Date: 2021-03-03T22:26:51+00:00

Actual source code: plexnatural.c
petsc-3.14.5 2021-03-03
Report Typos and Errors

      1: #include <petsc/private/dmpleximpl.h>

      3: /*@
      4:   DMPlexSetMigrationSF - Sets the SF for migrating from a parent DM into this DM

      6:   Input Parameters:
      7: + dm        - The DM
      8: - naturalSF - The PetscSF

     10:   Note: It is necessary to call this in order to have DMCreateSubDM() or DMCreateSuperDM() build the Global-To-Natural map

     12:   Level: intermediate

     14: .seealso: DMPlexDistribute(), DMPlexDistributeField(), DMPlexCreateMigrationSF(), DMPlexGetMigrationSF()
     15: @*/
     16: PetscErrorCode DMPlexSetMigrationSF(DM dm, PetscSF migrationSF)
     17: {
     20:   dm->sfMigration = migrationSF;
     21:   PetscObjectReference((PetscObject) migrationSF);
     22:   return(0);
     23: }

     25: /*@
     26:   DMPlexGetMigrationSF - Gets the SF for migrating from a parent DM into this DM

     28:   Input Parameter:
     29: . dm          - The DM

     31:   Output Parameter:
     32: . migrationSF - The PetscSF

     34:   Level: intermediate

     36: .seealso: DMPlexDistribute(), DMPlexDistributeField(), DMPlexCreateMigrationSF(), DMPlexSetMigrationSF
     37: @*/
     38: PetscErrorCode DMPlexGetMigrationSF(DM dm, PetscSF *migrationSF)
     39: {
     41:   *migrationSF = dm->sfMigration;
     42:   return(0);
     43: }

     45: /*@
     46:   DMPlexSetGlobalToNaturalSF - Sets the SF for mapping Global Vec to the Natural Vec

     48:   Input Parameters:
     49: + dm          - The DM
     50: - naturalSF   - The PetscSF

     52:   Level: intermediate

     54: .seealso: DMPlexDistribute(), DMPlexDistributeField(), DMPlexCreateGlobalToNaturalSF(), DMPlexGetGlobaltoNaturalSF()
     55: @*/
     56: PetscErrorCode DMPlexSetGlobalToNaturalSF(DM dm, PetscSF naturalSF)
     57: {
     60:   dm->sfNatural = naturalSF;
     61:   PetscObjectReference((PetscObject) naturalSF);
     62:   dm->useNatural = PETSC_TRUE;
     63:   return(0);
     64: }

     66: /*@
     67:   DMPlexGetGlobalToNaturalSF - Gets the SF for mapping Global Vec to the Natural Vec

     69:   Input Parameter:
     70: . dm          - The DM

     72:   Output Parameter:
     73: . naturalSF   - The PetscSF

     75:   Level: intermediate

     77: .seealso: DMPlexDistribute(), DMPlexDistributeField(), DMPlexCreateGlobalToNaturalSF(), DMPlexSetGlobaltoNaturalSF
     78: @*/
     79: PetscErrorCode DMPlexGetGlobalToNaturalSF(DM dm, PetscSF *naturalSF)
     80: {
     82:   *naturalSF = dm->sfNatural;
     83:   return(0);
     84: }

     86: /*@
     87:   DMPlexCreateGlobalToNaturalSF - Creates the SF for mapping Global Vec to the Natural Vec

     89:   Input Parameters:
     90: + dm          - The DM
     91: . section     - The PetscSection describing the Vec before the mesh was distributed
     92: - sfMigration - The PetscSF used to distribute the mesh

     94:   Output Parameter:
     95: . sfNatural   - PetscSF for mapping the Vec in PETSc ordering to the canonical ordering

     97:   Note: This is not typically called by the user.

     99:   Level: intermediate

    101: .seealso: DMPlexDistribute(), DMPlexDistributeField()
    102:  @*/
    103: PetscErrorCode DMPlexCreateGlobalToNaturalSF(DM dm, PetscSection section, PetscSF sfMigration, PetscSF *sfNatural)
    104: {
    105:   MPI_Comm       comm;
    106:   Vec            gv;
    107:   PetscSF        sf, sfEmbed, sfSeqToNatural, sfField, sfFieldInv;
    108:   PetscSection   gSection, sectionDist, gLocSection;
    109:   PetscInt      *spoints, *remoteOffsets;
    110:   PetscInt       ssize, pStart, pEnd, p;
    111:   PetscLayout    map;

    115:   PetscObjectGetComm((PetscObject) dm, &comm);
    116:   /* PetscPrintf(comm, "Point migration SF\n");
    117:    PetscSFView(sfMigration, 0); */
    118:   /* Create a new section from distributing the original section */
    119:   PetscSectionCreate(comm, &sectionDist);
    120:   PetscSFDistributeSection(sfMigration, section, &remoteOffsets, sectionDist);
    121:   /* PetscPrintf(comm, "Distributed Section\n");
    122:    PetscSectionView(sectionDist, PETSC_VIEWER_STDOUT_WORLD); */
    123:   DMSetLocalSection(dm, sectionDist);
    124:   /* Get a pruned version of migration SF */
    125:   DMGetGlobalSection(dm, &gSection);
    126:   PetscSectionGetChart(gSection, &pStart, &pEnd);
    127:   for (p = pStart, ssize = 0; p < pEnd; ++p) {
    128:     PetscInt dof, off;

    130:     PetscSectionGetDof(gSection, p, &dof);
    131:     PetscSectionGetOffset(gSection, p, &off);
    132:     if ((dof > 0) && (off >= 0)) ++ssize;
    133:   }
    134:   PetscMalloc1(ssize, &spoints);
    135:   for (p = pStart, ssize = 0; p < pEnd; ++p) {
    136:     PetscInt dof, off;

    138:     PetscSectionGetDof(gSection, p, &dof);
    139:     PetscSectionGetOffset(gSection, p, &off);
    140:     if ((dof > 0) && (off >= 0)) spoints[ssize++] = p;
    141:   }
    142:   PetscSFCreateEmbeddedLeafSF(sfMigration, ssize, spoints, &sfEmbed);
    143:   PetscFree(spoints);
    144:   /* PetscPrintf(comm, "Embedded SF\n");
    145:    PetscSFView(sfEmbed, 0); */
    146:   /* Create the SF for seq to natural */
    147:   DMGetGlobalVector(dm, &gv);
    148:   VecGetLayout(gv,&map);
    149:   /* Note that entries of gv are leaves in sfSeqToNatural, entries of the seq vec are roots */
    150:   PetscSFCreate(comm, &sfSeqToNatural);
    151:   PetscSFSetGraphWithPattern(sfSeqToNatural, map, PETSCSF_PATTERN_GATHER);
    152:   DMRestoreGlobalVector(dm, &gv);
    153:   /* PetscPrintf(comm, "Seq-to-Natural SF\n");
    154:    PetscSFView(sfSeqToNatural, 0); */
    155:   /* Create the SF associated with this section */
    156:   DMGetPointSF(dm, &sf);
    157:   PetscSectionCreateGlobalSection(sectionDist, sf, PETSC_FALSE, PETSC_TRUE, &gLocSection);
    158:   PetscSFCreateSectionSF(sfEmbed, section, remoteOffsets, gLocSection, &sfField);
    159:   PetscFree(remoteOffsets);
    160:   PetscSFDestroy(&sfEmbed);
    161:   PetscSectionDestroy(&gLocSection);
    162:   PetscSectionDestroy(&sectionDist);
    163:   /* PetscPrintf(comm, "Field SF\n");
    164:    PetscSFView(sfField, 0); */
    165:   /* Invert the field SF so it's now from distributed to sequential */
    166:   PetscSFCreateInverseSF(sfField, &sfFieldInv);
    167:   PetscSFDestroy(&sfField);
    168:   /* PetscPrintf(comm, "Inverse Field SF\n");
    169:    PetscSFView(sfFieldInv, 0); */
    170:   /* Multiply the sfFieldInv with the */
    171:   PetscSFComposeInverse(sfFieldInv, sfSeqToNatural, sfNatural);
    172:   PetscObjectViewFromOptions((PetscObject) *sfNatural, NULL, "-globaltonatural_sf_view");
    173:   /* Clean up */
    174:   PetscSFDestroy(&sfFieldInv);
    175:   PetscSFDestroy(&sfSeqToNatural);
    176:   return(0);
    177: }

    179: /*@
    180:   DMPlexGlobalToNaturalBegin - Rearranges a global Vector in the natural order.

    182:   Collective on dm

    184:   Input Parameters:
    185: + dm - The distributed DMPlex
    186: - gv - The global Vec

    188:   Output Parameters:
    189: . nv - Vec in the canonical ordering distributed over all processors associated with gv

    191:   Note: The user must call DMSetUseNatural(dm, PETSC_TRUE) before DMPlexDistribute().

    193:   Level: intermediate

    195: .seealso: DMPlexDistribute(), DMPlexDistributeField(), DMPlexNaturalToGlobalBegin(), DMPlexGlobalToNaturalEnd()
    196: @*/
    197: PetscErrorCode DMPlexGlobalToNaturalBegin(DM dm, Vec gv, Vec nv)
    198: {
    199:   const PetscScalar *inarray;
    200:   PetscScalar       *outarray;
    201:   PetscMPIInt        size;
    202:   PetscErrorCode     ierr;

    205:   PetscLogEventBegin(DMPLEX_GlobalToNaturalBegin,dm,0,0,0);
    206:   MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);
    207:   if (dm->sfNatural) {
    208:     VecGetArray(nv, &outarray);
    209:     VecGetArrayRead(gv, &inarray);
    210:     PetscSFBcastBegin(dm->sfNatural, MPIU_SCALAR, (PetscScalar *) inarray, outarray);
    211:     VecRestoreArrayRead(gv, &inarray);
    212:     VecRestoreArray(nv, &outarray);
    213:   } else if (size == 1) {
    214:     VecCopy(nv, gv);
    215:   } else if (dm->useNatural) SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "DM global to natural SF not present.\nIf DMPlexDistribute() was called, report to petsc-maint@mcs.anl.gov.\n");
    216:   else SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONGSTATE, "DM global to natural SF was not created.\nYou must call DMSetUseNatural() before DMPlexDistribute().\n");
    217:   PetscLogEventEnd(DMPLEX_GlobalToNaturalBegin,dm,0,0,0);
    218:   return(0);
    219: }

    221: /*@
    222:   DMPlexGlobalToNaturalEnd - Rearranges a global Vector in the natural order.

    224:   Collective on dm

    226:   Input Parameters:
    227: + dm - The distributed DMPlex
    228: - gv - The global Vec

    230:   Output Parameters:
    231: . nv - The natural Vec

    233:   Note: The user must call DMSetUseNatural(dm, PETSC_TRUE) before DMPlexDistribute().

    235:   Level: intermediate

    237:  .seealso: DMPlexDistribute(), DMPlexDistributeField(), DMPlexNaturalToGlobalBegin(), DMPlexGlobalToNaturalBegin()
    238:  @*/
    239: PetscErrorCode DMPlexGlobalToNaturalEnd(DM dm, Vec gv, Vec nv)
    240: {
    241:   const PetscScalar *inarray;
    242:   PetscScalar       *outarray;
    243:   PetscMPIInt        size;
    244:   PetscErrorCode     ierr;

    247:   PetscLogEventBegin(DMPLEX_GlobalToNaturalEnd,dm,0,0,0);
    248:   MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);
    249:   if (dm->sfNatural) {
    250:     VecGetArrayRead(gv, &inarray);
    251:     VecGetArray(nv, &outarray);
    252:     PetscSFBcastEnd(dm->sfNatural, MPIU_SCALAR, (PetscScalar *) inarray, outarray);
    253:     VecRestoreArrayRead(gv, &inarray);
    254:     VecRestoreArray(nv, &outarray);
    255:   } else if (size == 1) {
    256:   } else if (dm->useNatural) SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "DM global to natural SF not present.\nIf DMPlexDistribute() was called, report to petsc-maint@mcs.anl.gov.\n");
    257:   else SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONGSTATE, "DM global to natural SF was not created.\nYou must call DMSetUseNatural() before DMPlexDistribute().\n");
    258:   PetscLogEventEnd(DMPLEX_GlobalToNaturalEnd,dm,0,0,0);
    259:   return(0);
    260: }

    262: /*@
    263:   DMPlexNaturalToGlobalBegin - Rearranges a Vector in the natural order to the Global order.

    265:   Collective on dm

    267:   Input Parameters:
    268: + dm - The distributed DMPlex
    269: - nv - The natural Vec

    271:   Output Parameters:
    272: . gv - The global Vec

    274:   Note: The user must call DMSetUseNatural(dm, PETSC_TRUE) before DMPlexDistribute().

    276:   Level: intermediate

    278: .seealso: DMPlexDistribute(), DMPlexDistributeField(), DMPlexNaturalToGlobalBegin(),DMPlexGlobalToNaturalEnd()
    279: @*/
    280: PetscErrorCode DMPlexNaturalToGlobalBegin(DM dm, Vec nv, Vec gv)
    281: {
    282:   const PetscScalar *inarray;
    283:   PetscScalar       *outarray;
    284:   PetscMPIInt        size;
    285:   PetscErrorCode     ierr;

    288:   PetscLogEventBegin(DMPLEX_NaturalToGlobalBegin,dm,0,0,0);
    289:   MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);
    290:   if (dm->sfNatural) {
    291:     /* We only have acces to the SF that goes from Global to Natural.
    292:        Instead of inverting dm->sfNatural, we can call PetscSFReduceBegin/End with MPI_Op MPI_SUM.
    293:        Here the SUM really does nothing since sfNatural is one to one, as long as gV is set to zero first. */
    294:     VecZeroEntries(gv);
    295:     VecGetArray(gv, &outarray);
    296:     VecGetArrayRead(nv, &inarray);
    297:     PetscSFReduceBegin(dm->sfNatural, MPIU_SCALAR, (PetscScalar *) inarray, outarray, MPI_SUM);
    298:     VecRestoreArrayRead(nv, &inarray);
    299:     VecRestoreArray(gv, &outarray);
    300:   } else if (size == 1) {
    301:     VecCopy(nv, gv);
    302:   } else if (dm->useNatural) SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "DM global to natural SF not present.\nIf DMPlexDistribute() was called, report to petsc-maint@mcs.anl.gov.\n");
    303:   else SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONGSTATE, "DM global to natural SF was not created.\nYou must call DMSetUseNatural() before DMPlexDistribute().\n");
    304:   PetscLogEventEnd(DMPLEX_NaturalToGlobalBegin,dm,0,0,0);
    305:   return(0);
    306: }

    308: /*@
    309:   DMPlexNaturalToGlobalEnd - Rearranges a Vector in the natural order to the Global order.

    311:   Collective on dm

    313:   Input Parameters:
    314: + dm - The distributed DMPlex
    315: - nv - The natural Vec

    317:   Output Parameters:
    318: . gv - The global Vec

    320:   Note: The user must call DMSetUseNatural(dm, PETSC_TRUE) before DMPlexDistribute().

    322:   Level: intermediate

    324: .seealso: DMPlexDistribute(), DMPlexDistributeField(), DMPlexNaturalToGlobalBegin(), DMPlexGlobalToNaturalBegin()
    325:  @*/
    326: PetscErrorCode DMPlexNaturalToGlobalEnd(DM dm, Vec nv, Vec gv)
    327: {
    328:   const PetscScalar *inarray;
    329:   PetscScalar       *outarray;
    330:   PetscMPIInt        size;
    331:   PetscErrorCode     ierr;

    334:   PetscLogEventBegin(DMPLEX_NaturalToGlobalEnd,dm,0,0,0);
    335:   MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);
    336:   if (dm->sfNatural) {
    337:     VecGetArrayRead(nv, &inarray);
    338:     VecGetArray(gv, &outarray);
    339:     PetscSFReduceEnd(dm->sfNatural, MPIU_SCALAR, (PetscScalar *) inarray, outarray, MPI_SUM);
    340:     VecRestoreArrayRead(nv, &inarray);
    341:     VecRestoreArray(gv, &outarray);
    342:   } else if (size == 1) {
    343:   } else if (dm->useNatural) SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_PLIB, "DM global to natural SF not present.\nIf DMPlexDistribute() was called, report to petsc-maint@mcs.anl.gov.\n");
    344:   else SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONGSTATE, "DM global to natural SF was not created.\nYou must call DMSetUseNatural() before DMPlexDistribute().\n");
    345:   PetscLogEventEnd(DMPLEX_NaturalToGlobalEnd,dm,0,0,0);
    346:   return(0);
    347: }