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: static PetscErrorCode PetscViewerParseVersion_Private(PetscViewer, const char[], DMPlexStorageVersion *);
      8: static PetscErrorCode PetscViewerCheckVersion_Private(PetscViewer, DMPlexStorageVersion);
      9: static PetscErrorCode PetscViewerAttachVersion_Private(PetscViewer, const char[], DMPlexStorageVersion);
     10: static PetscErrorCode PetscViewerGetAttachedVersion_Private(PetscViewer, const char[], DMPlexStorageVersion *);

     12: PETSC_SINGLE_LIBRARY_INTERN PetscErrorCode VecView_MPI(Vec, PetscViewer);

     14: static PetscErrorCode PetscViewerPrintVersion_Private(PetscViewer viewer, DMPlexStorageVersion version, char str[], size_t len)
     15: {
     16:   PetscFunctionBegin;
     17:   PetscCall(PetscViewerCheckVersion_Private(viewer, version));
     18:   PetscCall(PetscSNPrintf(str, len, "%d.%d.%d", version->major, version->minor, version->subminor));
     19:   PetscFunctionReturn(PETSC_SUCCESS);
     20: }

     22: static PetscErrorCode PetscViewerParseVersion_Private(PetscViewer viewer, const char str[], DMPlexStorageVersion *version)
     23: {
     24:   PetscToken           t;
     25:   const char          *ts;
     26:   PetscInt             i;
     27:   PetscInt             ti[3];
     28:   DMPlexStorageVersion v;

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

     49: static PetscErrorCode PetscViewerAttachVersion_Private(PetscViewer viewer, const char key[], DMPlexStorageVersion v)
     50: {
     51:   PetscFunctionBegin;
     52:   PetscCall(PetscObjectContainerCompose((PetscObject)viewer, key, v, PetscCtxDestroyDefault));
     53:   PetscFunctionReturn(PETSC_SUCCESS);
     54: }

     56: static PetscErrorCode PetscViewerGetAttachedVersion_Private(PetscViewer viewer, const char key[], DMPlexStorageVersion *v)
     57: {
     58:   PetscContainer cont;

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

     67: /*
     68:   Version log:
     69:   1.0.0 legacy version (default if no "dmplex_storage_version" attribute found in file)
     70:   1.1.0 legacy version, but output VIZ by default
     71:   2.0.0 introduce versioning and multiple topologies
     72:   2.1.0 introduce distributions
     73:   3.0.0 new checkpointing format in Firedrake paper
     74:   3.1.0 new format with IS compression
     75: */
     76: static PetscErrorCode PetscViewerCheckVersion_Private(PetscViewer viewer, DMPlexStorageVersion version)
     77: {
     78:   PetscBool valid = PETSC_FALSE;

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

    141: static inline PetscBool DMPlexStorageVersionEQ(DMPlexStorageVersion version, int major, int minor, int subminor)
    142: {
    143:   return (PetscBool)(version->major == major && version->minor == minor && version->subminor == subminor);
    144: }

    146: static inline PetscBool DMPlexStorageVersionGE(DMPlexStorageVersion version, int major, int minor, int subminor)
    147: {
    148:   return (PetscBool)((version->major == major && version->minor == minor && version->subminor >= subminor) || (version->major == major && version->minor > minor) || version->major > major);
    149: }

    151: /*@C
    152:   PetscViewerHDF5SetDMPlexStorageVersionWriting - Set the storage version for writing

    154:   Logically collective

    156:   Input Parameters:
    157: + viewer  - The `PetscViewer`
    158: - version - The storage format version

    160:   Level: advanced

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

    165: .seealso: [](ch_dmbase), `DM`, `PetscViewerHDF5GetDMPlexStorageVersionWriting()`, `PetscViewerHDF5GetDMPlexStorageVersionReading()`, `PetscViewerHDF5SetDMPlexStorageVersionReading()`
    166: @*/
    167: PetscErrorCode PetscViewerHDF5SetDMPlexStorageVersionWriting(PetscViewer viewer, DMPlexStorageVersion version)
    168: {
    169:   const char           ATTR_NAME[] = "dmplex_storage_version";
    170:   DMPlexStorageVersion viewerVersion;
    171:   PetscBool            fileHasVersion;
    172:   char                 fileVersion[16], versionStr[16], viewerVersionStr[16];

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

    182:     PetscCall(PetscViewerPrintVersion_Private(viewer, viewerVersion, viewerVersionStr, 16));
    183:     PetscCall(PetscStrcmp(versionStr, viewerVersionStr, &flg));
    184:     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);
    185:   }

    187:   PetscCall(PetscViewerHDF5HasAttribute(viewer, NULL, ATTR_NAME, &fileHasVersion));
    188:   if (fileHasVersion) {
    189:     PetscBool flg;
    190:     char     *tmp;

    192:     PetscCall(PetscViewerHDF5ReadAttribute(viewer, "/", ATTR_NAME, PETSC_STRING, NULL, &tmp));
    193:     PetscCall(PetscStrncpy(fileVersion, tmp, sizeof(fileVersion)));
    194:     PetscCall(PetscFree(tmp));
    195:     PetscCall(PetscStrcmp(fileVersion, versionStr, &flg));
    196:     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);
    197:   } else {
    198:     PetscCall(PetscViewerHDF5WriteAttribute(viewer, "/", ATTR_NAME, PETSC_STRING, versionStr));
    199:   }
    200:   PetscCall(PetscNew(&viewerVersion));
    201:   viewerVersion->major    = version->major;
    202:   viewerVersion->minor    = version->minor;
    203:   viewerVersion->subminor = version->subminor;
    204:   PetscCall(PetscViewerAttachVersion_Private(viewer, DMPLEX_STORAGE_VERSION_WRITING_KEY, viewerVersion));
    205:   PetscFunctionReturn(PETSC_SUCCESS);
    206: }

    208: /*@C
    209:   PetscViewerHDF5GetDMPlexStorageVersionWriting - Get the storage version for writing

    211:   Logically collective

    213:   Input Parameter:
    214: . viewer - The `PetscViewer`

    216:   Output Parameter:
    217: . version - The storage format version

    219:   Options Database Keys:
    220: . -dm_plex_view_hdf5_storage_version <num> - Overrides the storage format version

    222:   Level: advanced

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

    227: .seealso: [](ch_dmbase), `DM`, `PetscViewerHDF5SetDMPlexStorageVersionWriting()`, `PetscViewerHDF5GetDMPlexStorageVersionReading()`, `PetscViewerHDF5SetDMPlexStorageVersionReading()`
    228: @*/
    229: PetscErrorCode PetscViewerHDF5GetDMPlexStorageVersionWriting(PetscViewer viewer, DMPlexStorageVersion *version)
    230: {
    231:   const char ATTR_NAME[] = "dmplex_storage_version";
    232:   PetscBool  fileHasVersion;
    233:   char       optVersion[16], fileVersion[16];

    235:   PetscFunctionBegin;
    237:   PetscAssertPointer(version, 2);
    238:   PetscCall(PetscViewerGetAttachedVersion_Private(viewer, DMPLEX_STORAGE_VERSION_WRITING_KEY, version));
    239:   if (*version) PetscFunctionReturn(PETSC_SUCCESS);

    241:   PetscCall(PetscStrncpy(fileVersion, DMPLEX_STORAGE_VERSION_STABLE, sizeof(fileVersion)));
    242:   PetscCall(PetscViewerHDF5HasAttribute(viewer, NULL, ATTR_NAME, &fileHasVersion));
    243:   if (fileHasVersion) {
    244:     char *tmp;

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

    259:     PetscCall(PetscStrcmp(fileVersion, optVersion, &flg));
    260:     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);
    261:   }
    262:   PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "petsc_version_git", PETSC_STRING, PETSC_VERSION_GIT));
    263:   PetscCall(PetscViewerParseVersion_Private(viewer, optVersion, version));
    264:   PetscCall(PetscViewerAttachVersion_Private(viewer, DMPLEX_STORAGE_VERSION_WRITING_KEY, *version));
    265:   PetscFunctionReturn(PETSC_SUCCESS);
    266: }

    268: /*@C
    269:   PetscViewerHDF5SetDMPlexStorageVersionReading - Set the storage version for reading

    271:   Logically collective

    273:   Input Parameters:
    274: + viewer  - The `PetscViewer`
    275: - version - The storage format version

    277:   Level: advanced

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

    282: .seealso: [](ch_dmbase), `DM`, `PetscViewerHDF5GetDMPlexStorageVersionReading()`, `PetscViewerHDF5GetDMPlexStorageVersionWriting()`, `PetscViewerHDF5SetDMPlexStorageVersionWriting()`
    283: @*/
    284: PetscErrorCode PetscViewerHDF5SetDMPlexStorageVersionReading(PetscViewer viewer, DMPlexStorageVersion version)
    285: {
    286:   const char           ATTR_NAME[] = "dmplex_storage_version";
    287:   DMPlexStorageVersion viewerVersion;
    288:   PetscBool            fileHasVersion;
    289:   char                 versionStr[16], viewerVersionStr[16];

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

    299:     PetscCall(PetscViewerPrintVersion_Private(viewer, viewerVersion, viewerVersionStr, 16));
    300:     PetscCall(PetscStrcmp(versionStr, viewerVersionStr, &flg));
    301:     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);
    302:   }

    304:   PetscCall(PetscViewerHDF5HasAttribute(viewer, NULL, ATTR_NAME, &fileHasVersion));
    305:   if (fileHasVersion) {
    306:     char     *fileVersion;
    307:     PetscBool flg;

    309:     PetscCall(PetscViewerHDF5ReadAttribute(viewer, "/", ATTR_NAME, PETSC_STRING, NULL, &fileVersion));
    310:     PetscCall(PetscStrcmp(fileVersion, versionStr, &flg));
    311:     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);
    312:     PetscCall(PetscFree(fileVersion));
    313:   }
    314:   PetscCall(PetscNew(&viewerVersion));
    315:   viewerVersion->major    = version->major;
    316:   viewerVersion->minor    = version->minor;
    317:   viewerVersion->subminor = version->subminor;
    318:   PetscCall(PetscViewerAttachVersion_Private(viewer, DMPLEX_STORAGE_VERSION_READING_KEY, viewerVersion));
    319:   PetscFunctionReturn(PETSC_SUCCESS);
    320: }

    322: /*@C
    323:   PetscViewerHDF5GetDMPlexStorageVersionReading - Get the storage version for reading

    325:   Logically collective

    327:   Input Parameter:
    328: . viewer - The `PetscViewer`

    330:   Output Parameter:
    331: . version - The storage format version

    333:   Options Database Keys:
    334: . -dm_plex_view_hdf5_storage_version <num> - Overrides the storage format version

    336:   Level: advanced

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

    341: .seealso: [](ch_dmbase), `DM`, `PetscViewerHDF5SetDMPlexStorageVersionReading()`, `PetscViewerHDF5GetDMPlexStorageVersionWriting()`, `PetscViewerHDF5SetDMPlexStorageVersionWriting()`
    342: @*/
    343: PetscErrorCode PetscViewerHDF5GetDMPlexStorageVersionReading(PetscViewer viewer, DMPlexStorageVersion *version)
    344: {
    345:   const char ATTR_NAME[] = "dmplex_storage_version";
    346:   char      *defaultVersion;
    347:   char      *versionString;

    349:   PetscFunctionBegin;
    351:   PetscAssertPointer(version, 2);
    352:   PetscCall(PetscViewerGetAttachedVersion_Private(viewer, DMPLEX_STORAGE_VERSION_READING_KEY, version));
    353:   if (*version) PetscFunctionReturn(PETSC_SUCCESS);

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

    365: static PetscErrorCode DMPlexGetHDF5Name_Private(DM dm, const char *name[])
    366: {
    367:   PetscFunctionBegin;
    368:   if (((PetscObject)dm)->name) {
    369:     PetscCall(PetscObjectGetName((PetscObject)dm, name));
    370:   } else {
    371:     *name = "plex";
    372:   }
    373:   PetscFunctionReturn(PETSC_SUCCESS);
    374: }

    376: PetscErrorCode DMSequenceGetLength_HDF5_Internal(DM dm, const char seqname[], PetscInt *seqlen, PetscViewer viewer)
    377: {
    378:   hid_t       file, group, dset, dspace;
    379:   hsize_t     rdim, *dims;
    380:   const char *groupname;
    381:   PetscBool   has;

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

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

    401: static PetscErrorCode DMSequenceView_HDF5(DM dm, const char seqname[], PetscInt seqnum, PetscScalar value, PetscViewer viewer)
    402: {
    403:   Vec         stamp;
    404:   PetscMPIInt rank;

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

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

    435: PetscErrorCode DMSequenceLoad_HDF5_Internal(DM dm, const char seqname[], PetscInt seqnum, PetscScalar *value, PetscViewer viewer)
    436: {
    437:   Vec         stamp;
    438:   PetscMPIInt rank;

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

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

    470: static PetscErrorCode DMPlexCreateCutVertexLabel_Private(DM dm, DMLabel cutLabel, DMLabel *cutVertexLabel)
    471: {
    472:   IS              cutcells = NULL;
    473:   const PetscInt *cutc;
    474:   PetscInt        cellHeight, vStart, vEnd, cStart, cEnd, c;

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

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

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

    510: PetscErrorCode VecView_Plex_Local_HDF5_Internal(Vec v, PetscViewer viewer)
    511: {
    512:   DMPlexStorageVersion version;
    513:   DM                   dm;
    514:   DM                   dmBC;
    515:   PetscSection         section, sectionGlobal;
    516:   Vec                  gv;
    517:   const char          *name;
    518:   PetscViewerFormat    format;
    519:   PetscInt             seqnum;
    520:   PetscReal            seqval;
    521:   PetscBool            isseq;

    523:   PetscFunctionBegin;
    524:   PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
    525:   PetscCall(PetscObjectTypeCompare((PetscObject)v, VECSEQ, &isseq));
    526:   PetscCall(VecGetDM(v, &dm));
    527:   PetscCall(DMGetLocalSection(dm, &section));
    528:   PetscCall(DMGetOutputSequenceNumber(dm, &seqnum, &seqval));
    529:   PetscCall(DMSequenceView_HDF5(dm, "time", seqnum, (PetscScalar)seqval, viewer));
    530:   if (seqnum >= 0) {
    531:     PetscCall(PetscViewerHDF5PushTimestepping(viewer));
    532:     PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum));
    533:   }
    534:   PetscCall(PetscViewerGetFormat(viewer, &format));
    535:   PetscCall(DMGetOutputDM(dm, &dmBC));
    536:   PetscCall(DMGetGlobalSection(dmBC, &sectionGlobal));
    537:   PetscCall(DMGetGlobalVector(dmBC, &gv));
    538:   PetscCall(PetscObjectGetName((PetscObject)v, &name));
    539:   PetscCall(PetscObjectSetName((PetscObject)gv, name));
    540:   PetscCall(DMLocalToGlobalBegin(dmBC, v, INSERT_VALUES, gv));
    541:   PetscCall(DMLocalToGlobalEnd(dmBC, v, INSERT_VALUES, gv));
    542:   PetscCall(PetscObjectTypeCompare((PetscObject)gv, VECSEQ, &isseq));
    543:   if (format == PETSC_VIEWER_HDF5_VIZ) {
    544:     /* Output visualization representation */
    545:     PetscInt numFields, f;
    546:     DMLabel  cutLabel, cutVertexLabel = NULL;

    548:     PetscCall(PetscSectionGetNumFields(section, &numFields));
    549:     PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel));
    550:     for (f = 0; f < numFields; ++f) {
    551:       Vec                      subv;
    552:       IS                       is;
    553:       const char              *fname, *fgroup, *componentName, *fname_def = "unnamed";
    554:       char                     subname[PETSC_MAX_PATH_LEN];
    555:       PetscInt                 Nc, Nt = 1;
    556:       PetscInt                *pStart, *pEnd;
    557:       PetscViewerVTKFieldType *ft;

    559:       if (DMPlexStorageVersionEQ(version, 1, 1, 0)) PetscCall(DMPlexGetFieldTypes_Internal(dm, section, f, &Nt, &pStart, &pEnd, &ft));
    560:       else {
    561:         PetscCall(PetscMalloc3(Nt, &pStart, Nt, &pEnd, Nt, &ft));
    562:         PetscCall(DMPlexGetFieldType_Internal(dm, section, f, &pStart[0], &pEnd[0], &ft[0]));
    563:       }
    564:       for (PetscInt t = 0; t < Nt; ++t) {
    565:         if (ft[t] == PETSC_VTK_INVALID) continue;
    566:         fgroup = (ft[t] == PETSC_VTK_POINT_VECTOR_FIELD) || (ft[t] == PETSC_VTK_POINT_FIELD) ? "/vertex_fields" : "/cell_fields";
    567:         PetscCall(PetscSectionGetFieldName(section, f, &fname));
    568:         if (!fname) fname = fname_def;

    570:         if (!t) {
    571:           PetscCall(PetscViewerHDF5PushGroup(viewer, fgroup));
    572:         } else {
    573:           char group[PETSC_MAX_PATH_LEN];

    575:           PetscCall(PetscSNPrintf(group, PETSC_MAX_PATH_LEN, "%s_%" PetscInt_FMT, fgroup, t));
    576:           PetscCall(PetscViewerHDF5PushGroup(viewer, group));
    577:         }

    579:         if (cutLabel) {
    580:           const PetscScalar *ga;
    581:           PetscScalar       *suba;
    582:           PetscInt           gstart, subSize = 0, extSize = 0, subOff = 0, newOff = 0;

    584:           PetscCall(DMPlexCreateCutVertexLabel_Private(dm, cutLabel, &cutVertexLabel));
    585:           PetscCall(PetscSectionGetFieldComponents(section, f, &Nc));
    586:           for (PetscInt p = pStart[t]; p < pEnd[t]; ++p) {
    587:             PetscInt gdof, fdof = 0, val;

    589:             PetscCall(PetscSectionGetDof(sectionGlobal, p, &gdof));
    590:             if (gdof > 0) PetscCall(PetscSectionGetFieldDof(section, p, f, &fdof));
    591:             subSize += fdof;
    592:             PetscCall(DMLabelGetValue(cutVertexLabel, p, &val));
    593:             if (val == 1) extSize += fdof;
    594:           }
    595:           PetscCall(VecCreate(PetscObjectComm((PetscObject)gv), &subv));
    596:           PetscCall(VecSetSizes(subv, subSize + extSize, PETSC_DETERMINE));
    597:           PetscCall(VecSetBlockSize(subv, Nc));
    598:           PetscCall(VecSetType(subv, VECSTANDARD));
    599:           PetscCall(VecGetOwnershipRange(gv, &gstart, NULL));
    600:           PetscCall(VecGetArrayRead(gv, &ga));
    601:           PetscCall(VecGetArray(subv, &suba));
    602:           for (PetscInt p = pStart[t]; p < pEnd[t]; ++p) {
    603:             PetscInt gdof, goff, val;

    605:             PetscCall(PetscSectionGetDof(sectionGlobal, p, &gdof));
    606:             if (gdof > 0) {
    607:               PetscInt fdof, fc, f2, poff = 0;

    609:               PetscCall(PetscSectionGetOffset(sectionGlobal, p, &goff));
    610:               /* Can get rid of this loop by storing field information in the global section */
    611:               for (f2 = 0; f2 < f; ++f2) {
    612:                 PetscCall(PetscSectionGetFieldDof(section, p, f2, &fdof));
    613:                 poff += fdof;
    614:               }
    615:               PetscCall(PetscSectionGetFieldDof(section, p, f, &fdof));
    616:               for (fc = 0; fc < fdof; ++fc, ++subOff) suba[subOff] = ga[goff + poff + fc - gstart];
    617:               PetscCall(DMLabelGetValue(cutVertexLabel, p, &val));
    618:               if (val == 1) {
    619:                 for (fc = 0; fc < fdof; ++fc, ++newOff) suba[subSize + newOff] = ga[goff + poff + fc - gstart];
    620:               }
    621:             }
    622:           }
    623:           PetscCall(VecRestoreArrayRead(gv, &ga));
    624:           PetscCall(VecRestoreArray(subv, &suba));
    625:           PetscCall(DMLabelDestroy(&cutVertexLabel));
    626:         } else {
    627:           PetscCall(PetscSectionGetField_Internal(section, sectionGlobal, gv, f, pStart[t], pEnd[t], &is, &subv));
    628:         }
    629:         PetscCall(PetscStrncpy(subname, name, sizeof(subname)));
    630:         PetscCall(PetscStrlcat(subname, "_", sizeof(subname)));
    631:         PetscCall(PetscStrlcat(subname, fname, sizeof(subname)));
    632:         PetscCall(PetscObjectSetName((PetscObject)subv, subname));
    633:         if (isseq) PetscCall(VecView_Seq(subv, viewer));
    634:         else PetscCall(VecView_MPI(subv, viewer));
    635:         if (ft[t] == PETSC_VTK_POINT_VECTOR_FIELD || ft[t] == PETSC_VTK_CELL_VECTOR_FIELD) {
    636:           PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)subv, "vector_field_type", PETSC_STRING, "vector"));
    637:         } else {
    638:           PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)subv, "vector_field_type", PETSC_STRING, "scalar"));
    639:         }

    641:         /* Output the component names in the field if available */
    642:         PetscCall(PetscSectionGetFieldComponents(section, f, &Nc));
    643:         for (PetscInt c = 0; c < Nc; ++c) {
    644:           char componentNameLabel[PETSC_MAX_PATH_LEN];
    645:           PetscCall(PetscSectionGetComponentName(section, f, c, &componentName));
    646:           PetscCall(PetscSNPrintf(componentNameLabel, sizeof(componentNameLabel), "componentName%" PetscInt_FMT, c));
    647:           PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)subv, componentNameLabel, PETSC_STRING, componentName));
    648:         }

    650:         if (cutLabel) PetscCall(VecDestroy(&subv));
    651:         else PetscCall(PetscSectionRestoreField_Internal(section, sectionGlobal, gv, f, pStart[t], pEnd[t], &is, &subv));
    652:         PetscCall(PetscViewerHDF5PopGroup(viewer));
    653:       }
    654:       if (!DMPlexStorageVersionEQ(version, 1, 1, 0)) PetscCall(PetscFree3(pStart, pEnd, ft));
    655:     }
    656:   } else {
    657:     /* Output full vector */
    658:     PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
    659:     if (isseq) PetscCall(VecView_Seq(gv, viewer));
    660:     else PetscCall(VecView_MPI(gv, viewer));
    661:     PetscCall(PetscViewerHDF5PopGroup(viewer));
    662:   }
    663:   if (seqnum >= 0) PetscCall(PetscViewerHDF5PopTimestepping(viewer));
    664:   PetscCall(DMRestoreGlobalVector(dmBC, &gv));
    665:   PetscFunctionReturn(PETSC_SUCCESS);
    666: }

    668: PetscErrorCode VecView_Plex_HDF5_Internal(Vec v, PetscViewer viewer)
    669: {
    670:   DMPlexStorageVersion version;
    671:   DM                   dm;
    672:   Vec                  locv;
    673:   PetscObject          isZero;
    674:   const char          *name;
    675:   PetscReal            time;

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

    681:   PetscCall(VecGetDM(v, &dm));
    682:   PetscCall(DMGetLocalVector(dm, &locv));
    683:   PetscCall(PetscObjectGetName((PetscObject)v, &name));
    684:   PetscCall(PetscObjectSetName((PetscObject)locv, name));
    685:   PetscCall(PetscObjectQuery((PetscObject)v, "__Vec_bc_zero__", &isZero));
    686:   PetscCall(PetscObjectCompose((PetscObject)locv, "__Vec_bc_zero__", isZero));
    687:   PetscCall(DMGlobalToLocalBegin(dm, v, INSERT_VALUES, locv));
    688:   PetscCall(DMGlobalToLocalEnd(dm, v, INSERT_VALUES, locv));
    689:   PetscCall(DMGetOutputSequenceNumber(dm, NULL, &time));
    690:   PetscCall(DMPlexInsertBoundaryValues(dm, PETSC_TRUE, locv, time, NULL, NULL, NULL));
    691:   PetscCall(VecView_Plex_Local_HDF5_Internal(locv, viewer));
    692:   if (DMPlexStorageVersionEQ(version, 1, 1, 0)) {
    693:     PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
    694:     PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_VIZ));
    695:     PetscCall(VecView_Plex_Local_HDF5_Internal(locv, viewer));
    696:     PetscCall(PetscViewerPopFormat(viewer));
    697:     PetscCall(PetscViewerHDF5PopGroup(viewer));
    698:   }
    699:   PetscCall(PetscObjectCompose((PetscObject)locv, "__Vec_bc_zero__", NULL));
    700:   PetscCall(DMRestoreLocalVector(dm, &locv));
    701:   PetscFunctionReturn(PETSC_SUCCESS);
    702: }

    704: PetscErrorCode VecView_Plex_HDF5_Native_Internal(Vec v, PetscViewer viewer)
    705: {
    706:   PetscBool isseq;

    708:   PetscFunctionBegin;
    709:   PetscCall(PetscObjectTypeCompare((PetscObject)v, VECSEQ, &isseq));
    710:   PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
    711:   if (isseq) PetscCall(VecView_Seq(v, viewer));
    712:   else PetscCall(VecView_MPI(v, viewer));
    713:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    714:   PetscFunctionReturn(PETSC_SUCCESS);
    715: }

    717: PetscErrorCode VecLoad_Plex_HDF5_Internal(Vec v, PetscViewer viewer)
    718: {
    719:   DM          dm;
    720:   Vec         locv;
    721:   const char *name;
    722:   PetscInt    seqnum;

    724:   PetscFunctionBegin;
    725:   PetscCall(VecGetDM(v, &dm));
    726:   PetscCall(DMGetLocalVector(dm, &locv));
    727:   PetscCall(PetscObjectGetName((PetscObject)v, &name));
    728:   PetscCall(PetscObjectSetName((PetscObject)locv, name));
    729:   PetscCall(DMGetOutputSequenceNumber(dm, &seqnum, NULL));
    730:   PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
    731:   if (seqnum >= 0) {
    732:     PetscCall(PetscViewerHDF5PushTimestepping(viewer));
    733:     PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum));
    734:   }
    735:   PetscCall(VecLoad_Plex_Local(locv, viewer));
    736:   if (seqnum >= 0) PetscCall(PetscViewerHDF5PopTimestepping(viewer));
    737:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    738:   PetscCall(DMLocalToGlobalBegin(dm, locv, INSERT_VALUES, v));
    739:   PetscCall(DMLocalToGlobalEnd(dm, locv, INSERT_VALUES, v));
    740:   PetscCall(DMRestoreLocalVector(dm, &locv));
    741:   PetscFunctionReturn(PETSC_SUCCESS);
    742: }

    744: PetscErrorCode VecLoad_Plex_HDF5_Native_Internal(Vec v, PetscViewer viewer)
    745: {
    746:   DM       dm;
    747:   PetscInt seqnum;

    749:   PetscFunctionBegin;
    750:   PetscCall(VecGetDM(v, &dm));
    751:   PetscCall(DMGetOutputSequenceNumber(dm, &seqnum, NULL));
    752:   PetscCall(PetscViewerHDF5PushGroup(viewer, "/fields"));
    753:   if (seqnum >= 0) {
    754:     PetscCall(PetscViewerHDF5PushTimestepping(viewer));
    755:     PetscCall(PetscViewerHDF5SetTimestep(viewer, seqnum));
    756:   }
    757:   PetscCall(VecLoad_Default(v, viewer));
    758:   if (seqnum >= 0) PetscCall(PetscViewerHDF5PopTimestepping(viewer));
    759:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    760:   PetscFunctionReturn(PETSC_SUCCESS);
    761: }

    763: static PetscErrorCode DMPlexDistributionView_HDF5_Private(DM dm, IS globalPointNumbers, PetscViewer viewer)
    764: {
    765:   DMPlexStorageVersion version;
    766:   MPI_Comm             comm;
    767:   PetscMPIInt          size, rank;
    768:   PetscInt             size_petsc_int;
    769:   const char          *topologydm_name, *distribution_name;
    770:   const PetscInt      *gpoint;
    771:   PetscInt             pStart, pEnd, p;
    772:   PetscSF              pointSF;
    773:   PetscInt             nroots, nleaves;
    774:   const PetscInt      *ilocal;
    775:   const PetscSFNode   *iremote;
    776:   IS                   chartSizesIS, ownersIS, gpointsIS;
    777:   PetscInt            *chartSize, *owners, *gpoints;
    778:   PetscBool            ocompress;

    780:   PetscFunctionBegin;
    781:   PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
    782:   PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
    783:   PetscCallMPI(MPI_Comm_size(comm, &size));
    784:   PetscCallMPI(MPI_Comm_rank(comm, &rank));
    785:   PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
    786:   PetscCall(DMPlexDistributionGetName(dm, &distribution_name));
    787:   if (!distribution_name) PetscFunctionReturn(PETSC_SUCCESS);
    788:   PetscCall(PetscLogEventBegin(DMPLEX_DistributionView, viewer, 0, 0, 0));
    789:   size_petsc_int = (PetscInt)size;
    790:   PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "comm_size", PETSC_INT, (void *)&size_petsc_int));
    791:   PetscCall(ISGetIndices(globalPointNumbers, &gpoint));
    792:   PetscCall(DMPlexGetChart(dm, &pStart, &pEnd));
    793:   PetscCall(PetscMalloc1(1, &chartSize));
    794:   *chartSize = pEnd - pStart;
    795:   PetscCall(PetscMalloc1(*chartSize, &owners));
    796:   PetscCall(PetscMalloc1(*chartSize, &gpoints));
    797:   PetscCall(DMGetPointSF(dm, &pointSF));
    798:   PetscCall(PetscSFGetGraph(pointSF, &nroots, &nleaves, &ilocal, &iremote));
    799:   for (p = pStart; p < pEnd; ++p) {
    800:     PetscInt gp = gpoint[p - pStart];

    802:     owners[p - pStart]  = rank;
    803:     gpoints[p - pStart] = (gp < 0 ? -(gp + 1) : gp);
    804:   }
    805:   for (p = 0; p < nleaves; ++p) {
    806:     PetscInt ilocalp = (ilocal ? ilocal[p] : p);

    808:     owners[ilocalp] = iremote[p].rank;
    809:   }
    810:   PetscCall(ISCreateGeneral(comm, 1, chartSize, PETSC_OWN_POINTER, &chartSizesIS));
    811:   PetscCall(ISCreateGeneral(comm, *chartSize, owners, PETSC_OWN_POINTER, &ownersIS));
    812:   PetscCall(ISCreateGeneral(comm, *chartSize, gpoints, PETSC_OWN_POINTER, &gpointsIS));
    813:   if (DMPlexStorageVersionGE(version, 3, 1, 0)) {
    814:     PetscCall(PetscViewerHDF5GetCompress(viewer, &ocompress));
    815:     PetscCall(PetscViewerHDF5SetCompress(viewer, PETSC_TRUE));
    816:   }
    817:   PetscCall(PetscObjectSetName((PetscObject)chartSizesIS, "chart_sizes"));
    818:   PetscCall(PetscObjectSetName((PetscObject)ownersIS, "owners"));
    819:   PetscCall(PetscObjectSetName((PetscObject)gpointsIS, "global_point_numbers"));
    820:   PetscCall(ISView(chartSizesIS, viewer));
    821:   PetscCall(ISView(ownersIS, viewer));
    822:   PetscCall(ISView(gpointsIS, viewer));
    823:   PetscCall(ISDestroy(&chartSizesIS));
    824:   PetscCall(ISDestroy(&ownersIS));
    825:   PetscCall(ISDestroy(&gpointsIS));
    826:   PetscCall(ISRestoreIndices(globalPointNumbers, &gpoint));
    827:   if (DMPlexStorageVersionGE(version, 3, 1, 0)) PetscCall(PetscViewerHDF5SetCompress(viewer, ocompress));
    828:   PetscCall(PetscLogEventEnd(DMPLEX_DistributionView, viewer, 0, 0, 0));
    829:   PetscFunctionReturn(PETSC_SUCCESS);
    830: }

    832: 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[])
    833: {
    834:   DMPlexStorageVersion version;
    835:   IS                   coneSizesIS, conesIS, orientationsIS;
    836:   PetscInt            *coneSizes, *cones, *orientations;
    837:   const PetscInt      *gpoint;
    838:   PetscInt             nPoints = 0, conesSize = 0;
    839:   PetscInt             p, c, s;
    840:   PetscBool            ocompress;
    841:   MPI_Comm             comm;

    843:   PetscFunctionBegin;
    844:   PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
    845:   PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
    846:   PetscCall(ISGetIndices(globalPointNumbers, &gpoint));
    847:   for (p = pStart; p < pEnd; ++p) {
    848:     if (gpoint[p] >= 0) {
    849:       PetscInt coneSize;

    851:       PetscCall(DMPlexGetConeSize(dm, p, &coneSize));
    852:       nPoints += 1;
    853:       conesSize += coneSize;
    854:     }
    855:   }
    856:   PetscCall(PetscMalloc1(nPoints, &coneSizes));
    857:   PetscCall(PetscMalloc1(conesSize, &cones));
    858:   PetscCall(PetscMalloc1(conesSize, &orientations));
    859:   for (p = pStart, c = 0, s = 0; p < pEnd; ++p) {
    860:     if (gpoint[p] >= 0) {
    861:       const PetscInt *cone, *ornt;
    862:       PetscInt        coneSize, cp;

    864:       PetscCall(DMPlexGetConeSize(dm, p, &coneSize));
    865:       PetscCall(DMPlexGetCone(dm, p, &cone));
    866:       PetscCall(DMPlexGetConeOrientation(dm, p, &ornt));
    867:       coneSizes[s] = coneSize;
    868:       for (cp = 0; cp < coneSize; ++cp, ++c) {
    869:         cones[c]        = gpoint[cone[cp]] < 0 ? -(gpoint[cone[cp]] + 1) : gpoint[cone[cp]];
    870:         orientations[c] = ornt[cp];
    871:       }
    872:       ++s;
    873:     }
    874:   }
    875:   PetscCheck(s == nPoints, PETSC_COMM_SELF, PETSC_ERR_LIB, "Total number of points %" PetscInt_FMT " != %" PetscInt_FMT, s, nPoints);
    876:   PetscCheck(c == conesSize, PETSC_COMM_SELF, PETSC_ERR_LIB, "Total number of cone points %" PetscInt_FMT " != %" PetscInt_FMT, c, conesSize);
    877:   PetscCall(ISCreateGeneral(comm, nPoints, coneSizes, PETSC_OWN_POINTER, &coneSizesIS));
    878:   PetscCall(ISCreateGeneral(comm, conesSize, cones, PETSC_OWN_POINTER, &conesIS));
    879:   PetscCall(ISCreateGeneral(comm, conesSize, orientations, PETSC_OWN_POINTER, &orientationsIS));
    880:   PetscCall(PetscObjectSetName((PetscObject)coneSizesIS, coneSizesName));
    881:   PetscCall(PetscObjectSetName((PetscObject)conesIS, conesName));
    882:   PetscCall(PetscObjectSetName((PetscObject)orientationsIS, orientationsName));
    883:   if (DMPlexStorageVersionGE(version, 3, 1, 0)) {
    884:     PetscCall(PetscViewerHDF5GetCompress(viewer, &ocompress));
    885:     PetscCall(PetscViewerHDF5SetCompress(viewer, PETSC_TRUE));
    886:   }
    887:   PetscCall(ISView(coneSizesIS, viewer));
    888:   PetscCall(ISView(conesIS, viewer));
    889:   PetscCall(ISView(orientationsIS, viewer));
    890:   PetscCall(ISDestroy(&coneSizesIS));
    891:   PetscCall(ISDestroy(&conesIS));
    892:   PetscCall(ISDestroy(&orientationsIS));
    893:   if (pointsName) {
    894:     IS        pointsIS;
    895:     PetscInt *points;

    897:     PetscCall(PetscMalloc1(nPoints, &points));
    898:     for (p = pStart, c = 0, s = 0; p < pEnd; ++p) {
    899:       if (gpoint[p] >= 0) {
    900:         points[s] = gpoint[p];
    901:         ++s;
    902:       }
    903:     }
    904:     PetscCall(ISCreateGeneral(comm, nPoints, points, PETSC_OWN_POINTER, &pointsIS));
    905:     PetscCall(PetscObjectSetName((PetscObject)pointsIS, pointsName));
    906:     PetscCall(ISView(pointsIS, viewer));
    907:     PetscCall(ISDestroy(&pointsIS));
    908:   }
    909:   PetscCall(ISRestoreIndices(globalPointNumbers, &gpoint));
    910:   if (DMPlexStorageVersionGE(version, 3, 1, 0)) PetscCall(PetscViewerHDF5SetCompress(viewer, ocompress));
    911:   PetscFunctionReturn(PETSC_SUCCESS);
    912: }

    914: static PetscErrorCode DMPlexTopologyView_HDF5_Legacy_Private(DM dm, IS globalPointNumbers, PetscViewer viewer)
    915: {
    916:   const char *pointsName, *coneSizesName, *conesName, *orientationsName;
    917:   PetscInt    pStart, pEnd, dim;

    919:   PetscFunctionBegin;
    920:   pointsName       = "order";
    921:   coneSizesName    = "cones";
    922:   conesName        = "cells";
    923:   orientationsName = "orientation";
    924:   PetscCall(DMPlexGetChart(dm, &pStart, &pEnd));
    925:   PetscCall(DMPlexTopologyView_HDF5_Inner_Private(dm, globalPointNumbers, viewer, pStart, pEnd, pointsName, coneSizesName, conesName, orientationsName));
    926:   PetscCall(DMGetDimension(dm, &dim));
    927:   PetscCall(PetscViewerHDF5WriteAttribute(viewer, conesName, "cell_dim", PETSC_INT, (void *)&dim));
    928:   PetscFunctionReturn(PETSC_SUCCESS);
    929: }

    931: //TODO get this numbering right away without needing this function
    932: /* Renumber global point numbers so that they are 0-based per stratum */
    933: static PetscErrorCode RenumberGlobalPointNumbersPerStratum_Private(DM dm, IS globalPointNumbers, IS *newGlobalPointNumbers, IS *strataPermutation)
    934: {
    935:   PetscInt        d, depth, p, n;
    936:   PetscInt       *offsets;
    937:   const PetscInt *gpn;
    938:   PetscInt       *ngpn;
    939:   MPI_Comm        comm;

    941:   PetscFunctionBegin;
    942:   PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
    943:   PetscCall(ISGetLocalSize(globalPointNumbers, &n));
    944:   PetscCall(ISGetIndices(globalPointNumbers, &gpn));
    945:   PetscCall(PetscMalloc1(n, &ngpn));
    946:   PetscCall(DMPlexGetDepth(dm, &depth));
    947:   PetscCall(PetscMalloc1(depth + 1, &offsets));
    948:   for (d = 0; d <= depth; d++) {
    949:     PetscInt pStart, pEnd;

    951:     PetscCall(DMPlexGetDepthStratum(dm, d, &pStart, &pEnd));
    952:     offsets[d] = PETSC_INT_MAX;
    953:     for (p = pStart; p < pEnd; p++) {
    954:       if (gpn[p] >= 0 && gpn[p] < offsets[d]) offsets[d] = gpn[p];
    955:     }
    956:   }
    957:   PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, offsets, depth + 1, MPIU_INT, MPI_MIN, comm));
    958:   for (d = 0; d <= depth; d++) {
    959:     PetscInt pStart, pEnd;

    961:     PetscCall(DMPlexGetDepthStratum(dm, d, &pStart, &pEnd));
    962:     for (p = pStart; p < pEnd; p++) ngpn[p] = gpn[p] - PetscSign(gpn[p]) * offsets[d];
    963:   }
    964:   PetscCall(ISRestoreIndices(globalPointNumbers, &gpn));
    965:   PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)globalPointNumbers), n, ngpn, PETSC_OWN_POINTER, newGlobalPointNumbers));
    966:   {
    967:     PetscInt *perm;

    969:     PetscCall(PetscMalloc1(depth + 1, &perm));
    970:     for (d = 0; d <= depth; d++) perm[d] = d;
    971:     PetscCall(PetscSortIntWithPermutation(depth + 1, offsets, perm));
    972:     PetscCall(ISCreateGeneral(PETSC_COMM_SELF, depth + 1, perm, PETSC_OWN_POINTER, strataPermutation));
    973:   }
    974:   PetscCall(PetscFree(offsets));
    975:   PetscFunctionReturn(PETSC_SUCCESS);
    976: }

    978: static PetscErrorCode DMPlexTopologyView_HDF5_Private(DM dm, IS globalPointNumbers, PetscViewer viewer)
    979: {
    980:   IS          globalPointNumbers0, strataPermutation;
    981:   const char *coneSizesName, *conesName, *orientationsName;
    982:   PetscInt    depth, d;
    983:   MPI_Comm    comm;

    985:   PetscFunctionBegin;
    986:   coneSizesName    = "cone_sizes";
    987:   conesName        = "cones";
    988:   orientationsName = "orientations";
    989:   PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
    990:   PetscCall(DMPlexGetDepth(dm, &depth));
    991:   {
    992:     PetscInt dim;

    994:     PetscCall(DMGetDimension(dm, &dim));
    995:     PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "cell_dim", PETSC_INT, &dim));
    996:     PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "depth", PETSC_INT, &depth));
    997:   }

    999:   PetscCall(RenumberGlobalPointNumbersPerStratum_Private(dm, globalPointNumbers, &globalPointNumbers0, &strataPermutation));
    1000:   /* TODO dirty trick to save serial IS using the same parallel viewer */
    1001:   {
    1002:     IS              spOnComm;
    1003:     PetscInt        n   = 0, N;
    1004:     const PetscInt *idx = NULL;
    1005:     const PetscInt *old;
    1006:     PetscMPIInt     rank;

    1008:     PetscCallMPI(MPI_Comm_rank(comm, &rank));
    1009:     PetscCall(ISGetLocalSize(strataPermutation, &N));
    1010:     PetscCall(ISGetIndices(strataPermutation, &old));
    1011:     if (!rank) {
    1012:       n   = N;
    1013:       idx = old;
    1014:     }
    1015:     PetscCall(ISCreateGeneral(comm, n, idx, PETSC_COPY_VALUES, &spOnComm));
    1016:     PetscCall(ISRestoreIndices(strataPermutation, &old));
    1017:     PetscCall(ISDestroy(&strataPermutation));
    1018:     strataPermutation = spOnComm;
    1019:   }
    1020:   PetscCall(PetscObjectSetName((PetscObject)strataPermutation, "permutation"));
    1021:   PetscCall(ISView(strataPermutation, viewer));
    1022:   PetscCall(PetscViewerHDF5PushGroup(viewer, "strata"));
    1023:   for (d = 0; d <= depth; d++) {
    1024:     PetscInt pStart, pEnd;
    1025:     char     group[128];

    1027:     PetscCall(PetscSNPrintf(group, sizeof(group), "%" PetscInt_FMT, d));
    1028:     PetscCall(PetscViewerHDF5PushGroup(viewer, group));
    1029:     PetscCall(DMPlexGetDepthStratum(dm, d, &pStart, &pEnd));
    1030:     PetscCall(DMPlexTopologyView_HDF5_Inner_Private(dm, globalPointNumbers0, viewer, pStart, pEnd, NULL, coneSizesName, conesName, orientationsName));
    1031:     PetscCall(PetscViewerHDF5PopGroup(viewer));
    1032:   }
    1033:   PetscCall(PetscViewerHDF5PopGroup(viewer)); /* strata */
    1034:   PetscCall(ISDestroy(&globalPointNumbers0));
    1035:   PetscCall(ISDestroy(&strataPermutation));
    1036:   PetscFunctionReturn(PETSC_SUCCESS);
    1037: }

    1039: PetscErrorCode DMPlexTopologyView_HDF5_Internal(DM dm, IS globalPointNumbers, PetscViewer viewer)
    1040: {
    1041:   DMPlexStorageVersion version;
    1042:   const char          *topologydm_name;
    1043:   char                 group[PETSC_MAX_PATH_LEN];

    1045:   PetscFunctionBegin;
    1046:   PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
    1047:   PetscCall(PetscInfo(dm, "Writing DM %s storage version %d.%d.%d\n", dm->hdr.name, version->major, version->minor, version->subminor));
    1048:   PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
    1049:   if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
    1050:     PetscCall(PetscSNPrintf(group, sizeof(group), "topologies/%s", topologydm_name));
    1051:   } else {
    1052:     PetscCall(PetscStrncpy(group, "/", sizeof(group)));
    1053:   }
    1054:   PetscCall(PetscViewerHDF5PushGroup(viewer, group));

    1056:   PetscCall(PetscViewerHDF5PushGroup(viewer, "topology"));
    1057:   if (version->major < 3) {
    1058:     PetscCall(DMPlexTopologyView_HDF5_Legacy_Private(dm, globalPointNumbers, viewer));
    1059:   } else {
    1060:     /* since DMPlexStorageVersion 3.0.0 */
    1061:     PetscCall(DMPlexTopologyView_HDF5_Private(dm, globalPointNumbers, viewer));
    1062:   }
    1063:   PetscCall(PetscViewerHDF5PopGroup(viewer)); /* "topology" */

    1065:   if (DMPlexStorageVersionGE(version, 2, 1, 0)) {
    1066:     const char *distribution_name;

    1068:     PetscCall(DMPlexDistributionGetName(dm, &distribution_name));
    1069:     PetscCall(PetscViewerHDF5PushGroup(viewer, "distributions"));
    1070:     PetscCall(PetscViewerHDF5WriteGroup(viewer, NULL));
    1071:     PetscCall(PetscViewerHDF5PushGroup(viewer, distribution_name));
    1072:     PetscCall(DMPlexDistributionView_HDF5_Private(dm, globalPointNumbers, viewer));
    1073:     PetscCall(PetscViewerHDF5PopGroup(viewer)); /* distribution_name */
    1074:     PetscCall(PetscViewerHDF5PopGroup(viewer)); /* "distributions" */
    1075:   }

    1077:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1078:   PetscFunctionReturn(PETSC_SUCCESS);
    1079: }

    1081: static PetscErrorCode CreateConesIS_Private(DM dm, PetscInt cStart, PetscInt cEnd, IS globalCellNumbers, PetscInt *numCorners, IS *cellIS)
    1082: {
    1083:   PetscSF         sfPoint;
    1084:   DMLabel         cutLabel, cutVertexLabel         = NULL;
    1085:   IS              globalVertexNumbers, cutvertices = NULL;
    1086:   const PetscInt *gcell, *gvertex, *cutverts = NULL;
    1087:   PetscInt       *vertices;
    1088:   PetscInt        conesSize = 0;
    1089:   PetscInt        dim, numCornersLocal = 0, cell, vStart, vEnd, vExtra = 0, v;

    1091:   PetscFunctionBegin;
    1092:   *numCorners = 0;
    1093:   PetscCall(DMGetDimension(dm, &dim));
    1094:   PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
    1095:   PetscCall(ISGetIndices(globalCellNumbers, &gcell));

    1097:   for (cell = cStart; cell < cEnd; ++cell) {
    1098:     PetscInt *closure = NULL;
    1099:     PetscInt  closureSize, v, Nc = 0;

    1101:     if (gcell[cell] < 0) continue;
    1102:     PetscCall(DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure));
    1103:     for (v = 0; v < closureSize * 2; v += 2) {
    1104:       if ((closure[v] >= vStart) && (closure[v] < vEnd)) ++Nc;
    1105:     }
    1106:     PetscCall(DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure));
    1107:     conesSize += Nc;
    1108:     if (!numCornersLocal) numCornersLocal = Nc;
    1109:     else if (numCornersLocal != Nc) numCornersLocal = 1;
    1110:   }
    1111:   PetscCallMPI(MPIU_Allreduce(&numCornersLocal, numCorners, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)dm)));
    1112:   PetscCheck(!numCornersLocal || !(numCornersLocal != *numCorners || *numCorners == 0), PETSC_COMM_SELF, PETSC_ERR_SUP, "Visualization topology currently only supports identical cell shapes");
    1113:   /* Handle periodic cuts by identifying vertices which should be duplicated */
    1114:   PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel));
    1115:   PetscCall(DMPlexCreateCutVertexLabel_Private(dm, cutLabel, &cutVertexLabel));
    1116:   if (cutVertexLabel) PetscCall(DMLabelGetStratumIS(cutVertexLabel, 1, &cutvertices));
    1117:   if (cutvertices) {
    1118:     PetscCall(ISGetIndices(cutvertices, &cutverts));
    1119:     PetscCall(ISGetLocalSize(cutvertices, &vExtra));
    1120:   }
    1121:   PetscCall(DMGetPointSF(dm, &sfPoint));
    1122:   if (cutLabel) {
    1123:     const PetscInt    *ilocal;
    1124:     const PetscSFNode *iremote;
    1125:     PetscInt           nroots, nleaves;

    1127:     PetscCall(PetscSFGetGraph(sfPoint, &nroots, &nleaves, &ilocal, &iremote));
    1128:     if (nleaves < 0) {
    1129:       PetscCall(PetscObjectReference((PetscObject)sfPoint));
    1130:     } else {
    1131:       PetscCall(PetscSFCreate(PetscObjectComm((PetscObject)sfPoint), &sfPoint));
    1132:       PetscCall(PetscSFSetGraph(sfPoint, nroots + vExtra, nleaves, (PetscInt *)ilocal, PETSC_COPY_VALUES, (PetscSFNode *)iremote, PETSC_COPY_VALUES));
    1133:     }
    1134:   } else {
    1135:     PetscCall(PetscObjectReference((PetscObject)sfPoint));
    1136:   }
    1137:   /* Number all vertices */
    1138:   PetscCall(DMPlexCreateNumbering_Plex(dm, vStart, vEnd + vExtra, 0, NULL, sfPoint, &globalVertexNumbers));
    1139:   PetscCall(PetscSFDestroy(&sfPoint));
    1140:   /* Create cones */
    1141:   PetscCall(ISGetIndices(globalVertexNumbers, &gvertex));
    1142:   PetscCall(PetscMalloc1(conesSize, &vertices));
    1143:   for (cell = cStart, v = 0; cell < cEnd; ++cell) {
    1144:     PetscInt *closure = NULL;
    1145:     PetscInt  closureSize, Nc = 0, p, value = -1;
    1146:     PetscBool replace;

    1148:     if (gcell[cell] < 0) continue;
    1149:     if (cutLabel) PetscCall(DMLabelGetValue(cutLabel, cell, &value));
    1150:     replace = (value == 2) ? PETSC_TRUE : PETSC_FALSE;
    1151:     PetscCall(DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure));
    1152:     for (p = 0; p < closureSize * 2; p += 2) {
    1153:       if ((closure[p] >= vStart) && (closure[p] < vEnd)) closure[Nc++] = closure[p];
    1154:     }
    1155:     PetscCall(DMPlexReorderCell(dm, cell, closure));
    1156:     for (p = 0; p < Nc; ++p) {
    1157:       PetscInt nv, gv = gvertex[closure[p] - vStart];

    1159:       if (replace) {
    1160:         PetscCall(PetscFindInt(closure[p], vExtra, cutverts, &nv));
    1161:         if (nv >= 0) gv = gvertex[vEnd - vStart + nv];
    1162:       }
    1163:       vertices[v++] = gv < 0 ? -(gv + 1) : gv;
    1164:     }
    1165:     PetscCall(DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure));
    1166:   }
    1167:   PetscCall(ISRestoreIndices(globalVertexNumbers, &gvertex));
    1168:   PetscCall(ISDestroy(&globalVertexNumbers));
    1169:   PetscCall(ISRestoreIndices(globalCellNumbers, &gcell));
    1170:   if (cutvertices) PetscCall(ISRestoreIndices(cutvertices, &cutverts));
    1171:   PetscCall(ISDestroy(&cutvertices));
    1172:   PetscCall(DMLabelDestroy(&cutVertexLabel));
    1173:   PetscCheck(v == conesSize, PETSC_COMM_SELF, PETSC_ERR_LIB, "Total number of cell vertices %" PetscInt_FMT " != %" PetscInt_FMT, v, conesSize);
    1174:   PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)dm), conesSize, vertices, PETSC_OWN_POINTER, cellIS));
    1175:   PetscCall(PetscLayoutSetBlockSize((*cellIS)->map, *numCorners));
    1176:   PetscCall(PetscObjectSetName((PetscObject)*cellIS, "cells"));
    1177:   PetscFunctionReturn(PETSC_SUCCESS);
    1178: }

    1180: static PetscErrorCode DMPlexTopologyView_HDF5_XDMF_Private(DM dm, IS globalCellNumbers, PetscViewer viewer)
    1181: {
    1182:   DM       cdm;
    1183:   DMLabel  depthLabel, ctLabel;
    1184:   IS       cellIS;
    1185:   PetscInt dim, depth, cellHeight, c, n = 0;

    1187:   PetscFunctionBegin;
    1188:   PetscCall(PetscViewerHDF5PushGroup(viewer, "/viz"));
    1189:   PetscCall(PetscViewerHDF5WriteGroup(viewer, NULL));

    1191:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1192:   PetscCall(DMGetDimension(dm, &dim));
    1193:   PetscCall(DMPlexGetDepth(dm, &depth));
    1194:   PetscCall(DMGetCoordinateDM(dm, &cdm));
    1195:   PetscCall(DMPlexGetVTKCellHeight(dm, &cellHeight));
    1196:   PetscCall(DMPlexGetDepthLabel(dm, &depthLabel));
    1197:   PetscCall(DMPlexGetCellTypeLabel(dm, &ctLabel));
    1198:   for (c = 0; c < DM_NUM_POLYTOPES; ++c) {
    1199:     const DMPolytopeType ict = (DMPolytopeType)c;
    1200:     PetscInt             pStart, pEnd, dep, numCorners;
    1201:     PetscBool            output = PETSC_FALSE, doOutput;

    1203:     if (ict == DM_POLYTOPE_FV_GHOST) continue;
    1204:     PetscCall(DMLabelGetStratumBounds(ctLabel, ict, &pStart, &pEnd));
    1205:     if (pStart >= 0) {
    1206:       PetscCall(DMLabelGetValue(depthLabel, pStart, &dep));
    1207:       if (dep == depth - cellHeight) output = PETSC_TRUE;
    1208:     }
    1209:     PetscCallMPI(MPIU_Allreduce(&output, &doOutput, 1, MPI_C_BOOL, MPI_LOR, PetscObjectComm((PetscObject)dm)));
    1210:     if (!doOutput) continue;
    1211:     PetscCall(CreateConesIS_Private(dm, pStart, pEnd, globalCellNumbers, &numCorners, &cellIS));
    1212:     if (!n) {
    1213:       PetscCall(PetscViewerHDF5PushGroup(viewer, "/viz/topology"));
    1214:     } else {
    1215:       char group[PETSC_MAX_PATH_LEN];

    1217:       PetscCall(PetscSNPrintf(group, PETSC_MAX_PATH_LEN, "/viz/topology_%" PetscInt_FMT, n));
    1218:       PetscCall(PetscViewerHDF5PushGroup(viewer, group));
    1219:     }
    1220:     PetscCall(ISView(cellIS, viewer));
    1221:     PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)cellIS, "cell_corners", PETSC_INT, (void *)&numCorners));
    1222:     PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)cellIS, "cell_dim", PETSC_INT, (void *)&dim));
    1223:     PetscCall(ISDestroy(&cellIS));
    1224:     PetscCall(PetscViewerHDF5PopGroup(viewer));
    1225:     ++n;
    1226:   }
    1227:   PetscFunctionReturn(PETSC_SUCCESS);
    1228: }

    1230: static PetscErrorCode DMPlexCoordinatesView_HDF5_Legacy_Private(DM dm, PetscViewer viewer)
    1231: {
    1232:   DM        cdm;
    1233:   Vec       coordinates, newcoords;
    1234:   PetscReal lengthScale;
    1235:   PetscInt  m, M, bs;

    1237:   PetscFunctionBegin;
    1238:   PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
    1239:   PetscCall(DMGetCoordinateDM(dm, &cdm));
    1240:   PetscCall(DMGetCoordinates(dm, &coordinates));
    1241:   PetscCall(VecCreate(PetscObjectComm((PetscObject)coordinates), &newcoords));
    1242:   PetscCall(PetscObjectSetName((PetscObject)newcoords, "vertices"));
    1243:   PetscCall(VecGetSize(coordinates, &M));
    1244:   PetscCall(VecGetLocalSize(coordinates, &m));
    1245:   PetscCall(VecSetSizes(newcoords, m, M));
    1246:   PetscCall(VecGetBlockSize(coordinates, &bs));
    1247:   PetscCall(VecSetBlockSize(newcoords, bs));
    1248:   PetscCall(VecSetType(newcoords, VECSTANDARD));
    1249:   PetscCall(VecCopy(coordinates, newcoords));
    1250:   PetscCall(VecScale(newcoords, lengthScale));
    1251:   /* Did not use DMGetGlobalVector() in order to bypass default group assignment */
    1252:   PetscCall(PetscViewerHDF5PushGroup(viewer, "/geometry"));
    1253:   PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_NATIVE));
    1254:   PetscCall(VecView(newcoords, viewer));
    1255:   PetscCall(PetscViewerPopFormat(viewer));
    1256:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1257:   PetscCall(VecDestroy(&newcoords));
    1258:   PetscFunctionReturn(PETSC_SUCCESS);
    1259: }

    1261: PetscErrorCode DMPlexCoordinatesView_HDF5_Internal(DM dm, PetscViewer viewer)
    1262: {
    1263:   DM                   cdm;
    1264:   Vec                  coords, newcoords;
    1265:   PetscInt             m, M, bs;
    1266:   PetscReal            lengthScale;
    1267:   PetscBool            viewSection = PETSC_TRUE, ocompress;
    1268:   const char          *topologydm_name, *coordinatedm_name, *coordinates_name;
    1269:   PetscViewerFormat    format;
    1270:   DMPlexStorageVersion version;

    1272:   PetscFunctionBegin;
    1273:   PetscCall(PetscViewerGetFormat(viewer, &format));
    1274:   PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
    1275:   if (!DMPlexStorageVersionGE(version, 2, 0, 0) || format == PETSC_VIEWER_HDF5_XDMF || format == PETSC_VIEWER_HDF5_VIZ) {
    1276:     PetscCall(DMPlexCoordinatesView_HDF5_Legacy_Private(dm, viewer));
    1277:     PetscFunctionReturn(PETSC_SUCCESS);
    1278:   }
    1279:   /* since 2.0.0 */
    1280:   if (DMPlexStorageVersionGE(version, 3, 1, 0)) {
    1281:     PetscCall(PetscViewerHDF5GetCompress(viewer, &ocompress));
    1282:     PetscCall(PetscViewerHDF5SetCompress(viewer, PETSC_TRUE));
    1283:   }
    1284:   PetscCall(PetscOptionsGetBool(NULL, dm->hdr.prefix, "-dm_plex_view_coordinate_section", &viewSection, NULL));
    1285:   PetscCall(DMGetCoordinateDM(dm, &cdm));
    1286:   PetscCall(DMGetCoordinates(dm, &coords));
    1287:   PetscCall(PetscObjectGetName((PetscObject)cdm, &coordinatedm_name));
    1288:   PetscCall(PetscObjectGetName((PetscObject)coords, &coordinates_name));
    1289:   PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
    1290:   PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
    1291:   PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
    1292:   PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "coordinateDMName", PETSC_STRING, coordinatedm_name));
    1293:   PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "coordinatesName", PETSC_STRING, coordinates_name));
    1294:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1295:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1296:   if (viewSection) PetscCall(DMPlexSectionView(dm, viewer, cdm));
    1297:   PetscCall(VecCreate(PetscObjectComm((PetscObject)coords), &newcoords));
    1298:   PetscCall(PetscObjectSetName((PetscObject)newcoords, coordinates_name));
    1299:   PetscCall(VecGetSize(coords, &M));
    1300:   PetscCall(VecGetLocalSize(coords, &m));
    1301:   PetscCall(VecSetSizes(newcoords, m, M));
    1302:   PetscCall(VecGetBlockSize(coords, &bs));
    1303:   PetscCall(VecSetBlockSize(newcoords, bs));
    1304:   PetscCall(VecSetType(newcoords, VECSTANDARD));
    1305:   PetscCall(VecCopy(coords, newcoords));
    1306:   PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
    1307:   PetscCall(VecScale(newcoords, lengthScale));
    1308:   PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_NATIVE));
    1309:   PetscCall(DMPlexGlobalVectorView(dm, viewer, cdm, newcoords));
    1310:   PetscCall(PetscViewerPopFormat(viewer));
    1311:   PetscCall(VecDestroy(&newcoords));
    1312:   if (DMPlexStorageVersionGE(version, 3, 1, 0)) PetscCall(PetscViewerHDF5SetCompress(viewer, ocompress));
    1313:   PetscFunctionReturn(PETSC_SUCCESS);
    1314: }

    1316: static PetscErrorCode DMPlexCoordinatesView_HDF5_XDMF_Private(DM dm, PetscViewer viewer)
    1317: {
    1318:   DM               cdm;
    1319:   Vec              coordinatesLocal, newcoords;
    1320:   PetscSection     cSection, cGlobalSection;
    1321:   PetscScalar     *coords, *ncoords;
    1322:   DMLabel          cutLabel, cutVertexLabel = NULL;
    1323:   const PetscReal *L;
    1324:   PetscReal        lengthScale;
    1325:   PetscInt         vStart, vEnd, v, bs, N, coordSize, dof, off, d;
    1326:   PetscBool        localized, embedded;

    1328:   PetscFunctionBegin;
    1329:   PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
    1330:   PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
    1331:   PetscCall(DMGetCoordinatesLocal(dm, &coordinatesLocal));
    1332:   PetscCall(VecGetBlockSize(coordinatesLocal, &bs));
    1333:   PetscCall(DMGetCoordinatesLocalized(dm, &localized));
    1334:   if (localized == PETSC_FALSE) PetscFunctionReturn(PETSC_SUCCESS);
    1335:   PetscCall(DMGetPeriodicity(dm, NULL, NULL, &L));
    1336:   PetscCall(DMGetCoordinateDM(dm, &cdm));
    1337:   PetscCall(DMGetLocalSection(cdm, &cSection));
    1338:   PetscCall(DMGetGlobalSection(cdm, &cGlobalSection));
    1339:   PetscCall(DMGetLabel(dm, "periodic_cut", &cutLabel));
    1340:   N = 0;

    1342:   PetscCall(DMPlexCreateCutVertexLabel_Private(dm, cutLabel, &cutVertexLabel));
    1343:   PetscCall(VecCreate(PetscObjectComm((PetscObject)dm), &newcoords));
    1344:   PetscCall(PetscSectionGetDof(cSection, vStart, &dof));
    1345:   PetscCall(PetscPrintf(PETSC_COMM_SELF, "DOF: %" PetscInt_FMT "\n", dof));
    1346:   embedded = (PetscBool)(L && dof == 2 && !cutLabel);
    1347:   if (cutVertexLabel) {
    1348:     PetscCall(DMLabelGetStratumSize(cutVertexLabel, 1, &v));
    1349:     N += dof * v;
    1350:   }
    1351:   for (v = vStart; v < vEnd; ++v) {
    1352:     PetscCall(PetscSectionGetDof(cGlobalSection, v, &dof));
    1353:     if (dof < 0) continue;
    1354:     if (embedded) N += dof + 1;
    1355:     else N += dof;
    1356:   }
    1357:   if (embedded) PetscCall(VecSetBlockSize(newcoords, bs + 1));
    1358:   else PetscCall(VecSetBlockSize(newcoords, bs));
    1359:   PetscCall(VecSetSizes(newcoords, N, PETSC_DETERMINE));
    1360:   PetscCall(VecSetType(newcoords, VECSTANDARD));
    1361:   PetscCall(VecGetArray(coordinatesLocal, &coords));
    1362:   PetscCall(VecGetArray(newcoords, &ncoords));
    1363:   coordSize = 0;
    1364:   for (v = vStart; v < vEnd; ++v) {
    1365:     PetscCall(PetscSectionGetDof(cGlobalSection, v, &dof));
    1366:     PetscCall(PetscSectionGetOffset(cSection, v, &off));
    1367:     if (dof < 0) continue;
    1368:     if (embedded) {
    1369:       if (L && (L[0] > 0.0) && (L[1] > 0.0)) {
    1370:         PetscReal theta, phi, r, R;
    1371:         /* XY-periodic */
    1372:         /* Suppose its an y-z circle, then
    1373:              \hat r = (0, cos(th), sin(th)) \hat x = (1, 0, 0)
    1374:            and the circle in that plane is
    1375:              \hat r cos(phi) + \hat x sin(phi) */
    1376:         theta                = 2.0 * PETSC_PI * PetscRealPart(coords[off + 1]) / L[1];
    1377:         phi                  = 2.0 * PETSC_PI * PetscRealPart(coords[off + 0]) / L[0];
    1378:         r                    = L[0] / (2.0 * PETSC_PI * 2.0 * L[1]);
    1379:         R                    = L[1] / (2.0 * PETSC_PI);
    1380:         ncoords[coordSize++] = PetscSinReal(phi) * r;
    1381:         ncoords[coordSize++] = -PetscCosReal(theta) * (R + r * PetscCosReal(phi));
    1382:         ncoords[coordSize++] = PetscSinReal(theta) * (R + r * PetscCosReal(phi));
    1383:       } else if (L && (L[0] > 0.0)) {
    1384:         /* X-periodic */
    1385:         ncoords[coordSize++] = -PetscCosReal(2.0 * PETSC_PI * PetscRealPart(coords[off + 0]) / L[0]) * (L[0] / (2.0 * PETSC_PI));
    1386:         ncoords[coordSize++] = coords[off + 1];
    1387:         ncoords[coordSize++] = PetscSinReal(2.0 * PETSC_PI * PetscRealPart(coords[off + 0]) / L[0]) * (L[0] / (2.0 * PETSC_PI));
    1388:       } else if (L && (L[1] > 0.0)) {
    1389:         /* Y-periodic */
    1390:         ncoords[coordSize++] = coords[off + 0];
    1391:         ncoords[coordSize++] = PetscSinReal(2.0 * PETSC_PI * PetscRealPart(coords[off + 1]) / L[1]) * (L[1] / (2.0 * PETSC_PI));
    1392:         ncoords[coordSize++] = -PetscCosReal(2.0 * PETSC_PI * PetscRealPart(coords[off + 1]) / L[1]) * (L[1] / (2.0 * PETSC_PI));
    1393: #if 0
    1394:       } else if ((bd[0] == DM_BOUNDARY_TWIST)) {
    1395:         PetscReal phi, r, R;
    1396:         /* Mobius strip */
    1397:         /* Suppose its an x-z circle, then
    1398:              \hat r = (-cos(phi), 0, sin(phi)) \hat y = (0, 1, 0)
    1399:            and in that plane we rotate by pi as we go around the circle
    1400:              \hat r cos(phi/2) + \hat y sin(phi/2) */
    1401:         phi   = 2.0*PETSC_PI*PetscRealPart(coords[off+0])/L[0];
    1402:         R     = L[0];
    1403:         r     = PetscRealPart(coords[off+1]) - L[1]/2.0;
    1404:         ncoords[coordSize++] = -PetscCosReal(phi) * (R + r * PetscCosReal(phi/2.0));
    1405:         ncoords[coordSize++] =  PetscSinReal(phi/2.0) * r;
    1406:         ncoords[coordSize++] =  PetscSinReal(phi) * (R + r * PetscCosReal(phi/2.0));
    1407: #endif
    1408:       } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Cannot handle periodicity in this domain");
    1409:     } else {
    1410:       for (d = 0; d < dof; ++d, ++coordSize) ncoords[coordSize] = coords[off + d];
    1411:     }
    1412:   }
    1413:   if (cutVertexLabel) {
    1414:     IS              vertices;
    1415:     const PetscInt *verts;
    1416:     PetscInt        n;

    1418:     PetscCall(DMLabelGetStratumIS(cutVertexLabel, 1, &vertices));
    1419:     if (vertices) {
    1420:       PetscCall(ISGetIndices(vertices, &verts));
    1421:       PetscCall(ISGetLocalSize(vertices, &n));
    1422:       for (v = 0; v < n; ++v) {
    1423:         PetscCall(PetscSectionGetDof(cSection, verts[v], &dof));
    1424:         PetscCall(PetscSectionGetOffset(cSection, verts[v], &off));
    1425:         for (d = 0; d < dof; ++d) ncoords[coordSize++] = coords[off + d] + ((L[d] > 0.) ? L[d] : 0.0);
    1426:       }
    1427:       PetscCall(ISRestoreIndices(vertices, &verts));
    1428:       PetscCall(ISDestroy(&vertices));
    1429:     }
    1430:   }
    1431:   PetscCheck(coordSize == N, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatched sizes: %" PetscInt_FMT " != %" PetscInt_FMT, coordSize, N);
    1432:   PetscCall(DMLabelDestroy(&cutVertexLabel));
    1433:   PetscCall(VecRestoreArray(coordinatesLocal, &coords));
    1434:   PetscCall(VecRestoreArray(newcoords, &ncoords));
    1435:   PetscCall(PetscObjectSetName((PetscObject)newcoords, "vertices"));
    1436:   PetscCall(VecScale(newcoords, lengthScale));
    1437:   PetscCall(PetscViewerHDF5PushGroup(viewer, "/viz"));
    1438:   PetscCall(PetscViewerHDF5WriteGroup(viewer, NULL));
    1439:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1440:   PetscCall(PetscViewerHDF5PushGroup(viewer, "/viz/geometry"));
    1441:   PetscCall(VecView(newcoords, viewer));
    1442:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1443:   PetscCall(VecDestroy(&newcoords));
    1444:   PetscFunctionReturn(PETSC_SUCCESS);
    1445: }

    1447: PetscErrorCode DMPlexLabelsView_HDF5_Internal(DM dm, IS globalPointNumbers, PetscViewer viewer)
    1448: {
    1449:   const char          *topologydm_name;
    1450:   const PetscInt      *gpoint;
    1451:   PetscInt             numLabels;
    1452:   PetscBool            omitCelltypes = PETSC_FALSE, ocompress;
    1453:   DMPlexStorageVersion version;
    1454:   char                 group[PETSC_MAX_PATH_LEN];

    1456:   PetscFunctionBegin;
    1457:   PetscCall(PetscOptionsGetBool(NULL, dm->hdr.prefix, "-dm_plex_omit_celltypes", &omitCelltypes, NULL));
    1458:   PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
    1459:   if (DMPlexStorageVersionGE(version, 3, 1, 0)) {
    1460:     PetscCall(PetscViewerHDF5GetCompress(viewer, &ocompress));
    1461:     PetscCall(PetscViewerHDF5SetCompress(viewer, PETSC_TRUE));
    1462:   }
    1463:   PetscCall(ISGetIndices(globalPointNumbers, &gpoint));
    1464:   PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
    1465:   if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
    1466:     PetscCall(PetscSNPrintf(group, sizeof(group), "topologies/%s/labels", topologydm_name));
    1467:   } else {
    1468:     PetscCall(PetscStrncpy(group, "/labels", sizeof(group)));
    1469:   }
    1470:   PetscCall(PetscViewerHDF5PushGroup(viewer, group));
    1471:   PetscCall(DMGetNumLabels(dm, &numLabels));
    1472:   for (PetscInt l = 0; l < numLabels; ++l) {
    1473:     DMLabel         label;
    1474:     const char     *name;
    1475:     IS              valueIS, pvalueIS, globalValueIS;
    1476:     const PetscInt *values;
    1477:     PetscInt        numValues, v;
    1478:     PetscBool       isDepth, isCelltype, output;

    1480:     PetscCall(DMGetLabelByNum(dm, l, &label));
    1481:     PetscCall(PetscObjectGetName((PetscObject)label, &name));
    1482:     PetscCall(DMGetLabelOutput(dm, name, &output));
    1483:     PetscCall(PetscStrncmp(name, "depth", 10, &isDepth));
    1484:     PetscCall(PetscStrncmp(name, "celltype", 10, &isCelltype));
    1485:     // TODO Should only filter out celltype if it can be calculated
    1486:     if (isDepth || (isCelltype && omitCelltypes) || !output) continue;
    1487:     PetscCall(PetscViewerHDF5PushGroup(viewer, name));
    1488:     PetscCall(DMLabelGetValueIS(label, &valueIS));
    1489:     /* Must copy to a new IS on the global comm */
    1490:     PetscCall(ISGetLocalSize(valueIS, &numValues));
    1491:     PetscCall(ISGetIndices(valueIS, &values));
    1492:     PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)dm), numValues, values, PETSC_COPY_VALUES, &pvalueIS));
    1493:     PetscCall(ISRestoreIndices(valueIS, &values));
    1494:     PetscCall(ISAllGather(pvalueIS, &globalValueIS));
    1495:     PetscCall(ISDestroy(&pvalueIS));
    1496:     PetscCall(ISSortRemoveDups(globalValueIS));
    1497:     PetscCall(ISGetLocalSize(globalValueIS, &numValues));
    1498:     PetscCall(ISGetIndices(globalValueIS, &values));
    1499:     for (v = 0; v < numValues; ++v) {
    1500:       IS              stratumIS, globalStratumIS;
    1501:       const PetscInt *spoints = NULL;
    1502:       PetscInt       *gspoints, n = 0, gn, p;
    1503:       const char     *iname = "indices";
    1504:       char            group[PETSC_MAX_PATH_LEN];

    1506:       PetscCall(PetscSNPrintf(group, sizeof(group), "%" PetscInt_FMT, values[v]));
    1507:       PetscCall(PetscViewerHDF5PushGroup(viewer, group));
    1508:       PetscCall(DMLabelGetStratumIS(label, values[v], &stratumIS));

    1510:       if (stratumIS) PetscCall(ISGetLocalSize(stratumIS, &n));
    1511:       if (stratumIS) PetscCall(ISGetIndices(stratumIS, &spoints));
    1512:       for (gn = 0, p = 0; p < n; ++p)
    1513:         if (gpoint[spoints[p]] >= 0) ++gn;
    1514:       PetscCall(PetscMalloc1(gn, &gspoints));
    1515:       for (gn = 0, p = 0; p < n; ++p)
    1516:         if (gpoint[spoints[p]] >= 0) gspoints[gn++] = gpoint[spoints[p]];
    1517:       if (stratumIS) PetscCall(ISRestoreIndices(stratumIS, &spoints));
    1518:       PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)dm), gn, gspoints, PETSC_OWN_POINTER, &globalStratumIS));
    1519:       PetscCall(PetscObjectSetName((PetscObject)globalStratumIS, iname));
    1520:       PetscCall(ISView(globalStratumIS, viewer));
    1521:       PetscCall(ISDestroy(&globalStratumIS));
    1522:       PetscCall(ISDestroy(&stratumIS));
    1523:       PetscCall(PetscViewerHDF5PopGroup(viewer));
    1524:     }
    1525:     PetscCall(ISRestoreIndices(globalValueIS, &values));
    1526:     PetscCall(ISDestroy(&globalValueIS));
    1527:     PetscCall(ISDestroy(&valueIS));
    1528:     PetscCall(PetscViewerHDF5PopGroup(viewer));
    1529:   }
    1530:   PetscCall(ISRestoreIndices(globalPointNumbers, &gpoint));
    1531:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1532:   if (DMPlexStorageVersionGE(version, 3, 1, 0)) PetscCall(PetscViewerHDF5SetCompress(viewer, ocompress));
    1533:   PetscFunctionReturn(PETSC_SUCCESS);
    1534: }

    1536: /* We only write cells and vertices. Does this screw up parallel reading? */
    1537: PetscErrorCode DMPlexView_HDF5_Internal(DM dm, PetscViewer viewer)
    1538: {
    1539:   IS                globalPointNumbers;
    1540:   PetscViewerFormat format;
    1541:   PetscBool         viz_geom = PETSC_FALSE, xdmf_topo = PETSC_FALSE, petsc_topo = PETSC_FALSE;

    1543:   PetscFunctionBegin;
    1544:   PetscCall(DMPlexCreatePointNumbering(dm, &globalPointNumbers));
    1545:   PetscCall(DMPlexCoordinatesView_HDF5_Internal(dm, viewer));

    1547:   PetscCall(PetscViewerGetFormat(viewer, &format));
    1548:   switch (format) {
    1549:   case PETSC_VIEWER_HDF5_VIZ:
    1550:     viz_geom  = PETSC_TRUE;
    1551:     xdmf_topo = PETSC_TRUE;
    1552:     break;
    1553:   case PETSC_VIEWER_HDF5_XDMF:
    1554:     xdmf_topo = PETSC_TRUE;
    1555:     break;
    1556:   case PETSC_VIEWER_HDF5_PETSC:
    1557:     petsc_topo = PETSC_TRUE;
    1558:     break;
    1559:   case PETSC_VIEWER_DEFAULT:
    1560:   case PETSC_VIEWER_NATIVE:
    1561:     viz_geom   = PETSC_TRUE;
    1562:     xdmf_topo  = PETSC_TRUE;
    1563:     petsc_topo = PETSC_TRUE;
    1564:     break;
    1565:   default:
    1566:     SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "PetscViewerFormat %s not supported for HDF5 output.", PetscViewerFormats[format]);
    1567:   }

    1569:   if (viz_geom) PetscCall(DMPlexCoordinatesView_HDF5_XDMF_Private(dm, viewer));
    1570:   if (xdmf_topo) PetscCall(DMPlexTopologyView_HDF5_XDMF_Private(dm, globalPointNumbers, viewer));
    1571:   if (petsc_topo) {
    1572:     PetscBool viewLabels = PETSC_TRUE;

    1574:     PetscCall(DMPlexTopologyView_HDF5_Internal(dm, globalPointNumbers, viewer));
    1575:     PetscCall(PetscOptionsGetBool(NULL, dm->hdr.prefix, "-dm_plex_view_labels", &viewLabels, NULL));
    1576:     if (viewLabels) PetscCall(DMPlexLabelsView_HDF5_Internal(dm, globalPointNumbers, viewer));
    1577:   }

    1579:   PetscCall(ISDestroy(&globalPointNumbers));
    1580:   PetscFunctionReturn(PETSC_SUCCESS);
    1581: }

    1583: PetscErrorCode DMPlexSectionView_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm)
    1584: {
    1585:   DMPlexStorageVersion version;
    1586:   MPI_Comm             comm;
    1587:   const char          *topologydm_name;
    1588:   const char          *sectiondm_name;
    1589:   PetscSection         gsection;
    1590:   PetscBool            ocompress;

    1592:   PetscFunctionBegin;
    1593:   PetscCall(PetscViewerHDF5GetDMPlexStorageVersionWriting(viewer, &version));
    1594:   if (DMPlexStorageVersionGE(version, 3, 1, 0)) {
    1595:     PetscCall(PetscViewerHDF5GetCompress(viewer, &ocompress));
    1596:     PetscCall(PetscViewerHDF5SetCompress(viewer, PETSC_TRUE));
    1597:   }
    1598:   PetscCall(PetscObjectGetComm((PetscObject)sectiondm, &comm));
    1599:   PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
    1600:   PetscCall(PetscObjectGetName((PetscObject)sectiondm, &sectiondm_name));
    1601:   PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
    1602:   PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
    1603:   PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
    1604:   PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
    1605:   PetscCall(DMGetGlobalSection(sectiondm, &gsection));
    1606:   /* Save raw section */
    1607:   PetscCall(PetscSectionView(gsection, viewer));
    1608:   /* Save plex wrapper */
    1609:   {
    1610:     PetscInt        pStart, pEnd, p, n;
    1611:     IS              globalPointNumbers;
    1612:     const PetscInt *gpoints;
    1613:     IS              orderIS;
    1614:     PetscInt       *order;

    1616:     PetscCall(PetscSectionGetChart(gsection, &pStart, &pEnd));
    1617:     PetscCall(DMPlexCreatePointNumbering(dm, &globalPointNumbers));
    1618:     PetscCall(ISGetIndices(globalPointNumbers, &gpoints));
    1619:     for (p = pStart, n = 0; p < pEnd; ++p)
    1620:       if (gpoints[p] >= 0) n++;
    1621:     /* "order" is an array of global point numbers.
    1622:        When loading, it is used with topology/order array
    1623:        to match section points with plex topology points. */
    1624:     PetscCall(PetscMalloc1(n, &order));
    1625:     for (p = pStart, n = 0; p < pEnd; ++p)
    1626:       if (gpoints[p] >= 0) order[n++] = gpoints[p];
    1627:     PetscCall(ISRestoreIndices(globalPointNumbers, &gpoints));
    1628:     PetscCall(ISDestroy(&globalPointNumbers));
    1629:     PetscCall(ISCreateGeneral(comm, n, order, PETSC_OWN_POINTER, &orderIS));
    1630:     PetscCall(PetscObjectSetName((PetscObject)orderIS, "order"));
    1631:     PetscCall(ISView(orderIS, viewer));
    1632:     PetscCall(ISDestroy(&orderIS));
    1633:   }
    1634:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1635:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1636:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1637:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1638:   if (DMPlexStorageVersionGE(version, 3, 1, 0)) PetscCall(PetscViewerHDF5SetCompress(viewer, ocompress));
    1639:   PetscFunctionReturn(PETSC_SUCCESS);
    1640: }

    1642: PetscErrorCode DMPlexGlobalVectorView_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm, Vec vec)
    1643: {
    1644:   const char *topologydm_name;
    1645:   const char *sectiondm_name;
    1646:   const char *vec_name;
    1647:   PetscInt    bs;

    1649:   PetscFunctionBegin;
    1650:   /* Check consistency */
    1651:   {
    1652:     PetscSF pointsf, pointsf1;

    1654:     PetscCall(DMGetPointSF(dm, &pointsf));
    1655:     PetscCall(DMGetPointSF(sectiondm, &pointsf1));
    1656:     PetscCheck(pointsf1 == pointsf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatching point SFs for dm and sectiondm");
    1657:   }
    1658:   PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
    1659:   PetscCall(PetscObjectGetName((PetscObject)sectiondm, &sectiondm_name));
    1660:   PetscCall(PetscObjectGetName((PetscObject)vec, &vec_name));
    1661:   PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
    1662:   PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
    1663:   PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
    1664:   PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
    1665:   PetscCall(PetscViewerHDF5PushGroup(viewer, "vecs"));
    1666:   PetscCall(PetscViewerHDF5PushGroup(viewer, vec_name));
    1667:   PetscCall(VecGetBlockSize(vec, &bs));
    1668:   PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "blockSize", PETSC_INT, (void *)&bs));
    1669:   PetscCall(VecSetBlockSize(vec, 1));
    1670:   /* VecView(vec, viewer) would call (*vec->opt->view)(vec, viewer), but,    */
    1671:   /* if vec was created with DMGet{Global, Local}Vector(), vec->opt->view    */
    1672:   /* is set to VecView_Plex, which would save vec in a predefined location.  */
    1673:   /* To save vec in where we want, we create a new Vec (temp) with           */
    1674:   /* VecCreate(), wrap the vec data in temp, and call VecView(temp, viewer). */
    1675:   {
    1676:     Vec                temp;
    1677:     const PetscScalar *array;
    1678:     PetscLayout        map;

    1680:     PetscCall(VecCreate(PetscObjectComm((PetscObject)vec), &temp));
    1681:     PetscCall(PetscObjectSetName((PetscObject)temp, vec_name));
    1682:     PetscCall(VecGetLayout(vec, &map));
    1683:     PetscCall(VecSetLayout(temp, map));
    1684:     PetscCall(VecSetUp(temp));
    1685:     PetscCall(VecGetArrayRead(vec, &array));
    1686:     PetscCall(VecPlaceArray(temp, array));
    1687:     PetscCall(VecView(temp, viewer));
    1688:     PetscCall(VecResetArray(temp));
    1689:     PetscCall(VecRestoreArrayRead(vec, &array));
    1690:     PetscCall(VecDestroy(&temp));
    1691:   }
    1692:   PetscCall(VecSetBlockSize(vec, bs));
    1693:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1694:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1695:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1696:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1697:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1698:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1699:   PetscFunctionReturn(PETSC_SUCCESS);
    1700: }

    1702: PetscErrorCode DMPlexLocalVectorView_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm, Vec vec)
    1703: {
    1704:   MPI_Comm     comm;
    1705:   const char  *topologydm_name;
    1706:   const char  *sectiondm_name;
    1707:   const char  *vec_name;
    1708:   PetscSection section;
    1709:   PetscBool    includesConstraints;
    1710:   Vec          gvec;
    1711:   PetscInt     m, bs;

    1713:   PetscFunctionBegin;
    1714:   PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
    1715:   /* Check consistency */
    1716:   {
    1717:     PetscSF pointsf, pointsf1;

    1719:     PetscCall(DMGetPointSF(dm, &pointsf));
    1720:     PetscCall(DMGetPointSF(sectiondm, &pointsf1));
    1721:     PetscCheck(pointsf1 == pointsf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatching point SFs for dm and sectiondm");
    1722:   }
    1723:   PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
    1724:   PetscCall(PetscObjectGetName((PetscObject)sectiondm, &sectiondm_name));
    1725:   PetscCall(PetscObjectGetName((PetscObject)vec, &vec_name));
    1726:   PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
    1727:   PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
    1728:   PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
    1729:   PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
    1730:   PetscCall(PetscViewerHDF5PushGroup(viewer, "vecs"));
    1731:   PetscCall(PetscViewerHDF5PushGroup(viewer, vec_name));
    1732:   PetscCall(VecGetBlockSize(vec, &bs));
    1733:   PetscCall(PetscViewerHDF5WriteAttribute(viewer, NULL, "blockSize", PETSC_INT, (void *)&bs));
    1734:   PetscCall(VecCreate(comm, &gvec));
    1735:   PetscCall(PetscObjectSetName((PetscObject)gvec, vec_name));
    1736:   PetscCall(DMGetGlobalSection(sectiondm, &section));
    1737:   PetscCall(PetscSectionGetIncludesConstraints(section, &includesConstraints));
    1738:   if (includesConstraints) PetscCall(PetscSectionGetStorageSize(section, &m));
    1739:   else PetscCall(PetscSectionGetConstrainedStorageSize(section, &m));
    1740:   PetscCall(VecSetSizes(gvec, m, PETSC_DECIDE));
    1741:   PetscCall(VecSetUp(gvec));
    1742:   PetscCall(DMLocalToGlobalBegin(sectiondm, vec, INSERT_VALUES, gvec));
    1743:   PetscCall(DMLocalToGlobalEnd(sectiondm, vec, INSERT_VALUES, gvec));
    1744:   PetscCall(VecView(gvec, viewer));
    1745:   PetscCall(VecDestroy(&gvec));
    1746:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1747:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1748:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1749:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1750:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1751:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1752:   PetscFunctionReturn(PETSC_SUCCESS);
    1753: }

    1755: struct _n_LoadLabelsCtx {
    1756:   MPI_Comm    comm;
    1757:   PetscMPIInt rank;
    1758:   DM          dm;
    1759:   PetscViewer viewer;
    1760:   DMLabel     label;
    1761:   PetscSF     sfXC;
    1762:   PetscLayout layoutX;
    1763: };
    1764: typedef struct _n_LoadLabelsCtx *LoadLabelsCtx;

    1766: static PetscErrorCode LoadLabelsCtxCreate(DM dm, PetscViewer viewer, PetscSF sfXC, LoadLabelsCtx *ctx)
    1767: {
    1768:   PetscFunctionBegin;
    1769:   PetscCall(PetscNew(ctx));
    1770:   PetscCall(PetscObjectReference((PetscObject)((*ctx)->dm = dm)));
    1771:   PetscCall(PetscObjectReference((PetscObject)((*ctx)->viewer = viewer)));
    1772:   PetscCall(PetscObjectGetComm((PetscObject)dm, &(*ctx)->comm));
    1773:   PetscCallMPI(MPI_Comm_rank((*ctx)->comm, &(*ctx)->rank));
    1774:   (*ctx)->sfXC = sfXC;
    1775:   if (sfXC) {
    1776:     PetscInt nX;

    1778:     PetscCall(PetscObjectReference((PetscObject)sfXC));
    1779:     PetscCall(PetscSFGetGraph(sfXC, &nX, NULL, NULL, NULL));
    1780:     PetscCall(PetscLayoutCreateFromSizes((*ctx)->comm, nX, PETSC_DECIDE, 1, &(*ctx)->layoutX));
    1781:   }
    1782:   PetscFunctionReturn(PETSC_SUCCESS);
    1783: }

    1785: static PetscErrorCode LoadLabelsCtxDestroy(LoadLabelsCtx *ctx)
    1786: {
    1787:   PetscFunctionBegin;
    1788:   if (!*ctx) PetscFunctionReturn(PETSC_SUCCESS);
    1789:   PetscCall(DMDestroy(&(*ctx)->dm));
    1790:   PetscCall(PetscViewerDestroy(&(*ctx)->viewer));
    1791:   PetscCall(PetscSFDestroy(&(*ctx)->sfXC));
    1792:   PetscCall(PetscLayoutDestroy(&(*ctx)->layoutX));
    1793:   PetscCall(PetscFree(*ctx));
    1794:   PetscFunctionReturn(PETSC_SUCCESS);
    1795: }

    1797: /*
    1798:     A: on-disk points
    1799:     X: global points [0, NX)
    1800:     C: distributed plex points
    1801: */
    1802: static herr_t ReadLabelStratumHDF5_Distribute_Private(IS stratumIS, LoadLabelsCtx ctx, IS *newStratumIS)
    1803: {
    1804:   MPI_Comm        comm    = ctx->comm;
    1805:   PetscSF         sfXC    = ctx->sfXC;
    1806:   PetscLayout     layoutX = ctx->layoutX;
    1807:   PetscSF         sfXA;
    1808:   const PetscInt *A_points;
    1809:   PetscInt        nX, nC;
    1810:   PetscInt        n;

    1812:   PetscFunctionBegin;
    1813:   PetscCall(PetscSFGetGraph(sfXC, &nX, &nC, NULL, NULL));
    1814:   PetscCall(ISGetLocalSize(stratumIS, &n));
    1815:   PetscCall(ISGetIndices(stratumIS, &A_points));
    1816:   PetscCall(PetscSFCreate(comm, &sfXA));
    1817:   PetscCall(PetscSFSetGraphLayout(sfXA, layoutX, n, NULL, PETSC_USE_POINTER, A_points));
    1818:   PetscCall(ISCreate(comm, newStratumIS));
    1819:   PetscCall(ISSetType(*newStratumIS, ISGENERAL));
    1820:   {
    1821:     PetscInt   i;
    1822:     PetscBool *A_mask, *X_mask, *C_mask;

    1824:     PetscCall(PetscCalloc3(n, &A_mask, nX, &X_mask, nC, &C_mask));
    1825:     for (i = 0; i < n; i++) A_mask[i] = PETSC_TRUE;
    1826:     PetscCall(PetscSFReduceBegin(sfXA, MPI_C_BOOL, A_mask, X_mask, MPI_REPLACE));
    1827:     PetscCall(PetscSFReduceEnd(sfXA, MPI_C_BOOL, A_mask, X_mask, MPI_REPLACE));
    1828:     PetscCall(PetscSFBcastBegin(sfXC, MPI_C_BOOL, X_mask, C_mask, MPI_LOR));
    1829:     PetscCall(PetscSFBcastEnd(sfXC, MPI_C_BOOL, X_mask, C_mask, MPI_LOR));
    1830:     PetscCall(ISGeneralSetIndicesFromMask(*newStratumIS, 0, nC, C_mask));
    1831:     PetscCall(PetscFree3(A_mask, X_mask, C_mask));
    1832:   }
    1833:   PetscCall(PetscSFDestroy(&sfXA));
    1834:   PetscCall(ISRestoreIndices(stratumIS, &A_points));
    1835:   PetscFunctionReturn(PETSC_SUCCESS);
    1836: }

    1838: static herr_t ReadLabelStratumHDF5_Static(hid_t g_id, const char *vname, const H5L_info_t *info, void *op_data)
    1839: {
    1840:   LoadLabelsCtx   ctx    = (LoadLabelsCtx)op_data;
    1841:   PetscViewer     viewer = ctx->viewer;
    1842:   DMLabel         label  = ctx->label;
    1843:   MPI_Comm        comm   = ctx->comm;
    1844:   IS              stratumIS;
    1845:   const PetscInt *ind;
    1846:   PetscInt        value, N, i;

    1848:   PetscCall(PetscOptionsStringToInt(vname, &value));
    1849:   PetscCall(ISCreate(comm, &stratumIS));
    1850:   PetscCall(PetscObjectSetName((PetscObject)stratumIS, "indices"));
    1851:   PetscCall(PetscViewerHDF5PushGroup(viewer, vname)); /* labels/<lname>/<vname> */

    1853:   if (!ctx->sfXC) {
    1854:     /* Force serial load */
    1855:     PetscCall(PetscViewerHDF5ReadSizes(viewer, "indices", NULL, &N));
    1856:     PetscCall(PetscLayoutSetLocalSize(stratumIS->map, !ctx->rank ? N : 0));
    1857:     PetscCall(PetscLayoutSetSize(stratumIS->map, N));
    1858:   }
    1859:   PetscCall(ISLoad(stratumIS, viewer));

    1861:   if (ctx->sfXC) {
    1862:     IS newStratumIS;

    1864:     PetscCallHDF5(ReadLabelStratumHDF5_Distribute_Private, (stratumIS, ctx, &newStratumIS));
    1865:     PetscCall(ISDestroy(&stratumIS));
    1866:     stratumIS = newStratumIS;
    1867:   }

    1869:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1870:   PetscCall(ISGetLocalSize(stratumIS, &N));
    1871:   PetscCall(ISGetIndices(stratumIS, &ind));
    1872:   for (i = 0; i < N; ++i) PetscCall(DMLabelSetValue(label, ind[i], value));
    1873:   PetscCall(ISRestoreIndices(stratumIS, &ind));
    1874:   PetscCall(ISDestroy(&stratumIS));
    1875:   return 0;
    1876: }

    1878: /* TODO: Fix this code, it is returning PETSc error codes when it should be translating them to herr_t codes */
    1879: static herr_t ReadLabelHDF5_Static(hid_t g_id, const char *lname, const H5L_info_t *info, void *op_data)
    1880: {
    1881:   LoadLabelsCtx  ctx = (LoadLabelsCtx)op_data;
    1882:   DM             dm  = ctx->dm;
    1883:   hsize_t        idx = 0;
    1884:   PetscErrorCode ierr;
    1885:   PetscBool      flg;
    1886:   herr_t         err;

    1888:   PetscCall(DMHasLabel(dm, lname, &flg));
    1889:   if (flg) PetscCall(DMRemoveLabel(dm, lname, NULL));
    1890:   ierr = DMCreateLabel(dm, lname);
    1891:   if (ierr) return (herr_t)ierr;
    1892:   ierr = DMGetLabel(dm, lname, &ctx->label);
    1893:   if (ierr) return (herr_t)ierr;
    1894:   ierr = PetscViewerHDF5PushGroup(ctx->viewer, lname);
    1895:   if (ierr) return (herr_t)ierr;
    1896:   /* Iterate over the label's strata */
    1897:   PetscCallHDF5Return(err, H5Literate_by_name, (g_id, lname, H5_INDEX_NAME, H5_ITER_NATIVE, &idx, ReadLabelStratumHDF5_Static, op_data, 0));
    1898:   ierr = PetscViewerHDF5PopGroup(ctx->viewer);
    1899:   if (ierr) return (herr_t)ierr;
    1900:   return err;
    1901: }

    1903: PetscErrorCode DMPlexLabelsLoad_HDF5_Internal(DM dm, PetscViewer viewer, PetscSF sfXC)
    1904: {
    1905:   const char          *topologydm_name;
    1906:   LoadLabelsCtx        ctx;
    1907:   hsize_t              idx = 0;
    1908:   char                 group[PETSC_MAX_PATH_LEN];
    1909:   DMPlexStorageVersion version;
    1910:   PetscBool            distributed, hasGroup;

    1912:   PetscFunctionBegin;
    1913:   PetscCall(DMPlexIsDistributed(dm, &distributed));
    1914:   if (distributed) PetscCheck(sfXC, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_NULL, "PetscSF must be given for parallel load");
    1915:   PetscCall(LoadLabelsCtxCreate(dm, viewer, sfXC, &ctx));
    1916:   PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
    1917:   PetscCall(PetscViewerHDF5GetDMPlexStorageVersionReading(viewer, &version));
    1918:   if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
    1919:     PetscCall(PetscSNPrintf(group, sizeof(group), "topologies/%s/labels", topologydm_name));
    1920:   } else {
    1921:     PetscCall(PetscStrncpy(group, "labels", sizeof(group)));
    1922:   }
    1923:   PetscCall(PetscViewerHDF5PushGroup(viewer, group));
    1924:   PetscCall(PetscViewerHDF5HasGroup(viewer, NULL, &hasGroup));
    1925:   if (hasGroup) {
    1926:     hid_t fileId, groupId;

    1928:     PetscCall(PetscViewerHDF5OpenGroup(viewer, NULL, &fileId, &groupId));
    1929:     /* Iterate over labels */
    1930:     PetscCallHDF5(H5Literate, (groupId, H5_INDEX_NAME, H5_ITER_NATIVE, &idx, ReadLabelHDF5_Static, ctx));
    1931:     PetscCallHDF5(H5Gclose, (groupId));
    1932:   }
    1933:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    1934:   PetscCall(LoadLabelsCtxDestroy(&ctx));
    1935:   PetscFunctionReturn(PETSC_SUCCESS);
    1936: }

    1938: static PetscErrorCode DMPlexDistributionLoad_HDF5_Private(DM dm, PetscViewer viewer, PetscSF sf, PetscSF *distsf, DM *distdm)
    1939: {
    1940:   MPI_Comm        comm;
    1941:   PetscMPIInt     size, rank;
    1942:   PetscInt        dist_size;
    1943:   const char     *distribution_name;
    1944:   PetscInt        p, lsize;
    1945:   IS              chartSizesIS, ownersIS, gpointsIS;
    1946:   const PetscInt *chartSize, *owners, *gpoints;
    1947:   PetscLayout     layout;
    1948:   PetscBool       has;

    1950:   PetscFunctionBegin;
    1951:   *distsf = NULL;
    1952:   *distdm = NULL;
    1953:   PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
    1954:   PetscCallMPI(MPI_Comm_size(comm, &size));
    1955:   PetscCallMPI(MPI_Comm_rank(comm, &rank));
    1956:   PetscCall(DMPlexDistributionGetName(dm, &distribution_name));
    1957:   if (!distribution_name) PetscFunctionReturn(PETSC_SUCCESS);
    1958:   PetscCall(PetscLogEventBegin(DMPLEX_DistributionLoad, viewer, 0, 0, 0));
    1959:   PetscCall(PetscViewerHDF5HasGroup(viewer, NULL, &has));
    1960:   if (!has) {
    1961:     const char *full_group;

    1963:     PetscCall(PetscViewerHDF5GetGroup(viewer, NULL, &full_group));
    1964:     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);
    1965:   }
    1966:   PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "comm_size", PETSC_INT, NULL, (void *)&dist_size));
    1967:   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);
    1968:   PetscCall(ISCreate(comm, &chartSizesIS));
    1969:   PetscCall(PetscObjectSetName((PetscObject)chartSizesIS, "chart_sizes"));
    1970:   PetscCall(ISCreate(comm, &ownersIS));
    1971:   PetscCall(PetscObjectSetName((PetscObject)ownersIS, "owners"));
    1972:   PetscCall(ISCreate(comm, &gpointsIS));
    1973:   PetscCall(PetscObjectSetName((PetscObject)gpointsIS, "global_point_numbers"));
    1974:   PetscCall(PetscLayoutSetLocalSize(chartSizesIS->map, 1));
    1975:   PetscCall(ISLoad(chartSizesIS, viewer));
    1976:   PetscCall(ISGetIndices(chartSizesIS, &chartSize));
    1977:   PetscCall(PetscLayoutSetLocalSize(ownersIS->map, *chartSize));
    1978:   PetscCall(PetscLayoutSetLocalSize(gpointsIS->map, *chartSize));
    1979:   PetscCall(ISLoad(ownersIS, viewer));
    1980:   PetscCall(ISLoad(gpointsIS, viewer));
    1981:   PetscCall(ISGetIndices(ownersIS, &owners));
    1982:   PetscCall(ISGetIndices(gpointsIS, &gpoints));
    1983:   PetscCall(PetscSFCreate(comm, distsf));
    1984:   PetscCall(PetscSFSetFromOptions(*distsf));
    1985:   PetscCall(PetscLayoutCreate(comm, &layout));
    1986:   PetscCall(PetscSFGetGraph(sf, &lsize, NULL, NULL, NULL));
    1987:   PetscCall(PetscLayoutSetLocalSize(layout, lsize));
    1988:   PetscCall(PetscLayoutSetBlockSize(layout, 1));
    1989:   PetscCall(PetscLayoutSetUp(layout));
    1990:   PetscCall(PetscSFSetGraphLayout(*distsf, layout, *chartSize, NULL, PETSC_OWN_POINTER, gpoints));
    1991:   PetscCall(PetscLayoutDestroy(&layout));
    1992:   /* Migrate DM */
    1993:   {
    1994:     PetscInt     pStart, pEnd;
    1995:     PetscSFNode *buffer0, *buffer1, *buffer2;

    1997:     PetscCall(DMPlexGetChart(dm, &pStart, &pEnd));
    1998:     PetscCall(PetscMalloc2(pEnd - pStart, &buffer0, lsize, &buffer1));
    1999:     PetscCall(PetscMalloc1(*chartSize, &buffer2));
    2000:     {
    2001:       PetscSF            workPointSF;
    2002:       PetscInt           workNroots, workNleaves;
    2003:       const PetscInt    *workIlocal;
    2004:       const PetscSFNode *workIremote;

    2006:       for (p = pStart; p < pEnd; ++p) {
    2007:         buffer0[p - pStart].rank  = rank;
    2008:         buffer0[p - pStart].index = p - pStart;
    2009:       }
    2010:       PetscCall(DMGetPointSF(dm, &workPointSF));
    2011:       PetscCall(PetscSFGetGraph(workPointSF, &workNroots, &workNleaves, &workIlocal, &workIremote));
    2012:       for (p = 0; p < workNleaves; ++p) {
    2013:         PetscInt workIlocalp = (workIlocal ? workIlocal[p] : p);

    2015:         buffer0[workIlocalp].rank = -1;
    2016:       }
    2017:     }
    2018:     for (p = 0; p < lsize; ++p) buffer1[p].rank = -1;
    2019:     for (p = 0; p < *chartSize; ++p) buffer2[p].rank = -1;
    2020:     PetscCall(PetscSFReduceBegin(sf, MPIU_SF_NODE, buffer0, buffer1, MPI_MAXLOC));
    2021:     PetscCall(PetscSFReduceEnd(sf, MPIU_SF_NODE, buffer0, buffer1, MPI_MAXLOC));
    2022:     PetscCall(PetscSFBcastBegin(*distsf, MPIU_SF_NODE, buffer1, buffer2, MPI_REPLACE));
    2023:     PetscCall(PetscSFBcastEnd(*distsf, MPIU_SF_NODE, buffer1, buffer2, MPI_REPLACE));
    2024:     if (PetscDefined(USE_DEBUG)) {
    2025:       for (p = 0; p < *chartSize; ++p) 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);
    2026:     }
    2027:     PetscCall(PetscFree2(buffer0, buffer1));
    2028:     PetscCall(DMCreate(comm, distdm));
    2029:     PetscCall(DMSetType(*distdm, DMPLEX));
    2030:     PetscCall(PetscObjectSetName((PetscObject)*distdm, ((PetscObject)dm)->name));
    2031:     PetscCall(DMPlexDistributionSetName(*distdm, distribution_name));
    2032:     {
    2033:       PetscSF migrationSF;

    2035:       PetscCall(PetscSFCreate(comm, &migrationSF));
    2036:       PetscCall(PetscSFSetFromOptions(migrationSF));
    2037:       PetscCall(PetscSFSetGraph(migrationSF, pEnd - pStart, *chartSize, NULL, PETSC_OWN_POINTER, buffer2, PETSC_OWN_POINTER));
    2038:       PetscCall(PetscSFSetUp(migrationSF));
    2039:       PetscCall(DMPlexMigrate(dm, migrationSF, *distdm));
    2040:       PetscCall(PetscSFDestroy(&migrationSF));
    2041:     }
    2042:   }
    2043:   /* Set pointSF */
    2044:   {
    2045:     PetscSF      pointSF;
    2046:     PetscInt    *ilocal, nleaves, q;
    2047:     PetscSFNode *iremote, *buffer0, *buffer1;

    2049:     PetscCall(PetscMalloc2(*chartSize, &buffer0, lsize, &buffer1));
    2050:     for (p = 0, nleaves = 0; p < *chartSize; ++p) {
    2051:       if (owners[p] == rank) {
    2052:         buffer0[p].rank = rank;
    2053:       } else {
    2054:         buffer0[p].rank = -1;
    2055:         nleaves++;
    2056:       }
    2057:       buffer0[p].index = p;
    2058:     }
    2059:     for (p = 0; p < lsize; ++p) buffer1[p].rank = -1;
    2060:     PetscCall(PetscSFReduceBegin(*distsf, MPIU_SF_NODE, buffer0, buffer1, MPI_MAXLOC));
    2061:     PetscCall(PetscSFReduceEnd(*distsf, MPIU_SF_NODE, buffer0, buffer1, MPI_MAXLOC));
    2062:     for (p = 0; p < *chartSize; ++p) buffer0[p].rank = -1;
    2063:     PetscCall(PetscSFBcastBegin(*distsf, MPIU_SF_NODE, buffer1, buffer0, MPI_REPLACE));
    2064:     PetscCall(PetscSFBcastEnd(*distsf, MPIU_SF_NODE, buffer1, buffer0, MPI_REPLACE));
    2065:     if (PetscDefined(USE_DEBUG)) {
    2066:       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);
    2067:     }
    2068:     PetscCall(PetscMalloc1(nleaves, &ilocal));
    2069:     PetscCall(PetscMalloc1(nleaves, &iremote));
    2070:     for (p = 0, q = 0; p < *chartSize; ++p) {
    2071:       if (buffer0[p].rank != rank) {
    2072:         ilocal[q]        = p;
    2073:         iremote[q].rank  = buffer0[p].rank;
    2074:         iremote[q].index = buffer0[p].index;
    2075:         q++;
    2076:       }
    2077:     }
    2078:     PetscCheck(q == nleaves, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatching leaf sizes: %" PetscInt_FMT " != %" PetscInt_FMT, q, nleaves);
    2079:     PetscCall(PetscFree2(buffer0, buffer1));
    2080:     PetscCall(PetscSFCreate(comm, &pointSF));
    2081:     PetscCall(PetscSFSetFromOptions(pointSF));
    2082:     PetscCall(PetscSFSetGraph(pointSF, *chartSize, nleaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER));
    2083:     PetscCall(DMSetPointSF(*distdm, pointSF));
    2084:     {
    2085:       DM cdm;

    2087:       PetscCall(DMGetCoordinateDM(*distdm, &cdm));
    2088:       PetscCall(DMSetPointSF(cdm, pointSF));
    2089:     }
    2090:     PetscCall(PetscSFDestroy(&pointSF));
    2091:   }
    2092:   PetscCall(ISRestoreIndices(chartSizesIS, &chartSize));
    2093:   PetscCall(ISRestoreIndices(ownersIS, &owners));
    2094:   PetscCall(ISRestoreIndices(gpointsIS, &gpoints));
    2095:   PetscCall(ISDestroy(&chartSizesIS));
    2096:   PetscCall(ISDestroy(&ownersIS));
    2097:   PetscCall(ISDestroy(&gpointsIS));
    2098:   /* Record that overlap has been manually created.               */
    2099:   /* This is to pass `DMPlexCheckPointSF()`, which checks that    */
    2100:   /* pointSF does not contain cells in the leaves if overlap = 0. */
    2101:   PetscCall(DMPlexSetOverlap_Plex(*distdm, NULL, DMPLEX_OVERLAP_MANUAL));
    2102:   PetscCall(DMPlexDistributeSetDefault(*distdm, PETSC_FALSE));
    2103:   PetscCall(DMPlexReorderSetDefault(*distdm, DM_REORDER_DEFAULT_FALSE));
    2104:   PetscCall(PetscLogEventEnd(DMPLEX_DistributionLoad, viewer, 0, 0, 0));
    2105:   PetscFunctionReturn(PETSC_SUCCESS);
    2106: }

    2108: // Serial load of topology
    2109: static PetscErrorCode DMPlexTopologyLoad_HDF5_Legacy_Private(DM dm, PetscViewer viewer, PetscSF *sf)
    2110: {
    2111:   MPI_Comm        comm;
    2112:   const char     *pointsName, *coneSizesName, *conesName, *orientationsName;
    2113:   IS              pointsIS, coneSizesIS, conesIS, orientationsIS;
    2114:   const PetscInt *points, *coneSizes, *cones, *orientations;
    2115:   PetscInt       *cone, *ornt;
    2116:   PetscInt        dim, N, Np, pEnd, p, q, maxConeSize = 0, c;
    2117:   PetscMPIInt     size, rank;

    2119:   PetscFunctionBegin;
    2120:   pointsName       = "order";
    2121:   coneSizesName    = "cones";
    2122:   conesName        = "cells";
    2123:   orientationsName = "orientation";
    2124:   PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
    2125:   PetscCallMPI(MPI_Comm_size(comm, &size));
    2126:   PetscCallMPI(MPI_Comm_rank(comm, &rank));
    2127:   PetscCall(ISCreate(comm, &pointsIS));
    2128:   PetscCall(PetscObjectSetName((PetscObject)pointsIS, pointsName));
    2129:   PetscCall(ISCreate(comm, &coneSizesIS));
    2130:   PetscCall(PetscObjectSetName((PetscObject)coneSizesIS, coneSizesName));
    2131:   PetscCall(ISCreate(comm, &conesIS));
    2132:   PetscCall(PetscObjectSetName((PetscObject)conesIS, conesName));
    2133:   PetscCall(ISCreate(comm, &orientationsIS));
    2134:   PetscCall(PetscObjectSetName((PetscObject)orientationsIS, orientationsName));
    2135:   PetscCall(PetscViewerHDF5ReadObjectAttribute(viewer, (PetscObject)conesIS, "cell_dim", PETSC_INT, NULL, &dim));
    2136:   PetscCall(DMSetDimension(dm, dim));
    2137:   {
    2138:     /* Force serial load */
    2139:     PetscCall(PetscInfo(dm, "Loading DM %s in serial\n", dm->hdr.name));
    2140:     PetscCall(PetscViewerHDF5ReadSizes(viewer, pointsName, NULL, &Np));
    2141:     PetscCall(PetscLayoutSetLocalSize(pointsIS->map, rank == 0 ? Np : 0));
    2142:     PetscCall(PetscLayoutSetSize(pointsIS->map, Np));
    2143:     pEnd = rank == 0 ? Np : 0;
    2144:     PetscCall(PetscViewerHDF5ReadSizes(viewer, coneSizesName, NULL, &Np));
    2145:     PetscCall(PetscLayoutSetLocalSize(coneSizesIS->map, rank == 0 ? Np : 0));
    2146:     PetscCall(PetscLayoutSetSize(coneSizesIS->map, Np));
    2147:     PetscCall(PetscViewerHDF5ReadSizes(viewer, conesName, NULL, &N));
    2148:     PetscCall(PetscLayoutSetLocalSize(conesIS->map, rank == 0 ? N : 0));
    2149:     PetscCall(PetscLayoutSetSize(conesIS->map, N));
    2150:     PetscCall(PetscViewerHDF5ReadSizes(viewer, orientationsName, NULL, &N));
    2151:     PetscCall(PetscLayoutSetLocalSize(orientationsIS->map, rank == 0 ? N : 0));
    2152:     PetscCall(PetscLayoutSetSize(orientationsIS->map, N));
    2153:   }
    2154:   PetscCall(ISLoad(pointsIS, viewer));
    2155:   PetscCall(ISLoad(coneSizesIS, viewer));
    2156:   PetscCall(ISLoad(conesIS, viewer));
    2157:   PetscCall(ISLoad(orientationsIS, viewer));
    2158:   /* Create Plex */
    2159:   PetscCall(DMPlexSetChart(dm, 0, pEnd));
    2160:   PetscCall(ISGetIndices(pointsIS, &points));
    2161:   PetscCall(ISGetIndices(coneSizesIS, &coneSizes));
    2162:   for (p = 0; p < pEnd; ++p) {
    2163:     PetscCall(DMPlexSetConeSize(dm, points[p], coneSizes[p]));
    2164:     maxConeSize = PetscMax(maxConeSize, coneSizes[p]);
    2165:   }
    2166:   PetscCall(DMSetUp(dm));
    2167:   PetscCall(ISGetIndices(conesIS, &cones));
    2168:   PetscCall(ISGetIndices(orientationsIS, &orientations));
    2169:   PetscCall(PetscMalloc2(maxConeSize, &cone, maxConeSize, &ornt));
    2170:   for (p = 0, q = 0; p < pEnd; ++p) {
    2171:     for (c = 0; c < coneSizes[p]; ++c, ++q) {
    2172:       cone[c] = cones[q];
    2173:       ornt[c] = orientations[q];
    2174:     }
    2175:     PetscCall(DMPlexSetCone(dm, points[p], cone));
    2176:     PetscCall(DMPlexSetConeOrientation(dm, points[p], ornt));
    2177:   }
    2178:   PetscCall(PetscFree2(cone, ornt));
    2179:   /* Create global section migration SF */
    2180:   if (sf) {
    2181:     PetscLayout layout;
    2182:     PetscInt   *globalIndices;

    2184:     PetscCall(PetscMalloc1(pEnd, &globalIndices));
    2185:     /* plex point == globalPointNumber in this case */
    2186:     for (p = 0; p < pEnd; ++p) globalIndices[p] = p;
    2187:     PetscCall(PetscLayoutCreate(comm, &layout));
    2188:     PetscCall(PetscLayoutSetSize(layout, Np));
    2189:     PetscCall(PetscLayoutSetBlockSize(layout, 1));
    2190:     PetscCall(PetscLayoutSetUp(layout));
    2191:     PetscCall(PetscSFCreate(comm, sf));
    2192:     PetscCall(PetscSFSetFromOptions(*sf));
    2193:     PetscCall(PetscSFSetGraphLayout(*sf, layout, pEnd, NULL, PETSC_OWN_POINTER, globalIndices));
    2194:     PetscCall(PetscLayoutDestroy(&layout));
    2195:     PetscCall(PetscFree(globalIndices));
    2196:   }
    2197:   /* Clean-up */
    2198:   PetscCall(ISRestoreIndices(pointsIS, &points));
    2199:   PetscCall(ISRestoreIndices(coneSizesIS, &coneSizes));
    2200:   PetscCall(ISRestoreIndices(conesIS, &cones));
    2201:   PetscCall(ISRestoreIndices(orientationsIS, &orientations));
    2202:   PetscCall(ISDestroy(&pointsIS));
    2203:   PetscCall(ISDestroy(&coneSizesIS));
    2204:   PetscCall(ISDestroy(&conesIS));
    2205:   PetscCall(ISDestroy(&orientationsIS));
    2206:   /* Fill in the rest of the topology structure */
    2207:   PetscCall(DMPlexSymmetrize(dm));
    2208:   PetscCall(DMPlexStratify(dm));
    2209:   PetscFunctionReturn(PETSC_SUCCESS);
    2210: }

    2212: /* Representation of two DMPlex strata in 0-based global numbering */
    2213: struct _n_PlexLayer {
    2214:   PetscInt     d;
    2215:   IS           conesIS, orientationsIS;
    2216:   PetscSection coneSizesSection;
    2217:   PetscLayout  vertexLayout;
    2218:   PetscSF      overlapSF, l2gSF; //TODO maybe confusing names (in DMPlex in general)
    2219:   PetscInt     offset, conesOffset, leafOffset;
    2220: };
    2221: typedef struct _n_PlexLayer *PlexLayer;

    2223: static PetscErrorCode PlexLayerDestroy(PlexLayer *layer)
    2224: {
    2225:   PetscFunctionBegin;
    2226:   if (!*layer) PetscFunctionReturn(PETSC_SUCCESS);
    2227:   PetscCall(PetscSectionDestroy(&(*layer)->coneSizesSection));
    2228:   PetscCall(ISDestroy(&(*layer)->conesIS));
    2229:   PetscCall(ISDestroy(&(*layer)->orientationsIS));
    2230:   PetscCall(PetscSFDestroy(&(*layer)->overlapSF));
    2231:   PetscCall(PetscSFDestroy(&(*layer)->l2gSF));
    2232:   PetscCall(PetscLayoutDestroy(&(*layer)->vertexLayout));
    2233:   PetscCall(PetscFree(*layer));
    2234:   PetscFunctionReturn(PETSC_SUCCESS);
    2235: }

    2237: static PetscErrorCode PlexLayerCreate_Private(PlexLayer *layer)
    2238: {
    2239:   PetscFunctionBegin;
    2240:   PetscCall(PetscNew(layer));
    2241:   (*layer)->d           = -1;
    2242:   (*layer)->offset      = -1;
    2243:   (*layer)->conesOffset = -1;
    2244:   (*layer)->leafOffset  = -1;
    2245:   PetscFunctionReturn(PETSC_SUCCESS);
    2246: }

    2248: // Parallel load of a depth stratum
    2249: static PetscErrorCode PlexLayerLoad_Private(PlexLayer layer, PetscViewer viewer, PetscInt d, PetscLayout pointsLayout)
    2250: {
    2251:   char         path[128];
    2252:   MPI_Comm     comm;
    2253:   const char  *coneSizesName, *conesName, *orientationsName;
    2254:   IS           coneSizesIS, conesIS, orientationsIS;
    2255:   PetscSection coneSizesSection;
    2256:   PetscLayout  vertexLayout = NULL;
    2257:   PetscInt     s;

    2259:   PetscFunctionBegin;
    2260:   coneSizesName    = "cone_sizes";
    2261:   conesName        = "cones";
    2262:   orientationsName = "orientations";
    2263:   PetscCall(PetscObjectGetComm((PetscObject)viewer, &comm));

    2265:   /* query size of next lower depth stratum (next lower dimension) */
    2266:   if (d > 0) {
    2267:     PetscInt NVertices;

    2269:     PetscCall(PetscSNPrintf(path, sizeof(path), "%" PetscInt_FMT "/%s", d - 1, coneSizesName));
    2270:     PetscCall(PetscViewerHDF5ReadSizes(viewer, path, NULL, &NVertices));
    2271:     PetscCall(PetscLayoutCreate(comm, &vertexLayout));
    2272:     PetscCall(PetscLayoutSetSize(vertexLayout, NVertices));
    2273:     PetscCall(PetscLayoutSetUp(vertexLayout));
    2274:   }

    2276:   PetscCall(PetscSNPrintf(path, sizeof(path), "%" PetscInt_FMT, d));
    2277:   PetscCall(PetscViewerHDF5PushGroup(viewer, path));

    2279:   /* create coneSizesSection from stored IS coneSizes */
    2280:   {
    2281:     const PetscInt *coneSizes;

    2283:     PetscCall(ISCreate(comm, &coneSizesIS));
    2284:     PetscCall(PetscObjectSetName((PetscObject)coneSizesIS, coneSizesName));
    2285:     if (pointsLayout) PetscCall(ISSetLayout(coneSizesIS, pointsLayout));
    2286:     PetscCall(ISLoad(coneSizesIS, viewer));
    2287:     if (!pointsLayout) PetscCall(ISGetLayout(coneSizesIS, &pointsLayout));
    2288:     PetscCall(ISGetIndices(coneSizesIS, &coneSizes));
    2289:     PetscCall(PetscSectionCreate(comm, &coneSizesSection));
    2290:     //TODO different start ?
    2291:     PetscCall(PetscSectionSetChart(coneSizesSection, 0, pointsLayout->n));
    2292:     for (s = 0; s < pointsLayout->n; ++s) PetscCall(PetscSectionSetDof(coneSizesSection, s, coneSizes[s]));
    2293:     PetscCall(PetscSectionSetUp(coneSizesSection));
    2294:     PetscCall(ISRestoreIndices(coneSizesIS, &coneSizes));
    2295:     {
    2296:       PetscLayout tmp = NULL;

    2298:       /* We need to keep the layout until the end of function */
    2299:       PetscCall(PetscLayoutReference((PetscLayout)pointsLayout, &tmp));
    2300:     }
    2301:     PetscCall(ISDestroy(&coneSizesIS));
    2302:   }

    2304:   /* use value layout of coneSizesSection as layout of cones and orientations */
    2305:   {
    2306:     PetscLayout conesLayout;

    2308:     PetscCall(PetscSectionGetValueLayout(comm, coneSizesSection, &conesLayout));
    2309:     PetscCall(ISCreate(comm, &conesIS));
    2310:     PetscCall(ISCreate(comm, &orientationsIS));
    2311:     PetscCall(PetscObjectSetName((PetscObject)conesIS, conesName));
    2312:     PetscCall(PetscObjectSetName((PetscObject)orientationsIS, orientationsName));
    2313:     PetscCall(PetscLayoutDuplicate(conesLayout, &conesIS->map));
    2314:     PetscCall(PetscLayoutDuplicate(conesLayout, &orientationsIS->map));
    2315:     PetscCall(ISLoad(conesIS, viewer));
    2316:     PetscCall(ISLoad(orientationsIS, viewer));
    2317:     PetscCall(PetscLayoutDestroy(&conesLayout));
    2318:   }

    2320:   /* check assertion that layout of points is the same as point layout of coneSizesSection */
    2321:   {
    2322:     PetscLayout pointsLayout0;
    2323:     PetscBool   flg;

    2325:     PetscCall(PetscSectionGetPointLayout(comm, coneSizesSection, &pointsLayout0));
    2326:     PetscCall(PetscLayoutCompare(pointsLayout, pointsLayout0, &flg));
    2327:     PetscCheck(flg, comm, PETSC_ERR_PLIB, "points layout != coneSizesSection point layout");
    2328:     PetscCall(PetscLayoutDestroy(&pointsLayout0));
    2329:   }
    2330:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    2331:   PetscCall(PetscLayoutDestroy(&pointsLayout));

    2333:   layer->d                = d;
    2334:   layer->conesIS          = conesIS;
    2335:   layer->coneSizesSection = coneSizesSection;
    2336:   layer->orientationsIS   = orientationsIS;
    2337:   layer->vertexLayout     = vertexLayout;
    2338:   PetscFunctionReturn(PETSC_SUCCESS);
    2339: }

    2341: static PetscErrorCode PlexLayerDistribute_Private(PlexLayer layer, PetscSF cellLocalToGlobalSF)
    2342: {
    2343:   IS           newConesIS, newOrientationsIS;
    2344:   PetscSection newConeSizesSection;
    2345:   MPI_Comm     comm;

    2347:   PetscFunctionBegin;
    2348:   PetscCall(PetscObjectGetComm((PetscObject)cellLocalToGlobalSF, &comm));
    2349:   PetscCall(PetscSectionCreate(comm, &newConeSizesSection));
    2350:   //TODO rename to something like ISDistribute() with optional PetscSection argument
    2351:   PetscCall(DMPlexDistributeFieldIS(NULL, cellLocalToGlobalSF, layer->coneSizesSection, layer->conesIS, newConeSizesSection, &newConesIS));
    2352:   PetscCall(DMPlexDistributeFieldIS(NULL, cellLocalToGlobalSF, layer->coneSizesSection, layer->orientationsIS, newConeSizesSection, &newOrientationsIS));

    2354:   PetscCall(PetscObjectSetName((PetscObject)newConeSizesSection, ((PetscObject)layer->coneSizesSection)->name));
    2355:   PetscCall(PetscObjectSetName((PetscObject)newConesIS, ((PetscObject)layer->conesIS)->name));
    2356:   PetscCall(PetscObjectSetName((PetscObject)newOrientationsIS, ((PetscObject)layer->orientationsIS)->name));
    2357:   PetscCall(PetscSectionDestroy(&layer->coneSizesSection));
    2358:   PetscCall(ISDestroy(&layer->conesIS));
    2359:   PetscCall(ISDestroy(&layer->orientationsIS));
    2360:   layer->coneSizesSection = newConeSizesSection;
    2361:   layer->conesIS          = newConesIS;
    2362:   layer->orientationsIS   = newOrientationsIS;
    2363:   PetscFunctionReturn(PETSC_SUCCESS);
    2364: }

    2366: //TODO share code with DMPlexBuildFromCellListParallel()
    2367: #include <petsc/private/hashseti.h>
    2368: static PetscErrorCode PlexLayerCreateSFs_Private(PlexLayer layer, PetscSF *vertexOverlapSF, PetscSF *sfXC)
    2369: {
    2370:   PetscLayout     vertexLayout     = layer->vertexLayout;
    2371:   PetscSection    coneSection      = layer->coneSizesSection;
    2372:   IS              cellVertexData   = layer->conesIS;
    2373:   IS              coneOrientations = layer->orientationsIS;
    2374:   PetscSF         vl2gSF, vOverlapSF;
    2375:   PetscInt       *verticesAdj;
    2376:   PetscInt        i, n, numVerticesAdj;
    2377:   const PetscInt *cvd, *co = NULL;
    2378:   MPI_Comm        comm;

    2380:   PetscFunctionBegin;
    2381:   PetscCall(PetscObjectGetComm((PetscObject)coneSection, &comm));
    2382:   PetscCall(PetscSectionGetStorageSize(coneSection, &n));
    2383:   {
    2384:     PetscInt n0;

    2386:     PetscCall(ISGetLocalSize(cellVertexData, &n0));
    2387:     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);
    2388:     PetscCall(ISGetIndices(cellVertexData, &cvd));
    2389:   }
    2390:   if (coneOrientations) {
    2391:     PetscInt n0;

    2393:     PetscCall(ISGetLocalSize(coneOrientations, &n0));
    2394:     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);
    2395:     PetscCall(ISGetIndices(coneOrientations, &co));
    2396:   }
    2397:   /* Get/check global number of vertices */
    2398:   {
    2399:     PetscInt NVerticesInCells = PETSC_INT_MIN;

    2401:     /* NVerticesInCells = max(cellVertexData) + 1 */
    2402:     for (i = 0; i < n; i++)
    2403:       if (cvd[i] > NVerticesInCells) NVerticesInCells = cvd[i];
    2404:     ++NVerticesInCells;
    2405:     PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, &NVerticesInCells, 1, MPIU_INT, MPI_MAX, comm));

    2407:     if (vertexLayout->n == PETSC_DECIDE && vertexLayout->N == PETSC_DECIDE) vertexLayout->N = NVerticesInCells;
    2408:     else
    2409:       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,
    2410:                  vertexLayout->N, NVerticesInCells);
    2411:     PetscCall(PetscLayoutSetUp(vertexLayout));
    2412:   }
    2413:   /* Find locally unique vertices in cellVertexData */
    2414:   {
    2415:     PetscHSetI vhash;
    2416:     PetscInt   off = 0;

    2418:     PetscCall(PetscHSetICreate(&vhash));
    2419:     for (i = 0; i < n; ++i) PetscCall(PetscHSetIAdd(vhash, cvd[i]));
    2420:     PetscCall(PetscHSetIGetSize(vhash, &numVerticesAdj));
    2421:     PetscCall(PetscMalloc1(numVerticesAdj, &verticesAdj));
    2422:     PetscCall(PetscHSetIGetElems(vhash, &off, verticesAdj));
    2423:     PetscAssert(off == numVerticesAdj, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Assertion failed: off == numVerticesAdj (%" PetscInt_FMT " != %" PetscInt_FMT ")", off, numVerticesAdj);
    2424:     PetscCall(PetscHSetIDestroy(&vhash));
    2425:   }
    2426:   /* We must sort vertices to preserve numbering */
    2427:   PetscCall(PetscSortInt(numVerticesAdj, verticesAdj));
    2428:   /* Connect locally unique vertices with star forest */
    2429:   PetscCall(PetscSFCreateByMatchingIndices(vertexLayout, numVerticesAdj, verticesAdj, NULL, 0, numVerticesAdj, verticesAdj, NULL, 0, &vl2gSF, &vOverlapSF));
    2430:   PetscCall(PetscObjectSetName((PetscObject)vOverlapSF, "overlapSF"));
    2431:   PetscCall(PetscObjectSetName((PetscObject)vl2gSF, "localToGlobalSF"));

    2433:   PetscCall(PetscFree(verticesAdj));
    2434:   *vertexOverlapSF = vOverlapSF;
    2435:   *sfXC            = vl2gSF;
    2436:   PetscFunctionReturn(PETSC_SUCCESS);
    2437: }

    2439: static PetscErrorCode PlexLayerCreateCellSFs_Private(PlexLayer layer, PetscSF *cellOverlapSF, PetscSF *cellLocalToGlobalSF)
    2440: {
    2441:   PetscSection coneSection = layer->coneSizesSection;
    2442:   PetscInt     nCells;
    2443:   MPI_Comm     comm;

    2445:   PetscFunctionBegin;
    2446:   PetscCall(PetscObjectGetComm((PetscObject)coneSection, &comm));
    2447:   {
    2448:     PetscInt cStart;

    2450:     PetscCall(PetscSectionGetChart(coneSection, &cStart, &nCells));
    2451:     PetscCheck(cStart == 0, comm, PETSC_ERR_ARG_OUTOFRANGE, "coneSection must start at 0");
    2452:   }
    2453:   /* Create overlapSF as empty SF with the right number of roots */
    2454:   PetscCall(PetscSFCreate(comm, cellOverlapSF));
    2455:   PetscCall(PetscSFSetGraph(*cellOverlapSF, nCells, 0, NULL, PETSC_USE_POINTER, NULL, PETSC_USE_POINTER));
    2456:   PetscCall(PetscSFSetUp(*cellOverlapSF));
    2457:   /* Create localToGlobalSF as identity mapping */
    2458:   {
    2459:     PetscLayout map;

    2461:     PetscCall(PetscLayoutCreateFromSizes(comm, nCells, PETSC_DECIDE, 1, &map));
    2462:     PetscCall(PetscSFCreateFromLayouts(map, map, cellLocalToGlobalSF));
    2463:     PetscCall(PetscSFSetUp(*cellLocalToGlobalSF));
    2464:     PetscCall(PetscLayoutDestroy(&map));
    2465:   }
    2466:   PetscFunctionReturn(PETSC_SUCCESS);
    2467: }

    2469: static PetscErrorCode DMPlexTopologyBuildFromLayers_Private(DM dm, PetscInt depth, PlexLayer *layers, IS strataPermutation)
    2470: {
    2471:   const PetscInt *permArr;
    2472:   PetscInt        d, nPoints;
    2473:   MPI_Comm        comm;

    2475:   PetscFunctionBegin;
    2476:   PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
    2477:   PetscCall(ISGetIndices(strataPermutation, &permArr));

    2479:   /* Count points, strata offsets and cones offsets (taking strataPermutation into account) */
    2480:   {
    2481:     PetscInt stratumOffset = 0;
    2482:     PetscInt conesOffset   = 0;

    2484:     for (d = 0; d <= depth; d++) {
    2485:       const PetscInt  e = permArr[d];
    2486:       const PlexLayer l = layers[e];
    2487:       PetscInt        lo, n, size;

    2489:       PetscCall(PetscSectionGetChart(l->coneSizesSection, &lo, &n));
    2490:       PetscCall(PetscSectionGetStorageSize(l->coneSizesSection, &size));
    2491:       PetscCheck(lo == 0, comm, PETSC_ERR_PLIB, "starting point should be 0 in coneSizesSection %" PetscInt_FMT, d);
    2492:       l->offset      = stratumOffset;
    2493:       l->conesOffset = conesOffset;
    2494:       stratumOffset += n;
    2495:       conesOffset += size;
    2496:     }
    2497:     nPoints = stratumOffset;
    2498:   }

    2500:   /* Set interval for all plex points */
    2501:   //TODO we should store starting point of plex
    2502:   PetscCall(DMPlexSetChart(dm, 0, nPoints));

    2504:   /* Set up plex coneSection from layer coneSections */
    2505:   {
    2506:     PetscSection coneSection;

    2508:     PetscCall(DMPlexGetConeSection(dm, &coneSection));
    2509:     for (d = 0; d <= depth; d++) {
    2510:       const PlexLayer l = layers[d];
    2511:       PetscInt        n, q;

    2513:       PetscCall(PetscSectionGetChart(l->coneSizesSection, NULL, &n));
    2514:       for (q = 0; q < n; q++) {
    2515:         const PetscInt p = l->offset + q;
    2516:         PetscInt       coneSize;

    2518:         PetscCall(PetscSectionGetDof(l->coneSizesSection, q, &coneSize));
    2519:         PetscCall(PetscSectionSetDof(coneSection, p, coneSize));
    2520:       }
    2521:     }
    2522:   }
    2523:   //TODO this is terrible, DMSetUp_Plex() should be DMPlexSetUpSections() or so
    2524:   PetscCall(DMSetUp(dm));

    2526:   /* Renumber cones points from layer-global numbering to plex-local numbering */
    2527:   {
    2528:     PetscInt *cones, *ornts;

    2530:     PetscCall(DMPlexGetCones(dm, &cones));
    2531:     PetscCall(DMPlexGetConeOrientations(dm, &ornts));
    2532:     for (d = 1; d <= depth; d++) {
    2533:       const PlexLayer l = layers[d];
    2534:       PetscInt        i, lConesSize;
    2535:       PetscInt       *lCones;
    2536:       const PetscInt *lOrnts;
    2537:       PetscInt       *pCones = &cones[l->conesOffset];
    2538:       PetscInt       *pOrnts = &ornts[l->conesOffset];

    2540:       PetscCall(PetscSectionGetStorageSize(l->coneSizesSection, &lConesSize));
    2541:       /* Get cones in local plex numbering */
    2542:       {
    2543:         ISLocalToGlobalMapping l2g;
    2544:         PetscLayout            vertexLayout = l->vertexLayout;
    2545:         PetscSF                vertexSF     = layers[d - 1]->l2gSF; /* vertices of this layer are cells of previous layer */
    2546:         const PetscInt        *gCones;
    2547:         PetscInt               lConesSize0;

    2549:         PetscCall(ISGetLocalSize(l->conesIS, &lConesSize0));
    2550:         PetscCheck(lConesSize0 == lConesSize, comm, PETSC_ERR_PLIB, "layer %" PetscInt_FMT " size(conesIS) = %" PetscInt_FMT " != %" PetscInt_FMT " = storageSize(coneSizesSection)", d, lConesSize0, lConesSize);
    2551:         PetscCall(ISGetLocalSize(l->orientationsIS, &lConesSize0));
    2552:         PetscCheck(lConesSize0 == lConesSize, comm, PETSC_ERR_PLIB, "layer %" PetscInt_FMT " size(orientationsIS) = %" PetscInt_FMT " != %" PetscInt_FMT " = storageSize(coneSizesSection)", d, lConesSize0, lConesSize);

    2554:         PetscCall(PetscMalloc1(lConesSize, &lCones));
    2555:         PetscCall(ISGetIndices(l->conesIS, &gCones));
    2556:         PetscCall(ISLocalToGlobalMappingCreateSF(vertexSF, vertexLayout->rstart, &l2g));
    2557:         PetscCall(ISGlobalToLocalMappingApply(l2g, IS_GTOLM_MASK, lConesSize, gCones, &lConesSize0, lCones));
    2558:         PetscCheck(lConesSize0 == lConesSize, comm, PETSC_ERR_PLIB, "global to local does not cover all indices (%" PetscInt_FMT " of %" PetscInt_FMT ")", lConesSize0, lConesSize);
    2559:         PetscCall(ISLocalToGlobalMappingDestroy(&l2g));
    2560:         PetscCall(ISRestoreIndices(l->conesIS, &gCones));
    2561:       }
    2562:       PetscCall(ISGetIndices(l->orientationsIS, &lOrnts));
    2563:       /* Set cones, need to add stratum offset */
    2564:       for (i = 0; i < lConesSize; i++) {
    2565:         pCones[i] = lCones[i] + layers[d - 1]->offset; /* cone points of current layer are points of previous layer */
    2566:         pOrnts[i] = lOrnts[i];
    2567:       }
    2568:       PetscCall(PetscFree(lCones));
    2569:       PetscCall(ISRestoreIndices(l->orientationsIS, &lOrnts));
    2570:     }
    2571:   }
    2572:   PetscCall(DMPlexSymmetrize(dm));
    2573:   PetscCall(DMPlexStratify(dm));
    2574:   PetscCall(ISRestoreIndices(strataPermutation, &permArr));
    2575:   PetscFunctionReturn(PETSC_SUCCESS);
    2576: }

    2578: static PetscErrorCode PlexLayerConcatenateSFs_Private(MPI_Comm comm, PetscInt depth, PlexLayer layers[], IS strataPermutation, PetscSF *overlapSF, PetscSF *l2gSF)
    2579: {
    2580:   PetscInt        d;
    2581:   PetscSF        *osfs, *lsfs;
    2582:   PetscInt       *leafOffsets;
    2583:   const PetscInt *permArr;

    2585:   PetscFunctionBegin;
    2586:   PetscCall(ISGetIndices(strataPermutation, &permArr));
    2587:   PetscCall(PetscCalloc3(depth + 1, &osfs, depth + 1, &lsfs, depth + 1, &leafOffsets));
    2588:   for (d = 0; d <= depth; d++) {
    2589:     const PetscInt e = permArr[d];

    2591:     PetscAssert(e == layers[e]->d, PETSC_COMM_SELF, PETSC_ERR_PLIB, "assertion: e == layers[e]->d");
    2592:     osfs[d]        = layers[e]->overlapSF;
    2593:     lsfs[d]        = layers[e]->l2gSF;
    2594:     leafOffsets[d] = layers[e]->offset;
    2595:   }
    2596:   PetscCall(PetscSFConcatenate(comm, depth + 1, osfs, PETSCSF_CONCATENATE_ROOTMODE_LOCAL, leafOffsets, overlapSF));
    2597:   PetscCall(PetscSFConcatenate(comm, depth + 1, lsfs, PETSCSF_CONCATENATE_ROOTMODE_GLOBAL, leafOffsets, l2gSF));
    2598:   PetscCall(PetscFree3(osfs, lsfs, leafOffsets));
    2599:   PetscCall(ISRestoreIndices(strataPermutation, &permArr));
    2600:   PetscFunctionReturn(PETSC_SUCCESS);
    2601: }

    2603: // Parallel load of topology
    2604: static PetscErrorCode DMPlexTopologyLoad_HDF5_Private(DM dm, PetscViewer viewer, PetscSF *sfXC)
    2605: {
    2606:   PlexLayer  *layers;
    2607:   IS          strataPermutation;
    2608:   PetscLayout pointsLayout;
    2609:   PetscInt    depth;
    2610:   PetscInt    d;
    2611:   MPI_Comm    comm;

    2613:   PetscFunctionBegin;
    2614:   {
    2615:     PetscInt dim;

    2617:     PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "depth", PETSC_INT, NULL, &depth));
    2618:     PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "cell_dim", PETSC_INT, NULL, &dim));
    2619:     PetscCall(DMSetDimension(dm, dim));
    2620:   }
    2621:   PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));

    2623:   PetscCall(PetscInfo(dm, "Loading DM %s in parallel\n", dm->hdr.name));
    2624:   {
    2625:     IS spOnComm;

    2627:     PetscCall(ISCreate(comm, &spOnComm));
    2628:     PetscCall(PetscObjectSetName((PetscObject)spOnComm, "permutation"));
    2629:     PetscCall(ISLoad(spOnComm, viewer));
    2630:     /* have the same serial IS on every rank */
    2631:     PetscCall(ISAllGather(spOnComm, &strataPermutation));
    2632:     PetscCall(PetscObjectSetName((PetscObject)strataPermutation, ((PetscObject)spOnComm)->name));
    2633:     PetscCall(ISDestroy(&spOnComm));
    2634:   }

    2636:   /* Create layers, load raw data for each layer */
    2637:   PetscCall(PetscViewerHDF5PushGroup(viewer, "strata"));
    2638:   PetscCall(PetscMalloc1(depth + 1, &layers));
    2639:   for (d = depth, pointsLayout = NULL; d >= 0; pointsLayout = layers[d]->vertexLayout, d--) {
    2640:     PetscCall(PlexLayerCreate_Private(&layers[d]));
    2641:     PetscCall(PlexLayerLoad_Private(layers[d], viewer, d, pointsLayout));
    2642:   }
    2643:   PetscCall(PetscViewerHDF5PopGroup(viewer)); /* strata */

    2645:   for (d = depth; d >= 0; d--) {
    2646:     /* Redistribute cells and vertices for each applicable layer */
    2647:     if (d < depth) PetscCall(PlexLayerDistribute_Private(layers[d], layers[d]->l2gSF));
    2648:     /* Create vertex overlap SF and vertex localToGlobal SF for each applicable layer */
    2649:     if (d > 0) PetscCall(PlexLayerCreateSFs_Private(layers[d], &layers[d - 1]->overlapSF, &layers[d - 1]->l2gSF));
    2650:   }
    2651:   /* Build trivial SFs for the cell layer as well */
    2652:   PetscCall(PlexLayerCreateCellSFs_Private(layers[depth], &layers[depth]->overlapSF, &layers[depth]->l2gSF));

    2654:   /* Build DMPlex topology from the layers */
    2655:   PetscCall(DMPlexTopologyBuildFromLayers_Private(dm, depth, layers, strataPermutation));

    2657:   /* Build overall point SF alias overlap SF */
    2658:   {
    2659:     PetscSF overlapSF;

    2661:     PetscCall(PlexLayerConcatenateSFs_Private(comm, depth, layers, strataPermutation, &overlapSF, sfXC));
    2662:     PetscCall(DMSetPointSF(dm, overlapSF));
    2663:     PetscCall(PetscSFDestroy(&overlapSF));
    2664:   }

    2666:   for (d = depth; d >= 0; d--) PetscCall(PlexLayerDestroy(&layers[d]));
    2667:   PetscCall(PetscFree(layers));
    2668:   PetscCall(ISDestroy(&strataPermutation));
    2669:   PetscFunctionReturn(PETSC_SUCCESS);
    2670: }

    2672: PetscErrorCode DMPlexTopologyLoad_HDF5_Internal(DM dm, PetscViewer viewer, PetscSF *sfXC)
    2673: {
    2674:   DMPlexStorageVersion version;
    2675:   const char          *topologydm_name;
    2676:   char                 group[PETSC_MAX_PATH_LEN];
    2677:   PetscSF              sfwork = NULL;

    2679:   PetscFunctionBegin;
    2680:   PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
    2681:   PetscCall(PetscViewerHDF5GetDMPlexStorageVersionReading(viewer, &version));
    2682:   if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
    2683:     PetscCall(PetscSNPrintf(group, sizeof(group), "topologies/%s", topologydm_name));
    2684:   } else {
    2685:     PetscCall(PetscStrncpy(group, "/", sizeof(group)));
    2686:   }
    2687:   PetscCall(PetscViewerHDF5PushGroup(viewer, group));

    2689:   PetscCall(PetscViewerHDF5PushGroup(viewer, "topology"));
    2690:   if (version->major < 3) {
    2691:     PetscCall(DMPlexTopologyLoad_HDF5_Legacy_Private(dm, viewer, &sfwork));
    2692:   } else {
    2693:     /* since DMPlexStorageVersion 3.0.0 */
    2694:     PetscCall(DMPlexTopologyLoad_HDF5_Private(dm, viewer, &sfwork));
    2695:   }
    2696:   PetscCall(PetscViewerHDF5PopGroup(viewer)); /* "topology" */

    2698:   if (DMPlexStorageVersionGE(version, 2, 0, 0)) {
    2699:     DM          distdm;
    2700:     PetscSF     distsf;
    2701:     const char *distribution_name;
    2702:     PetscBool   exists;

    2704:     PetscCall(DMPlexDistributionGetName(dm, &distribution_name));
    2705:     /* this group is guaranteed to be present since DMPlexStorageVersion 2.1.0 */
    2706:     PetscCall(PetscViewerHDF5PushGroup(viewer, "distributions"));
    2707:     PetscCall(PetscViewerHDF5HasGroup(viewer, NULL, &exists));
    2708:     if (exists) {
    2709:       PetscCall(PetscViewerHDF5PushGroup(viewer, distribution_name));
    2710:       PetscCall(DMPlexDistributionLoad_HDF5_Private(dm, viewer, sfwork, &distsf, &distdm));
    2711:       if (distdm) {
    2712:         PetscCall(DMPlexReplace_Internal(dm, &distdm));
    2713:         PetscCall(PetscSFDestroy(&sfwork));
    2714:         sfwork = distsf;
    2715:       }
    2716:       PetscCall(PetscViewerHDF5PopGroup(viewer)); /* distribution_name */
    2717:     }
    2718:     PetscCall(PetscViewerHDF5PopGroup(viewer)); /* "distributions" */
    2719:   }
    2720:   if (sfXC) {
    2721:     *sfXC = sfwork;
    2722:   } else {
    2723:     PetscCall(PetscSFDestroy(&sfwork));
    2724:   }

    2726:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    2727:   PetscFunctionReturn(PETSC_SUCCESS);
    2728: }

    2730: /* If the file is old, it not only has different path to the coordinates, but   */
    2731: /* does not contain coordinateDMs, so must fall back to the old implementation. */
    2732: static PetscErrorCode DMPlexCoordinatesLoad_HDF5_Legacy_Private(DM dm, PetscViewer viewer)
    2733: {
    2734:   PetscSection coordSection;
    2735:   Vec          coordinates;
    2736:   PetscReal    lengthScale;
    2737:   PetscInt     spatialDim, N, numVertices, vStart, vEnd, v;
    2738:   PetscMPIInt  rank;

    2740:   PetscFunctionBegin;
    2741:   PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank));
    2742:   /* Read geometry */
    2743:   PetscCall(PetscViewerHDF5PushGroup(viewer, "/geometry"));
    2744:   PetscCall(VecCreate(PetscObjectComm((PetscObject)dm), &coordinates));
    2745:   PetscCall(PetscObjectSetName((PetscObject)coordinates, "vertices"));
    2746:   {
    2747:     /* Force serial load */
    2748:     PetscCall(PetscViewerHDF5ReadSizes(viewer, "vertices", &spatialDim, &N));
    2749:     PetscCall(VecSetSizes(coordinates, rank == 0 ? N : 0, N));
    2750:     PetscCall(VecSetBlockSize(coordinates, spatialDim));
    2751:   }
    2752:   PetscCall(VecLoad(coordinates, viewer));
    2753:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    2754:   PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
    2755:   PetscCall(VecScale(coordinates, 1.0 / lengthScale));
    2756:   PetscCall(VecGetLocalSize(coordinates, &numVertices));
    2757:   PetscCall(VecGetBlockSize(coordinates, &spatialDim));
    2758:   numVertices /= spatialDim;
    2759:   /* Create coordinates */
    2760:   PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
    2761:   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);
    2762:   PetscCall(DMGetCoordinateSection(dm, &coordSection));
    2763:   PetscCall(PetscSectionSetNumFields(coordSection, 1));
    2764:   PetscCall(PetscSectionSetFieldComponents(coordSection, 0, spatialDim));
    2765:   PetscCall(PetscSectionSetChart(coordSection, vStart, vEnd));
    2766:   for (v = vStart; v < vEnd; ++v) {
    2767:     PetscCall(PetscSectionSetDof(coordSection, v, spatialDim));
    2768:     PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, spatialDim));
    2769:   }
    2770:   PetscCall(PetscSectionSetUp(coordSection));
    2771:   PetscCall(DMSetCoordinates(dm, coordinates));
    2772:   PetscCall(VecDestroy(&coordinates));
    2773:   PetscFunctionReturn(PETSC_SUCCESS);
    2774: }

    2776: PetscErrorCode DMPlexCoordinatesLoad_HDF5_Internal(DM dm, PetscViewer viewer, PetscSF sfXC)
    2777: {
    2778:   DMPlexStorageVersion version;
    2779:   DM                   cdm;
    2780:   Vec                  coords;
    2781:   PetscInt             blockSize;
    2782:   PetscReal            lengthScale;
    2783:   PetscSF              lsf;
    2784:   const char          *topologydm_name;
    2785:   char                *coordinatedm_name, *coordinates_name;

    2787:   PetscFunctionBegin;
    2788:   PetscCall(PetscViewerHDF5GetDMPlexStorageVersionReading(viewer, &version));
    2789:   if (!DMPlexStorageVersionGE(version, 2, 0, 0)) {
    2790:     PetscCall(DMPlexCoordinatesLoad_HDF5_Legacy_Private(dm, viewer));
    2791:     PetscFunctionReturn(PETSC_SUCCESS);
    2792:   }
    2793:   /* else: since DMPlexStorageVersion 2.0.0 */
    2794:   PetscCheck(sfXC, PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_NULL, "PetscSF must be given for parallel load");
    2795:   PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
    2796:   PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
    2797:   PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
    2798:   PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "coordinateDMName", PETSC_STRING, NULL, &coordinatedm_name));
    2799:   PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "coordinatesName", PETSC_STRING, NULL, &coordinates_name));
    2800:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    2801:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    2802:   PetscCall(DMGetCoordinateDM(dm, &cdm));
    2803:   PetscCall(PetscObjectSetName((PetscObject)cdm, coordinatedm_name));
    2804:   PetscCall(PetscFree(coordinatedm_name));
    2805:   /* lsf: on-disk data -> in-memory local vector associated with cdm's local section */
    2806:   PetscCall(DMPlexSectionLoad(dm, viewer, cdm, sfXC, NULL, &lsf));
    2807:   PetscCall(DMCreateLocalVector(cdm, &coords));
    2808:   PetscCall(PetscObjectSetName((PetscObject)coords, coordinates_name));
    2809:   PetscCall(PetscFree(coordinates_name));
    2810:   PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_NATIVE));
    2811:   PetscCall(DMPlexLocalVectorLoad(dm, viewer, cdm, lsf, coords));
    2812:   PetscCall(PetscViewerPopFormat(viewer));
    2813:   PetscCall(DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale));
    2814:   PetscCall(VecScale(coords, 1.0 / lengthScale));
    2815:   PetscCall(DMSetCoordinatesLocal(dm, coords));
    2816:   PetscCall(VecGetBlockSize(coords, &blockSize));
    2817:   PetscCall(DMSetCoordinateDim(dm, blockSize));
    2818:   PetscCall(VecDestroy(&coords));
    2819:   PetscCall(PetscSFDestroy(&lsf));
    2820:   PetscFunctionReturn(PETSC_SUCCESS);
    2821: }

    2823: PetscErrorCode DMPlexLoad_HDF5_Internal(DM dm, PetscViewer viewer)
    2824: {
    2825:   DMPlexStorageVersion version;

    2827:   PetscFunctionBegin;
    2828:   PetscCall(PetscViewerHDF5GetDMPlexStorageVersionReading(viewer, &version));
    2829:   PetscCall(PetscInfo(dm, "Loading DM %s storage version %d.%d.%d\n", dm->hdr.name, version->major, version->minor, version->subminor));
    2830:   if (!DMPlexStorageVersionGE(version, 2, 0, 0)) {
    2831:     PetscCall(DMPlexTopologyLoad_HDF5_Internal(dm, viewer, NULL));
    2832:     PetscCall(DMPlexLabelsLoad_HDF5_Internal(dm, viewer, NULL));
    2833:     PetscCall(DMPlexCoordinatesLoad_HDF5_Legacy_Private(dm, viewer));
    2834:   } else {
    2835:     PetscSF sfXC;

    2837:     /* since DMPlexStorageVersion 2.0.0 */
    2838:     PetscCall(DMPlexTopologyLoad_HDF5_Internal(dm, viewer, &sfXC));
    2839:     PetscCall(DMPlexLabelsLoad_HDF5_Internal(dm, viewer, sfXC));
    2840:     PetscCall(DMPlexCoordinatesLoad_HDF5_Internal(dm, viewer, sfXC));
    2841:     PetscCall(PetscSFDestroy(&sfXC));
    2842:   }
    2843:   PetscFunctionReturn(PETSC_SUCCESS);
    2844: }

    2846: static PetscErrorCode DMPlexSectionLoad_HDF5_Internal_CreateDataSF(PetscSection rootSection, PetscLayout layout, PetscInt globalOffsets[], PetscSection leafSection, PetscSF *sectionSF)
    2847: {
    2848:   MPI_Comm  comm;
    2849:   PetscInt  pStart, pEnd, p, m;
    2850:   PetscInt *goffs, *ilocal;
    2851:   PetscBool rootIncludeConstraints, leafIncludeConstraints;

    2853:   PetscFunctionBegin;
    2854:   PetscCall(PetscObjectGetComm((PetscObject)leafSection, &comm));
    2855:   PetscCall(PetscSectionGetChart(leafSection, &pStart, &pEnd));
    2856:   PetscCall(PetscSectionGetIncludesConstraints(rootSection, &rootIncludeConstraints));
    2857:   PetscCall(PetscSectionGetIncludesConstraints(leafSection, &leafIncludeConstraints));
    2858:   if (rootIncludeConstraints && leafIncludeConstraints) PetscCall(PetscSectionGetStorageSize(leafSection, &m));
    2859:   else PetscCall(PetscSectionGetConstrainedStorageSize(leafSection, &m));
    2860:   PetscCall(PetscMalloc1(m, &ilocal));
    2861:   PetscCall(PetscMalloc1(m, &goffs));
    2862:   /* Currently, PetscSFDistributeSection() returns globalOffsets[] only */
    2863:   /* for the top-level section (not for each field), so one must have   */
    2864:   /* rootSection->pointMajor == PETSC_TRUE.                             */
    2865:   PetscCheck(rootSection->pointMajor, PETSC_COMM_SELF, PETSC_ERR_SUP, "No support for field major ordering");
    2866:   /* Currently, we also assume that leafSection->pointMajor == PETSC_TRUE. */
    2867:   PetscCheck(leafSection->pointMajor, PETSC_COMM_SELF, PETSC_ERR_SUP, "No support for field major ordering");
    2868:   for (p = pStart, m = 0; p < pEnd; ++p) {
    2869:     PetscInt        dof, cdof, i, j, off, goff;
    2870:     const PetscInt *cinds;

    2872:     PetscCall(PetscSectionGetDof(leafSection, p, &dof));
    2873:     if (dof < 0) continue;
    2874:     goff = globalOffsets[p - pStart];
    2875:     PetscCall(PetscSectionGetOffset(leafSection, p, &off));
    2876:     PetscCall(PetscSectionGetConstraintDof(leafSection, p, &cdof));
    2877:     PetscCall(PetscSectionGetConstraintIndices(leafSection, p, &cinds));
    2878:     for (i = 0, j = 0; i < dof; ++i) {
    2879:       PetscBool constrained = (PetscBool)(j < cdof && i == cinds[j]);

    2881:       if (!constrained || (leafIncludeConstraints && rootIncludeConstraints)) {
    2882:         ilocal[m]  = off++;
    2883:         goffs[m++] = goff++;
    2884:       } else if (leafIncludeConstraints && !rootIncludeConstraints) ++off;
    2885:       else if (!leafIncludeConstraints && rootIncludeConstraints) ++goff;
    2886:       if (constrained) ++j;
    2887:     }
    2888:   }
    2889:   PetscCall(PetscSFCreate(comm, sectionSF));
    2890:   PetscCall(PetscSFSetFromOptions(*sectionSF));
    2891:   PetscCall(PetscSFSetGraphLayout(*sectionSF, layout, m, ilocal, PETSC_OWN_POINTER, goffs));
    2892:   PetscCall(PetscFree(goffs));
    2893:   PetscFunctionReturn(PETSC_SUCCESS);
    2894: }

    2896: PetscErrorCode DMPlexSectionLoad_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm, PetscSF sfXB, PetscSF *gsf, PetscSF *lsf)
    2897: {
    2898:   MPI_Comm     comm;
    2899:   PetscMPIInt  size, rank;
    2900:   const char  *topologydm_name;
    2901:   const char  *sectiondm_name;
    2902:   PetscSection sectionA, sectionB;
    2903:   PetscBool    has;
    2904:   PetscInt     nX, n, i;
    2905:   PetscSF      sfAB;

    2907:   PetscFunctionBegin;
    2908:   PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
    2909:   PetscCallMPI(MPI_Comm_size(comm, &size));
    2910:   PetscCallMPI(MPI_Comm_rank(comm, &rank));
    2911:   PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
    2912:   PetscCall(PetscObjectGetName((PetscObject)sectiondm, &sectiondm_name));
    2913:   PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
    2914:   PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
    2915:   PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
    2916:   PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
    2917:   /* A: on-disk points                        */
    2918:   /* X: list of global point numbers, [0, NX) */
    2919:   /* B: plex points                           */
    2920:   /* Load raw section (sectionA)              */
    2921:   PetscCall(PetscSectionCreate(comm, &sectionA));
    2922:   PetscCall(PetscViewerHDF5HasGroup(viewer, "section", &has));
    2923:   if (has) PetscCall(PetscSectionLoad(sectionA, viewer));
    2924:   else {
    2925:     // TODO If section is missing, create the default affine section with dim dofs on each vertex. Use PetscSplitOwnership() to split vertices.
    2926:     //   How do I know the total number of vertices?
    2927:     PetscInt dim, Nf = 1, Nv, nv = PETSC_DECIDE;

    2929:     PetscCall(DMGetDimension(dm, &dim));
    2930:     PetscCall(DMPlexGetDepthStratumGlobalSize(dm, 0, &Nv));
    2931:     PetscCall(PetscSectionSetNumFields(sectionA, Nf));
    2932:     PetscCall(PetscSectionSetFieldName(sectionA, 0, "Cartesian"));
    2933:     PetscCall(PetscSectionSetFieldComponents(sectionA, 0, dim));
    2934:     for (PetscInt c = 0; c < dim; ++c) {
    2935:       char axis = 'X' + (char)c;

    2937:       PetscCall(PetscSectionSetComponentName(sectionA, 0, c, &axis));
    2938:     }
    2939:     PetscCall(PetscSplitOwnership(comm, &nv, &Nv));
    2940:     PetscCall(PetscSectionSetChart(sectionA, 0, nv));
    2941:     for (PetscInt p = 0; p < nv; ++p) {
    2942:       PetscCall(PetscSectionSetDof(sectionA, p, dim));
    2943:       PetscCall(PetscSectionSetFieldDof(sectionA, p, 0, dim));
    2944:     }
    2945:     PetscCall(PetscSectionSetUp(sectionA));
    2946:   }
    2947:   PetscCall(PetscSectionGetChart(sectionA, NULL, &n));
    2948: /* Create sfAB: A -> B */
    2949: #if defined(PETSC_USE_DEBUG)
    2950:   {
    2951:     PetscInt N, N1;

    2953:     PetscCall(PetscViewerHDF5ReadSizes(viewer, "order", NULL, &N1));
    2954:     PetscCallMPI(MPIU_Allreduce(&n, &N, 1, MPIU_INT, MPI_SUM, comm));
    2955:     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);
    2956:   }
    2957: #endif
    2958:   {
    2959:     IS              orderIS;
    2960:     const PetscInt *gpoints;
    2961:     PetscSF         sfXA, sfAX;
    2962:     PetscLayout     layout;
    2963:     PetscSFNode    *owners, *buffer;
    2964:     PetscInt        nleaves;
    2965:     PetscInt       *ilocal;
    2966:     PetscSFNode    *iremote;

    2968:     /* Create sfAX: A -> X */
    2969:     PetscCall(ISCreate(comm, &orderIS));
    2970:     PetscCall(PetscObjectSetName((PetscObject)orderIS, "order"));
    2971:     PetscCall(PetscLayoutSetLocalSize(orderIS->map, n));
    2972:     PetscCall(ISLoad(orderIS, viewer));
    2973:     PetscCall(PetscLayoutCreate(comm, &layout));
    2974:     PetscCall(PetscSFGetGraph(sfXB, &nX, NULL, NULL, NULL));
    2975:     PetscCall(PetscLayoutSetLocalSize(layout, nX));
    2976:     PetscCall(PetscLayoutSetBlockSize(layout, 1));
    2977:     PetscCall(PetscLayoutSetUp(layout));
    2978:     PetscCall(PetscSFCreate(comm, &sfXA));
    2979:     PetscCall(ISGetIndices(orderIS, &gpoints));
    2980:     PetscCall(PetscSFSetGraphLayout(sfXA, layout, n, NULL, PETSC_OWN_POINTER, gpoints));
    2981:     PetscCall(ISRestoreIndices(orderIS, &gpoints));
    2982:     PetscCall(ISDestroy(&orderIS));
    2983:     PetscCall(PetscLayoutDestroy(&layout));
    2984:     PetscCall(PetscMalloc1(n, &owners));
    2985:     PetscCall(PetscMalloc1(nX, &buffer));
    2986:     for (i = 0; i < n; ++i) {
    2987:       owners[i].rank  = rank;
    2988:       owners[i].index = i;
    2989:     }
    2990:     for (i = 0; i < nX; ++i) {
    2991:       buffer[i].rank  = -1;
    2992:       buffer[i].index = -1;
    2993:     }
    2994:     PetscCall(PetscSFReduceBegin(sfXA, MPIU_SF_NODE, owners, buffer, MPI_MAXLOC));
    2995:     PetscCall(PetscSFReduceEnd(sfXA, MPIU_SF_NODE, owners, buffer, MPI_MAXLOC));
    2996:     PetscCall(PetscSFDestroy(&sfXA));
    2997:     PetscCall(PetscFree(owners));
    2998:     for (i = 0, nleaves = 0; i < nX; ++i)
    2999:       if (buffer[i].rank >= 0) nleaves++;
    3000:     PetscCall(PetscMalloc1(nleaves, &ilocal));
    3001:     PetscCall(PetscMalloc1(nleaves, &iremote));
    3002:     for (i = 0, nleaves = 0; i < nX; ++i) {
    3003:       if (buffer[i].rank >= 0) {
    3004:         ilocal[nleaves]        = i;
    3005:         iremote[nleaves].rank  = buffer[i].rank;
    3006:         iremote[nleaves].index = buffer[i].index;
    3007:         nleaves++;
    3008:       }
    3009:     }
    3010:     PetscCall(PetscFree(buffer));
    3011:     PetscCall(PetscSFCreate(comm, &sfAX));
    3012:     PetscCall(PetscSFSetFromOptions(sfAX));
    3013:     PetscCall(PetscSFSetGraph(sfAX, n, nleaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER));
    3014:     PetscCall(PetscSFCompose(sfAX, sfXB, &sfAB));
    3015:     PetscCall(PetscSFDestroy(&sfAX));
    3016:   }
    3017:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    3018:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    3019:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    3020:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    3021:   /* Create plex section (sectionB) */
    3022:   PetscCall(DMGetLocalSection(sectiondm, &sectionB));
    3023:   if (lsf || gsf) {
    3024:     PetscLayout layout;
    3025:     PetscInt    M, m;
    3026:     PetscInt   *offsetsA;
    3027:     PetscBool   includesConstraintsA;

    3029:     PetscCall(PetscSFDistributeSection(sfAB, sectionA, &offsetsA, sectionB));
    3030:     PetscCall(PetscSectionGetIncludesConstraints(sectionA, &includesConstraintsA));
    3031:     if (includesConstraintsA) PetscCall(PetscSectionGetStorageSize(sectionA, &m));
    3032:     else PetscCall(PetscSectionGetConstrainedStorageSize(sectionA, &m));
    3033:     PetscCallMPI(MPIU_Allreduce(&m, &M, 1, MPIU_INT, MPI_SUM, comm));
    3034:     PetscCall(PetscLayoutCreate(comm, &layout));
    3035:     PetscCall(PetscLayoutSetSize(layout, M));
    3036:     PetscCall(PetscLayoutSetUp(layout));
    3037:     if (lsf) {
    3038:       PetscSF lsfABdata;

    3040:       PetscCall(DMPlexSectionLoad_HDF5_Internal_CreateDataSF(sectionA, layout, offsetsA, sectionB, &lsfABdata));
    3041:       *lsf = lsfABdata;
    3042:     }
    3043:     if (gsf) {
    3044:       PetscSection gsectionB, gsectionB1;
    3045:       PetscBool    includesConstraintsB;
    3046:       PetscSF      gsfABdata, pointsf;

    3048:       PetscCall(DMGetGlobalSection(sectiondm, &gsectionB1));
    3049:       PetscCall(PetscSectionGetIncludesConstraints(gsectionB1, &includesConstraintsB));
    3050:       PetscCall(DMGetPointSF(sectiondm, &pointsf));
    3051:       PetscCall(PetscSectionCreateGlobalSection(sectionB, pointsf, PETSC_TRUE, includesConstraintsB, PETSC_TRUE, &gsectionB));
    3052:       PetscCall(DMPlexSectionLoad_HDF5_Internal_CreateDataSF(sectionA, layout, offsetsA, gsectionB, &gsfABdata));
    3053:       PetscCall(PetscSectionDestroy(&gsectionB));
    3054:       *gsf = gsfABdata;
    3055:     }
    3056:     PetscCall(PetscLayoutDestroy(&layout));
    3057:     PetscCall(PetscFree(offsetsA));
    3058:   } else {
    3059:     PetscCall(PetscSFDistributeSection(sfAB, sectionA, NULL, sectionB));
    3060:   }
    3061:   PetscCall(PetscSFDestroy(&sfAB));
    3062:   PetscCall(PetscSectionDestroy(&sectionA));
    3063:   PetscFunctionReturn(PETSC_SUCCESS);
    3064: }

    3066: PetscErrorCode DMPlexVecLoad_HDF5_Internal(DM dm, PetscViewer viewer, DM sectiondm, PetscSF sf, Vec vec)
    3067: {
    3068:   MPI_Comm           comm;
    3069:   const char        *topologydm_name;
    3070:   const char        *sectiondm_name;
    3071:   const char        *vec_name;
    3072:   Vec                vecA;
    3073:   PetscInt           mA, m, bs;
    3074:   const PetscInt    *ilocal;
    3075:   const PetscScalar *src;
    3076:   PetscScalar       *dest;

    3078:   PetscFunctionBegin;
    3079:   PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
    3080:   PetscCall(DMPlexGetHDF5Name_Private(dm, &topologydm_name));
    3081:   PetscCall(PetscObjectGetName((PetscObject)sectiondm, &sectiondm_name));
    3082:   PetscCall(PetscObjectGetName((PetscObject)vec, &vec_name));
    3083:   PetscCall(PetscViewerHDF5PushGroup(viewer, "topologies"));
    3084:   PetscCall(PetscViewerHDF5PushGroup(viewer, topologydm_name));
    3085:   PetscCall(PetscViewerHDF5PushGroup(viewer, "dms"));
    3086:   PetscCall(PetscViewerHDF5PushGroup(viewer, sectiondm_name));
    3087:   PetscCall(PetscViewerHDF5PushGroup(viewer, "vecs"));
    3088:   PetscCall(PetscViewerHDF5PushGroup(viewer, vec_name));
    3089:   PetscCall(VecCreate(comm, &vecA));
    3090:   PetscCall(PetscObjectSetName((PetscObject)vecA, vec_name));
    3091:   PetscCall(PetscSFGetGraph(sf, &mA, &m, &ilocal, NULL));
    3092:   /* Check consistency */
    3093:   {
    3094:     PetscSF  pointsf, pointsf1;
    3095:     PetscInt m1, i, j;

    3097:     PetscCall(DMGetPointSF(dm, &pointsf));
    3098:     PetscCall(DMGetPointSF(sectiondm, &pointsf1));
    3099:     PetscCheck(pointsf1 == pointsf, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Mismatching point SFs for dm and sectiondm");
    3100: #if defined(PETSC_USE_DEBUG)
    3101:     {
    3102:       PetscInt MA, MA1;

    3104:       PetscCallMPI(MPIU_Allreduce(&mA, &MA, 1, MPIU_INT, MPI_SUM, comm));
    3105:       PetscCall(PetscViewerHDF5ReadSizes(viewer, vec_name, NULL, &MA1));
    3106:       PetscCheck(MA1 == MA, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Total SF root size (%" PetscInt_FMT ") != On-disk vector data size (%" PetscInt_FMT ")", MA, MA1);
    3107:     }
    3108: #endif
    3109:     PetscCall(VecGetLocalSize(vec, &m1));
    3110:     PetscCheck(m1 >= m, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Target vector size (%" PetscInt_FMT ") < SF leaf size (%" PetscInt_FMT ")", m1, m);
    3111:     for (i = 0; i < m; ++i) {
    3112:       j = ilocal ? ilocal[i] : i;
    3113:       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);
    3114:     }
    3115:   }
    3116:   PetscCall(VecSetSizes(vecA, mA, PETSC_DECIDE));
    3117:   PetscCall(VecLoad(vecA, viewer));
    3118:   PetscCall(VecGetArrayRead(vecA, &src));
    3119:   PetscCall(VecGetArray(vec, &dest));
    3120:   PetscCall(PetscSFBcastBegin(sf, MPIU_SCALAR, src, dest, MPI_REPLACE));
    3121:   PetscCall(PetscSFBcastEnd(sf, MPIU_SCALAR, src, dest, MPI_REPLACE));
    3122:   PetscCall(VecRestoreArray(vec, &dest));
    3123:   PetscCall(VecRestoreArrayRead(vecA, &src));
    3124:   PetscCall(VecDestroy(&vecA));
    3125:   PetscCall(PetscViewerHDF5ReadAttribute(viewer, NULL, "blockSize", PETSC_INT, NULL, (void *)&bs));
    3126:   PetscCall(VecSetBlockSize(vec, bs));
    3127:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    3128:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    3129:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    3130:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    3131:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    3132:   PetscCall(PetscViewerHDF5PopGroup(viewer));
    3133:   PetscFunctionReturn(PETSC_SUCCESS);
    3134: }