Date: 2025-03-29T05:58:52+00:00

Actual source code: general.c

      1: /*
      2:      Provides the functions for index sets (IS) defined by a list of integers.
      3: */
      4: #include <../src/vec/is/is/impls/general/general.h>
      5: #include <petsc/private/viewerhdf5impl.h>

      7: static PetscErrorCode ISDuplicate_General(IS is, IS *newIS)
      8: {
      9:   IS_General *sub = (IS_General *)is->data;
     10:   PetscInt    n, bs;

     12:   PetscFunctionBegin;
     13:   PetscCall(PetscLayoutGetLocalSize(is->map, &n));
     14:   PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)is), n, sub->idx, PETSC_COPY_VALUES, newIS));
     15:   PetscCall(PetscLayoutGetBlockSize(is->map, &bs));
     16:   PetscCall(PetscLayoutSetBlockSize((*newIS)->map, bs));
     17:   PetscFunctionReturn(PETSC_SUCCESS);
     18: }

     20: static PetscErrorCode ISDestroy_General(IS is)
     21: {
     22:   IS_General *is_general = (IS_General *)is->data;

     24:   PetscFunctionBegin;
     25:   if (is_general->allocated) PetscCall(PetscFree(is_general->idx));
     26:   PetscCall(PetscObjectComposeFunction((PetscObject)is, "ISGeneralSetIndices_C", NULL));
     27:   PetscCall(PetscObjectComposeFunction((PetscObject)is, "ISGeneralFilter_C", NULL));
     28:   PetscCall(PetscObjectComposeFunction((PetscObject)is, "ISGeneralSetIndicesFromMask_C", NULL));
     29:   PetscCall(PetscObjectComposeFunction((PetscObject)is, "ISShift_C", NULL));
     30:   PetscCall(PetscFree(is->data));
     31:   PetscFunctionReturn(PETSC_SUCCESS);
     32: }

     34: static PetscErrorCode ISCopy_General(IS is, IS isy)
     35: {
     36:   IS_General *is_general = (IS_General *)is->data, *isy_general = (IS_General *)isy->data;
     37:   PetscInt    n;

     39:   PetscFunctionBegin;
     40:   PetscCall(PetscLayoutGetLocalSize(is->map, &n));
     41:   PetscCall(PetscArraycpy(isy_general->idx, is_general->idx, n));
     42:   PetscFunctionReturn(PETSC_SUCCESS);
     43: }

     45: static PetscErrorCode ISShift_General(IS is, PetscInt shift, IS isy)
     46: {
     47:   IS_General *is_general = (IS_General *)is->data, *isy_general = (IS_General *)isy->data;
     48:   PetscInt    i, n;

     50:   PetscFunctionBegin;
     51:   PetscCall(PetscLayoutGetLocalSize(is->map, &n));
     52:   for (i = 0; i < n; i++) isy_general->idx[i] = is_general->idx[i] + shift;
     53:   PetscFunctionReturn(PETSC_SUCCESS);
     54: }

     56: static PetscErrorCode ISOnComm_General(IS is, MPI_Comm comm, PetscCopyMode mode, IS *newis)
     57: {
     58:   IS_General *sub = (IS_General *)is->data;
     59:   PetscInt    n;

     61:   PetscFunctionBegin;
     62:   PetscCheck(mode != PETSC_OWN_POINTER, comm, PETSC_ERR_ARG_WRONG, "Cannot use PETSC_OWN_POINTER");
     63:   PetscCall(PetscLayoutGetLocalSize(is->map, &n));
     64:   PetscCall(ISCreateGeneral(comm, n, sub->idx, mode, newis));
     65:   PetscFunctionReturn(PETSC_SUCCESS);
     66: }

     68: static PetscErrorCode ISSetBlockSize_General(IS is, PetscInt bs)
     69: {
     70:   PetscFunctionBegin;
     71:   PetscCall(PetscLayoutSetBlockSize(is->map, bs));
     72:   PetscFunctionReturn(PETSC_SUCCESS);
     73: }

     75: static PetscErrorCode ISContiguousLocal_General(IS is, PetscInt gstart, PetscInt gend, PetscInt *start, PetscBool *contig)
     76: {
     77:   IS_General *sub = (IS_General *)is->data;
     78:   PetscInt    n, i, p;

     80:   PetscFunctionBegin;
     81:   *start  = 0;
     82:   *contig = PETSC_TRUE;
     83:   PetscCall(PetscLayoutGetLocalSize(is->map, &n));
     84:   if (!n) PetscFunctionReturn(PETSC_SUCCESS);
     85:   p = sub->idx[0];
     86:   if (p < gstart) goto nomatch;
     87:   *start = p - gstart;
     88:   if (n > gend - p) goto nomatch;
     89:   for (i = 1; i < n; i++, p++) {
     90:     if (sub->idx[i] != p + 1) goto nomatch;
     91:   }
     92:   PetscFunctionReturn(PETSC_SUCCESS);
     93: nomatch:
     94:   *start  = -1;
     95:   *contig = PETSC_FALSE;
     96:   PetscFunctionReturn(PETSC_SUCCESS);
     97: }

     99: static PetscErrorCode ISLocate_General(IS is, PetscInt key, PetscInt *location)
    100: {
    101:   IS_General *sub = (IS_General *)is->data;
    102:   PetscInt    numIdx, i;
    103:   PetscBool   sorted;

    105:   PetscFunctionBegin;
    106:   PetscCall(PetscLayoutGetLocalSize(is->map, &numIdx));
    107:   PetscCall(ISGetInfo(is, IS_SORTED, IS_LOCAL, PETSC_TRUE, &sorted));
    108:   if (sorted) PetscCall(PetscFindInt(key, numIdx, sub->idx, location));
    109:   else {
    110:     const PetscInt *idx = sub->idx;

    112:     *location = -1;
    113:     for (i = 0; i < numIdx; i++) {
    114:       if (idx[i] == key) {
    115:         *location = i;
    116:         PetscFunctionReturn(PETSC_SUCCESS);
    117:       }
    118:     }
    119:   }
    120:   PetscFunctionReturn(PETSC_SUCCESS);
    121: }

    123: static PetscErrorCode ISGetIndices_General(IS in, const PetscInt *idx[])
    124: {
    125:   IS_General *sub = (IS_General *)in->data;

    127:   PetscFunctionBegin;
    128:   *idx = sub->idx;
    129:   PetscFunctionReturn(PETSC_SUCCESS);
    130: }

    132: static PetscErrorCode ISRestoreIndices_General(IS in, const PetscInt *idx[])
    133: {
    134:   IS_General *sub = (IS_General *)in->data;

    136:   PetscFunctionBegin;
    137:   /* F90Array1dCreate() inside ISRestoreArray() does not keep array when zero length array */
    138:   PetscCheck(in->map->n <= 0 || *idx == sub->idx, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Must restore with value from ISGetIndices()");
    139:   PetscFunctionReturn(PETSC_SUCCESS);
    140: }

    142: static PetscErrorCode ISInvertPermutation_General(IS is, PetscInt nlocal, IS *isout)
    143: {
    144:   IS_General     *sub = (IS_General *)is->data;
    145:   PetscInt        i, *ii, n, nstart;
    146:   const PetscInt *idx = sub->idx;
    147:   PetscMPIInt     size;
    148:   IS              istmp, nistmp;

    150:   PetscFunctionBegin;
    151:   PetscCall(PetscLayoutGetLocalSize(is->map, &n));
    152:   PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)is), &size));
    153:   if (size == 1) {
    154:     PetscCall(PetscMalloc1(n, &ii));
    155:     for (i = 0; i < n; i++) ii[idx[i]] = i;
    156:     PetscCall(ISCreateGeneral(PETSC_COMM_SELF, n, ii, PETSC_OWN_POINTER, isout));
    157:     PetscCall(ISSetPermutation(*isout));
    158:   } else {
    159:     /* crude, nonscalable get entire IS on each processor */
    160:     PetscCall(ISAllGather(is, &istmp));
    161:     PetscCall(ISSetPermutation(istmp));
    162:     PetscCall(ISInvertPermutation(istmp, PETSC_DECIDE, &nistmp));
    163:     PetscCall(ISDestroy(&istmp));
    164:     /* get the part we need */
    165:     if (nlocal == PETSC_DECIDE) nlocal = n;
    166:     PetscCallMPI(MPI_Scan(&nlocal, &nstart, 1, MPIU_INT, MPI_SUM, PetscObjectComm((PetscObject)is)));
    167:     if (PetscDefined(USE_DEBUG)) {
    168:       PetscInt    N;
    169:       PetscMPIInt rank;
    170:       PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)is), &rank));
    171:       PetscCall(PetscLayoutGetSize(is->map, &N));
    172:       PetscCheck((rank != size - 1) || (nstart == N), PETSC_COMM_SELF, PETSC_ERR_ARG_INCOMP, "Sum of nlocal lengths %" PetscInt_FMT " != total IS length %" PetscInt_FMT, nstart, N);
    173:     }
    174:     nstart -= nlocal;
    175:     PetscCall(ISGetIndices(nistmp, &idx));
    176:     PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)is), nlocal, idx + nstart, PETSC_COPY_VALUES, isout));
    177:     PetscCall(ISRestoreIndices(nistmp, &idx));
    178:     PetscCall(ISDestroy(&nistmp));
    179:   }
    180:   PetscFunctionReturn(PETSC_SUCCESS);
    181: }

    183: /*
    184:   FindRun_Private - Determine whether a run exists in the sequence

    186:   Input Parameters;
    187: + indices   - An array of indices
    188: . len       - The length of `indices`
    189: . off       - The offset into `indices`
    190: - minRunLen - The minimum size of a run

    192:   Output Parameters:
    193: + runLen - The length of the run, with 0 meaning no run was found
    194: . step   - The step between consecutive run values
    195: - val    - The initial run value

    197:   Note:
    198:   We define a run as an arithmetic progression of at least `minRunLen` values, where zero is a valid step.
    199: */
    200: static PetscErrorCode ISFindRun_Private(const PetscInt indices[], PetscInt len, PetscInt off, PetscInt minRunLen, PetscInt *runLen, PetscInt *step, PetscInt *val)
    201: {
    202:   PetscInt o = off, s, l;

    204:   PetscFunctionBegin;
    205:   *runLen = 0;
    206:   // We need at least 2 values for a run
    207:   if (len - off < PetscMax(minRunLen, 2)) PetscFunctionReturn(PETSC_SUCCESS);
    208:   s = indices[o + 1] - indices[o];
    209:   l = 2;
    210:   ++o;
    211:   while (o < len - 1 && (s == indices[o + 1] - indices[o])) {
    212:     ++l;
    213:     ++o;
    214:   }
    215:   if (runLen) *runLen = l;
    216:   if (step) *step = s;
    217:   if (val) *val = indices[off];
    218:   PetscFunctionReturn(PETSC_SUCCESS);
    219: }

    221: static PetscErrorCode ISGeneralCheckCompress(IS is, PetscBool *compress)
    222: {
    223:   const PetscInt  minRun    = 8;
    224:   PetscBool       lcompress = PETSC_TRUE;
    225:   const PetscInt *idx;
    226:   PetscInt        n, off = 0;

    228:   PetscFunctionBegin;
    229:   *compress = PETSC_FALSE;
    230:   if (!is->compressOutput) PetscFunctionReturn(PETSC_SUCCESS);
    231:   PetscCall(ISGetIndices(is, &idx));
    232:   PetscCall(ISGetLocalSize(is, &n));
    233:   while (off < n) {
    234:     PetscInt len;

    236:     PetscCall(ISFindRun_Private(idx, n, off, minRun, &len, NULL, NULL));
    237:     if (!len) {
    238:       lcompress = PETSC_FALSE;
    239:       break;
    240:     }
    241:     off += len;
    242:   }
    243:   PetscCallMPI(MPI_Allreduce(&lcompress, compress, 1, MPIU_BOOL, MPI_LAND, PetscObjectComm((PetscObject)is)));
    244:   PetscFunctionReturn(PETSC_SUCCESS);
    245: }

    247: #if defined(PETSC_HAVE_HDF5)
    248: // Run length encode the IS
    249: static PetscErrorCode ISGeneralCompress(IS is, IS *cis)
    250: {
    251:   const PetscInt *idx;
    252:   const PetscInt  minRun = 8;
    253:   PetscInt        runs   = 0;
    254:   PetscInt        off    = 0;
    255:   PetscInt       *cidx, n, r;
    256:   const char     *name;
    257:   MPI_Comm        comm;

    259:   PetscFunctionBegin;
    260:   PetscCall(PetscObjectGetComm((PetscObject)is, &comm));
    261:   PetscCall(ISGetIndices(is, &idx));
    262:   PetscCall(ISGetLocalSize(is, &n));
    263:   if (!n) runs = 0;
    264:   // Count runs
    265:   while (off < n) {
    266:     PetscInt len;

    268:     PetscCall(ISFindRun_Private(idx, n, off, minRun, &len, NULL, NULL));
    269:     PetscCheck(len, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Compression failed to find a run at offset %" PetscInt_FMT, off);
    270:     ++runs;
    271:     off += len;
    272:   }
    273:   // Construct compressed set
    274:   PetscCall(PetscMalloc1(runs * 3, &cidx));
    275:   off = 0;
    276:   r   = 0;
    277:   while (off < n) {
    278:     PetscCall(ISFindRun_Private(idx, n, off, minRun, &cidx[r * 3 + 0], &cidx[r * 3 + 1], &cidx[r * 3 + 2]));
    279:     PetscCheck(cidx[r * 3 + 0], PETSC_COMM_SELF, PETSC_ERR_PLIB, "Compression failed to find a run at offset %" PetscInt_FMT, off);
    280:     off += cidx[r * 3 + 0];
    281:     ++r;
    282:   }
    283:   PetscCheck(r == runs, comm, PETSC_ERR_PLIB, "The number of runs %" PetscInt_FMT " != %" PetscInt_FMT " computed chunks", runs, r);
    284:   PetscCheck(off == n, comm, PETSC_ERR_PLIB, "The local size %" PetscInt_FMT " != %" PetscInt_FMT " total encoded size", n, off);
    285:   PetscCall(ISCreateGeneral(comm, runs * 3, cidx, PETSC_OWN_POINTER, cis));
    286:   PetscCall(PetscLayoutSetBlockSize((*cis)->map, 3));
    287:   PetscCall(PetscObjectGetName((PetscObject)is, &name));
    288:   PetscCall(PetscObjectSetName((PetscObject)*cis, name));
    289:   PetscFunctionReturn(PETSC_SUCCESS);
    290: }

    292: static PetscErrorCode ISView_General_HDF5(IS is, PetscViewer viewer)
    293: {
    294:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data;
    295:   hid_t             filespace;  /* file dataspace identifier */
    296:   hid_t             chunkspace; /* chunk dataset property identifier */
    297:   hid_t             dset_id;    /* dataset identifier */
    298:   hid_t             memspace;   /* memory dataspace identifier */
    299:   hid_t             inttype;    /* int type (H5T_NATIVE_INT or H5T_NATIVE_LLONG) */
    300:   hid_t             file_id, group;
    301:   hsize_t           dim, maxDims[3], dims[3], chunkDims[3], count[3], offset[3];
    302:   PetscBool         timestepping;
    303:   PetscInt          bs, N, n, timestep = PETSC_INT_MIN, low;
    304:   hsize_t           chunksize;
    305:   const PetscInt   *ind;
    306:   const char       *isname;

    308:   PetscFunctionBegin;
    309:   PetscCall(ISGetBlockSize(is, &bs));
    310:   bs = PetscMax(bs, 1); /* If N = 0, bs  = 0 as well */
    311:   PetscCall(PetscViewerHDF5OpenGroup(viewer, NULL, &file_id, &group));
    312:   PetscCall(PetscViewerHDF5IsTimestepping(viewer, &timestepping));
    313:   if (timestepping) PetscCall(PetscViewerHDF5GetTimestep(viewer, &timestep));

    315:   /* Create the dataspace for the dataset.
    316:    *
    317:    * dims - holds the current dimensions of the dataset
    318:    *
    319:    * maxDims - holds the maximum dimensions of the dataset (unlimited
    320:    * for the number of time steps with the current dimensions for the
    321:    * other dimensions; so only additional time steps can be added).
    322:    *
    323:    * chunkDims - holds the size of a single time step (required to
    324:    * permit extending dataset).
    325:    */
    326:   dim       = 0;
    327:   chunksize = 1;
    328:   if (timestep >= 0) {
    329:     dims[dim]      = timestep + 1;
    330:     maxDims[dim]   = H5S_UNLIMITED;
    331:     chunkDims[dim] = 1;
    332:     ++dim;
    333:   }
    334:   PetscCall(ISGetSize(is, &N));
    335:   PetscCall(ISGetLocalSize(is, &n));
    336:   PetscCall(PetscHDF5IntCast(N / bs, dims + dim));

    338:   maxDims[dim]   = dims[dim];
    339:   chunkDims[dim] = PetscMax(1, dims[dim]);
    340:   chunksize *= chunkDims[dim];
    341:   ++dim;
    342:   if (bs >= 1) {
    343:     dims[dim]      = bs;
    344:     maxDims[dim]   = dims[dim];
    345:     chunkDims[dim] = dims[dim];
    346:     chunksize *= chunkDims[dim];
    347:     ++dim;
    348:   }
    349:   /* hdf5 chunks must be less than 4GB */
    350:   if (chunksize > PETSC_HDF5_MAX_CHUNKSIZE / 64) {
    351:     if (bs >= 1) {
    352:       if (chunkDims[dim - 2] > (hsize_t)PetscSqrtReal((PetscReal)(PETSC_HDF5_MAX_CHUNKSIZE / 64))) chunkDims[dim - 2] = (hsize_t)PetscSqrtReal((PetscReal)(PETSC_HDF5_MAX_CHUNKSIZE / 64));
    353:       if (chunkDims[dim - 1] > (hsize_t)PetscSqrtReal((PetscReal)(PETSC_HDF5_MAX_CHUNKSIZE / 64))) chunkDims[dim - 1] = (hsize_t)PetscSqrtReal((PetscReal)(PETSC_HDF5_MAX_CHUNKSIZE / 64));
    354:     } else {
    355:       chunkDims[dim - 1] = PETSC_HDF5_MAX_CHUNKSIZE / 64;
    356:     }
    357:   }
    358:   PetscCallHDF5Return(filespace, H5Screate_simple, ((int)dim, dims, maxDims));

    360:   #if defined(PETSC_USE_64BIT_INDICES)
    361:   inttype = H5T_NATIVE_LLONG;
    362:   #else
    363:   inttype = H5T_NATIVE_INT;
    364:   #endif

    366:   /* Create the dataset with default properties and close filespace */
    367:   PetscCall(PetscObjectGetName((PetscObject)is, &isname));
    368:   if (!H5Lexists(group, isname, H5P_DEFAULT)) {
    369:     /* Create chunk */
    370:     PetscCallHDF5Return(chunkspace, H5Pcreate, (H5P_DATASET_CREATE));
    371:     PetscCallHDF5(H5Pset_chunk, (chunkspace, (int)dim, chunkDims));

    373:     PetscCallHDF5Return(dset_id, H5Dcreate2, (group, isname, inttype, filespace, H5P_DEFAULT, chunkspace, H5P_DEFAULT));
    374:     PetscCallHDF5(H5Pclose, (chunkspace));
    375:   } else {
    376:     PetscCallHDF5Return(dset_id, H5Dopen2, (group, isname, H5P_DEFAULT));
    377:     PetscCallHDF5(H5Dset_extent, (dset_id, dims));
    378:   }
    379:   PetscCallHDF5(H5Sclose, (filespace));

    381:   /* Each process defines a dataset and writes it to the hyperslab in the file */
    382:   dim = 0;
    383:   if (timestep >= 0) {
    384:     count[dim] = 1;
    385:     ++dim;
    386:   }
    387:   PetscCall(PetscHDF5IntCast(n / bs, count + dim));
    388:   ++dim;
    389:   if (bs >= 1) {
    390:     count[dim] = bs;
    391:     ++dim;
    392:   }
    393:   if (n > 0 || H5_VERSION_GE(1, 10, 0)) {
    394:     PetscCallHDF5Return(memspace, H5Screate_simple, ((int)dim, count, NULL));
    395:   } else {
    396:     /* Can't create dataspace with zero for any dimension, so create null dataspace. */
    397:     PetscCallHDF5Return(memspace, H5Screate, (H5S_NULL));
    398:   }

    400:   /* Select hyperslab in the file */
    401:   PetscCall(PetscLayoutGetRange(is->map, &low, NULL));
    402:   dim = 0;
    403:   if (timestep >= 0) {
    404:     offset[dim] = timestep;
    405:     ++dim;
    406:   }
    407:   PetscCall(PetscHDF5IntCast(low / bs, offset + dim));
    408:   ++dim;
    409:   if (bs >= 1) {
    410:     offset[dim] = 0;
    411:     ++dim;
    412:   }
    413:   if (n > 0 || H5_VERSION_GE(1, 10, 0)) {
    414:     PetscCallHDF5Return(filespace, H5Dget_space, (dset_id));
    415:     PetscCallHDF5(H5Sselect_hyperslab, (filespace, H5S_SELECT_SET, offset, NULL, count, NULL));
    416:   } else {
    417:     /* Create null filespace to match null memspace. */
    418:     PetscCallHDF5Return(filespace, H5Screate, (H5S_NULL));
    419:   }

    421:   PetscCall(ISGetIndices(is, &ind));
    422:   PetscCallHDF5(H5Dwrite, (dset_id, inttype, memspace, filespace, hdf5->dxpl_id, ind));
    423:   PetscCallHDF5(H5Fflush, (file_id, H5F_SCOPE_GLOBAL));
    424:   PetscCall(ISRestoreIndices(is, &ind));

    426:   /* Close/release resources */
    427:   PetscCallHDF5(H5Gclose, (group));
    428:   PetscCallHDF5(H5Sclose, (filespace));
    429:   PetscCallHDF5(H5Sclose, (memspace));
    430:   PetscCallHDF5(H5Dclose, (dset_id));

    432:   if (timestepping) PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)is, "timestepping", PETSC_BOOL, &timestepping));
    433:   PetscCall(PetscInfo(is, "Wrote IS object with name %s\n", isname));
    434:   PetscFunctionReturn(PETSC_SUCCESS);
    435: }

    437: static PetscErrorCode ISView_General_HDF5_Compressed(IS is, PetscViewer viewer)
    438: {
    439:   const PetscBool compressed = PETSC_TRUE;
    440:   const char     *isname;
    441:   IS              cis;
    442:   PetscBool       timestepping;

    444:   PetscFunctionBegin;
    445:   PetscCall(PetscViewerHDF5IsTimestepping(viewer, &timestepping));
    446:   PetscCheck(!timestepping, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONG, "Timestepping not supported for compressed writing");

    448:   PetscCall(ISGeneralCompress(is, &cis));
    449:   PetscCall(ISView_General_HDF5(cis, viewer));
    450:   PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)cis, "compressed", PETSC_BOOL, &compressed));
    451:   PetscCall(ISDestroy(&cis));

    453:   PetscCall(PetscObjectGetName((PetscObject)is, &isname));
    454:   PetscCall(PetscInfo(is, "Wrote compressed IS object with name %s\n", isname));
    455:   PetscFunctionReturn(PETSC_SUCCESS);
    456: }
    457: #endif

    459: static PetscErrorCode ISView_General(IS is, PetscViewer viewer)
    460: {
    461:   IS_General *sub = (IS_General *)is->data;
    462:   PetscInt   *idx = sub->idx, n;
    463:   PetscBool   iascii, isbinary, ishdf5, compress;

    465:   PetscFunctionBegin;
    466:   PetscCall(PetscLayoutGetLocalSize(is->map, &n));
    467:   PetscCall(ISGeneralCheckCompress(is, &compress));
    468:   PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERASCII, &iascii));
    469:   PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERBINARY, &isbinary));
    470:   PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5));
    471:   if (iascii) {
    472:     MPI_Comm          comm;
    473:     PetscMPIInt       rank, size;
    474:     PetscViewerFormat fmt;
    475:     PetscBool         isperm;

    477:     PetscCall(PetscObjectGetComm((PetscObject)viewer, &comm));
    478:     PetscCallMPI(MPI_Comm_rank(comm, &rank));
    479:     PetscCallMPI(MPI_Comm_size(comm, &size));

    481:     PetscCall(PetscViewerGetFormat(viewer, &fmt));
    482:     PetscCall(ISGetInfo(is, IS_PERMUTATION, IS_LOCAL, PETSC_FALSE, &isperm));
    483:     if (isperm && fmt != PETSC_VIEWER_ASCII_MATLAB) PetscCall(PetscViewerASCIIPrintf(viewer, "Index set is permutation\n"));
    484:     PetscCall(PetscViewerASCIIPushSynchronized(viewer));
    485:     if (size > 1) {
    486:       if (fmt == PETSC_VIEWER_ASCII_MATLAB) {
    487:         const char *name;

    489:         PetscCall(PetscObjectGetName((PetscObject)is, &name));
    490:         PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "%s_%d = [...\n", name, rank));
    491:         for (PetscInt i = 0; i < n; i++) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "%" PetscInt_FMT "\n", idx[i] + 1));
    492:         PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "];\n"));
    493:       } else {
    494:         PetscInt st = 0;

    496:         if (fmt == PETSC_VIEWER_ASCII_INDEX) st = is->map->rstart;
    497:         PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "[%d] Number of indices in set %" PetscInt_FMT "\n", rank, n));
    498:         for (PetscInt i = 0; i < n; i++) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "[%d] %" PetscInt_FMT " %" PetscInt_FMT "\n", rank, i + st, idx[i]));
    499:       }
    500:     } else {
    501:       if (fmt == PETSC_VIEWER_ASCII_MATLAB) {
    502:         const char *name;

    504:         PetscCall(PetscObjectGetName((PetscObject)is, &name));
    505:         PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "%s = [...\n", name));
    506:         for (PetscInt i = 0; i < n; i++) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "%" PetscInt_FMT "\n", idx[i] + 1));
    507:         PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "];\n"));
    508:       } else {
    509:         PetscInt st = 0;

    511:         if (fmt == PETSC_VIEWER_ASCII_INDEX) st = is->map->rstart;
    512:         PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "Number of indices in set %" PetscInt_FMT "\n", n));
    513:         for (PetscInt i = 0; i < n; i++) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "%" PetscInt_FMT " %" PetscInt_FMT "\n", i + st, idx[i]));
    514:       }
    515:     }
    516:     PetscCall(PetscViewerFlush(viewer));
    517:     PetscCall(PetscViewerASCIIPopSynchronized(viewer));
    518:   } else if (isbinary) {
    519:     PetscCall(ISView_Binary(is, viewer));
    520:   } else if (ishdf5) {
    521: #if defined(PETSC_HAVE_HDF5)
    522:     if (compress) PetscCall(ISView_General_HDF5_Compressed(is, viewer));
    523:     else PetscCall(ISView_General_HDF5(is, viewer));
    524: #endif
    525:   }
    526:   PetscFunctionReturn(PETSC_SUCCESS);
    527: }

    529: static PetscErrorCode ISSort_General(IS is)
    530: {
    531:   IS_General *sub = (IS_General *)is->data;
    532:   PetscInt    n;

    534:   PetscFunctionBegin;
    535:   PetscCall(PetscLayoutGetLocalSize(is->map, &n));
    536:   PetscCall(PetscIntSortSemiOrdered(n, sub->idx));
    537:   PetscFunctionReturn(PETSC_SUCCESS);
    538: }

    540: static PetscErrorCode ISSortRemoveDups_General(IS is)
    541: {
    542:   IS_General *sub = (IS_General *)is->data;
    543:   PetscLayout map;
    544:   PetscInt    n;
    545:   PetscBool   sorted;

    547:   PetscFunctionBegin;
    548:   PetscCall(PetscLayoutGetLocalSize(is->map, &n));
    549:   PetscCall(ISGetInfo(is, IS_SORTED, IS_LOCAL, PETSC_TRUE, &sorted));
    550:   if (sorted) {
    551:     PetscCall(PetscSortedRemoveDupsInt(&n, sub->idx));
    552:   } else {
    553:     PetscCall(PetscSortRemoveDupsInt(&n, sub->idx));
    554:   }
    555:   PetscCall(PetscLayoutCreateFromSizes(PetscObjectComm((PetscObject)is), n, PETSC_DECIDE, is->map->bs, &map));
    556:   PetscCall(PetscLayoutDestroy(&is->map));
    557:   is->map = map;
    558:   PetscFunctionReturn(PETSC_SUCCESS);
    559: }

    561: static PetscErrorCode ISSorted_General(IS is, PetscBool *flg)
    562: {
    563:   PetscFunctionBegin;
    564:   PetscCall(ISGetInfo(is, IS_SORTED, IS_LOCAL, PETSC_TRUE, flg));
    565:   PetscFunctionReturn(PETSC_SUCCESS);
    566: }

    568: static PetscErrorCode ISToGeneral_General(IS is)
    569: {
    570:   PetscFunctionBegin;
    571:   PetscFunctionReturn(PETSC_SUCCESS);
    572: }

    574: // clang-format off
    575: static const struct _ISOps myops = {
    576:   PetscDesignatedInitializer(getindices, ISGetIndices_General),
    577:   PetscDesignatedInitializer(restoreindices, ISRestoreIndices_General),
    578:   PetscDesignatedInitializer(invertpermutation, ISInvertPermutation_General),
    579:   PetscDesignatedInitializer(sort, ISSort_General),
    580:   PetscDesignatedInitializer(sortremovedups, ISSortRemoveDups_General),
    581:   PetscDesignatedInitializer(sorted, ISSorted_General),
    582:   PetscDesignatedInitializer(duplicate, ISDuplicate_General),
    583:   PetscDesignatedInitializer(destroy, ISDestroy_General),
    584:   PetscDesignatedInitializer(view, ISView_General),
    585:   PetscDesignatedInitializer(load, ISLoad_Default),
    586:   PetscDesignatedInitializer(copy, ISCopy_General),
    587:   PetscDesignatedInitializer(togeneral, ISToGeneral_General),
    588:   PetscDesignatedInitializer(oncomm, ISOnComm_General),
    589:   PetscDesignatedInitializer(setblocksize, ISSetBlockSize_General),
    590:   PetscDesignatedInitializer(contiguous, ISContiguousLocal_General),
    591:   PetscDesignatedInitializer(locate, ISLocate_General),
    592:   /* no specializations of {sorted,unique,perm,interval}{local,global} because the default
    593:    * checks in ISGetInfo_XXX in index.c are exactly what we would do for ISGeneral */
    594:   PetscDesignatedInitializer(sortedlocal, NULL),
    595:   PetscDesignatedInitializer(sortedglobal, NULL),
    596:   PetscDesignatedInitializer(uniquelocal, NULL),
    597:   PetscDesignatedInitializer(uniqueglobal, NULL),
    598:   PetscDesignatedInitializer(permlocal, NULL),
    599:   PetscDesignatedInitializer(permglobal, NULL),
    600:   PetscDesignatedInitializer(intervallocal, NULL),
    601:   PetscDesignatedInitializer(intervalglobal, NULL)
    602: };
    603: // clang-format on

    605: PETSC_INTERN PetscErrorCode ISSetUp_General(IS is)
    606: {
    607:   IS_General     *sub = (IS_General *)is->data;
    608:   const PetscInt *idx = sub->idx;
    609:   PetscInt        n, i, min, max;

    611:   PetscFunctionBegin;
    612:   PetscCall(PetscLayoutGetLocalSize(is->map, &n));

    614:   if (n) {
    615:     min = max = idx[0];
    616:     for (i = 1; i < n; i++) {
    617:       if (idx[i] < min) min = idx[i];
    618:       if (idx[i] > max) max = idx[i];
    619:     }
    620:     is->min = min;
    621:     is->max = max;
    622:   } else {
    623:     is->min = PETSC_INT_MAX;
    624:     is->max = PETSC_INT_MIN;
    625:   }
    626:   PetscFunctionReturn(PETSC_SUCCESS);
    627: }

    629: /*@
    630:   ISCreateGeneral - Creates a data structure for an index set containing a list of integers.

    632:   Collective

    634:   Input Parameters:
    635: + comm - the MPI communicator
    636: . n    - the length of the index set
    637: . idx  - the list of integers
    638: - mode - `PETSC_COPY_VALUES`, `PETSC_OWN_POINTER`, or `PETSC_USE_POINTER`; see `PetscCopyMode` for meaning of this flag.

    640:   Output Parameter:
    641: . is - the new index set

    643:   Level: beginner

    645:   Notes:
    646:   When the communicator is not `MPI_COMM_SELF`, the operations on IS are NOT
    647:   conceptually the same as `MPI_Group` operations. The `IS` are then
    648:   distributed sets of indices and thus certain operations on them are
    649:   collective.

    651:   Use `ISGeneralSetIndices()` to provide indices to an already existing `IS` of `ISType` `ISGENERAL`

    653: .seealso: [](sec_scatter), `IS`, `ISGENERAL`, `ISCreateStride()`, `ISCreateBlock()`, `ISAllGather()`, `PETSC_COPY_VALUES`, `PETSC_OWN_POINTER`,
    654:           `PETSC_USE_POINTER`, `PetscCopyMode`, `ISGeneralSetIndicesFromMask()`
    655: @*/
    656: PetscErrorCode ISCreateGeneral(MPI_Comm comm, PetscInt n, const PetscInt idx[], PetscCopyMode mode, IS *is)
    657: {
    658:   PetscFunctionBegin;
    659:   PetscCall(ISCreate(comm, is));
    660:   PetscCall(ISSetType(*is, ISGENERAL));
    661:   PetscCall(ISGeneralSetIndices(*is, n, idx, mode));
    662:   PetscFunctionReturn(PETSC_SUCCESS);
    663: }

    665: /*@
    666:   ISGeneralSetIndices - Sets the indices for an `ISGENERAL` index set

    668:   Logically Collective

    670:   Input Parameters:
    671: + is   - the index set
    672: . n    - the length of the index set
    673: . idx  - the list of integers
    674: - mode - see `PetscCopyMode` for meaning of this flag.

    676:   Level: beginner

    678:   Note:
    679:   Use `ISCreateGeneral()` to create the `IS` and set its indices in a single function call

    681: .seealso: [](sec_scatter), `IS`, `ISBLOCK`, `ISCreateGeneral()`, `ISGeneralSetIndicesFromMask()`, `ISBlockSetIndices()`, `ISGENERAL`, `PetscCopyMode`
    682: @*/
    683: PetscErrorCode ISGeneralSetIndices(IS is, PetscInt n, const PetscInt idx[], PetscCopyMode mode)
    684: {
    685:   PetscFunctionBegin;
    687:   PetscCheck(n >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "length < 0");
    688:   if (n) PetscAssertPointer(idx, 3);
    689:   PetscCall(ISClearInfoCache(is, PETSC_FALSE));
    690:   PetscUseMethod(is, "ISGeneralSetIndices_C", (IS, PetscInt, const PetscInt[], PetscCopyMode), (is, n, idx, mode));
    691:   PetscFunctionReturn(PETSC_SUCCESS);
    692: }

    694: static PetscErrorCode ISGeneralSetIndices_General(IS is, PetscInt n, const PetscInt idx[], PetscCopyMode mode)
    695: {
    696:   PetscLayout map;
    697:   IS_General *sub = (IS_General *)is->data;

    699:   PetscFunctionBegin;
    700:   PetscCall(PetscLayoutCreateFromSizes(PetscObjectComm((PetscObject)is), n, PETSC_DECIDE, is->map->bs, &map));
    701:   PetscCall(PetscLayoutDestroy(&is->map));
    702:   is->map = map;

    704:   if (sub->allocated) PetscCall(PetscFree(sub->idx));
    705:   if (mode == PETSC_COPY_VALUES) {
    706:     PetscCall(PetscMalloc1(n, &sub->idx));
    707:     PetscCall(PetscArraycpy(sub->idx, idx, n));
    708:     sub->allocated = PETSC_TRUE;
    709:   } else if (mode == PETSC_OWN_POINTER) {
    710:     sub->idx       = (PetscInt *)idx;
    711:     sub->allocated = PETSC_TRUE;
    712:   } else {
    713:     sub->idx       = (PetscInt *)idx;
    714:     sub->allocated = PETSC_FALSE;
    715:   }

    717:   PetscCall(ISSetUp_General(is));
    718:   PetscCall(ISViewFromOptions(is, NULL, "-is_view"));
    719:   PetscFunctionReturn(PETSC_SUCCESS);
    720: }

    722: /*@
    723:   ISGeneralSetIndicesFromMask - Sets the indices for an `ISGENERAL` index set using a boolean mask

    725:   Collective

    727:   Input Parameters:
    728: + is     - the index set
    729: . rstart - the range start index (inclusive)
    730: . rend   - the range end index (exclusive)
    731: - mask   - the boolean mask array of length rend-rstart, indices will be set for each `PETSC_TRUE` value in the array

    733:   Level: beginner

    735:   Note:
    736:   The mask array may be freed by the user after this call.

    738:   Example:
    739: .vb
    740:    PetscBool mask[] = {PETSC_FALSE, PETSC_TRUE, PETSC_FALSE, PETSC_FALSE, PETSC_TRUE};
    741:    ISGeneralSetIndicesFromMask(is,10,15,mask);
    742: .ve
    743:   will feed the `IS` with indices
    744: .vb
    745:   {11, 14}
    746: .ve
    747:   locally.

    749: .seealso: [](sec_scatter), `IS`, `ISCreateGeneral()`, `ISGeneralSetIndices()`, `ISGENERAL`
    750: @*/
    751: PetscErrorCode ISGeneralSetIndicesFromMask(IS is, PetscInt rstart, PetscInt rend, const PetscBool mask[])
    752: {
    753:   PetscFunctionBegin;
    755:   PetscCheck(rstart <= rend, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "rstart %" PetscInt_FMT " must be less than or equal to rend %" PetscInt_FMT, rstart, rend);
    756:   if (rend - rstart) PetscAssertPointer(mask, 4);
    757:   PetscCall(ISClearInfoCache(is, PETSC_FALSE));
    758:   PetscUseMethod(is, "ISGeneralSetIndicesFromMask_C", (IS, PetscInt, PetscInt, const PetscBool[]), (is, rstart, rend, mask));
    759:   PetscFunctionReturn(PETSC_SUCCESS);
    760: }

    762: static PetscErrorCode ISGeneralSetIndicesFromMask_General(IS is, PetscInt rstart, PetscInt rend, const PetscBool mask[])
    763: {
    764:   PetscInt  i, nidx;
    765:   PetscInt *idx;

    767:   PetscFunctionBegin;
    768:   for (i = 0, nidx = 0; i < rend - rstart; i++)
    769:     if (mask[i]) nidx++;
    770:   PetscCall(PetscMalloc1(nidx, &idx));
    771:   for (i = 0, nidx = 0; i < rend - rstart; i++) {
    772:     if (mask[i]) {
    773:       idx[nidx] = i + rstart;
    774:       nidx++;
    775:     }
    776:   }
    777:   PetscCall(ISGeneralSetIndices_General(is, nidx, idx, PETSC_OWN_POINTER));
    778:   PetscFunctionReturn(PETSC_SUCCESS);
    779: }

    781: static PetscErrorCode ISGeneralFilter_General(IS is, PetscInt start, PetscInt end)
    782: {
    783:   IS_General *sub = (IS_General *)is->data;
    784:   PetscInt   *idx = sub->idx, *idxnew;
    785:   PetscInt    i, n = is->map->n, nnew = 0, o;

    787:   PetscFunctionBegin;
    788:   for (i = 0; i < n; ++i)
    789:     if (idx[i] >= start && idx[i] < end) nnew++;
    790:   PetscCall(PetscMalloc1(nnew, &idxnew));
    791:   for (o = 0, i = 0; i < n; i++) {
    792:     if (idx[i] >= start && idx[i] < end) idxnew[o++] = idx[i];
    793:   }
    794:   PetscCall(ISGeneralSetIndices_General(is, nnew, idxnew, PETSC_OWN_POINTER));
    795:   PetscFunctionReturn(PETSC_SUCCESS);
    796: }

    798: /*@
    799:   ISGeneralFilter - Remove all indices outside of [start, end) from an `ISGENERAL`

    801:   Collective

    803:   Input Parameters:
    804: + is    - the index set
    805: . start - the lowest index kept
    806: - end   - one more than the highest index kept, `start` $\le$ `end`

    808:   Level: beginner

    810: .seealso: [](sec_scatter), `IS`, `ISGENERAL`, `ISCreateGeneral()`, `ISGeneralSetIndices()`
    811: @*/
    812: PetscErrorCode ISGeneralFilter(IS is, PetscInt start, PetscInt end)
    813: {
    814:   PetscFunctionBegin;
    816:   PetscCheck(start <= end, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "start %" PetscInt_FMT " must be less than or equal to end %" PetscInt_FMT, start, end);
    817:   PetscCall(ISClearInfoCache(is, PETSC_FALSE));
    818:   PetscUseMethod(is, "ISGeneralFilter_C", (IS, PetscInt, PetscInt), (is, start, end));
    819:   PetscFunctionReturn(PETSC_SUCCESS);
    820: }

    822: PETSC_INTERN PetscErrorCode ISCreate_General(IS is)
    823: {
    824:   IS_General *sub;

    826:   PetscFunctionBegin;
    827:   PetscCall(PetscNew(&sub));
    828:   is->data   = (void *)sub;
    829:   is->ops[0] = myops;
    830:   PetscCall(PetscObjectComposeFunction((PetscObject)is, "ISGeneralSetIndices_C", ISGeneralSetIndices_General));
    831:   PetscCall(PetscObjectComposeFunction((PetscObject)is, "ISGeneralSetIndicesFromMask_C", ISGeneralSetIndicesFromMask_General));
    832:   PetscCall(PetscObjectComposeFunction((PetscObject)is, "ISGeneralFilter_C", ISGeneralFilter_General));
    833:   PetscCall(PetscObjectComposeFunction((PetscObject)is, "ISShift_C", ISShift_General));
    834:   PetscFunctionReturn(PETSC_SUCCESS);
    835: }