Actual source code: sliced.c

      1: #include <petscdmsliced.h>
      2: #include <petscmat.h>
      3: #include <petsc/private/dmimpl.h>

      5: /* CSR storage of the nonzero structure of a bs*bs matrix */
      6: typedef struct {
      7:   PetscInt bs, nz, *i, *j;
      8: } DMSlicedBlockFills;

     10: typedef struct {
     11:   PetscInt            bs, n, N, Nghosts, *ghosts;
     12:   PetscInt            d_nz, o_nz, *d_nnz, *o_nnz;
     13:   DMSlicedBlockFills *dfill, *ofill;
     14: } DM_Sliced;

     16: static PetscErrorCode DMCreateMatrix_Sliced(DM dm, Mat *J)
     17: {
     18:   PetscInt              *globals, *sd_nnz, *so_nnz, rstart, bs, i;
     19:   ISLocalToGlobalMapping lmap;
     20:   PetscBool              aij   = PETSC_FALSE;
     21:   DM_Sliced             *slice = (DM_Sliced *)dm->data;

     23:   PetscFunctionBegin;
     24:   bs = slice->bs;
     25:   PetscCall(MatCreate(PetscObjectComm((PetscObject)dm), J));
     26:   PetscCall(MatSetSizes(*J, slice->n * bs, slice->n * bs, PETSC_DETERMINE, PETSC_DETERMINE));
     27:   PetscCall(MatSetBlockSize(*J, bs));
     28:   PetscCall(MatSetType(*J, dm->mattype));
     29:   PetscCall(MatSeqBAIJSetPreallocation(*J, bs, slice->d_nz, slice->d_nnz));
     30:   PetscCall(MatMPIBAIJSetPreallocation(*J, bs, slice->d_nz, slice->d_nnz, slice->o_nz, slice->o_nnz));
     31:   /* In general, we have to do extra work to preallocate for scalar (AIJ) matrices so we check whether it will do any
     32:   * good before going on with it. */
     33:   PetscCall(PetscObjectHasFunction((PetscObject)*J, "MatMPIAIJSetPreallocation_C", &aij));
     34:   if (!aij) PetscCall(PetscObjectHasFunction((PetscObject)*J, "MatSeqAIJSetPreallocation_C", &aij));
     35:   if (aij) {
     36:     if (bs == 1) {
     37:       PetscCall(MatSeqAIJSetPreallocation(*J, slice->d_nz, slice->d_nnz));
     38:       PetscCall(MatMPIAIJSetPreallocation(*J, slice->d_nz, slice->d_nnz, slice->o_nz, slice->o_nnz));
     39:     } else if (!slice->d_nnz) {
     40:       PetscCall(MatSeqAIJSetPreallocation(*J, slice->d_nz * bs, NULL));
     41:       PetscCall(MatMPIAIJSetPreallocation(*J, slice->d_nz * bs, NULL, slice->o_nz * bs, NULL));
     42:     } else {
     43:       /* The user has provided preallocation per block-row, convert it to per scalar-row respecting DMSlicedSetBlockFills() if applicable */
     44:       PetscCall(PetscMalloc2(slice->n * bs, &sd_nnz, (!!slice->o_nnz) * slice->n * bs, &so_nnz));
     45:       for (i = 0; i < slice->n * bs; i++) {
     46:         sd_nnz[i] = (slice->d_nnz[i / bs] - 1) * (slice->ofill ? slice->ofill->i[i % bs + 1] - slice->ofill->i[i % bs] : bs) + (slice->dfill ? slice->dfill->i[i % bs + 1] - slice->dfill->i[i % bs] : bs);
     47:         if (so_nnz) so_nnz[i] = slice->o_nnz[i / bs] * (slice->ofill ? slice->ofill->i[i % bs + 1] - slice->ofill->i[i % bs] : bs);
     48:       }
     49:       PetscCall(MatSeqAIJSetPreallocation(*J, slice->d_nz * bs, sd_nnz));
     50:       PetscCall(MatMPIAIJSetPreallocation(*J, slice->d_nz * bs, sd_nnz, slice->o_nz * bs, so_nnz));
     51:       PetscCall(PetscFree2(sd_nnz, so_nnz));
     52:     }
     53:   }

     55:   /* Set up the local to global map.  For the scalar map, we have to translate to entry-wise indexing instead of block-wise. */
     56:   PetscCall(PetscMalloc1(slice->n + slice->Nghosts, &globals));
     57:   PetscCall(MatGetOwnershipRange(*J, &rstart, NULL));
     58:   for (i = 0; i < slice->n; i++) globals[i] = rstart / bs + i;

     60:   for (i = 0; i < slice->Nghosts; i++) globals[slice->n + i] = slice->ghosts[i];
     61:   PetscCall(ISLocalToGlobalMappingCreate(PETSC_COMM_SELF, bs, slice->n + slice->Nghosts, globals, PETSC_OWN_POINTER, &lmap));
     62:   PetscCall(MatSetLocalToGlobalMapping(*J, lmap, lmap));
     63:   PetscCall(ISLocalToGlobalMappingDestroy(&lmap));
     64:   PetscCall(MatSetDM(*J, dm));
     65:   PetscFunctionReturn(PETSC_SUCCESS);
     66: }

     68: /*@
     69:   DMSlicedSetGhosts - Sets the global indices of other processes elements that will
     70:   be ghosts on this process

     72:   Not Collective

     74:   Input Parameters:
     75: + dm      - the `DMSLICED` object
     76: . bs      - block size
     77: . nlocal  - number of local (owned, non-ghost) blocks
     78: . Nghosts - number of ghost blocks on this process
     79: - ghosts  - global indices of each ghost block

     81:   Level: advanced

     83: .seealso: `DM`, `DMSLICED`, `DMDestroy()`, `DMCreateGlobalVector()`
     84: @*/
     85: PetscErrorCode DMSlicedSetGhosts(DM dm, PetscInt bs, PetscInt nlocal, PetscInt Nghosts, const PetscInt ghosts[])
     86: {
     87:   DM_Sliced *slice = (DM_Sliced *)dm->data;

     89:   PetscFunctionBegin;
     91:   PetscCall(PetscFree(slice->ghosts));
     92:   PetscCall(PetscMalloc1(Nghosts, &slice->ghosts));
     93:   PetscCall(PetscArraycpy(slice->ghosts, ghosts, Nghosts));
     94:   slice->bs      = bs;
     95:   slice->n       = nlocal;
     96:   slice->Nghosts = Nghosts;
     97:   PetscFunctionReturn(PETSC_SUCCESS);
     98: }

    100: /*@
    101:   DMSlicedSetPreallocation - sets the matrix memory preallocation for matrices computed by `DMSLICED`

    103:   Not Collective

    105:   Input Parameters:
    106: + dm    - the `DM` object
    107: . d_nz  - number of block nonzeros per block row in diagonal portion of local
    108:           submatrix  (same for all local rows)
    109: . d_nnz - array containing the number of block nonzeros in the various block rows
    110:           of the in diagonal portion of the local (possibly different for each block
    111:           row) or `NULL`.
    112: . o_nz  - number of block nonzeros per block row in the off-diagonal portion of local
    113:           submatrix (same for all local rows).
    114: - o_nnz - array containing the number of nonzeros in the various block rows of the
    115:           off-diagonal portion of the local submatrix (possibly different for
    116:           each block row) or `NULL`.

    118:   Level: advanced

    120:   Note:
    121:   See `MatMPIBAIJSetPreallocation()` for more details on preallocation.  If a scalar matrix (`MATAIJ`) is
    122:   obtained with `DMSlicedGetMatrix()`, the correct preallocation will be set, respecting `DMSlicedSetBlockFills()`.

    124: .seealso: `DM`, `DMSLICED`, `DMDestroy()`, `DMCreateGlobalVector()`, `MatMPIAIJSetPreallocation()`,
    125:          `MatMPIBAIJSetPreallocation()`, `DMSlicedGetMatrix()`, `DMSlicedSetBlockFills()`
    126: @*/
    127: PetscErrorCode DMSlicedSetPreallocation(DM dm, PetscInt d_nz, const PetscInt d_nnz[], PetscInt o_nz, const PetscInt o_nnz[])
    128: {
    129:   DM_Sliced *slice = (DM_Sliced *)dm->data;

    131:   PetscFunctionBegin;
    133:   slice->d_nz  = d_nz;
    134:   slice->d_nnz = (PetscInt *)d_nnz;
    135:   slice->o_nz  = o_nz;
    136:   slice->o_nnz = (PetscInt *)o_nnz;
    137:   PetscFunctionReturn(PETSC_SUCCESS);
    138: }

    140: static PetscErrorCode DMSlicedSetBlockFills_Private(PetscInt bs, const PetscInt *fill, DMSlicedBlockFills **inf)
    141: {
    142:   PetscInt            i, j, nz, *fi, *fj;
    143:   DMSlicedBlockFills *f;

    145:   PetscFunctionBegin;
    146:   PetscAssertPointer(inf, 3);
    147:   if (*inf) PetscCall(PetscFree3(*inf, (*inf)->i, (*inf)->j));
    148:   if (!fill) PetscFunctionReturn(PETSC_SUCCESS);
    149:   for (i = 0, nz = 0; i < bs * bs; i++)
    150:     if (fill[i]) nz++;
    151:   PetscCall(PetscMalloc3(1, &f, bs + 1, &fi, nz, &fj));
    152:   f->bs = bs;
    153:   f->nz = nz;
    154:   f->i  = fi;
    155:   f->j  = fj;
    156:   for (i = 0, nz = 0; i < bs; i++) {
    157:     fi[i] = nz;
    158:     for (j = 0; j < bs; j++)
    159:       if (fill[i * bs + j]) fj[nz++] = j;
    160:   }
    161:   fi[i] = nz;
    162:   *inf  = f;
    163:   PetscFunctionReturn(PETSC_SUCCESS);
    164: }

    166: /*@
    167:   DMSlicedSetBlockFills - Sets the fill pattern in each block for a multi-component problem
    168:   of the matrix returned by `DMSlicedGetMatrix()`.

    170:   Logically Collective

    172:   Input Parameters:
    173: + dm    - the `DM` object
    174: . dfill - the fill pattern in the diagonal block (may be `NULL`, means use dense block)
    175: - ofill - the fill pattern in the off-diagonal blocks

    177:   Level: advanced

    179:   Note:
    180:   This only makes sense for multicomponent problems using scalar matrix formats (AIJ).
    181:   See `DMDASetBlockFills()` for example usage.

    183: .seealso: `DM`, `DMSLICED`, `DMSlicedGetMatrix()`, `DMDASetBlockFills()`
    184: @*/
    185: PetscErrorCode DMSlicedSetBlockFills(DM dm, const PetscInt dfill[], const PetscInt ofill[])
    186: {
    187:   DM_Sliced *slice = (DM_Sliced *)dm->data;

    189:   PetscFunctionBegin;
    191:   PetscCall(DMSlicedSetBlockFills_Private(slice->bs, dfill, &slice->dfill));
    192:   PetscCall(DMSlicedSetBlockFills_Private(slice->bs, ofill, &slice->ofill));
    193:   PetscFunctionReturn(PETSC_SUCCESS);
    194: }

    196: static PetscErrorCode DMDestroy_Sliced(DM dm)
    197: {
    198:   DM_Sliced *slice = (DM_Sliced *)dm->data;

    200:   PetscFunctionBegin;
    201:   PetscCall(PetscFree(slice->ghosts));
    202:   if (slice->dfill) PetscCall(PetscFree3(slice->dfill, slice->dfill->i, slice->dfill->j));
    203:   if (slice->ofill) PetscCall(PetscFree3(slice->ofill, slice->ofill->i, slice->ofill->j));
    204:   /* This was originally freed in DMDestroy(), but that prevents reference counting of backend objects */
    205:   PetscCall(PetscFree(slice));
    206:   PetscFunctionReturn(PETSC_SUCCESS);
    207: }

    209: static PetscErrorCode DMCreateGlobalVector_Sliced(DM dm, Vec *gvec)
    210: {
    211:   DM_Sliced *slice = (DM_Sliced *)dm->data;

    213:   PetscFunctionBegin;
    215:   PetscAssertPointer(gvec, 2);
    216:   *gvec = NULL;
    217:   PetscCall(VecCreateGhostBlock(PetscObjectComm((PetscObject)dm), slice->bs, slice->n * slice->bs, PETSC_DETERMINE, slice->Nghosts, slice->ghosts, gvec));
    218:   PetscCall(VecSetDM(*gvec, dm));
    219:   PetscFunctionReturn(PETSC_SUCCESS);
    220: }

    222: static PetscErrorCode DMGlobalToLocalBegin_Sliced(DM da, Vec g, InsertMode mode, Vec l)
    223: {
    224:   PetscBool flg;

    226:   PetscFunctionBegin;
    227:   PetscCall(VecGhostIsLocalForm(g, l, &flg));
    228:   PetscCheck(flg, PetscObjectComm((PetscObject)da), PETSC_ERR_ARG_WRONG, "Local vector is not local form of global vector");
    229:   PetscCall(VecGhostUpdateEnd(g, mode, SCATTER_FORWARD));
    230:   PetscCall(VecGhostUpdateBegin(g, mode, SCATTER_FORWARD));
    231:   PetscFunctionReturn(PETSC_SUCCESS);
    232: }

    234: static PetscErrorCode DMGlobalToLocalEnd_Sliced(DM da, Vec g, InsertMode mode, Vec l)
    235: {
    236:   PetscBool flg;

    238:   PetscFunctionBegin;
    239:   PetscCall(VecGhostIsLocalForm(g, l, &flg));
    240:   PetscCheck(flg, PetscObjectComm((PetscObject)da), PETSC_ERR_ARG_WRONG, "Local vector is not local form of global vector");
    241:   PetscCall(VecGhostUpdateEnd(g, mode, SCATTER_FORWARD));
    242:   PetscFunctionReturn(PETSC_SUCCESS);
    243: }

    245: /*MC
    246:    DMSLICED = "sliced" - A `DM` object that is used to manage data for a general graph. Uses `VecCreateGhost()` ghosted vectors for storing the fields

    248:    See `DMCreateSliced()` for details.

    250:   Level: intermediate

    252: .seealso: `DMType`, `DMCOMPOSITE`, `DMCreateSliced()`, `DMCreate()`
    253: M*/

    255: PETSC_EXTERN PetscErrorCode DMCreate_Sliced(DM p)
    256: {
    257:   DM_Sliced *slice;

    259:   PetscFunctionBegin;
    260:   PetscCall(PetscNew(&slice));
    261:   p->data = slice;

    263:   p->ops->createglobalvector = DMCreateGlobalVector_Sliced;
    264:   p->ops->creatematrix       = DMCreateMatrix_Sliced;
    265:   p->ops->globaltolocalbegin = DMGlobalToLocalBegin_Sliced;
    266:   p->ops->globaltolocalend   = DMGlobalToLocalEnd_Sliced;
    267:   p->ops->destroy            = DMDestroy_Sliced;
    268:   PetscFunctionReturn(PETSC_SUCCESS);
    269: }

    271: /*@
    272:   DMSlicedCreate - Creates a `DM` object, used to manage data for a unstructured problem

    274:   Collective

    276:   Input Parameters:
    277: + comm    - the processors that will share the global vector
    278: . bs      - the block size
    279: . nlocal  - number of vector entries on this process
    280: . Nghosts - number of ghost points needed on this process
    281: . ghosts  - global indices of all ghost points for this process
    282: . d_nnz   - matrix preallocation information representing coupling within this process
    283: - o_nnz   - matrix preallocation information representing coupling between this process and other processes

    285:   Output Parameter:
    286: . dm - the slice object

    288:   Level: advanced

    290:   Notes:
    291:   This `DM` does not support `DMCreateLocalVector()`, `DMGlobalToLocalBegin()`, and `DMGlobalToLocalEnd()` instead one directly uses
    292:   `VecGhostGetLocalForm()` and `VecGhostRestoreLocalForm()` to access the local representation and `VecGhostUpdateBegin()` and `VecGhostUpdateEnd()` to update
    293:   the ghost points.

    295:   One can use `DMGlobalToLocalBegin()`, and `DMGlobalToLocalEnd()` instead of `VecGhostUpdateBegin()` and `VecGhostUpdateEnd()`.

    297: .seealso: `DM`, `DMSLICED`, `DMDestroy()`, `DMCreateGlobalVector()`, `DMSetType()`, `DMSlicedSetGhosts()`, `DMSlicedSetPreallocation()`,
    298:           `VecGhostUpdateBegin()`, `VecGhostUpdateEnd()`,
    299:           `VecGhostGetLocalForm()`, `VecGhostRestoreLocalForm()`
    300: @*/
    301: PetscErrorCode DMSlicedCreate(MPI_Comm comm, PetscInt bs, PetscInt nlocal, PetscInt Nghosts, const PetscInt ghosts[], const PetscInt d_nnz[], const PetscInt o_nnz[], DM *dm)
    302: {
    303:   PetscFunctionBegin;
    304:   PetscAssertPointer(dm, 8);
    305:   PetscCall(DMCreate(comm, dm));
    306:   PetscCall(DMSetType(*dm, DMSLICED));
    307:   PetscCall(DMSlicedSetGhosts(*dm, bs, nlocal, Nghosts, ghosts));
    308:   if (d_nnz) PetscCall(DMSlicedSetPreallocation(*dm, 0, d_nnz, 0, o_nnz));
    309:   PetscFunctionReturn(PETSC_SUCCESS);
    310: }