Actual source code: sliced.c

petsc-3.8.2 2017-11-09
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  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:   PetscErrorCode         ierr;
 19:   PetscInt               *globals,*sd_nnz,*so_nnz,rstart,bs,i;
 20:   ISLocalToGlobalMapping lmap;
 21:   void                   (*aij)(void) = NULL;
 22:   DM_Sliced              *slice = (DM_Sliced*)dm->data;

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

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

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

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

 79:     Not Collective

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

 88:     Level: advanced

 90: .seealso DMDestroy(), DMCreateGlobalVector()

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

100:   PetscFree(slice->ghosts);
101:   PetscMalloc1(Nghosts,&slice->ghosts);
102:   PetscMemcpy(slice->ghosts,ghosts,Nghosts*sizeof(PetscInt));
103:   slice->bs      = bs;
104:   slice->n       = nlocal;
105:   slice->Nghosts = Nghosts;
106:   return(0);
107: }

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

112:     Not Collective

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

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

131:     Level: advanced

133: .seealso DMDestroy(), DMCreateGlobalVector(), MatMPIAIJSetPreallocation(),
134:          MatMPIBAIJSetPreallocation(), DMSlicedGetMatrix(), DMSlicedSetBlockFills()

136: @*/
137: PetscErrorCode  DMSlicedSetPreallocation(DM dm,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[])
138: {
139:   DM_Sliced *slice = (DM_Sliced*)dm->data;

143:   slice->d_nz  = d_nz;
144:   slice->d_nnz = (PetscInt*)d_nnz;
145:   slice->o_nz  = o_nz;
146:   slice->o_nnz = (PetscInt*)o_nnz;
147:   return(0);
148: }

150: static PetscErrorCode DMSlicedSetBlockFills_Private(PetscInt bs,const PetscInt *fill,DMSlicedBlockFills **inf)
151: {
152:   PetscErrorCode     ierr;
153:   PetscInt           i,j,nz,*fi,*fj;
154:   DMSlicedBlockFills *f;

158:   if (*inf) {PetscFree3(*inf,(*inf)->i,(*inf)->j);}
159:   if (!fill) return(0);
160:   for (i=0,nz=0; i<bs*bs; i++) if (fill[i]) nz++;
161:   PetscMalloc3(1,&f,bs+1,&fi,nz,&fj);
162:   f->bs = bs;
163:   f->nz = nz;
164:   f->i  = fi;
165:   f->j  = fj;
166:   for (i=0,nz=0; i<bs; i++) {
167:     fi[i] = nz;
168:     for (j=0; j<bs; j++) if (fill[i*bs+j]) fj[nz++] = j;
169:   }
170:   fi[i] = nz;
171:   *inf  = f;
172:   return(0);
173: }

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

179:     Logically Collective on DM

181:     Input Parameter:
182: +   sliced - the DM object
183: .   dfill - the fill pattern in the diagonal block (may be NULL, means use dense block)
184: -   ofill - the fill pattern in the off-diagonal blocks

186:     Notes:
187:     This only makes sense for multicomponent problems using scalar matrix formats (AIJ).
188:     See DMDASetBlockFills() for example usage.

190:     Level: advanced

192: .seealso DMSlicedGetMatrix(), DMDASetBlockFills()
193: @*/
194: PetscErrorCode  DMSlicedSetBlockFills(DM dm,const PetscInt *dfill,const PetscInt *ofill)
195: {
196:   DM_Sliced      *slice = (DM_Sliced*)dm->data;

201:   DMSlicedSetBlockFills_Private(slice->bs,dfill,&slice->dfill);
202:   DMSlicedSetBlockFills_Private(slice->bs,ofill,&slice->ofill);
203:   return(0);
204: }

206: static PetscErrorCode  DMDestroy_Sliced(DM dm)
207: {
209:   DM_Sliced      *slice = (DM_Sliced*)dm->data;

212:   PetscFree(slice->ghosts);
213:   if (slice->dfill) {PetscFree3(slice->dfill,slice->dfill->i,slice->dfill->j);}
214:   if (slice->ofill) {PetscFree3(slice->ofill,slice->ofill->i,slice->ofill->j);}
215:   /* This was originally freed in DMDestroy(), but that prevents reference counting of backend objects */
216:   PetscFree(slice);
217:   return(0);
218: }

220: static PetscErrorCode  DMCreateGlobalVector_Sliced(DM dm,Vec *gvec)
221: {
223:   DM_Sliced      *slice = (DM_Sliced*)dm->data;

228:   *gvec = 0;
229:   VecCreateGhostBlock(PetscObjectComm((PetscObject)dm),slice->bs,slice->n*slice->bs,PETSC_DETERMINE,slice->Nghosts,slice->ghosts,gvec);
230:   VecSetDM(*gvec,dm);
231:   return(0);
232: }

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

240:   VecGhostIsLocalForm(g,l,&flg);
241:   if (!flg) SETERRQ(PetscObjectComm((PetscObject)da),PETSC_ERR_ARG_WRONG,"Local vector is not local form of global vector");
242:   VecGhostUpdateEnd(g,mode,SCATTER_FORWARD);
243:   VecGhostUpdateBegin(g,mode,SCATTER_FORWARD);
244:   return(0);
245: }

247: static PetscErrorCode  DMGlobalToLocalEnd_Sliced(DM da,Vec g,InsertMode mode,Vec l)
248: {
250:   PetscBool      flg;

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

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

262:    See DMCreateSliced() for details.

264:   Level: intermediate

266: .seealso: DMType, DMCOMPOSITE, DMCreateSliced(), DMCreate()
267: M*/

269: PETSC_EXTERN PetscErrorCode DMCreate_Sliced(DM p)
270: {
272:   DM_Sliced      *slice;

275:   PetscNewLog(p,&slice);
276:   p->data = slice;

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

280:   p->ops->createglobalvector = DMCreateGlobalVector_Sliced;
281:   p->ops->creatematrix       = DMCreateMatrix_Sliced;
282:   p->ops->globaltolocalbegin = DMGlobalToLocalBegin_Sliced;
283:   p->ops->globaltolocalend   = DMGlobalToLocalEnd_Sliced;
284:   p->ops->destroy            = DMDestroy_Sliced;
285:   return(0);
286: }

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

291:     Collective on MPI_Comm

293:     Input Parameter:
294: +   comm - the processors that will share the global vector
295: .   bs - the block size
296: .   nlocal - number of vector entries on this process
297: .   Nghosts - number of ghost points needed on this process
298: .   ghosts - global indices of all ghost points for this process
299: .   d_nnz - matrix preallocation information representing coupling within this process
300: -   o_nnz - matrix preallocation information representing coupling between this process and other processes

302:     Output Parameters:
303: .   slice - the slice object

305:     Notes:
306:         This DM does not support DMCreateLocalVector(), DMGlobalToLocalBegin(), and DMGlobalToLocalEnd() instead one directly uses
307:         VecGhostGetLocalForm() and VecGhostRestoreLocalForm() to access the local representation and VecGhostUpdateBegin() and VecGhostUpdateEnd() to update
308:         the ghost points.

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

312:     Level: advanced

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

317: @*/
318: PetscErrorCode  DMSlicedCreate(MPI_Comm comm,PetscInt bs,PetscInt nlocal,PetscInt Nghosts,const PetscInt ghosts[], const PetscInt d_nnz[],const PetscInt o_nnz[],DM *dm)
319: {

324:   DMCreate(comm,dm);
325:   DMSetType(*dm,DMSLICED);
326:   DMSlicedSetGhosts(*dm,bs,nlocal,Nghosts,ghosts);
327:   if (d_nnz) {
328:     DMSlicedSetPreallocation(*dm,0, d_nnz,0,o_nnz);
329:   }
330:   return(0);
331: }