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

     23:   bs   = slice->bs;
     24:   MatCreate(PetscObjectComm((PetscObject)dm),J);
     25:   MatSetSizes(*J,slice->n*bs,slice->n*bs,PETSC_DETERMINE,PETSC_DETERMINE);
     26:   MatSetBlockSize(*J,bs);
     27:   MatSetType(*J,dm->mattype);
     28:   MatSeqBAIJSetPreallocation(*J,bs,slice->d_nz,slice->d_nnz);
     29:   MatMPIBAIJSetPreallocation(*J,bs,slice->d_nz,slice->d_nnz,slice->o_nz,slice->o_nnz);
     30:   /* In general, we have to do extra work to preallocate for scalar (AIJ) matrices so we check whether it will do any
     31:   * good before going on with it. */
     32:   PetscObjectQueryFunction((PetscObject)*J,"MatMPIAIJSetPreallocation_C",&aij);
     33:   if (!aij) {
     34:     PetscObjectQueryFunction((PetscObject)*J,"MatSeqAIJSetPreallocation_C",&aij);
     35:   }
     36:   if (aij) {
     37:     if (bs == 1) {
     38:       MatSeqAIJSetPreallocation(*J,slice->d_nz,slice->d_nnz);
     39:       MatMPIAIJSetPreallocation(*J,slice->d_nz,slice->d_nnz,slice->o_nz,slice->o_nnz);
     40:     } else if (!slice->d_nnz) {
     41:       MatSeqAIJSetPreallocation(*J,slice->d_nz*bs,NULL);
     42:       MatMPIAIJSetPreallocation(*J,slice->d_nz*bs,NULL,slice->o_nz*bs,NULL);
     43:     } else {
     44:       /* The user has provided preallocation per block-row, convert it to per scalar-row respecting DMSlicedSetBlockFills() if applicable */
     45:       PetscMalloc2(slice->n*bs,&sd_nnz,(!!slice->o_nnz)*slice->n*bs,&so_nnz);
     46:       for (i=0; i<slice->n*bs; i++) {
     47:         sd_nnz[i] = (slice->d_nnz[i/bs]-1) * (slice->ofill ? slice->ofill->i[i%bs+1]-slice->ofill->i[i%bs] : bs)
     48:                                            + (slice->dfill ? slice->dfill->i[i%bs+1]-slice->dfill->i[i%bs] : bs);
     49:         if (so_nnz) {
     50:           so_nnz[i] = slice->o_nnz[i/bs] * (slice->ofill ? slice->ofill->i[i%bs+1]-slice->ofill->i[i%bs] : bs);
     51:         }
     52:       }
     53:       MatSeqAIJSetPreallocation(*J,slice->d_nz*bs,sd_nnz);
     54:       MatMPIAIJSetPreallocation(*J,slice->d_nz*bs,sd_nnz,slice->o_nz*bs,so_nnz);
     55:       PetscFree2(sd_nnz,so_nnz);
     56:     }
     57:   }

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

     64:   for (i=0; i<slice->Nghosts; i++) {
     65:     globals[slice->n+i] = slice->ghosts[i];
     66:   }
     67:   ISLocalToGlobalMappingCreate(PETSC_COMM_SELF,bs,slice->n+slice->Nghosts,globals,PETSC_OWN_POINTER,&lmap);
     68:   MatSetLocalToGlobalMapping(*J,lmap,lmap);
     69:   ISLocalToGlobalMappingDestroy(&lmap);
     70:   MatSetDM(*J,dm);
     71:   return 0;
     72: }

     74: /*@C
     75:     DMSlicedSetGhosts - Sets the global indices of other processes elements that will
     76:       be ghosts on this process

     78:     Not Collective

     80:     Input Parameters:
     81: +    slice - the DM object
     82: .    bs - block size
     83: .    nlocal - number of local (owned, non-ghost) blocks
     84: .    Nghosts - number of ghost blocks on this process
     85: -    ghosts - global indices of each ghost block

     87:     Level: advanced

     89: .seealso DMDestroy(), DMCreateGlobalVector()

     91: @*/
     92: PetscErrorCode  DMSlicedSetGhosts(DM dm,PetscInt bs,PetscInt nlocal,PetscInt Nghosts,const PetscInt ghosts[])
     93: {
     94:   DM_Sliced      *slice = (DM_Sliced*)dm->data;

     97:   PetscFree(slice->ghosts);
     98:   PetscMalloc1(Nghosts,&slice->ghosts);
     99:   PetscArraycpy(slice->ghosts,ghosts,Nghosts);
    100:   slice->bs      = bs;
    101:   slice->n       = nlocal;
    102:   slice->Nghosts = Nghosts;
    103:   return 0;
    104: }

    106: /*@C
    107:     DMSlicedSetPreallocation - sets the matrix memory preallocation for matrices computed by DMSliced

    109:     Not Collective

    111:     Input Parameters:
    112: +    slice - the DM object
    113: .    d_nz  - number of block nonzeros per block row in diagonal portion of local
    114:            submatrix  (same for all local rows)
    115: .    d_nnz - array containing the number of block nonzeros in the various block rows
    116:            of the in diagonal portion of the local (possibly different for each block
    117:            row) or NULL.
    118: .    o_nz  - number of block nonzeros per block row in the off-diagonal portion of local
    119:            submatrix (same for all local rows).
    120: -    o_nnz - array containing the number of nonzeros in the various block rows of the
    121:            off-diagonal portion of the local submatrix (possibly different for
    122:            each block row) or NULL.

    124:     Notes:
    125:     See MatMPIBAIJSetPreallocation() for more details on preallocation.  If a scalar matrix (AIJ) is
    126:     obtained with DMSlicedGetMatrix(), the correct preallocation will be set, respecting DMSlicedSetBlockFills().

    128:     Level: advanced

    130: .seealso DMDestroy(), DMCreateGlobalVector(), MatMPIAIJSetPreallocation(),
    131:          MatMPIBAIJSetPreallocation(), DMSlicedGetMatrix(), DMSlicedSetBlockFills()

    133: @*/
    134: PetscErrorCode  DMSlicedSetPreallocation(DM dm,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[])
    135: {
    136:   DM_Sliced *slice = (DM_Sliced*)dm->data;

    139:   slice->d_nz  = d_nz;
    140:   slice->d_nnz = (PetscInt*)d_nnz;
    141:   slice->o_nz  = o_nz;
    142:   slice->o_nnz = (PetscInt*)o_nnz;
    143:   return 0;
    144: }

    146: static PetscErrorCode DMSlicedSetBlockFills_Private(PetscInt bs,const PetscInt *fill,DMSlicedBlockFills **inf)
    147: {
    148:   PetscInt           i,j,nz,*fi,*fj;
    149:   DMSlicedBlockFills *f;

    152:   if (*inf) PetscFree3(*inf,(*inf)->i,(*inf)->j);
    153:   if (!fill) return 0;
    154:   for (i=0,nz=0; i<bs*bs; i++) if (fill[i]) nz++;
    155:   PetscMalloc3(1,&f,bs+1,&fi,nz,&fj);
    156:   f->bs = bs;
    157:   f->nz = nz;
    158:   f->i  = fi;
    159:   f->j  = fj;
    160:   for (i=0,nz=0; i<bs; i++) {
    161:     fi[i] = nz;
    162:     for (j=0; j<bs; j++) if (fill[i*bs+j]) fj[nz++] = j;
    163:   }
    164:   fi[i] = nz;
    165:   *inf  = f;
    166:   return 0;
    167: }

    169: /*@C
    170:     DMSlicedSetBlockFills - Sets the fill pattern in each block for a multi-component problem
    171:     of the matrix returned by DMSlicedGetMatrix().

    173:     Logically Collective on dm

    175:     Input Parameters:
    176: +   sliced - the DM object
    177: .   dfill - the fill pattern in the diagonal block (may be NULL, means use dense block)
    178: -   ofill - the fill pattern in the off-diagonal blocks

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

    184:     Level: advanced

    186: .seealso DMSlicedGetMatrix(), DMDASetBlockFills()
    187: @*/
    188: PetscErrorCode  DMSlicedSetBlockFills(DM dm,const PetscInt *dfill,const PetscInt *ofill)
    189: {
    190:   DM_Sliced      *slice = (DM_Sliced*)dm->data;

    193:   DMSlicedSetBlockFills_Private(slice->bs,dfill,&slice->dfill);
    194:   DMSlicedSetBlockFills_Private(slice->bs,ofill,&slice->ofill);
    195:   return 0;
    196: }

    198: static PetscErrorCode  DMDestroy_Sliced(DM dm)
    199: {
    200:   DM_Sliced      *slice = (DM_Sliced*)dm->data;

    202:   PetscFree(slice->ghosts);
    203:   if (slice->dfill) PetscFree3(slice->dfill,slice->dfill->i,slice->dfill->j);
    204:   if (slice->ofill) PetscFree3(slice->ofill,slice->ofill->i,slice->ofill->j);
    205:   /* This was originally freed in DMDestroy(), but that prevents reference counting of backend objects */
    206:   PetscFree(slice);
    207:   return 0;
    208: }

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

    216:   *gvec = NULL;
    217:   VecCreateGhostBlock(PetscObjectComm((PetscObject)dm),slice->bs,slice->n*slice->bs,PETSC_DETERMINE,slice->Nghosts,slice->ghosts,gvec);
    218:   VecSetDM(*gvec,dm);
    219:   return 0;
    220: }

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

    226:   VecGhostIsLocalForm(g,l,&flg);
    228:   VecGhostUpdateEnd(g,mode,SCATTER_FORWARD);
    229:   VecGhostUpdateBegin(g,mode,SCATTER_FORWARD);
    230:   return 0;
    231: }

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

    237:   VecGhostIsLocalForm(g,l,&flg);
    239:   VecGhostUpdateEnd(g,mode,SCATTER_FORWARD);
    240:   return 0;
    241: }

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

    246:    See DMCreateSliced() for details.

    248:   Level: intermediate

    250: .seealso: DMType, DMCOMPOSITE, DMCreateSliced(), DMCreate()
    251: M*/

    253: PETSC_EXTERN PetscErrorCode DMCreate_Sliced(DM p)
    254: {
    255:   DM_Sliced      *slice;

    257:   PetscNewLog(p,&slice);
    258:   p->data = slice;

    260:   p->ops->createglobalvector = DMCreateGlobalVector_Sliced;
    261:   p->ops->creatematrix       = DMCreateMatrix_Sliced;
    262:   p->ops->globaltolocalbegin = DMGlobalToLocalBegin_Sliced;
    263:   p->ops->globaltolocalend   = DMGlobalToLocalEnd_Sliced;
    264:   p->ops->destroy            = DMDestroy_Sliced;
    265:   return 0;
    266: }

    268: /*@C
    269:     DMSlicedCreate - Creates a DM object, used to manage data for a unstructured problem

    271:     Collective

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

    282:     Output Parameters:
    283: .   slice - the slice object

    285:     Notes:
    286:         This DM does not support DMCreateLocalVector(), DMGlobalToLocalBegin(), and DMGlobalToLocalEnd() instead one directly uses
    287:         VecGhostGetLocalForm() and VecGhostRestoreLocalForm() to access the local representation and VecGhostUpdateBegin() and VecGhostUpdateEnd() to update
    288:         the ghost points.

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

    292:     Level: advanced

    294: .seealso DMDestroy(), DMCreateGlobalVector(), DMSetType(), DMSLICED, DMSlicedSetGhosts(), DMSlicedSetPreallocation(), VecGhostUpdateBegin(), VecGhostUpdateEnd(),
    295:          VecGhostGetLocalForm(), VecGhostRestoreLocalForm()

    297: @*/
    298: PetscErrorCode  DMSlicedCreate(MPI_Comm comm,PetscInt bs,PetscInt nlocal,PetscInt Nghosts,const PetscInt ghosts[], const PetscInt d_nnz[],const PetscInt o_nnz[],DM *dm)
    299: {
    301:   DMCreate(comm,dm);
    302:   DMSetType(*dm,DMSLICED);
    303:   DMSlicedSetGhosts(*dm,bs,nlocal,Nghosts,ghosts);
    304:   if (d_nnz) {
    305:     DMSlicedSetPreallocation(*dm,0, d_nnz,0,o_nnz);
    306:   }
    307:   return 0;
    308: }