocalToGlobalBegin(sectiondm, vec, INSERT_VALUES, gvec));
    1700:   PetscCall(DMLocalToGlobalEnd(sectiondm, vec, INSERT_VALUES, gvec));
    1701:   PetscCall(VecView(gvec, viewer));
    1702:   PetscCall(VecDestroy(&gvec));
    1703:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1704:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1705:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1706:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1707:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1708:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1709:   PetscFunctionReturn(PETSC_SUCCESS);
    1710: }

    1712: struct _n_LoadLabelsCtx {
    1713:   MPI_Comm    comm;
    1714:   PetscMPIInt rank;
    1715:   DM          dm;
    1716:   PetscViewer viewer;
    1717:   DMLabel     label;
    1718:   PetscSF     sfXC;
    1719:   PetscLayout layoutX;
    1720: };
    1721: typedef struct _n_LoadLabelsCtx *LoadLabelsCtx;

    1723: static PetscErrorCode LoadLabelsCtxCreate(DM dm, PetscViewer viewer, PetscSF sfXC, LoadLabelsCtx *ctx)
    1724: {
    1725:   PetscFunctionBegin;
    1726:   PetscCall(PetscNew(ctx));
    1727:   PetscCall(PetscObjectReference((PetscObject)((*ctx)->dm = dm)));
    1728:   PetscCall(PetscObjectReference((PetscObject)((*ctx)->viewer = viewer)));
    1729:   PetscCall(PetscObjectGetComm((PetscObject)dm, &(*ctx)->comm));
    1730:   PetscCallMPI(MPI_Comm_rank((*ctx)->comm, &(*ctx)->rank));
    1731:   (*ctx)->sfXC = sfXC;
    1732:   if (sfXC) {
    1733:     PetscInt nX;

    1735:     PetscCall(PetscObjectReference((PetscObject)sfXC));
    1736:     PetscCall(PetscSFGetGraph(sfXC, &nX, NULL, NULL, NULL));
    1737:     PetscCall(PetscLayoutCreateFromSizes((*ctx)->comm, nX, PETSC_DECIDE, 1, &(*ctx)->layoutX));
    1738:   }
    1739:   PetscFunctionReturn(PETSC_SUCCESS);
    1740: }

    1742: static PetscErrorCode LoadLabelsCtxDestroy(LoadLabelsCtx *ctx)
    1743: {
    1744:   PetscFunctionBegin;
    1745:   if (!*ctx) PetscFunctionReturn(PETSC_SUCCESS);
    1746:   PetscCall(DMDestroy(&(*ctx)->dm));
    1747:   PetscCall(PetscViewerDestroy(&(*ctx)->viewer));
    1748:   PetscCall(PetscSFDestroy(&(*ctx)->sfXC));
    1749:   PetscCall(PetscLayoutDestroy(&(*ctx)->layoutX));
    1750:   PetscCall(PetscFree(*ctx));
    1751:   PetscFunctionReturn(PETSC_SUCCESS);
    1752: }

    1754: /*
    1755:     A: on-disk points
    1756:     X: global points [0, NX)
    1757:     C: distributed plex points
    1758: */
    1759: static herr_t ReadLabelStratumHDF5_Distribute_Private(IS stratumIS, LoadLabelsCtx ctx, IS *newStratumIS)
    1760: {
    1761:   MPI_Comm        comm    = ctx->comm;
    1762:   PetscSF         sfXC    = ctx->sfXC;
    1763:   PetscLayout     layoutX = ctx->layoutX;
    1764:   PetscSF         sfXA;
    1765:   const PetscInt *A_points;
    1766:   PetscInt        nX, nC;
    1767:   PetscInt        n;

    1769:   PetscFunctionBegin;
    1770:   PetscCall(PetscSFGetGraph(sfXC, &nX, &nC, NULL, NULL));
    1771:   PetscCall(ISGetLocalSize(stratumIS, &n));
    1772:   PetscCall(ISGetIndices(stratumIS, &A_points));
    1773:   PetscCall(PetscSFCreate(comm, &sfXA));
    1774:   PetscCall(PetscSFSetGraphLayout(sfXA, layoutX, n, NULL, PETSC_USE_POINTER, A_points));
    1775:   PetscCall(ISCreate(comm, newStratumIS));
    1776:   PetscCall(ISSetType(*newStratumIS, ISGENERAL));
    1777:   {
    1778:     PetscInt   i;
    1779:     PetscBool *A_mask, *X_mask, *C_mask;

    1781:     PetscCall(PetscCalloc3(n, &A_mask, nX, &X_mask, nC, &C_mask));
    1782:     for (i = 0; i < n; i++) A_mask[i] = PETSC_TRUE;
    1783:     PetscCall(PetscSFReduceBegin(sfXA, MPIU_BOOL, A_mask, X_mask, MPI_REPLACE));
    1784:     PetscCall(PetscSFReduceEnd(sfXA, MPIU_BOOL, A_mask, X_mask, MPI_REPLACE));
    1785:     PetscCall(PetscSFBcastBegin(sfXC, MPIU_BOOL, X_mask, C_mask, MPI_LOR));
    1786:     PetscCall(PetscSFBcastEnd(sfXC, MPIU_BOOL, X_mask, C_mask, MPI_LOR));
    1787:     PetscCall(ISGeneralSetIndicesFromMask(*newStratumIS, 0, nC, C_mask));
    1788:     PetscCall(PetscFree3(A_mask, X_mask, C_mask));
    1789:   }
    1790:   PetscCall(PetscSFDestroy(&sfXA));
    1791:   PetscCall(ISRestoreIndices(stratumIS, &A_points));
    1792:   PetscFunctionReturn(PETSC_SUCCESS);
    1793: }

    1795: static herr_t ReadLabelStratumHDF5_Static(hid_t g_id, const char *vname, const H5L_info_t *info, void *op_data)
    1796: {
    1797:   LoadLabelsCtx   ctx    = (LoadLabelsCtx)op_data;
    1798:   PetscViewer     viewer = ctx->viewer;
    1799:   DMLabel         label  = ctx->label;
    1800:   MPI_Comm        comm   = ctx->comm;
    1801:   IS              stratumIS;
    1802:   const PetscInt *ind;
    1803:   PetscInt        value, N, i;

    1805:   PetscCall(PetscOptionsStringToInt(vname, &value));
    1806:   PetscCall(ISCreate(comm, &stratumIS));
    1807:   PetscCall(PetscObjectSetName((PetscObject)stratumIS, "indices"));
    1808:   PetscCall(PetscViewerHDF5PushGroup(viewer, vname)); /* labels/<lname>/<vname> */

    1810:   if (!ctx->sfXC) {
    1811:     /* Force serial load */
    1812:     PetscCall(PetscViewerHDF5ReadSizes(viewer, "indices", NULL, &N));
    1813:     PetscCall(PetscLayoutSetLocalSize(stratumIS->map, !ctx->rank ? N : 0));
    1814:     PetscCall(PetscLayoutSetSize(stratumIS->map, N));
    1815:   }
    1816:   PetscCall(ISLoad(stratumIS, viewer));

    1818:   if (ctx->sfXC) {
    1819:     IS newStratumIS;

    1821:     PetscCallHDF5(ReadLabelStratumHDF5_Distribute_Private, (stratumIS, ctx, &newStratumIS));
    1822:     PetscCall(ISDestroy(&stratumIS));
    1823:     stratumIS = newStratumIS;
    1824:   }

    1826:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1827:   PetscCall(ISGetLocalSize(stratumIS, &N));
    1828:   PetscCall(ISGetIndices(stratumIS, &ind));
    1829:   for (i = 0; i < N; ++i) PetscCall(DMLabelSetValue(label, ind[i], value));
    1830:   PetscCall(ISRestoreIndices(stratumIS, &ind));
    1831:   PetscCall(ISDestroy(&stratumIS));
    1832:   return 0;
    1833: }

    1835: /* TODO: Fix this code, it is returning PETSc error codes when it should be translating them to herr_t codes */
    1836: static herr_t ReadLabelHDF5_Static(hid_t g_id, const char *lname, const H5L_info_t *info, void *op_data)
    1837: {
    1838:   LoadLabelsCtx  ctx = (LoadLabelsCtx)op_data;
    1839:   DM             dm  = ctx->dm;
    1840:   hsize_t        idx = 0;
    1841:   PetscErrorCode ierr;
    1842:   PetscBool      flg;
    1843:   herr_t         err;

    1845:   PetscCall(DMHasLabel(dm, lname, &flg));
    1846:   if (flg) PetscCall(DMRemoveLabel(dm, lname, NULL));
    1847:   ierr = DMCreateLabel(dm, lname);
    1848:   if (ierr) return (herr_t)ierr;
    1849:   ierr = DMGetLabel(dm, lname, &ctx->label);
    1850:   if (ierr) return (herr_t)ierr;
    1851:   ierr = PetscViewerHDF5PushGroup(ctx->viewer, lname);
    1852:   if (ierr) return (herr_t)ierr;
    1853:   /* Iterate over the label's strata */
    1854:   PetscCallHDF5Return(err, H5Literate_by_name, (g_id, lname, H5_INDEX_NAME, H5_ITER_NATIVE, &idx, ReadLabelStratumHDF5_Static, op_data, 0));
    1855:   ierr = PetscViewerHDF5PopGroup(ctx->viewer);
    1856:   if (ierr) return (herr_t)ierr;
    1857:   return err;
    1858: }

    1860: PetscErrorCode DMPlexLabelsLoad_HDF5_Internal(DM dm, PetscViewer viewer, PetscSF sfXC)
    1861: {
    1862:   const char          *topologydm_name;
    1863:   LoadLabelsCtx        ctx;
    1864:   hsize_t              idx = 0;
    1865:   char                 group[PETSC_MAX_PATH_LEN];
    1866:   DMPlexStorageVersion version;
    1867:   PetscBool            distributed, hasGroup;

    1869:   PetscFunctionBegin;
    1870:   PetscCall(DMPlexIsDistributed(dm, &distributed));
    1871:   if (distributed) PetscCheck(sfXC, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_NULL, "PetscSF must be given for parallel load");
    1872:   PetscCall(LoadLabelsCtxCreate(dm, viewer, sfXC, &ctx));
    1873:   PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
    1874:   PetscCall(PetscViewerHDF5GetDMPlexStorageVersionReading(viewer, &version));
    1875:   if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
    1876:     PetscCall(PetscSNPrintf(group, sizeof(group), "topologies/%s/labels", topologydm_name));
    1877:   } else {
    1878:     PetscCall(PetscStrncpy(group, "labels", sizeof(group)));
    1879:   }
    1880:   PetscCall(PetscViewerHDF5PushGroup(viewer, group));
    1881:   PetscCall(PetscViewerHDF5HasGroup(viewer, NULL, &hasGroup));
    1882:   if (hasGroup) {
    1883:     hid_t fileId, groupId;

    1885:     PetscCall(PetscViewerHDF5OpenGroup(viewer, NULL, &fileId, &groupId));
    1886:     /* Iterate over labels */
    1887:     PetscCallHDF5(H5Literate, (groupId, H5_INDEX_NAME, H5_ITER_NATIVE, &idx, ReadLabelHDF5_Static, ctx));
    1888:     PetscCallHDF5(H5Gclose, (groupId));
    1889:   }
    1890:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1891:   PetscCall(LoadLabelsCtxDestroy(&ctx));
    1892:   PetscFunctionReturn(PETSC_SUCCESS);
    1893: }

    1895: static PetscErrorCode DMPlexDistributionLoad_HDF5_Private(DM dm, PetscViewer viewer, PetscSF sf, PetscSF *distsf, DM *distdm)
    1896: {
    1897:   MPI_Comm        comm;
    1898:   PetscMPIInt     size, rank;
    1899:   PetscInt        dist_size;
    1900:   const char     *distribution_name;
    1901:   PetscInt        p, lsize;
    1902:   IS              chartSizesIS, ownersIS, gpointsIS;
    1903:   const PetscInt *chartSize, *owners, *gpoints;
    1904:   PetscLayout     layout;
    1905:   PetscBool       has;

    1907:   PetscFunctionBegin;
    1908:   *distsf = NULL;
    1909:   *distdm = NULL;
    1910:   PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
    1911:   PetscCallMPI(MPI_Comm_size(comm, &size));
    1912:   PetscCallMPI(MPI_Comm_rank(comm, &rank));
    1913:   PetscCall(DMPlexDistributionGetName(dm, &distribution_name));
    1914:   if (!distribution_name) PetscFunctionReturn(PETSC_SUCCESS);
    1915:   PetscCall(PetscLogEventBegin(DMPLEX_DistributionLoad, viewer, 0, 0, 0));
    1916:   PetscCall(PetscViewerHDF5HasGroup(viewer, NULL, &has));
    1917:   if (!has) {
    1918:     char *full_group;

    1920:     PetscCall(PetscViewerHDF5GetGroup(viewer, NULL, &full_group));
    1921:     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);
    1922:   }
    1923:   PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "comm_size", PETSC_INT, NULL, (void *)&dist_size));
    1924:   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);
    1925:   PetscCall(ISCreate(comm, &chartSizesIS));
    1926:   PetscCall(PetscObjectSetName((PetscObject)chartSizesIS, "chart_sizes"));
    1927:   PetscCall(ISCreate(comm, &ownersIS));
    1928:   PetscCall(PetscObjectSetName((PetscObject)ownersIS, "owners"));
    1929:   PetscCall(ISCreate(comm, &gpointsIS));
    1930:   PetscCall(PetscObjectSetName((PetscObject)gpointsIS, "global_point_numbers"));
    1931:   PetscCall(PetscLayoutSetLocalSize(chartSizesIS->map, 1));
    1932:   PetscCall(ISLoad(chartSizesIS, viewer));
    1933:   PetscCall(ISGetIndices(chartSizesIS, &chartSize));
    1934:   PetscCall(PetscLayoutSetLocalSize(ownersIS->map, *chartSize));
    1935:   PetscCall(PetscLayoutSetLocalSize(gpointsIS->map, *chartSize));
    1936:   PetscCall(ISLoad(ownersIS, viewer));
    1937:   PetscCall(ISLoad(gpointsIS, viewer));
    1938:   PetscCall(ISGetIndices(ownersIS, &owners));
    1939:   PetscCall(ISGetIndices(gpointsIS, &gpoints));
    1940:   PetscCall(PetscSFCreate(comm, distsf));
    1941:   PetscCall(PetscSFSetFromOptions(*distsf));
    1942:   PetscCall(PetscLayoutCreate(comm, &layout));
    1943:   PetscCall(PetscSFGetGraph(sf, &lsize, NULL, NULL, NULL));
    1944:   PetscCall(PetscLayoutSetLocalSize(layout, lsize));
    1945:   PetscCall(PetscLayoutSetBlockSize(layout, 1));
    1946:   PetscCall(PetscLayoutSetUp(layout));
    1947:   PetscCall(PetscSFSetGraphLayout(*distsf, layout, *chartSize, NULL, PETSC_OWN_POINTER, gpoints));
    1948:   PetscCall(PetscLayoutDestroy(&layout));
    1949:   /* Migrate DM */
    1950:   {
    1951:     PetscInt     pStart, pEnd;
    1952:     PetscSFNode *buffer0, *buffer1, *buffer2;

    1954:     PetscCall(DMPlexGetChart(dm, &pStart, &pEnd));
    1955:     PetscCall(PetscMalloc2(pEnd - pStart, &buffer0, lsize, &buffer1));
    1956:     PetscCall(PetscMalloc1(*chartSize, &buffer2));
    1957:     {
    1958:       PetscSF            workPointSF;
    1959:       PetscInt           workNroots, workNleaves;
    1960:       const PetscInt    *workIlocal;
    1961:       const PetscSFNode *workIremote;

    1963:       for (p = pStart; p < pEnd; ++p) {
    1964:         buffer0[p - pStart].rank  = rank;
    1965:         buffer0[p - pStart].index = p - pStart;
    1966:       }
    1967:       PetscCall(DMGetPointSF(dm, &workPointSF));
    1968:       PetscCall(PetscSFGetGraph(workPointSF, &workNroots, &workNleaves, &workIlocal, &workIremote));
    1969:       for (p = 0; p < workNleaves; ++p) {
    1970:         PetscInt workIlocalp = (workIlocal ? workIlocal[p] : p);

    1972:         buffer0[workIlocalp].rank = -1;
    1973:       }
    1974:     }
    1975:     for (p = 0; p < lsize; ++p) buffer1[p].rank = -1;
    1976:     for (p = 0; p < *chartSize; ++p) buffer2[p].rank = -1;
    1977:     PetscCall(PetscSFReduceBegin(sf, MPIU_SF_NODE, buffer0, buffer1, MPI_MAXLOC));
    1978:     PetscCall(PetscSFReduceEnd(sf, MPIU_SF_NODE, buffer0, buffer1, MPI_MAXLOC));
    1979:     PetscCall(PetscSFBcastBegin(*distsf, MPIU_SF_NODE, buffer1, buffer2, MPI_REPLACE));
    1980:     PetscCall(PetscSFBcastEnd(*distsf, MPIU_SF_NODE, buffer1, buffer2, MPI_REPLACE));
    1981:     if (PetscDefined(USE_DEBUG)) {
    1982:       for (p = 0; p < *chartSize; ++p) {
    1983:         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);
    1984:       }
    1985:     }
    1986:     PetscCall(PetscFree2(buffer0, buffer1));
    1987:     PetscCall(DMCreate(comm, distdm));
    1988:     PetscCall(DMSetType(*distdm, DMPLEX));
    1989:     PetscCall(PetscObjectSetName((PetscObject)*distdm, ((PetscObject)dm)->name));
    1990:     PetscCall(DMPlexDistributionSetName(*distdm, distribution_name));
    1991:     {
    1992:       PetscSF migrationSF;

    1994:       PetscCall(PetscSFCreate(comm, &migrationSF));
    1995:       PetscCall(PetscSFSetFromOptions(migrationSF));
    1996:       PetscCall(PetscSFSetGraph(migrationSF, pEnd - pStart, *chartSize, NULL, PETSC_OWN_POINTER, buffer2, PETSC_OWN_POINTER));
    1997:       PetscCall(PetscSFSetUp(migrationSF));
    1998:       PetscCall(DMPlexMigrate(dm, migrationSF, *distdm));
    1999:       PetscCall(PetscSFDestroy(&migrationSF));
    2000:     }
    2001:   }
    2002:   /* Set pointSF */
    2003:   {
    2004:     PetscSF      pointSF;
    2005:     PetscInt    *ilocal, nleaves, q;
    2006:     PetscSFNode *iremote, *buffer0, *buffer1;

    2008:     PetscCall(PetscMalloc2(*chartSize, &buffer0, lsize, &buffer1));
    2009:     for (p = 0, nleaves = 0; p < *chartSize; ++p) {
    2010:       if (owners[p] == rank) {
    2011:         buffer0[p].rank = rank;
    2012:       } else {
    2013:         buffer0[p].rank = -1;
    2014:         nleaves++;
    2015:       }
    2016:       buffer0[p].index = p;
    2017:     }
    2018:     for (p = 0; p < lsize; ++p) buffer1[p].rank = -1;
    2019:     PetscCall(PetscSFReduceBegin(*distsf, MPIU_SF_NODE, buffer0, buffer1, MPI_MAXLOC));
    2020:     PetscCall(PetscSFReduceEnd(*distsf, MPIU_SF_NODE, buffer0, buffer1, MPI_MAXLOC));
    2021:     for (p = 0; p < *chartSize; ++p) buffer0[p].rank = -1;
    2022:     PetscCall(PetscSFBcastBegin(*distsf, MPIU_SF_NODE, buffer1, buffer0, MPI_REPLACE));
    2023:     PetscCall(PetscSFBcastEnd(*distsf, MPIU_SF_NODE, buffer1, buffer0, MPI_REPLACE));
    2024:     if (PetscDefined(USE_DEBUG)) {
    2025:       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);
    2026:     }
    2027:     PetscCall(PetscMalloc1(nleaves, &ilocal));
    2028:     PetscCall(PetscMalloc1(nleaves, &iremote));
    2029:     for (p = 0, q = 0; p < *chartSize; ++p) {
    2030:       if (buffer0[p].rank != rank) {
    2031:         ilocal[q]        = p;
    2032:         iremote[q].rank  = buffer0[p].rank;
    2033:         iremote[q].index = buffer0[p].index;
    2034:         q++;
    2035:       }
    2036:     }
    2037:     PetscCheck(q == nleaves, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatching leaf sizes: %" PetscInt_FMT " != %" PetscInt_FMT, q, nleaves);
    2038:     PetscCall(PetscFree2(buffer0, buffer1));
    2039:     PetscCall(PetscSFCreate(comm, &pointSF));
    2040:     PetscCall(PetscSFSetFromOptions(pointSF));
    2041:     PetscCall(PetscSFSetGraph(pointSF, *chartSize, nleaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER));
    2042:     PetscCall(DMSetPointSF(*distdm, pointSF));
    2043:     {
    2044:       DM cdm;

    2046:       PetscCall(DMGetCoordinateDM(*distdm, &cdm));
    2047:       PetscCall(DMSetPointSF(cdm, pointSF));
    2048:     }
    2049:     PetscCall(PetscSFDestroy(&pointSF));
    2050:   }
    2051:   PetscCall(ISRestoreIndices(chartSizesIS, &chartSize));
    2052:   PetscCall(ISRestoreIndices(ownersIS, &owners));
    2053:   PetscCall(ISRestoreIndices(gpointsIS, &gpoints));
    2054:   PetscCall(ISDestroy(&chartSizesIS));
    2055:   PetscCall(ISDestroy(&ownersIS));
    2056:   PetscCall(ISDestroy(&gpointsIS));
    2057:   /* Record that overlap has been manually created.               */
    2058:   /* This is to pass `DMPlexCheckPointSF()`, which checks that    */
    2059:   /* pointSF does not contain cells in the leaves if overlap = 0. */
    2060:   PetscCall(DMPlexSetOverlap_Plex(*distdm, NULL, DMPLEX_OVERLAP_MANUAL));
    2061:   PetscCall(DMPlexDistributeSetDefault(*distdm, PETSC_FALSE));
    2062:   PetscCall(DMPlexReorderSetDefault(*distdm, DM_REORDER_DEFAULT_FALSE));
    2063:   PetscCall(PetscLogEventEnd(DMPLEX_DistributionLoad, viewer, 0, 0, 0));
    2064:   PetscFunctionReturn(PETSC_SUCCESS);
    2065: }

    2067: // Serial load of topology
    2068: static PetscErrorCode DMPlexTopologyLoad_HDF5_Legacy_Private(DM dm, PetscViewer viewer, PetscSF *sf)
    2069: {
    2070:   MPI_Comm        comm;
    2071:   const char     *pointsName, *coneSizesName, *conesName, *orientationsName;
    2072:   IS              pointsIS, coneSizesIS, conesIS, orientationsIS;
    2073:   const PetscInt *points, *coneSizes, *cones, *orientations;
    2074:   PetscInt       *cone, *ornt;
    2075:   PetscInt        dim, N, Np, pEnd, p, q, maxConeSize = 0, c;
    2076:   PetscMPIInt     size, rank;

    2078:   PetscFunctionBegin;
    2079:   pointsName       = "order";
    2080:   coneSizesName    = "cones";
    2081:   conesName        = "cells";
    2082:   orientationsName = "orientation";
    2083:   PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
    2084:   PetscCallMPI(MPI_Comm_size(comm, &size));
    2085:   PetscCallMPI(MPI_Comm_rank(comm, &rank));
    2086:   PetscCall(ISCreate(comm, &pointsIS));
    2087:   PetscCall(PetscObjectSetName((PetscObject)pointsIS, pointsName));
    2088:   PetscCall(ISCreate(comm, &coneSizesIS));
    2089:   PetscCall(PetscObjectSetName((PetscObject)coneSizesIS, coneSizesName));
    2090:   PetscCall(ISCreate(comm, &conesIS));
    2091:   PetscCall(PetscObjectSetName((PetscObject)conesIS, conesName));
    2092:   PetscCall(ISCreate(comm, &orientationsIS));
    2093:   PetscCall(PetscObjectSetName((PetscObject)orientationsIS, orientationsName));
    2094:   PetscCall(PetscViewerHDF5ReadObjectAttribute(viewer, (PetscObject)conesIS, "cell_dim", PETSC_INT, NULL, &dim));
    2095:   PetscCall(DMSetDimension(dm, dim));
    2096:   {
    2097:     /* Force serial load */
    2098:     PetscCall(PetscInfo(dm, "Loading DM %s in serial\n", dm->hdr.name));
    2099:     PetscCall(PetscViewerHDF5ReadSizes(viewer, pointsName, NULL, &Np));
    2100:     PetscCall(PetscLayoutSetLocalSize(pointsIS->map, rank == 0 ? Np : 0));
    2101:     PetscCall(PetscLayoutSetSize(pointsIS->map, Np));
    2102:     pEnd = rank == 0 ? Np : 0;
    2103:     PetscCall(PetscViewerHDF5ReadSizes(viewer, coneSizesName, NULL, &Np));
    2104:     PetscCall(PetscLayoutSetLocalSize(coneSizesIS->map, rank == 0 ? Np : 0));
    2105:     PetscCall(PetscLayoutSetSize(coneSizesIS->map, Np));
    2106:     PetscCall(PetscViewerHDF5ReadSizes(viewer, conesName, NULL, &N));
    2107:     PetscCall(PetscLayoutSetLocalSize(conesIS->map, rank == 0 ? N : 0));
    2108:     PetscCall(PetscLayoutSetSize(conesIS->map, N));
    2109:     PetscCall(PetscViewerHDF5ReadSizes(viewer, orientationsName, NULL, &N));
    2110:     PetscCall(PetscLayoutSetLocalSize(orientationsIS->map, rank == 0 ? N : 0));
    2111:     PetscCall(PetscLayoutSetSize(orientationsIS->map, N));
    2112:   }
    2113:   PetscCall(ISLoad(pointsIS, viewer));
    2114:   PetscCall(ISLoad(coneSizesIS, viewer));
    2115:   PetscCall(ISLoad(conesIS, viewer));
    2116:   PetscCall(ISLoad(orientationsIS, viewer));
    2117:   /* Create Plex */
    2118:   PetscCall(DMPlexSetChart(dm, 0, pEnd));
    2119:   PetscCall(ISGetIndices(pointsIS, &points));
    2120:   PetscCall(ISGetIndices(coneSizesIS, &coneSizes));
    2121:   for (p = 0; p < pEnd; ++p) {
    2122:     PetscCall(DMPlexSetConeSize(dm, points[p], coneSizes[p]));
    2123:     maxConeSize = PetscMax(maxConeSize, coneSizes[p]);
    2124:   }
    2125:   PetscCall(DMSetUp(dm));
    2126:   PetscCall(ISGetIndices(conesIS, &cones));
    2127:   PetscCall(ISGetIndices(orientationsIS, &orientations));
    2128:   PetscCall(PetscMalloc2(maxConeSize, &cone, maxConeSize, &ornt));
    2129:   for (p = 0, q = 0; p < pEnd; ++p) {
    2130:     for (c = 0; c < coneSizes[p]; ++c, ++q) {
    2131:       cone[c] = cones[q];
    2132:       ornt[c] = orientations[q];
    2133:     }
    2134:     PetscCall(DMPlexSetCone(dm, points[p], cone));
    2135:     PetscCall(DMPlexSetConeOrientation(dm, points[p], ornt));
    2136:   }
    2137:   PetscCall(PetscFree2(cone, ornt));
    2138:   /* Create global section migration SF */
    2139:   if (sf) {
    2140:     PetscLayout layout;
    2141:     PetscInt   *globalIndices;

    2143:     PetscCall(PetscMalloc1(pEnd, &globalIndices));
    2144:     /* plex point == globalPointNumber in this case */
    2145:     for (p = 0; p < pEnd; ++p) globalIndices[p] = p;
    2146:     PetscCall(PetscLayoutCreate(comm, &layout));
    2147:     PetscCall(PetscLayoutSetSize(layout, Np));
    2148:     PetscCall(PetscLayoutSetBlockSize(layout, 1));
    2149:     PetscCall(PetscLayoutSetUp(layout));
    2150:     PetscCall(PetscSFCreate(comm, sf));
    2151:     PetscCall(PetscSFSetFromOptions(*sf));
    2152:     PetscCall(PetscSFSetGraphLayout(*sf, layout, pEnd, NULL, PETSC_OWN_POINTER, globalIndices));
    2153:     PetscCall(PetscLayoutDestroy(&layout));
    2154:     PetscCall(PetscFree(globalIndices));
    2155:   }
    2156:   /* Clean-up */
    2157:   PetscCall(ISRestoreIndices(pointsIS, &points));
    2158:   PetscCall(ISRestoreIndices(coneSizesIS, &coneSizes));
    2159:   PetscCall(ISRestoreIndices(conesIS, &cones));
    2160:   PetscCall(ISRestoreIndices(orientationsIS, &orientations));
    2161:   PetscCall(ISDestroy(&pointsIS));
    2162:   PetscCall(ISDestroy(&coneSizesIS));
    2163:   PetscCall(ISDestroy(&conesIS));
    2164:   PetscCall(ISDestroy(&orientationsIS));
    2165:   /* Fill in the rest of the topology structure */
    2166:   PetscCall(DMPlexSymmetrize(dm));
    2167:   PetscCall(DMPlexStratify(dm));
    2168:   PetscFunctionReturn(PETSC_SUCCESS);
    2169: }

    2171: /* Representation of two DMPlex strata in 0-based global numbering */
    2172: struct _n_PlexLayer {
    2173:   PetscInt     d;
    2174:   IS           conesIS, orientationsIS;
    2175:   PetscSection coneSizesSection;
    2176:   PetscLayout  vertexLayout;
    2177:   PetscSF      overlapSF, l2gSF; //TODO maybe confusing names (in DMPlex in general)
    2178:   PetscInt     offset, conesOffset, leafOffset;
    2179: };
    2180: typedef struct _n_PlexLayer *PlexLayer;

    2182: static PetscErrorCode PlexLayerDestroy(PlexLayer *layer)
    2183: {
    2184:   PetscFunctionBegin;
    2185:   if (!*layer) PetscFunctionReturn(PETSC_SUCCESS);
    2186:   PetscCall(PetscSectionDestroy(&(*layer)->coneSizesSection));
    2187:   PetscCall(ISDestroy(&(*layer)->conesIS));
    2188:   PetscCall(ISDestroy(&(*layer)->orientationsIS));
    2189:   PetscCall(PetscSFDestroy(&(*layer)->overlapSF));
    2190:   PetscCall(PetscSFDestroy(&(*layer)->l2gSF));
    2191:   PetscCall(PetscLayoutDestroy(&(*layer)->vertexLayout));
    2192:   PetscCall(PetscFree(*layer));
    2193:   PetscFunctionReturn(PETSC_SUCCESS);
    2194: }

    2196: static PetscErrorCode PlexLayerCreate_Private(PlexLayer *layer)
    2197: {
    2198:   PetscFunctionBegin;
    2199:   PetscCall(PetscNew(layer));
    2200:   (*layer)->d           = -1;
    2201:   (*layer)->offset      = -1;
    2202:   (*layer)->conesOffset = -1;
    2203:   (*layer)->leafOffset  = -1;
    2204:   PetscFunctionReturn(PETSC_SUCCESS);
    2205: }

    2207: // Parallel load of a depth stratum
    2208: static PetscErrorCode PlexLayerLoad_Private(PlexLayer layer, PetscViewer viewer, PetscInt d, PetscLayout pointsLayout)
    2209: {
    2210:   char         path[128];
    2211:   MPI_Comm     comm;
    2212:   const char  *coneSizesName, *conesName, *orientationsName;
    2213:   IS           coneSizesIS, conesIS, orientationsIS;
    2214:   PetscSection coneSizesSection;
    2215:   PetscLayout  vertexLayout = NULL;
    2216:   PetscInt     s;

    2218:   PetscFunctionBegin;
    2219:   coneSizesName    = "cone_sizes";
    2220:   conesName        = "cones";
    2221:   orientationsName = "orientations";
    2222:   PetscCall(PetscObjectGetComm((PetscObject)viewer, &comm));

    2224:   /* query size of next lower depth stratum (next lower dimension) */
    2225:   if (d > 0) {
    2226:     PetscInt NVertices;

    2228:     PetscCall(PetscSNPrintf(path, sizeof(path), "%" PetscInt_FMT "/%s", d - 1, coneSizesName));
    2229:     PetscCall(PetscViewerHDF5ReadSizes(viewer, path, NULL, &NVertices));
    2230:     PetscCall(PetscLayoutCreate(comm, &vertexLayout));
    2231:     PetscCall(PetscLayoutSetSize(vertexLayout, NVertices));
    2232:     PetscCall(PetscLayoutSetUp(vertexLayout));
    2233:   }

    2235:   PetscCall(PetscSNPrintf(path, sizeof(path), "%" PetscInt_FMT, d));
    2236:   PetscCall(PetscViewerHDF5PushGroup(viewer, path));

    2238:   /* create coneSizesSection from stored IS coneSizes */
    2239:   {
    2240:     const PetscInt *coneSizes;

    2242:     PetscCall(ISCreate(comm, &coneSizesIS));
    2243:     PetscCall(PetscObjectSetName((PetscObject)coneSizesIS, coneSizesName));
    2244:     if (pointsLayout) PetscCall(ISSetLayout(coneSizesIS, pointsLayout));
    2245:     PetscCall(ISLoad(coneSizesIS, viewer));
    2246:     if (!pointsLayout) PetscCall(ISGetLayout(coneSizesIS, &pointsLayout));
    2247:     PetscCall(ISGetIndices(coneSizesIS, &coneSizes));
    2248:     PetscCall(PetscSectionCreate(comm, &coneSizesSection));
    2249:     //TODO different start ?
    2250:     PetscCall(PetscSectionSetChart(coneSizesSection, 0, pointsLayout->n));
    2251:     for (s = 0; s < pointsLayout->n; ++s) PetscCall(PetscSectionSetDof(coneSizesSection, s, coneSizes[s]));
    2252:     PetscCall(PetscSectionSetUp(coneSizesSection));
    2253:     PetscCall(ISRestoreIndices(coneSizesIS, &coneSizes));
    2254:     {
    2255:       PetscLayout tmp = NULL;

    2257:       /* We need to keep the layout until the end of function */
    2258:       PetscCall(PetscLayoutReference((PetscLayout)pointsLayout, &tmp));
    2259:     }
    2260:     PetscCall(ISDestroy(&coneSizesIS));
    2261:   }

    2263:   /* use value layout of coneSizesSection as layout of cones and orientations */
    2264:   {
    2265:     PetscLayout conesLayout;

    2267:     PetscCall(PetscSectionGetValueLayout(comm, coneSizesSection, &conesLayout));
    2268:     PetscCall(ISCreate(comm, &conesIS));
    2269:     PetscCall(ISCreate(comm, &orientationsIS));
    2270:     PetscCall(PetscObjectSetName((PetscObject)conesIS, conesName));
    2271:     PetscCall(PetscObjectSetName((PetscObject)orientationsIS, orientationsName));
    2272:     PetscCall(PetscLayoutDuplicate(conesLayout, &conesIS->map));
    2273:     PetscCall(PetscLayoutDuplicate(conesLayout, &orientationsIS->map));
    2274:     PetscCall(ISLoad(conesIS, viewer));
    2275:     PetscCall(ISLoad(orientationsIS, viewer));
    2276:     PetscCall(PetscLayoutDestroy(&conesLayout));
    2277:   }

    2279:   /* check assertion that layout of points is the same as point layout of coneSizesSection */
    2280:   {
    2281:     PetscLayout pointsLayout0;
    2282:     PetscBool   flg;

    2284:     PetscCall(PetscSectionGetPointLayout(comm, coneSizesSection, &pointsLayout0));
    2285:     PetscCall(PetscLayoutCompare(pointsLayout, pointsLayout0, &flg));
    2286:     PetscCheck(flg, comm, PETSC_ERR_PLIB, "points layout != coneSizesSection point layout");
    2287:     PetscCall(PetscLayoutDestroy(&pointsLayout0));
    2288:   }
    2289:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    2290:   PetscCall(PetscLayoutDestroy(&pointsLayout));

    2292:   layer->d                = d;
    2293:   layer->conesIS          = conesIS;
    2294:   layer->coneSizesSection = coneSizesSection;
    2295:   layer->orientationsIS   = orientationsIS;
    2296:   layer->vertexLayout     = vertexLayout;
    2297:   PetscFunctionReturn(PETSC_SUCCESS);
    2298: }

    2300: static PetscErrorCode PlexLayerDistribute_Private(PlexLayer layer, PetscSF cellLocalToGlobalSF)
    2301: {
    2302:   IS           newConesIS, newOrientationsIS;
    2303:   PetscSection newConeSizesSection;
    2304:   MPI_Comm     comm;

    2306:   PetscFunctionBegin;
    2307:   PetscCall(PetscObjectGetComm((PetscObject)cellLocalToGlobalSF, &comm));
    2308:   PetscCall(PetscSectionCreate(comm, &newConeSizesSection));
    2309:   //TODO rename to something like ISDistribute() with optional PetscSection argument
    2310:   PetscCall(DMPlexDistributeFieldIS(NULL, cellLocalToGlobalSF, layer->coneSizesSection, layer->conesIS, newConeSizesSection, &newConesIS));
    2311:   PetscCall(DMPlexDistributeFieldIS(NULL, cellLocalToGlobalSF, layer->coneSizesSection, layer->orientationsIS, newConeSizesSection, &newOrientationsIS));

    2313:   PetscCall(PetscObjectSetName((PetscObject)newConeSizesSection, ((PetscObject)layer->coneSizesSection)->name));
    2314:   PetscCall(PetscObjectSetName((PetscObject)newConesIS, ((PetscObject)layer->conesIS)->name));
    2315:   PetscCall(PetscObjectSetName((PetscObject)newOrientationsIS, ((PetscObject)layer->orientationsIS)->name));
    2316:   PetscCall(PetscSectionDestroy(&layer->coneSizesSection));
    2317:   PetscCall(ISDestroy(&layer->conesIS));
    2318:   PetscCall(ISDestroy(&layer->orientationsIS));
    2319:   layer->coneSizesSection = newConeSizesSection;
    2320:   layer->conesIS          = newConesIS;
    2321:   layer->orientationsIS   = newOrientationsIS;
    2322:   PetscFunctionReturn(PETSC_SUCCESS);
    2323: }

    2325: //TODO share code with DMPlexBuildFromCellListParallel()
    2326: #include <petsc/private/hashseti.h>
    2327: static PetscErrorCode PlexLayerCreateSFs_Private(PlexLayer layer, PetscSF *vertexOverlapSF, PetscSF *sfXC)
    2328: {
    2329:   PetscLayout     vertexLayout     = layer->vertexLayout;
    2330:   PetscSection    coneSection      = layer->coneSizesSection;
    2331:   IS              cellVertexData   = layer->conesIS;
    2332:   IS              coneOrientations = layer->orientationsIS;
    2333:   PetscSF         vl2gSF, vOverlapSF;
    2334:   PetscInt       *verticesAdj;
    2335:   PetscInt        i, n, numVerticesAdj;
    2336:   const PetscInt *cvd, *co = NULL;
    2337:   MPI_Comm        comm;

    2339:   PetscFunctionBegin;
    2340:   PetscCall(PetscObjectGetComm((PetscObject)coneSection, &comm));
    2341:   PetscCall(PetscSectionGetStorageSize(coneSection, &n));
    2342:   {
    2343:     PetscInt n0;

    2345:     PetscCall(ISGetLocalSize(cellVertexData, &n0));
    2346:     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);
    2347:     PetscCall(ISGetIndices(cellVertexData, &cvd));
    2348:   }
    2349:   if (coneOrientations) {
    2350:     PetscInt n0;

    2352:     PetscCall(ISGetLocalSize(coneOrientations, &n0));
    2353:     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);
    2354:     PetscCall(ISGetIndices(coneOrientations, &co));
    2355:   }
    2356:   /* Get/check global number of vertices */
    2357:   {
    2358:     PetscInt NVerticesInCells = PETSC_INT_MIN;

    2360:     /* NVerticesInCells = max(cellVertexData) + 1 */
    2361:     for (i = 0; i < n; i++)
    2362:       if (cvd[i] > NVerticesInCells) NVerticesInCells = cvd[i];
    2363:     ++NVerticesInCells;
    2364:     PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, &NVerticesInCells, 1, MPIU_INT, MPI_MAX, comm));

    2366:     if (vertexLayout->n == PETSC_DECIDE && vertexLayout->N == PETSC_DECIDE) vertexLayout->N = NVerticesInCells;
    2367:     else
    2368:       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,
    2369:                  vertexLayout->N, NVerticesInCells);
    2370:     PetscCall(PetscLayoutSetUp(vertexLayout));
    2371:   }
    2372:   /* Find locally unique vertices in cellVertexData */
    2373:   {
    2374:     PetscHSetI vhash;
    2375:     PetscInt   off = 0;

    2377:     PetscCall(PetscHSetICreate(&vhash));
    2378:     for (i = 0; i < n; ++i) PetscCall(PetscHSetIAdd(vhash, cvd[i]));
    2379:     PetscCall(PetscHSetIGetSize(vhash, &numVerticesAdj));
    2380:     PetscCall(PetscMalloc1(numVerticesAdj, &verticesAdj));
    2381:     PetscCall(PetscHSetIGetElems(vhash, &off, verticesAdj));
    2382:     PetscAssert(off == numVerticesAdj, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Assertion failed: off == numVerticesAdj (%" PetscInt_FMT " != %" PetscInt_FMT ")", off, numVerticesAdj);
    2383:     PetscCall(PetscHSetIDestroy(&vhash));
    2384:   }
    2385:   /* We must sort vertices to preserve numbering */
    2386:   PetscCall(PetscSortInt(numVerticesAdj, verticesAdj));
    2387:   /* Connect locally unique vertices with star forest */
    2388:   PetscCall(PetscSFCreateByMatchingIndices(vertexLayout, numVerticesAdj, verticesAdj, NULL, 0, numVerticesAdj, verticesAdj, NULL, 0, &vl2gSF, &vOverlapSF));
    2389:   PetscCall(PetscObjectSetName((PetscObject)vOverlapSF, "overlapSF"));
    2390:   PetscCall(PetscObjectSetName((PetscObject)vl2gSF, "localToGlobalSF"));

    2392:   PetscCall(PetscFree(verticesAdj));
    2393:   *vertexOverlapSF = vOverlapSF;
    2394:   *sfXC            = vl2gSF;
    2395:   PetscFunctionReturn(PETSC_SUCCESS);
    2396: }

    2398: static PetscErrorCode PlexLayerCreateCellSFs_Private(PlexLayer layer, PetscSF *cellOverlapSF, PetscSF *cellLocalToGlobalSF)
    2399: {
    2400:   PetscSection coneSection = layer->coneSizesSection;
    2401:   PetscInt     nCells;
    2402:   MPI_Comm     comm;

    2404:   PetscFunctionBegin;
    2405:   PetscCall(PetscObjectGetComm((PetscObject)coneSection, &comm));
    2406:   {
    2407:     PetscInt cStart;

    2409:     PetscCall(PetscSectionGetChart(coneSection, &cStart, &nCells));
    2410:     PetscCheck(cStart == 0, comm, PETSC_ERR_ARG_OUTOFRANGE, "coneSection must start at 0");
    2411:   }
    2412:   /* Create overlapSF as empty SF with the right number of roots */
    2413:   PetscCall(PetscSFCreate(comm, cellOverlapSF));
    2414:   PetscCall(PetscSFSetGraph(*cellOverlapSF, nCells, 0, NULL, PETSC_USE_POINTER, NULL, PETSC_USE_POINTER));
    2415:   PetscCall(PetscSFSetUp(*cellOverlapSF));
    2416:   /* Create localToGlobalSF as identity mapping */
    2417:   {
    2418:     PetscLayout map;

    2420:     PetscCall(PetscLayoutCreateFromSizes(comm, nCells, PETSC_DECIDE, 1, &map));
    2421:     PetscCall(PetscSFCreateFromLayouts(map, map, cellLocalToGlobalSF));
    2422:     PetscCall(PetscSFSetUp(*cellLocalToGlobalSF));
    2423:     PetscCall(PetscLayoutDestroy(&map));
    2424:   }
    2425:   PetscFunctionReturn(PETSC_SUCCESS);
    2426: }

    2428: static PetscErrorCode DMPlexTopologyBuildFromLayers_Private(DM dm, PetscInt depth, PlexLayer *layers, IS strataPermutation)
    2429: {
    2430:   const PetscInt *permArr;
    2431:   PetscInt        d, nPoints;
    2432:   MPI_Comm        comm;

    2434:   PetscFunctionBegin;
    2435:   PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
    2436:   PetscCall(ISGetIndices(strataPermutation, &permArr));

    2438:   /* Count points, strata offsets and cones offsets (taking strataPermutation into account) */
    2439:   {
    2440:     PetscInt stratumOffset = 0;
    2441:     PetscInt conesOffset   = 0;

    2443:     for (d = 0; d <= depth; d++) {
    2444:       const PetscInt  e = permArr[d];
    2445:       const PlexLayer l = layers[e];
    2446:       PetscInt        lo, n, size;

    2448:       PetscCall(PetscSectionGetChart(l->coneSizesSection, &lo, &n));
    2449:       PetscCall(PetscSectionGetStorageSize(l->coneSizesSection, &size));
    2450:       PetscCheck(lo == 0, comm, PETSC_ERR_PLIB, "starting point should be 0 in coneSizesSection %" PetscInt_FMT, d);
    2451:       l->offset      = stratumOffset;
    2452:       l->conesOffset = conesOffset;
    2453:       stratumOffset += n;
    2454:       conesOffset += size;
    2455:     }
    2456:     nPoints = stratumOffset;
    2457:   }

    2459:   /* Set interval for all plex points */
    2460:   //TODO we should store starting point of plex
    2461:   PetscCall(DMPlexSetChart(dm, 0, nPoints));

    2463:   /* Set up plex coneSection from layer coneSections */
    2464:   {
    2465:     PetscSection coneSection;

    2467:     PetscCall(DMPlexGetConeSection(dm, &coneSection));
    2468:     for (d = 0; d <= depth; d++) {
    2469:       const PlexLayer l = layers[d];
    2470:       PetscInt        n, q;

    2472:       PetscCall(PetscSectionGetChart(l->coneSizesSection, NULL, &n));
    2473:       for (q = 0; q < n; q++) {
    2474:         const PetscInt p = l->offset + q;
    2475:         PetscInt       coneSize;

    2477:         PetscCall(PetscSectionGetDof(l->coneSizesSection, q, &coneSize));
    2478:         PetscCall(PetscSectionSetDof(coneSection, p, coneSize));
    2479:       }
    2480:     }
    2481:   }
    2482:   //TODO this is terrible, DMSetUp_Plex() should be DMPlexSetUpSections() or so
    2483:   PetscCall(DMSetUp(dm));

    2485:   /* Renumber cones points from layer-global numbering to plex-local numbering */
    2486:   {
    2487:     PetscInt *cones, *ornts;

    2489:     PetscCall(DMPlexGetCones(dm, &cones));
    2490:     PetscCall(DMPlexGetConeOrientations(dm, &ornts));
    2491:     for (d = 1; d <= depth; d++) {
    2492:       const PlexLayer l = layers[d];
    2493:       PetscInt        i, lConesSize;
    2494:       PetscInt       *lCones;
    2495:       const PetscInt *lOrnts;
    2496:       PetscInt       *pCones = &cones[l->conesOffset];
    2497:       PetscInt       *pOrnts = &ornts[l->conesOffset];

    2499:       PetscCall(PetscSectionGetStorageSize(l->coneSizesSection, &lConesSize));
    2500:       /* Get cones in local plex numbering */
    2501:       {
    2502:         ISLocalToGlobalMapping l2g;
    2503:         PetscLayout            vertexLayout = l->vertexLayout;
    2504:         PetscSF                vertexSF     = layers[d - 1]->l2gSF; /* vertices of this layer are cells of previous layer */
    2505:         const PetscInt        *gCones;
    2506:         PetscInt               lConesSize0;

    2508:         PetscCall(ISGetLocalSize(l->conesIS, &lConesSize0));
    2509:         PetscCheck(lConesSize0 == lConesSize, comm, PETSC_ERR_PLIB, "layer %" PetscInt_FMT " size(conesIS) = %" PetscInt_FMT " != %" PetscInt_FMT " = storageSize(coneSizesSection)", d, lConesSize0, lConesSize);
    2510:         PetscCall(ISGetLocalSize(l->orientationsIS, &lConesSize0));
    2511:         PetscCheck(lConesSize0 == lConesSize, comm, PETSC_ERR_PLIB, "layer %" PetscInt_FMT " size(orientationsIS) = %" PetscInt_FMT " != %" PetscInt_FMT " = storageSize(coneSizesSection)", d, lConesSize0, lConesSize);

    2513:         PetscCall(PetscMalloc1(lConesSize, &lCones));
    2514:         PetscCall(ISGetIndices(l->conesIS, &gCones));
    2515:         PetscCall(ISLocalToGlobalMappingCreateSF(vertexSF, vertexLayout->rstart, &l2g));
    2516:         PetscCall(ISGlobalToLocalMappingApply(l2g, IS_GTOLM_MASK, lConesSize, gCones, &lConesSize0, lCones));
    2517:         PetscCheck(lConesSize0 == lConesSize, comm, PETSC_ERR_PLIB, "global to local does not cover all indices (%" PetscInt_FMT " of %" PetscInt_FMT ")", lConesSize0, lConesSize);
    2518:         PetscCall(ISLocalToGlobalMappingDestroy(&l2g));
    2519:         PetscCall(ISRestoreIndices(l->conesIS, &gCones));
    2520:       }
    2521:       PetscCall(ISGetIndices(l->orientationsIS, &lOrnts));
    2522:       /* Set cones, need to add stratum offset */
    2523:       for (i = 0; i < lConesSize; i++) {
    2524:         pCones[i] = lCones[i] + layers[d - 1]->offset; /* cone points of current layer are points of previous layer */
    2525:         pOrnts[i] = lOrnts[i];
    2526:       }
    2527:       PetscCall(PetscFree(lCones));
    2528:       PetscCall(ISRestoreIndices(l->orientationsIS, &lOrnts));
    2529:     }
    2530:   }
    2531:   PetscCall(DMPlexSymmetrize(dm));
    2532:   PetscCall(DMPlexStratify(dm));
    2533:   PetscCall(ISRestoreIndices(strataPermutation, &permArr));
    2534:   PetscFunctionReturn(PETSC_SUCCESS);
    2535: }

    2537: static PetscErrorCode PlexLayerConcatenateSFs_Private(MPI_Comm comm, PetscInt depth, PlexLayer layers[], IS strataPermutation, PetscSF *overlapSF, PetscSF *l2gSF)
    2538: {
    2539:   PetscInt        d;
    2540:   PetscSF        *osfs, *lsfs;
    2541:   PetscInt       *leafOffsets;
    2542:   const PetscInt *permArr;

    2544:   PetscFunctionBegin;
    2545:   PetscCall(ISGetIndices(strataPermutation, &permArr));
    2546:   PetscCall(PetscCalloc3(depth + 1, &osfs, depth + 1, &lsfs, depth + 1, &leafOffsets));
    2547:   for (d = 0; d <= depth; d++) {
    2548:     const PetscInt e = permArr[d];

    2550:     PetscAssert(e == layers[e]->d, PETSC_COMM_SELF, PETSC_ERR_PLIB, "assertion: e == layers[e]->d");
    2551:     osfs[d]        = layers[e]->overlapSF;
    2552:     lsfs[d]        = layers[e]->l2gSF;
    2553:     leafOffsets[d] = layers[e]->offset;
    2554:   }
    2555:   PetscCall(PetscSFConcatenate(comm, depth + 1, osfs, PETSCSF_CONCATENATE_ROOTMODE_LOCAL, leafOffsets, overlapSF));
    2556:   PetscCall(PetscSFConcatenate(comm, depth + 1, lsfs, PETSCSF_CONCATENATE_ROOTMODE_GLOBAL, leafOffsets, l2gSF));
    2557:   PetscCall(PetscFree3(osfs, lsfs, leafOffsets));
    2558:   PetscCall(ISRestoreIndices(strataPermutation, &permArr));
    2559:   PetscFunctionReturn(PETSC_SUCCESS);
    2560: }

    2562: // Parallel load of topology
    2563: static PetscErrorCode DMPlexTopologyLoad_HDF5_Private(DM dm, PetscViewer viewer, PetscSF *sfXC)
    2564: {
    2565:   PlexLayer  *layers;
    2566:   IS          strataPermutation;
    2567:   PetscLayout pointsLayout;
    2568:   PetscInt    depth;
    2569:   PetscInt    d;
    2570:   MPI_Comm    comm;

    2572:   PetscFunctionBegin;
    2573:   {
    2574:     PetscInt dim;

    2576:     PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "depth", PETSC_INT, NULL, &depth));
    2577:     PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "cell_dim", PETSC_INT, NULL, &dim));
    2578:     PetscCall(DMSetDimension(dm, dim));
    2579:   }
    2580:   PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));

    2582:   PetscCall(PetscInfo(dm, "Loading DM %s in parallel\n", dm->hdr.name));
    2583:   {
    2584:     IS spOnComm;

    2586:     PetscCall(ISCreate(comm, &spOnComm));
    2587:     PetscCall(PetscObjectSetName((PetscObject)spOnComm, "permutation"));
    2588:     PetscCall(ISLoad(spOnComm, viewer));
    2589:     /* have the same serial IS on every rank */
    2590:     PetscCall(ISAllGather(spOnComm, &strataPermutation));
    2591:     PetscCall(PetscObjectSetName((PetscObject)strataPermutation, ((PetscObject)spOnComm)->name));
    2592:     PetscCall(ISDestroy(&spOnComm));
    2593:   }

    2595:   /* Create layers, load raw data for each layer */
    2596:   PetscCall(PetscViewerHDF5PushGroup(viewer, "strata"));
    2597:   PetscCall(PetscMalloc1(depth + 1, &layers));
    2598:   for (d = depth, pointsLayout = NULL; d >= 0; pointsLayout = layers[d]->vertexLayout, d--) {
    2599:     PetscCall(PlexLayerCreate_Private(&layers[d]));
    2600:     PetscCall(PlexLayerLoad_Private(layers[d], viewer, d, pointsLayout));
    2601:   }
    2602:   PetscCall(PetscViewerHDF5PopGroup(viewer)); /* strata */

    2604:   for (d = depth; d >= 0; d--) {
    2605:     /* Redistribute cells and vertices for each applicable layer */
    2606:     if (d < depth) PetscCall(PlexLayerDistribute_Private(layers[d], layers[d]->l2gSF));
    2607:     /* Create vertex overlap SF and vertex localToGlobal SF for each applicable layer */
    2608:     if (d > 0) PetscCall(PlexLayerCreateSFs_Private(layers[d], &layers[d - 1]->overlapSF, &layers[d - 1]->l2gSF));
    2609:   }
    2610:   /* Build trivial SFs for the cell layer as well */
    2611:   PetscCall(PlexLayerCreateCellSFs_Private(layers[depth], &layers[depth]->overlapSF, &layers[depth]->l2gSF));

    2613:   /* Build DMPlex topology from the layers */
    2614:   PetscCall(DMPlexTopologyBuildFromLayers_Private(dm, depth, layers, strataPermutation));

    2616:   /* Build overall point SF alias overlap SF */
    2617:   {
    2618:     PetscSF overlapSF;

    2620:     PetscCall(PlexLayerConcatenateSFs_Private(comm, depth, layers, strataPermutation, &overlapSF, sfXC));
    2621:     PetscCall(DMSetPointSF(dm, overlapSF));
    2622:     PetscCall(PetscSFDestroy(&overlapSF));
    2623:   }

    2625:   for (d = depth; d >= 0; d--) PetscCall(PlexLayerDestroy(&layers[d]));
    2626:   PetscCall(PetscFree(layers));
    2627:   PetscCall(ISDestroy(&strataPermutation));
    2628:   PetscFunctionReturn(PETSC_SUCCESS);
    2629: }

    2631: PetscErrorCode DMPlexTopologyLoad_HDF5_Internal(DM dm, PetscViewer viewer, PetscSF *sfXC)
    2632: {
    2633:   DMPlexStorageVersion version;
    2634:   const char          *topologydm_name;
    2635:   char                 group[PETSC_MAX_PATH_LEN];
    2636:   PetscSF              sfwork = NULL;

    2638:   PetscFunctionBegin;
    2639:   PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
    2640:   PetscCall(PetscViewerHDF5GetDMPlexStorageVersionReading(viewer, &version));
    2641:   if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
    2642:     PetscCall(PetscSNPrintf(group, sizeof(group), "topologies/%s", topologydm_name));
    2643:   } else {
    2644:     PetscCall(PetscStrncpy(group, "/", sizeof(group)));
    2645:   }
    2646:   PetscCall(PetscViewerHDF5PushGroup(viewer, group));

    2648:   PetscCall(PetscViewerHDF5PushGroup(viewer, "topology"));
    2649:   if (version->major < 3) {
    2650:     PetscCall(DMPlexTopologyLoad_HDF5_Legacy_Private(dm, viewer, &sfwork));
    2651:   } else {
    2652:     /* since DMPlexStorageVersion 3.0.0 */
    2653:     PetscCall(DMPlexTopologyLoad_HDF5_Private(dm, viewer, &sfwork));
    2654:   }
    2655:   PetscCall(PetscViewerHDF5PopGroup(viewer)); /* "topology" */

    2657:   if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
    2658:     DM          distdm;
    2659:     PetscSF     distsf;
    2660:     const char *distribution_name;
    2661:     PetscBool   exists;

    2663:     PetscCall(DMPlexDistributionGetName(dm, &distribution_name));
    2664:     /* this group is guaranteed to be present since DMPlexStorageVersion 2.1.0 */
    2665:     PetscCall(PetscViewerHDF5PushGroup(viewer, "distributions"));
    2666:     PetscCall(PetscViewerHDF5HasGroup(viewer, NULL, &exists));
    2667:     if (exists) {
    2668:       PetscCall(PetscViewerHDF5PushGroup(viewer, distribution_name));
    2669:       PetscCall(DMPlexDistributionLoad_HDF5_Private(dm, viewer, sfwork, &distsf, &distdm));
    2670:       if (distdm) {
    2671:         PetscCall(DMPlexReplace_Internal(dm, &distdm));
    2672:         PetscCall(PetscSFDestroy(&sfwork));
    2673:         sfwork = distsf;
    2674:       }
    2675:       PetscCall(PetscViewerHDF5PopGroup(viewer)); /* distribution_name */
    2676:     }
    2677:     PetscCall(PetscViewerHDF5PopGroup(viewer)); /* "distributions" */
    2678:   }
    2679:   if (sfXC) {
    2680:     *sfXC = sfwork;
    2681:   } else {
    2682:     PetscCall(PetscSFDestroy(&sfwork));
    2683:   }

    2685:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    2686:   PetscFunctionReturn(PETSC_SUCCESS);
    2687: }

    2689: /* If the file is old, it not only has different path to the coordinates, but   */
    2690: /* does not contain coordinateDMs, so must fall back to the old implementation. */
    2691: static PetscErrorCode DMPlexCoordinatesLoad_HDF5_Legacy_Private(DM dm, PetscViewer viewer)
    2692: {
    2693:   PetscSection coordSection;
    2694:   Vec          coordinates;
    2695:   PetscReal    lengthScale;
    2696:   PetscInt     spatialDim, N, numVertices, vStart, vEnd, v;
    2697:   PetscMPIInt  rank;

    2699:   PetscFunctionBegin;
    2700:   PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank));
    2701:   /* Read geometry */
    2702:   PetscCall(PetscViewerHDF5PushGroup(viewer, "/geometry"));
    2703:   PetscCall(VecCreate(PetscObjectComm((PetscObject)dm), &coordinates));
    2704:   PetscCall(PetscObjectSetName((PetscObject)coordinates, "vertices"));
    2705:   {
    2706:     /* Force serial load */
    2707:     PetscCall(PetscViewerHDF5ReadSizes(viewer, "vertices", &spatialDim, &N));
    2708:     PetscCall(VecSetSizes(coordinates, rank == 0 ? N : 0, N));
    2709:     PetscCall(VecSetBlockSize(coordinates, spatialDim));
    2710:   }
    2711:   PetscCall(VecLoad(coordinates, viewer));
    2712:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    2713:   PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
    2714:   PetscCall(VecScale(coordinates, 1.0 / lengthScale));
    2715:   PetscCall(VecGetLocalSize(coordinates, &numVertices));
    2716:   PetscCall(VecGetBlockSize(coordinates, &spatialDim));
    2717:   numVertices /= spatialDim;
    2718:   /* Create coordinates */
    2719:   PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
    2720:   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);
    2721:   PetscCall(DMGetCoordinateSection(dm, &coordSection));
    2722:   PetscCall(PetscSectionSetNumFields(coordSection, 1));
    2723:   PetscCall(PetscSectionSetFieldComponents(coordSection, 0, spatialDim));
    2724:   PetscCall(PetscSectionSetChart(coordSection, vStart, vEnd));
    2725:   for (v = vStart; v < vEnd; ++v) {
    2726:     PetscCall(PetscSectionSetDof(coordSection, v, spatialDim));
    2727:     PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, spatialDim));
    2728:   }
    2729:   PetscCall(PetscSectionSetUp(coordSection));
    2730:   PetscCall(DMSetCoordinates(dm, coordinates));
    2731:   PetscCall(VecDestroy(&coordinates));
    2732:   PetscFunctionReturn(PETSC_SUCCESS);
    2733: }

    2735: PetscErrorCode DMPlexCoordinatesLoad_HDF5_Internal(DM dm, PetscViewer viewer, PetscSF sfXC)
    2736: {
    2737:   DMPlexStorageVersion version;
    2738:   DM                   cdm;
    2739:   Vec                  coords;
    2740:   PetscInt             blockSize;
    2741:   PetscReal            lengthScale;
    2742:   PetscSF              lsf;
    2743:   const char          *topologydm_name;
    2744:   char                *coordinatedm_name, *coordinates_name;

    2746:   PetscFunctionBegin;
    2747:   PetscCall(PetscViewerHDF5GetDMPlexStorageVersionReading(viewer, &version));
    2748:   if (!DMPlexStorageVersionGE(version, 2, 0, 0)) {
    2749:     PetscCall(DMPlexCoordinatesLoad_HDF5_Legacy_Private(dm, viewer));
    2750:     PetscFunctionReturn(PETSC_SUCCESS);
    2751:   }
    2752:   /* else: since DMPlexStorageVersion 2.0.0 */
    2753:   PetscCheck(sfXC, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_NULL, "PetscSF must be given for parallel load");
    2754:   PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
    2755:   PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
    2756:   PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
    2757:   PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "coordinateDMName", PETSC_STRING, NULL, &coordinatedm_name));
    2758:   PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "coordinatesName", PETSC_STRING, NULL, &coordinates_name));
    2759:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    2760:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    2761:   PetscCall(DMGetCoordinateDM(dm, &cdm));
    2762:   PetscCall(PetscObjectSetName((PetscObject)cdm, coordinatedm_name));
    2763:   PetscCall(PetscFree(coordinatedm_name));
    2764:   /* lsf: on-disk data -> in-memory local vector associated with cdm's local section */
    2765:   PetscCall(DMPlexSectionLoad(dm, viewer, cdm, sfXC, NULL, &lsf));
    2766:   PetscCall(DMCreateLocalVector(cdm, &coords));
    2767:   PetscCall(PetscObjectSetName((PetscObject)coords, coordinates_name));
    2768:   PetscCall(PetscFree(coordinates_name));
    2769:   PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_NATIVE));
    2770:   PetscCall(DMPlexLocalVectorLoad(dm, viewer, cdm, lsf, coords));
    2771:   PetscCall(PetscViewerPopFormat(viewer));
    2772:   PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
    2773:   PetscCall(VecScale(coords, 1.0 / lengthScale));
    2774:   PetscCall(DMSetCoordinatesLocal(dm, coords));
    2775:   PetscCall(VecGetBlockSize(coords, &blockSize));
    2776:   PetscCall(DMSetCoordinateDim(dm, blockSize));
    2777:   PetscCall(VecDestroy(&coords));
    2778:   PetscCall(PetscSFDestroy(&lsf));
    2779:   PetscFunctionReturn(PETSC_SUCCESS);
    2780: }

    2782: PetscErrorCode DMPlexLoad_HDF5_Internal(DM dm, PetscViewer viewer)
    2783: {
    2784:   DMPlexStorageVersion version;

    2786:   PetscFunctionBegin;
    2787:   PetscCall(PetscViewerHDF5GetDMPlexStorageVersionReading(viewer, &version));
    2788:   PetscCall(PetscInfo(dm, "Loading DM %s storage version %d.%d.%d\n", dm->hdr.name, version->major, version->minor, version->subminor));
    2789:   if (!DMPlexStorageVersionGE(version, 2, 0, 0)) {
    2790:     PetscCall(DMPlexTopologyLoad_HDF5_Internal(dm, viewer, NULL));
    2791:     PetscCall(DMPlexLabelsLoad_HDF5_Internal(dm, viewer, NULL));
    2792:     PetscCall(DMPlexCoordinatesLoad_HDF5_Legacy_Private(dm, viewer));
    2793:   } else {
    2794:     PetscSF sfXC;

    2796:     /* since DMPlexStorageVersion 2.0.0 */
    2797:     PetscCall(DMPlexTopologyLoad_HDF5_Internal(dm, viewer, &sfXC));
    2798:     PetscCall(DMPlexLabelsLoad_HDF5_Internal(dm, viewer, sfXC));
    2799:     PetscCall(DMPlexCoordinatesLoad_HDF5_Internal(dm, viewer, sfXC));
    2800:     PetscCall(PetscSFDestroy(&sfXC));
    2801:   }
    2802:   PetscFunctionReturn(PETSC_SUCCESS);
    2803: }

    2805: static PetscErrorCode DMPlexSectionLoad_HDF5_Internal_CreateDataSF(PetscSection rootSection, PetscLayout layout, PetscInt globalOffsets[], PetscSection leafSection, PetscSF *sectionSF)
    2806: {
    2807:   MPI_Comm  comm;
    2808:   PetscInt  pStart, pEnd, p, m;
    2809:   PetscInt *goffs, *ilocal;
    2810:   PetscBool rootIncludeConstraints, leafIncludeConstraints;

    2812:   PetscFunctionBegin;
    2813:   PetscCall(PetscObjectGetComm((PetscObject)leafSection, &comm));
    2814:   PetscCall(PetscSectionGetChart(leafSection, &pStart, &pEnd));
    2815:   PetscCall(PetscSectionGetIncludesConstraints(rootSection, &rootIncludeConstraints));
    2816:   PetscCall(PetscSectionGetIncludesConstraints(leafSection, &leafIncludeConstraints));
    2817:   if (rootIncludeConstraints && leafIncludeConstraints) PetscCall(PetscSectionGetStorageSize(leafSection, &m));
    2818:   else PetscCall(PetscSectionGetConstrainedStorageSize(leafSection, &m));
    2819:   PetscCall(PetscMalloc1(m, &ilocal));
    2820:   PetscCall(PetscMalloc1(m, &goffs));
    2821:   /* Currently, PetscSFDistributeSection() returns globalOffsets[] only */
    2822:   /* for the top-level section (not for each field), so one must have   */
    2823:   /* rootSection->pointMajor == PETSC_TRUE.                             */
    2824:   PetscCheck(rootSection->pointMajor, PETSC_COMM_SELF, PETSC_ERR_SUP, "No support for field major ordering");
    2825:   /* Currently, we also assume that leafSection->pointMajor == PETSC_TRUE. */
    2826:   PetscCheck(leafSection->pointMajor, PETSC_COMM_SELF, PETSC_ERR_SUP, "No support for field major ordering");
    2827:   for (p = pStart, m = 0; p < pEnd; ++p) {
    2828:     PetscInt        dof, cdof, i, j, off, goff;
    2829:     const PetscInt *cinds;

    2831:     PetscCall(PetscSectionGetDof(leafSection, p, &dof));
    2832:     if (dof < 0) continue;
    2833:     goff = globalOffsets[p - pStart];
    2834:     PetscCall(PetscSectionGetOffset(leafSection, p, &off));
    2835:     PetscCall(PetscSectionGetConstraintDof(leafSection, p, &cdof));
    2836:     PetscCall(PetscSectionGetConstraintIndices(leafSection, p, &cinds));
    2837:     for (i = 0, j = 0; i < dof; ++i) {
    2838:       PetscBool constrained = (PetscBool)(j < cdof && i == cinds[j]);

    2840:       if (!constrained || (leafIncludeConstraints && rootIncludeConstraints)) {
    2841:         ilocal[m]  = off++;
    2842:         goffs[m++] = goff++;
    2843:       } else if (leafIncludeConstraints && !rootIncludeConstraints) ++off;
    2844:       else if (!leafIncludeConstraints && rootIncludeConstraints) ++goff;
    2845:       if (constrained) ++j;
    2846:     }
    2847:   }
    2848:   PetscCall(PetscSFCreate(comm, sectionSF));
    2849:   PetscCall(PetscSFSetFromOptions(*sectionSF));
    2850:   PetscCall(PetscSFSetGraphLayout(*sectionSF, layout, m, ilocal, PETSC_OWN_POINTER, goffs));
    2851:   PetscCall(PetscFree(goffs));
    2852:   PetscFunctionReturn(PETSC_SUCCESS);
    2853: }

    2855: PetscErrorCode DMPlexSectionLoad_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm, PetscSF sfXB, PetscSF *gsf, PetscSF *lsf)
    2856: {
    2857:   MPI_Comm     comm;
    2858:   PetscMPIInt  size, rank;
    2859:   const char  *topologydm_name;
    2860:   const char  *sectiondm_name;
    2861:   PetscSection sectionA, sectionB;
    2862:   PetscBool    has;
    2863:   PetscInt     nX, n, i;
    2864:   PetscSF      sfAB;

    2866:   PetscFunctionBegin;
    2867:   PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
    2868:   PetscCallMPI(MPI_Comm_size(comm, &size));
    2869:   PetscCallMPI(MPI_Comm_rank(comm, &rank));
    2870:   PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
    2871:   PetscCall(PetscObjectGetName((PetscObject)sectiondm, &sectiondm_name));
    2872:   PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
    2873:   PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
    2874:   PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
    2875:   PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
    2876:   /* A: on-disk points                        */
    2877:   /* X: list of global point numbers, [0, NX) */
    2878:   /* B: plex points                           */
    2879:   /* Load raw section (sectionA)              */
    2880:   PetscCall(PetscSectionCreate(comm, &sectionA));
    2881:   PetscCall(PetscViewerHDF5HasGroup(viewer, "section", &has));
    2882:   if (has) PetscCall(PetscSectionLoad(sectionA, viewer));
    2883:   else {
    2884:     // TODO If section is missing, create the default affine section with dim dofs on each vertex. Use PetscSplitOwnership() to split vertices.
    2885:     //   How do I know the total number of vertices?
    2886:     PetscInt dim, Nf = 1, Nv, nv = PETSC_DECIDE;

    2888:     PetscCall(DMGetDimension(dm, &dim));
    2889:     PetscCall(DMPlexGetDepthStratumGlobalSize(dm, 0, &Nv));
    2890:     PetscCall(PetscSectionSetNumFields(sectionA, Nf));
    2891:     PetscCall(PetscSectionSetFieldName(sectionA, 0, "Cartesian"));
    2892:     PetscCall(PetscSectionSetFieldComponents(sectionA, 0, dim));
    2893:     for (PetscInt c = 0; c < dim; ++c) {
    2894:       char axis = 'X' + (char)c;

    2896:       PetscCall(PetscSectionSetComponentName(sectionA, 0, c, &axis));
    2897:     }
    2898:     PetscCall(PetscSplitOwnership(comm, &nv, &Nv));
    2899:     PetscCall(PetscSectionSetChart(sectionA, 0, nv));
    2900:     for (PetscInt p = 0; p < nv; ++p) {
    2901:       PetscCall(PetscSectionSetDof(sectionA, p, dim));
    2902:       PetscCall(PetscSectionSetFieldDof(sectionA, p, 0, dim));
    2903:     }
    2904:     PetscCall(PetscSectionSetUp(sectionA));
    2905:   }
    2906:   PetscCall(PetscSectionGetChart(sectionA, NULL, &n));
    2907: /* Create sfAB: A -> B */
    2908: #if defined(PETSC_USE_DEBUG)
    2909:   {
    2910:     PetscInt N, N1;

    2912:     PetscCall(PetscViewerHDF5ReadSizes(viewer, "order", NULL, &N1));
    2913:     PetscCallMPI(MPIU_Allreduce(&n, &N, 1, MPIU_INT, MPI_SUM, comm));
    2914:     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);
    2915:   }
    2916: #endif
    2917:   {
    2918:     IS              orderIS;
    2919:     const PetscInt *gpoints;
    2920:     PetscSF         sfXA, sfAX;
    2921:     PetscLayout     layout;
    2922:     PetscSFNode    *owners, *buffer;
    2923:     PetscInt        nleaves;
    2924:     PetscInt       *ilocal;
    2925:     PetscSFNode    *iremote;

    2927:     /* Create sfAX: A -> X */
    2928:     PetscCall(ISCreate(comm, &orderIS));
    2929:     PetscCall(PetscObjectSetName((PetscObject)orderIS, "order"));
    2930:     PetscCall(PetscLayoutSetLocalSize(orderIS->map, n));
    2931:     PetscCall(ISLoad(orderIS, viewer));
    2932:     PetscCall(PetscLayoutCreate(comm, &layout));
    2933:     PetscCall(PetscSFGetGraph(sfXB, &nX, NULL, NULL, NULL));
    2934:     PetscCall(PetscLayoutSetLocalSize(layout, nX));
    2935:     PetscCall(PetscLayoutSetBlockSize(layout, 1));
    2936:     PetscCall(PetscLayoutSetUp(layout));
    2937:     PetscCall(PetscSFCreate(comm, &sfXA));
    2938:     PetscCall(ISGetIndices(orderIS, &gpoints));
    2939:     PetscCall(PetscSFSetGraphLayout(sfXA, layout, n, NULL, PETSC_OWN_POINTER, gpoints));
    2940:     PetscCall(ISRestoreIndices(orderIS, &gpoints));
    2941:     PetscCall(ISDestroy(&orderIS));
    2942:     PetscCall(PetscLayoutDestroy(&layout));
    2943:     PetscCall(PetscMalloc1(n, &owners));
    2944:     PetscCall(PetscMalloc1(nX, &buffer));
    2945:     for (i = 0; i < n; ++i) {
    2946:       owners[i].rank  = rank;
    2947:       owners[i].index = i;
    2948:     }
    2949:     for (i = 0; i < nX; ++i) {
    2950:       buffer[i].rank  = -1;
    2951:       buffer[i].index = -1;
    2952:     }
    2953:     PetscCall(PetscSFReduceBegin(sfXA, MPIU_SF_NODE, owners, buffer, MPI_MAXLOC));
    2954:     PetscCall(PetscSFReduceEnd(sfXA, MPIU_SF_NODE, owners, buffer, MPI_MAXLOC));
    2955:     PetscCall(PetscSFDestroy(&sfXA));
    2956:     PetscCall(PetscFree(owners));
    2957:     for (i = 0, nleaves = 0; i < nX; ++i)
    2958:       if (buffer[i].rank >= 0) nleaves++;
    2959:     PetscCall(PetscMalloc1(nleaves, &ilocal));
    2960:     PetscCall(PetscMalloc1(nleaves, &iremote));
    2961:     for (i = 0, nleaves = 0; i < nX; ++i) {
    2962:       if (buffer[i].rank >= 0) {
    2963:         ilocal[nleaves]        = i;
    2964:         iremote[nleaves].rank  = buffer[i].rank;
    2965:         iremote[nleaves].index = buffer[i].index;
    2966:         nleaves++;
    2967:       }
    2968:     }
    2969:     PetscCall(PetscFree(buffer));
    2970:     PetscCall(PetscSFCreate(comm, &sfAX));
    2971:     PetscCall(PetscSFSetFromOptions(sfAX));
    2972:     PetscCall(PetscSFSetGraph(sfAX, n, nleaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER));
    2973:     PetscCall(PetscSFCompose(sfAX, sfXB, &sfAB));
    2974:     PetscCall(PetscSFDestroy(&sfAX));
    2975:   }
    2976:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    2977:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    2978:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    2979:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    2980:   /* Create plex section (sectionB) */
    2981:   PetscCall(DMGetLocalSection(sectiondm, &sectionB));
    2982:   if (lsf || gsf) {
    2983:     PetscLayout layout;
    2984:     PetscInt    M, m;
    2985:     PetscInt   *offsetsA;
    2986:     PetscBool   includesConstraintsA;

    2988:     PetscCall(PetscSFDistributeSection(sfAB, sectionA, &offsetsA, sectionB));
    2989:     PetscCall(PetscSectionGetIncludesConstraints(sectionA, &includesConstraintsA));
    2990:     if (includesConstraintsA) PetscCall(PetscSectionGetStorageSize(sectionA, &m));
    2991:     else PetscCall(PetscSectionGetConstrainedStorageSize(sectionA, &m));
    2992:     PetscCallMPI(MPIU_Allreduce(&m, &M, 1, MPIU_INT, MPI_SUM, comm));
    2993:     PetscCall(PetscLayoutCreate(comm, &layout));
    2994:     PetscCall(PetscLayoutSetSize(layout, M));
    2995:     PetscCall(PetscLayoutSetUp(layout));
    2996:     if (lsf) {
    2997:       PetscSF lsfABdata;

    2999:       PetscCall(DMPlexSectionLoad_HDF5_Internal_CreateDataSF(sectionA, layout, offsetsA, sectionB, &lsfABdata));
    3000:       *lsf = lsfABdata;
    3001:     }
    3002:     if (gsf) {
    3003:       PetscSection gsectionB, gsectionB1;
    3004:       PetscBool    includesConstraintsB;
    3005:       PetscSF      gsfABdata, pointsf;

    3007:       PetscCall(DMGetGlobalSection(sectiondm, &gsectionB1));
    3008:       PetscCall(PetscSectionGetIncludesConstraints(gsectionB1, &includesConstraintsB));
    3009:       PetscCall(DMGetPointSF(sectiondm, &pointsf));
    3010:       PetscCall(PetscSectionCreateGlobalSection(sectionB, pointsf, PETSC_TRUE, includesConstraintsB, PETSC_TRUE, &gsectionB));
    3011:       PetscCall(DMPlexSectionLoad_HDF5_Internal_CreateDataSF(sectionA, layout, offsetsA, gsectionB, &gsfABdata));
    3012:       PetscCall(PetscSectionDestroy(&gsectionB));
    3013:       *gsf = gsfABdata;
    3014:     }
    3015:     PetscCall(PetscLayoutDestroy(&layout));
    3016:     PetscCall(PetscFree(offsetsA));
    3017:   } else {
    3018:     PetscCall(PetscSFDistributeSection(sfAB, sectionA, NULL, sectionB));
    3019:   }
    3020:   PetscCall(PetscSFDestroy(&sfAB));
    3021:   PetscCall(PetscSectionDestroy(&sectionA));
    3022:   PetscFunctionReturn(PETSC_SUCCESS);
    3023: }

    3025: PetscErrorCode DMPlexVecLoad_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm, PetscSF sf, Vec vec)
    3026: {
    3027:   MPI_Comm           comm;
    3028:   const char        *topologydm_name;
    3029:   const char        *sectiondm_name;
    3030:   const char        *vec_name;
    3031:   Vec                vecA;
    3032:   PetscInt           mA, m, bs;
    3033:   const PetscInt    *ilocal;
    3034:   const PetscScalar *src;
    3035:   PetscScalar       *dest;

    3037:   PetscFunctionBegin;
    3038:   PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
    3039:   PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
    3040:   PetscCall(PetscObjectGetName((PetscObject)sectiondm, &sectiondm_name));
    3041:   PetscCall(PetscObjectGetName((PetscObject)vec, &vec_name));
    3042:   PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
    3043:   PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
    3044:   PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
    3045:   PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
    3046:   PetscCall(PetscViewerHDF5PushGroup(viewer, "vecs"));
    3047:   PetscCall(PetscViewerHDF5PushGroup(viewer, vec_name));
    3048:   PetscCall(VecCreate(comm, &vecA));
    3049:   PetscCall(PetscObjectSetName((PetscObject)vecA, vec_name));
    3050:   PetscCall(PetscSFGetGraph(sf, &mA, &m, &ilocal, NULL));
    3051:   /* Check consistency */
    3052:   {
    3053:     PetscSF  pointsf, pointsf1;
    3054:     PetscInt m1, i, j;

    3056:     PetscCall(DMGetPointSF(dm, &pointsf));
    3057:     PetscCall(DMGetPointSF(sectiondm, &pointsf1));
    3058:     PetscCheck(pointsf1 == pointsf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatching point SFs for dm and sectiondm");
    3059: #if defined(PETSC_USE_DEBUG)
    3060:     {
    3061:       PetscInt MA, MA1;

    3063:       PetscCallMPI(MPIU_Allreduce(&mA, &MA, 1, MPIU_INT, MPI_SUM, comm));
    3064:       PetscCall(PetscViewerHDF5ReadSizes(viewer, vec_name, NULL, &MA1));
    3065:       PetscCheck(MA1 == MA, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Total SF root size (%" PetscInt_FMT ") != On-disk vector data size (%" PetscInt_FMT ")", MA, MA1);
    3066:     }
    3067: #endif
    3068:     PetscCall(VecGetLocalSize(vec, &m1));
    3069:     PetscCheck(m1 >= m, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Target vector size (%" PetscInt_FMT ") < SF leaf size (%" PetscInt_FMT ")", m1, m);
    3070:     for (i = 0; i < m; ++i) {
    3071:       j = ilocal ? ilocal[i] : i;
    3072:       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);
    3073:     }
    3074:   }
    3075:   PetscCall(VecSetSizes(vecA, mA, PETSC_DECIDE));
    3076:   PetscCall(VecLoad(vecA, viewer));
    3077:   PetscCall(VecGetArrayRead(vecA, &src));
    3078:   PetscCall(VecGetArray(vec, &dest));
    3079:   PetscCall(PetscSFBcastBegin(sf, MPIU_SCALAR, src, dest, MPI_REPLACE));
    3080:   PetscCall(PetscSFBcastEnd(sf, MPIU_SCALAR, src, dest, MPI_REPLACE));
    3081:   PetscCall(VecRestoreArray(vec, &dest));
    3082:   PetscCall(VecRestoreArrayRead(vecA, &src));
    3083:   PetscCall(VecDestroy(&vecA));
    3084:   PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "blockSize", PETSC_INT, NULL, (void *)&bs));
    3085:   PetscCall(VecSetBlockSize(vec, bs));
    3086:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    3087:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    3088:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    3089:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    3090:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    3091:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    3092:   PetscFunctionReturn(PETSC_SUCCESS);
    3093: }