Date: 2015-10-02T22:13:59+00:00

Actual source code: sliced.c
petsc-3.6.2 2015-10-02
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      1: #include <petscdmsliced.h>      /*I      "petscdmsliced.h" I*/
      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;

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

     27:   bs   = slice->bs;
     28:   MatCreate(PetscObjectComm((PetscObject)dm),J);
     29:   MatSetSizes(*J,slice->n*bs,slice->n*bs,PETSC_DETERMINE,PETSC_DETERMINE);
     30:   MatSetBlockSize(*J,bs);
     31:   MatSetType(*J,dm->mattype);
     32:   MatSeqBAIJSetPreallocation(*J,bs,slice->d_nz,slice->d_nnz);
     33:   MatMPIBAIJSetPreallocation(*J,bs,slice->d_nz,slice->d_nnz,slice->o_nz,slice->o_nnz);
     34:   /* In general, we have to do extra work to preallocate for scalar (AIJ) matrices so we check whether it will do any
     35:   * good before going on with it. */
     36:   PetscObjectQueryFunction((PetscObject)*J,"MatMPIAIJSetPreallocation_C",&aij);
     37:   if (!aij) {
     38:     PetscObjectQueryFunction((PetscObject)*J,"MatSeqAIJSetPreallocation_C",&aij);
     39:   }
     40:   if (aij) {
     41:     if (bs == 1) {
     42:       MatSeqAIJSetPreallocation(*J,slice->d_nz,slice->d_nnz);
     43:       MatMPIAIJSetPreallocation(*J,slice->d_nz,slice->d_nnz,slice->o_nz,slice->o_nnz);
     44:     } else if (!slice->d_nnz) {
     45:       MatSeqAIJSetPreallocation(*J,slice->d_nz*bs,NULL);
     46:       MatMPIAIJSetPreallocation(*J,slice->d_nz*bs,NULL,slice->o_nz*bs,NULL);
     47:     } else {
     48:       /* The user has provided preallocation per block-row, convert it to per scalar-row respecting DMSlicedSetBlockFills() if applicable */
     49:       PetscMalloc2(slice->n*bs,&sd_nnz,(!!slice->o_nnz)*slice->n*bs,&so_nnz);
     50:       for (i=0; i<slice->n*bs; i++) {
     51:         sd_nnz[i] = (slice->d_nnz[i/bs]-1) * (slice->ofill ? slice->ofill->i[i%bs+1]-slice->ofill->i[i%bs] : bs)
     52:                                            + (slice->dfill ? slice->dfill->i[i%bs+1]-slice->dfill->i[i%bs] : bs);
     53:         if (so_nnz) {
     54:           so_nnz[i] = slice->o_nnz[i/bs] * (slice->ofill ? slice->ofill->i[i%bs+1]-slice->ofill->i[i%bs] : bs);
     55:         }
     56:       }
     57:       MatSeqAIJSetPreallocation(*J,slice->d_nz*bs,sd_nnz);
     58:       MatMPIAIJSetPreallocation(*J,slice->d_nz*bs,sd_nnz,slice->o_nz*bs,so_nnz);
     59:       PetscFree2(sd_nnz,so_nnz);
     60:     }
     61:   }

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

     68:   for (i=0; i<slice->Nghosts; i++) {
     69:     globals[slice->n+i] = slice->ghosts[i];
     70:   }
     71:   ISLocalToGlobalMappingCreate(PETSC_COMM_SELF,bs,slice->n+slice->Nghosts,globals,PETSC_OWN_POINTER,&lmap);
     72:   MatSetLocalToGlobalMapping(*J,lmap,lmap);
     73:   ISLocalToGlobalMappingDestroy(&lmap);
     74:   return(0);
     75: }

     79: /*@C
     80:     DMSlicedSetGhosts - Sets the global indices of other processes elements that will
     81:       be ghosts on this process

     83:     Not Collective

     85:     Input Parameters:
     86: +    slice - the DM object
     87: .    bs - block size
     88: .    nlocal - number of local (owned, non-ghost) blocks
     89: .    Nghosts - number of ghost blocks on this process
     90: -    ghosts - global indices of each ghost block

     92:     Level: advanced

     94: .seealso DMDestroy(), DMCreateGlobalVector()

     96: @*/
     97: PetscErrorCode  DMSlicedSetGhosts(DM dm,PetscInt bs,PetscInt nlocal,PetscInt Nghosts,const PetscInt ghosts[])
     98: {
    100:   DM_Sliced      *slice = (DM_Sliced*)dm->data;

    104:   PetscFree(slice->ghosts);
    105:   PetscMalloc1(Nghosts,&slice->ghosts);
    106:   PetscMemcpy(slice->ghosts,ghosts,Nghosts*sizeof(PetscInt));
    107:   slice->bs      = bs;
    108:   slice->n       = nlocal;
    109:   slice->Nghosts = Nghosts;
    110:   return(0);
    111: }

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

    118:     Not Collective

    120:     Input Parameters:
    121: +    slice - the DM object
    122: .    d_nz  - number of block nonzeros per block row in diagonal portion of local
    123:            submatrix  (same for all local rows)
    124: .    d_nnz - array containing the number of block nonzeros in the various block rows
    125:            of the in diagonal portion of the local (possibly different for each block
    126:            row) or NULL.
    127: .    o_nz  - number of block nonzeros per block row in the off-diagonal portion of local
    128:            submatrix (same for all local rows).
    129: -    o_nnz - array containing the number of nonzeros in the various block rows of the
    130:            off-diagonal portion of the local submatrix (possibly different for
    131:            each block row) or NULL.

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

    137:     Level: advanced

    139: .seealso DMDestroy(), DMCreateGlobalVector(), MatMPIAIJSetPreallocation(),
    140:          MatMPIBAIJSetPreallocation(), DMSlicedGetMatrix(), DMSlicedSetBlockFills()

    142: @*/
    143: PetscErrorCode  DMSlicedSetPreallocation(DM dm,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[])
    144: {
    145:   DM_Sliced *slice = (DM_Sliced*)dm->data;

    149:   slice->d_nz  = d_nz;
    150:   slice->d_nnz = (PetscInt*)d_nnz;
    151:   slice->o_nz  = o_nz;
    152:   slice->o_nnz = (PetscInt*)o_nnz;
    153:   return(0);
    154: }

    158: static PetscErrorCode DMSlicedSetBlockFills_Private(PetscInt bs,const PetscInt *fill,DMSlicedBlockFills **inf)
    159: {
    160:   PetscErrorCode     ierr;
    161:   PetscInt           i,j,nz,*fi,*fj;
    162:   DMSlicedBlockFills *f;

    166:   if (*inf) {PetscFree3((*inf)->i,(*inf)->j,*inf);}
    167:   if (!fill) return(0);
    168:   for (i=0,nz=0; i<bs*bs; i++) if (fill[i]) nz++;
    169:   PetscMalloc3(1,&f,bs+1,&fi,nz,&fj);
    170:   f->bs = bs;
    171:   f->nz = nz;
    172:   f->i  = fi;
    173:   f->j  = fj;
    174:   for (i=0,nz=0; i<bs; i++) {
    175:     fi[i] = nz;
    176:     for (j=0; j<bs; j++) if (fill[i*bs+j]) fj[nz++] = j;
    177:   }
    178:   fi[i] = nz;
    179:   *inf  = f;
    180:   return(0);
    181: }

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

    189:     Logically Collective on DM

    191:     Input Parameter:
    192: +   sliced - the DM object
    193: .   dfill - the fill pattern in the diagonal block (may be NULL, means use dense block)
    194: -   ofill - the fill pattern in the off-diagonal blocks

    196:     Notes:
    197:     This only makes sense for multicomponent problems using scalar matrix formats (AIJ).
    198:     See DMDASetBlockFills() for example usage.

    200:     Level: advanced

    202: .seealso DMSlicedGetMatrix(), DMDASetBlockFills()
    203: @*/
    204: PetscErrorCode  DMSlicedSetBlockFills(DM dm,const PetscInt *dfill,const PetscInt *ofill)
    205: {
    206:   DM_Sliced      *slice = (DM_Sliced*)dm->data;

    211:   DMSlicedSetBlockFills_Private(slice->bs,dfill,&slice->dfill);
    212:   DMSlicedSetBlockFills_Private(slice->bs,ofill,&slice->ofill);
    213:   return(0);
    214: }

    218: static PetscErrorCode  DMDestroy_Sliced(DM dm)
    219: {
    221:   DM_Sliced      *slice = (DM_Sliced*)dm->data;

    224:   PetscFree(slice->ghosts);
    225:   if (slice->dfill) {PetscFree3(slice->dfill,slice->dfill->i,slice->dfill->j);}
    226:   if (slice->ofill) {PetscFree3(slice->ofill,slice->ofill->i,slice->ofill->j);}
    227:   /* This was originally freed in DMDestroy(), but that prevents reference counting of backend objects */
    228:   PetscFree(slice);
    229:   return(0);
    230: }

    234: static PetscErrorCode  DMCreateGlobalVector_Sliced(DM dm,Vec *gvec)
    235: {
    237:   DM_Sliced      *slice = (DM_Sliced*)dm->data;

    242:   *gvec = 0;
    243:   VecCreateGhostBlock(PetscObjectComm((PetscObject)dm),slice->bs,slice->n*slice->bs,PETSC_DETERMINE,slice->Nghosts,slice->ghosts,gvec);
    244:   VecSetDM(*gvec,dm);
    245:   return(0);
    246: }

    250: static PetscErrorCode  DMGlobalToLocalBegin_Sliced(DM da,Vec g,InsertMode mode,Vec l)
    251: {
    253:   PetscBool      flg;

    256:   VecGhostIsLocalForm(g,l,&flg);
    257:   if (!flg) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_ARG_WRONG,"Local vector is not local form of global vector");
    258:   VecGhostUpdateEnd(g,mode,SCATTER_FORWARD);
    259:   VecGhostUpdateBegin(g,mode,SCATTER_FORWARD);
    260:   return(0);
    261: }

    265: static PetscErrorCode  DMGlobalToLocalEnd_Sliced(DM da,Vec g,InsertMode mode,Vec l)
    266: {
    268:   PetscBool      flg;

    271:   VecGhostIsLocalForm(g,l,&flg);
    272:   if (!flg) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_ARG_WRONG,"Local vector is not local form of global vector");
    273:   VecGhostUpdateEnd(g,mode,SCATTER_FORWARD);
    274:   return(0);
    275: }

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

    280:    See DMCreateSliced() for details.

    282:   Level: intermediate

    284: .seealso: DMType, DMCOMPOSITE, DMCreateSliced(), DMCreate()
    285: M*/

    289: PETSC_EXTERN PetscErrorCode DMCreate_Sliced(DM p)
    290: {
    292:   DM_Sliced      *slice;

    295:   PetscNewLog(p,&slice);
    296:   p->data = slice;

    298:   PetscObjectChangeTypeName((PetscObject)p,DMSLICED);

    300:   p->ops->createglobalvector = DMCreateGlobalVector_Sliced;
    301:   p->ops->creatematrix       = DMCreateMatrix_Sliced;
    302:   p->ops->globaltolocalbegin = DMGlobalToLocalBegin_Sliced;
    303:   p->ops->globaltolocalend   = DMGlobalToLocalEnd_Sliced;
    304:   p->ops->destroy            = DMDestroy_Sliced;
    305:   return(0);
    306: }

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

    313:     Collective on MPI_Comm

    315:     Input Parameter:
    316: +   comm - the processors that will share the global vector
    317: .   bs - the block size
    318: .   nlocal - number of vector entries on this process
    319: .   Nghosts - number of ghost points needed on this process
    320: .   ghosts - global indices of all ghost points for this process
    321: .   d_nnz - matrix preallocation information representing coupling within this process
    322: -   o_nnz - matrix preallocation information representing coupling between this process and other processes

    324:     Output Parameters:
    325: .   slice - the slice object

    327:     Notes:
    328:         This DM does not support DMCreateLocalVector(), DMGlobalToLocalBegin(), and DMGlobalToLocalEnd() instead one directly uses
    329:         VecGhostGetLocalForm() and VecGhostRestoreLocalForm() to access the local representation and VecGhostUpdateBegin() and VecGhostUpdateEnd() to update
    330:         the ghost points.

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

    334:     Level: advanced

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

    339: @*/
    340: PetscErrorCode  DMSlicedCreate(MPI_Comm comm,PetscInt bs,PetscInt nlocal,PetscInt Nghosts,const PetscInt ghosts[], const PetscInt d_nnz[],const PetscInt o_nnz[],DM *dm)
    341: {

    346:   DMCreate(comm,dm);
    347:   DMSetType(*dm,DMSLICED);
    348:   DMSlicedSetGhosts(*dm,bs,nlocal,Nghosts,ghosts);
    349:   if (d_nnz) {
    350:     DMSlicedSetPreallocation(*dm,0, d_nnz,0,o_nnz);
    351:   }
    352:   return(0);
    353: }