Actual source code: pbvec.c
petsc-3.7.1 2016-05-15
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      2: /*
      3:    This file contains routines for Parallel vector operations.
      4:  */
      5: #include <petscoptions.h>
      6: #include <../src/vec/vec/impls/mpi/pvecimpl.h>   /*I  "petscvec.h"   I*/

     10: static PetscErrorCode VecDot_MPI(Vec xin,Vec yin,PetscScalar *z)
     11: {
     12:   PetscScalar    sum,work;

     16:   VecDot_Seq(xin,yin,&work);
     17:   MPIU_Allreduce(&work,&sum,1,MPIU_SCALAR,MPIU_SUM,PetscObjectComm((PetscObject)xin));
     18:   *z   = sum;
     19:   return(0);
     20: }

     24: static PetscErrorCode VecTDot_MPI(Vec xin,Vec yin,PetscScalar *z)
     25: {
     26:   PetscScalar    sum,work;

     30:   VecTDot_Seq(xin,yin,&work);
     31:   MPIU_Allreduce(&work,&sum,1,MPIU_SCALAR,MPIU_SUM,PetscObjectComm((PetscObject)xin));
     32:   *z   = sum;
     33:   return(0);
     34: }

     36: extern PetscErrorCode VecView_MPI_Draw(Vec,PetscViewer);

     40: static PetscErrorCode VecPlaceArray_MPI(Vec vin,const PetscScalar *a)
     41: {
     43:   Vec_MPI        *v = (Vec_MPI*)vin->data;

     46:   if (v->unplacedarray) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"VecPlaceArray() was already called on this vector, without a call to VecResetArray()");
     47:   v->unplacedarray = v->array;  /* save previous array so reset can bring it back */
     48:   v->array         = (PetscScalar*)a;
     49:   if (v->localrep) {
     50:     VecPlaceArray(v->localrep,a);
     51:   }
     52:   return(0);
     53: }

     55: extern PetscErrorCode VecGetValues_MPI(Vec,PetscInt,const PetscInt[],PetscScalar[]);

     59: static PetscErrorCode VecDuplicate_MPI(Vec win,Vec *v)
     60: {
     62:   Vec_MPI        *vw,*w = (Vec_MPI*)win->data;
     63:   PetscScalar    *array;

     66:   VecCreate(PetscObjectComm((PetscObject)win),v);
     67:   PetscLayoutReference(win->map,&(*v)->map);

     69:   VecCreate_MPI_Private(*v,PETSC_TRUE,w->nghost,0);
     70:   vw   = (Vec_MPI*)(*v)->data;
     71:   PetscMemcpy((*v)->ops,win->ops,sizeof(struct _VecOps));

     73:   /* save local representation of the parallel vector (and scatter) if it exists */
     74:   if (w->localrep) {
     75:     VecGetArray(*v,&array);
     76:     VecCreateSeqWithArray(PETSC_COMM_SELF,PetscAbs(win->map->bs),win->map->n+w->nghost,array,&vw->localrep);
     77:     PetscMemcpy(vw->localrep->ops,w->localrep->ops,sizeof(struct _VecOps));
     78:     VecRestoreArray(*v,&array);
     79:     PetscLogObjectParent((PetscObject)*v,(PetscObject)vw->localrep);

     81:     vw->localupdate = w->localupdate;
     82:     if (vw->localupdate) {
     83:       PetscObjectReference((PetscObject)vw->localupdate);
     84:     }
     85:   }

     87:   /* New vector should inherit stashing property of parent */
     88:   (*v)->stash.donotstash   = win->stash.donotstash;
     89:   (*v)->stash.ignorenegidx = win->stash.ignorenegidx;

     91:   PetscObjectListDuplicate(((PetscObject)win)->olist,&((PetscObject)(*v))->olist);
     92:   PetscFunctionListDuplicate(((PetscObject)win)->qlist,&((PetscObject)(*v))->qlist);

     94:   (*v)->map->bs   = PetscAbs(win->map->bs);
     95:   (*v)->bstash.bs = win->bstash.bs;
     96:   return(0);
     97: }

    102: static PetscErrorCode VecSetOption_MPI(Vec V,VecOption op,PetscBool flag)
    103: {
    104:   Vec_MPI        *v = (Vec_MPI*)V->data;
    106:   switch (op) {
    107:   case VEC_IGNORE_OFF_PROC_ENTRIES: V->stash.donotstash = flag;
    108:     break;
    109:   case VEC_IGNORE_NEGATIVE_INDICES: V->stash.ignorenegidx = flag;
    110:     break;
    111:   case VEC_SUBSET_OFF_PROC_ENTRIES: v->assembly_subset = flag;
    112:     break;
    113:   }
    114:   return(0);
    115: }

    120: static PetscErrorCode VecResetArray_MPI(Vec vin)
    121: {
    122:   Vec_MPI        *v = (Vec_MPI*)vin->data;

    126:   v->array         = v->unplacedarray;
    127:   v->unplacedarray = 0;
    128:   if (v->localrep) {
    129:     VecResetArray(v->localrep);
    130:   }
    131:   return(0);
    132: }

    136: static PetscErrorCode VecAssemblySend_MPI_Private(MPI_Comm comm,const PetscMPIInt tag[],PetscMPIInt rankid,PetscMPIInt rank,void *sdata,MPI_Request req[],void *ctx)
    137: {
    138:   Vec X = (Vec)ctx;
    139:   Vec_MPI *x = (Vec_MPI*)X->data;
    140:   VecAssemblyHeader *hdr = (VecAssemblyHeader*)sdata;
    141:   PetscInt bs = X->map->bs;

    145:   /* x->recvhdr only exists when we are reusing a communication network.  In that case, some messages can be empty, but
    146:    * we have to send them this time if we sent them before because the receiver is expecting them. */
    147:   if (hdr->count || (x->recvhdr && x->sendptrs[rankid].ints)) {
    148:     MPI_Isend(x->sendptrs[rankid].ints,hdr->count,MPIU_INT,rank,tag[0],comm,&req[0]);
    149:     MPI_Isend(x->sendptrs[rankid].scalars,hdr->count,MPIU_SCALAR,rank,tag[1],comm,&req[1]);
    150:   }
    151:   if (hdr->bcount || (x->recvhdr && x->sendptrs[rankid].intb)) {
    152:     MPI_Isend(x->sendptrs[rankid].intb,hdr->bcount,MPIU_INT,rank,tag[2],comm,&req[2]);
    153:     MPI_Isend(x->sendptrs[rankid].scalarb,hdr->bcount*bs,MPIU_SCALAR,rank,tag[3],comm,&req[3]);
    154:   }
    155:   return(0);
    156: }

    160: static PetscErrorCode VecAssemblyRecv_MPI_Private(MPI_Comm comm,const PetscMPIInt tag[],PetscMPIInt rank,void *rdata,MPI_Request req[],void *ctx)
    161: {
    162:   Vec X = (Vec)ctx;
    163:   Vec_MPI *x = (Vec_MPI*)X->data;
    164:   VecAssemblyHeader *hdr = (VecAssemblyHeader*)rdata;
    166:   PetscInt bs = X->map->bs;
    167:   VecAssemblyFrame *frame;

    170:   PetscSegBufferGet(x->segrecvframe,1,&frame);

    172:   if (hdr->count) {
    173:     PetscSegBufferGet(x->segrecvint,hdr->count,&frame->ints);
    174:     MPI_Irecv(frame->ints,hdr->count,MPIU_INT,rank,tag[0],comm,&req[0]);
    175:     PetscSegBufferGet(x->segrecvscalar,hdr->count,&frame->scalars);
    176:     MPI_Irecv(frame->scalars,hdr->count,MPIU_SCALAR,rank,tag[1],comm,&req[1]);
    177:     frame->pendings = 2;
    178:   } else {
    179:     frame->ints = NULL;
    180:     frame->scalars = NULL;
    181:     frame->pendings = 0;
    182:   }

    184:   if (hdr->bcount) {
    185:     PetscSegBufferGet(x->segrecvint,hdr->bcount,&frame->intb);
    186:     MPI_Irecv(frame->intb,hdr->bcount,MPIU_INT,rank,tag[2],comm,&req[2]);
    187:     PetscSegBufferGet(x->segrecvscalar,hdr->bcount*bs,&frame->scalarb);
    188:     MPI_Irecv(frame->scalarb,hdr->bcount*bs,MPIU_SCALAR,rank,tag[3],comm,&req[3]);
    189:     frame->pendingb = 2;
    190:   } else {
    191:     frame->intb = NULL;
    192:     frame->scalarb = NULL;
    193:     frame->pendingb = 0;
    194:   }
    195:   return(0);
    196: }

    200: static PetscErrorCode VecAssemblyBegin_MPI_BTS(Vec X)
    201: {
    202:   Vec_MPI        *x = (Vec_MPI*)X->data;
    204:   MPI_Comm       comm;
    205:   PetscInt       i,j,jb,bs;

    208:   if (X->stash.donotstash) return(0);

    210:   PetscObjectGetComm((PetscObject)X,&comm);
    211:   VecGetBlockSize(X,&bs);
    212: #if defined(PETSC_USE_DEBUG)
    213:   {
    214:     InsertMode addv;
    215:     MPIU_Allreduce((PetscEnum*)&X->stash.insertmode,(PetscEnum*)&addv,1,MPIU_ENUM,MPI_BOR,comm);
    216:     if (addv == (ADD_VALUES|INSERT_VALUES)) SETERRQ(comm,PETSC_ERR_ARG_NOTSAMETYPE,"Some processors inserted values while others added");
    217:   }
    218: #endif
    219:   X->bstash.insertmode = X->stash.insertmode; /* Block stash implicitly tracks InsertMode of scalar stash */

    221:   VecStashSortCompress_Private(&X->stash);
    222:   VecStashSortCompress_Private(&X->bstash);

    224:   if (!x->sendranks) {
    225:     PetscMPIInt nowners,bnowners,*owners,*bowners;
    226:     PetscInt ntmp;
    227:     VecStashGetOwnerList_Private(&X->stash,X->map,&nowners,&owners);
    228:     VecStashGetOwnerList_Private(&X->bstash,X->map,&bnowners,&bowners);
    229:     PetscMergeMPIIntArray(nowners,owners,bnowners,bowners,&ntmp,&x->sendranks);
    230:     x->nsendranks = ntmp;
    231:     PetscFree(owners);
    232:     PetscFree(bowners);
    233:     PetscMalloc1(x->nsendranks,&x->sendhdr);
    234:     PetscCalloc1(x->nsendranks,&x->sendptrs);
    235:   }
    236:   for (i=0,j=0,jb=0; i<x->nsendranks; i++) {
    237:     PetscMPIInt rank = x->sendranks[i];
    238:     x->sendhdr[i].insertmode = X->stash.insertmode;
    239:     /* Initialize pointers for non-empty stashes the first time around.  Subsequent assemblies with
    240:      * VEC_SUBSET_OFF_PROC_ENTRIES will leave the old pointers (dangling because the stash has been collected) when
    241:      * there is nothing new to send, so that size-zero messages get sent instead. */
    242:     x->sendhdr[i].count = 0;
    243:     if (X->stash.n) {
    244:       x->sendptrs[i].ints    = &X->stash.idx[j];
    245:       x->sendptrs[i].scalars = &X->stash.array[j];
    246:       for ( ; j<X->stash.n && X->stash.idx[j] < X->map->range[rank+1]; j++) x->sendhdr[i].count++;
    247:     }
    248:     x->sendhdr[i].bcount = 0;
    249:     if (X->bstash.n) {
    250:       x->sendptrs[i].intb    = &X->bstash.idx[jb];
    251:       x->sendptrs[i].scalarb = &X->bstash.array[jb*bs];
    252:       for ( ; jb<X->bstash.n && X->bstash.idx[jb]*bs < X->map->range[rank+1]; jb++) x->sendhdr[i].bcount++;
    253:     }
    254:   }

    256:   if (!x->segrecvint) {PetscSegBufferCreate(sizeof(PetscInt),1000,&x->segrecvint);}
    257:   if (!x->segrecvscalar) {PetscSegBufferCreate(sizeof(PetscScalar),1000,&x->segrecvscalar);}
    258:   if (!x->segrecvframe) {PetscSegBufferCreate(sizeof(VecAssemblyFrame),50,&x->segrecvframe);}
    259:   if (x->recvhdr) {             /* VEC_SUBSET_OFF_PROC_ENTRIES and this is not the first assembly */
    260:     PetscMPIInt tag[4];
    261:     if (!x->assembly_subset) SETERRQ(comm,PETSC_ERR_PLIB,"Attempt to reuse rendezvous when not VEC_SUBSET_OFF_PROC_ENTRIES");
    262:     for (i=0; i<4; i++) {PetscCommGetNewTag(comm,&tag[i]);}
    263:     for (i=0; i<x->nsendranks; i++) {
    264:       VecAssemblySend_MPI_Private(comm,tag,i,x->sendranks[i],x->sendhdr+i,x->sendreqs+4*i,X);
    265:     }
    266:     for (i=0; i<x->nrecvranks; i++) {
    267:       VecAssemblyRecv_MPI_Private(comm,tag,x->recvranks[i],x->recvhdr+i,x->recvreqs+4*i,X);
    268:     }
    269:     x->use_status = PETSC_TRUE;
    270:   } else {                      /* First time */
    271:     PetscCommBuildTwoSidedFReq(comm,3,MPIU_INT,x->nsendranks,x->sendranks,(PetscInt*)x->sendhdr,&x->nrecvranks,&x->recvranks,&x->recvhdr,4,&x->sendreqs,&x->recvreqs,VecAssemblySend_MPI_Private,VecAssemblyRecv_MPI_Private,X);
    272:     x->use_status = PETSC_FALSE;
    273:   }

    275:   {
    276:     PetscInt nstash,reallocs;
    277:     VecStashGetInfo_Private(&X->stash,&nstash,&reallocs);
    278:     PetscInfo2(X,"Stash has %D entries, uses %D mallocs.\n",nstash,reallocs);
    279:     VecStashGetInfo_Private(&X->bstash,&nstash,&reallocs);
    280:     PetscInfo2(X,"Block-Stash has %D entries, uses %D mallocs.\n",nstash,reallocs);
    281:   }
    282:   return(0);
    283: }

    287: static PetscErrorCode VecAssemblyEnd_MPI_BTS(Vec X)
    288: {
    289:   Vec_MPI *x = (Vec_MPI*)X->data;
    290:   PetscInt bs = X->map->bs;
    291:   PetscMPIInt npending,*some_indices,r;
    292:   MPI_Status  *some_statuses;
    293:   PetscScalar *xarray;
    295:   VecAssemblyFrame *frame;

    298:   if (X->stash.donotstash) {
    299:     X->stash.insertmode = NOT_SET_VALUES;
    300:     X->bstash.insertmode = NOT_SET_VALUES;
    301:     return(0);
    302:   }

    304:   VecGetArray(X,&xarray);
    305:   PetscSegBufferExtractInPlace(x->segrecvframe,&frame);
    306:   PetscMalloc2(4*x->nrecvranks,&some_indices,x->use_status?4*x->nrecvranks:0,&some_statuses);
    307:   for (r=0,npending=0; r<x->nrecvranks; r++) npending += frame[r].pendings + frame[r].pendingb;
    308:   while (npending>0) {
    309:     PetscMPIInt ndone,ii;
    310:     /* Filling MPI_Status fields requires some resources from the MPI library.  We skip it on the first assembly, or
    311:      * when VEC_SUBSET_OFF_PROC_ENTRIES has not been set, because we could exchange exact sizes in the initial
    312:      * rendezvous.  When the rendezvous is elided, however, we use MPI_Status to get actual message lengths, so that
    313:      * subsequent assembly can set a proper subset of the values. */
    314:     MPI_Waitsome(4*x->nrecvranks,x->recvreqs,&ndone,some_indices,x->use_status?some_statuses:MPI_STATUSES_IGNORE);
    315:     for (ii=0; ii<ndone; ii++) {
    316:       PetscInt i = some_indices[ii]/4,j,k;
    317:       InsertMode imode = (InsertMode)x->recvhdr[i].insertmode;
    318:       PetscInt *recvint;
    319:       PetscScalar *recvscalar;
    320:       PetscBool intmsg = (PetscBool)(some_indices[ii]%2 == 0);
    321:       PetscBool blockmsg = (PetscBool)((some_indices[ii]%4)/2 == 1);
    322:       npending--;
    323:       if (!blockmsg) { /* Scalar stash */
    324:         PetscMPIInt count;
    325:         if (--frame[i].pendings > 0) continue;
    326:         if (x->use_status) {
    327:           MPI_Get_count(&some_statuses[ii],intmsg ? MPIU_INT : MPIU_SCALAR,&count);
    328:         } else count = x->recvhdr[i].count;
    329:         for (j=0,recvint=frame[i].ints,recvscalar=frame[i].scalars; j<count; j++,recvint++) {
    330:           PetscInt loc = *recvint - X->map->rstart;
    331:           if (*recvint < X->map->rstart || X->map->rend <= *recvint) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Received vector entry %D out of local range [%D,%D)]",*recvint,X->map->rstart,X->map->rend);
    332:           switch (imode) {
    333:           case ADD_VALUES:
    334:             xarray[loc] += *recvscalar++;
    335:             break;
    336:           case INSERT_VALUES:
    337:             xarray[loc] = *recvscalar++;
    338:             break;
    339:           default: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Insert mode not supported 0x%x",imode);
    340:           }
    341:         }
    342:       } else {                  /* Block stash */
    343:         PetscMPIInt count;
    344:         if (--frame[i].pendingb > 0) continue;
    345:         if (x->use_status) {
    346:           MPI_Get_count(&some_statuses[ii],intmsg ? MPIU_INT : MPIU_SCALAR,&count);
    347:           if (!intmsg) count /= bs; /* Convert from number of scalars to number of blocks */
    348:         } else count = x->recvhdr[i].bcount;
    349:         for (j=0,recvint=frame[i].intb,recvscalar=frame[i].scalarb; j<count; j++,recvint++) {
    350:           PetscInt loc = (*recvint)*bs - X->map->rstart;
    351:           switch (imode) {
    352:           case ADD_VALUES:
    353:             for (k=loc; k<loc+bs; k++) xarray[k] += *recvscalar++;
    354:             break;
    355:           case INSERT_VALUES:
    356:             for (k=loc; k<loc+bs; k++) xarray[k] = *recvscalar++;
    357:             break;
    358:           default: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Insert mode not supported 0x%x",imode);
    359:           }
    360:         }
    361:       }
    362:     }
    363:   }
    364:   VecRestoreArray(X,&xarray);
    365:   MPI_Waitall(4*x->nsendranks,x->sendreqs,MPI_STATUSES_IGNORE);
    366:   PetscFree2(some_indices,some_statuses);
    367:   if (x->assembly_subset) {
    368:     void *dummy;                /* reset segbuffers */
    369:     PetscSegBufferExtractInPlace(x->segrecvint,&dummy);
    370:     PetscSegBufferExtractInPlace(x->segrecvscalar,&dummy);
    371:   } else {
    372:     VecAssemblyReset_MPI(X);
    373:   }

    375:   X->stash.insertmode = NOT_SET_VALUES;
    376:   X->bstash.insertmode = NOT_SET_VALUES;
    377:   VecStashScatterEnd_Private(&X->stash);
    378:   VecStashScatterEnd_Private(&X->bstash);
    379:   return(0);
    380: }

    384: PetscErrorCode VecAssemblyReset_MPI(Vec X)
    385: {
    386:   Vec_MPI *x = (Vec_MPI*)X->data;

    390:   PetscFree(x->sendreqs);
    391:   PetscFree(x->recvreqs);
    392:   PetscFree(x->sendranks);
    393:   PetscFree(x->recvranks);
    394:   PetscFree(x->sendhdr);
    395:   PetscFree(x->recvhdr);
    396:   PetscFree(x->sendptrs);
    397:   PetscSegBufferDestroy(&x->segrecvint);
    398:   PetscSegBufferDestroy(&x->segrecvscalar);
    399:   PetscSegBufferDestroy(&x->segrecvframe);
    400:   return(0);
    401: }

    406: static PetscErrorCode VecSetFromOptions_MPI(PetscOptionItems *PetscOptionsObject,Vec X)
    407: {
    409:   PetscBool      flg = PETSC_FALSE,set;

    412:   PetscOptionsHead(PetscOptionsObject,"VecMPI Options");
    413:   PetscOptionsBool("-vec_assembly_bts","Use BuildTwoSided version of assembly","",flg,&flg,&set);
    414:   if (set) {
    415:     X->ops->assemblybegin = flg ? VecAssemblyBegin_MPI_BTS : VecAssemblyBegin_MPI;
    416:     X->ops->assemblyend   = flg ? VecAssemblyEnd_MPI_BTS   : VecAssemblyEnd_MPI;
    417:   }
    418:   PetscOptionsTail();
    419:   return(0);
    420: }

    423: static struct _VecOps DvOps = { VecDuplicate_MPI, /* 1 */
    424:                                 VecDuplicateVecs_Default,
    425:                                 VecDestroyVecs_Default,
    426:                                 VecDot_MPI,
    427:                                 VecMDot_MPI,
    428:                                 VecNorm_MPI,
    429:                                 VecTDot_MPI,
    430:                                 VecMTDot_MPI,
    431:                                 VecScale_Seq,
    432:                                 VecCopy_Seq, /* 10 */
    433:                                 VecSet_Seq,
    434:                                 VecSwap_Seq,
    435:                                 VecAXPY_Seq,
    436:                                 VecAXPBY_Seq,
    437:                                 VecMAXPY_Seq,
    438:                                 VecAYPX_Seq,
    439:                                 VecWAXPY_Seq,
    440:                                 VecAXPBYPCZ_Seq,
    441:                                 VecPointwiseMult_Seq,
    442:                                 VecPointwiseDivide_Seq,
    443:                                 VecSetValues_MPI, /* 20 */
    444:                                 VecAssemblyBegin_MPI_BTS,
    445:                                 VecAssemblyEnd_MPI_BTS,
    446:                                 0,
    447:                                 VecGetSize_MPI,
    448:                                 VecGetSize_Seq,
    449:                                 0,
    450:                                 VecMax_MPI,
    451:                                 VecMin_MPI,
    452:                                 VecSetRandom_Seq,
    453:                                 VecSetOption_MPI,
    454:                                 VecSetValuesBlocked_MPI,
    455:                                 VecDestroy_MPI,
    456:                                 VecView_MPI,
    457:                                 VecPlaceArray_MPI,
    458:                                 VecReplaceArray_Seq,
    459:                                 VecDot_Seq,
    460:                                 VecTDot_Seq,
    461:                                 VecNorm_Seq,
    462:                                 VecMDot_Seq,
    463:                                 VecMTDot_Seq,
    464:                                 VecLoad_Default,
    465:                                 VecReciprocal_Default,
    466:                                 VecConjugate_Seq,
    467:                                 0,
    468:                                 0,
    469:                                 VecResetArray_MPI,
    470:                                 VecSetFromOptions_MPI,/*set from options */
    471:                                 VecMaxPointwiseDivide_Seq,
    472:                                 VecPointwiseMax_Seq,
    473:                                 VecPointwiseMaxAbs_Seq,
    474:                                 VecPointwiseMin_Seq,
    475:                                 VecGetValues_MPI,
    476:                                 0,
    477:                                 0,
    478:                                 0,
    479:                                 0,
    480:                                 0,
    481:                                 0,
    482:                                 VecStrideGather_Default,
    483:                                 VecStrideScatter_Default,
    484:                                 0,
    485:                                 0,
    486:                                 0,
    487:                                 0,
    488:                                 0,
    489:                                 VecStrideSubSetGather_Default,
    490:                                 VecStrideSubSetScatter_Default,
    491:                                 0,
    492:                                 0
    493: };

    497: /*
    498:     VecCreate_MPI_Private - Basic create routine called by VecCreate_MPI() (i.e. VecCreateMPI()),
    499:     VecCreateMPIWithArray(), VecCreate_Shared() (i.e. VecCreateShared()), VecCreateGhost(),
    500:     VecDuplicate_MPI(), VecCreateGhostWithArray(), VecDuplicate_MPI(), and VecDuplicate_Shared()

    502:     If alloc is true and array is NULL then this routine allocates the space, otherwise
    503:     no space is allocated.
    504: */
    505: PetscErrorCode VecCreate_MPI_Private(Vec v,PetscBool alloc,PetscInt nghost,const PetscScalar array[])
    506: {
    507:   Vec_MPI        *s;

    511:   PetscNewLog(v,&s);
    512:   v->data        = (void*)s;
    513:   PetscMemcpy(v->ops,&DvOps,sizeof(DvOps));
    514:   s->nghost      = nghost;
    515:   v->petscnative = PETSC_TRUE;

    517:   PetscLayoutSetUp(v->map);

    519:   s->array           = (PetscScalar*)array;
    520:   s->array_allocated = 0;
    521:   if (alloc && !array) {
    522:     PetscInt n = v->map->n+nghost;
    523:     PetscMalloc1(n,&s->array);
    524:     PetscLogObjectMemory((PetscObject)v,n*sizeof(PetscScalar));
    525:     PetscMemzero(s->array,n*sizeof(PetscScalar));
    526:     s->array_allocated = s->array;
    527:   }

    529:   /* By default parallel vectors do not have local representation */
    530:   s->localrep    = 0;
    531:   s->localupdate = 0;

    533:   v->stash.insertmode = NOT_SET_VALUES;
    534:   v->bstash.insertmode = NOT_SET_VALUES;
    535:   /* create the stashes. The block-size for bstash is set later when
    536:      VecSetValuesBlocked is called.
    537:   */
    538:   VecStashCreate_Private(PetscObjectComm((PetscObject)v),1,&v->stash);
    539:   VecStashCreate_Private(PetscObjectComm((PetscObject)v),PetscAbs(v->map->bs),&v->bstash);

    541: #if defined(PETSC_HAVE_MATLAB_ENGINE)
    542:   PetscObjectComposeFunction((PetscObject)v,"PetscMatlabEnginePut_C",VecMatlabEnginePut_Default);
    543:   PetscObjectComposeFunction((PetscObject)v,"PetscMatlabEngineGet_C",VecMatlabEngineGet_Default);
    544: #endif
    545:   PetscObjectChangeTypeName((PetscObject)v,VECMPI);
    546:   return(0);
    547: }

    549: /*MC
    550:    VECMPI - VECMPI = "mpi" - The basic parallel vector

    552:    Options Database Keys:
    553: . -vec_type mpi - sets the vector type to VECMPI during a call to VecSetFromOptions()

    555:   Level: beginner

    557: .seealso: VecCreate(), VecSetType(), VecSetFromOptions(), VecCreateMpiWithArray(), VECMPI, VecType, VecCreateMPI(), VecCreateMpi()
    558: M*/

    562: PETSC_EXTERN PetscErrorCode VecCreate_MPI(Vec vv)
    563: {

    567:   VecCreate_MPI_Private(vv,PETSC_TRUE,0,0);
    568:   return(0);
    569: }

    571: /*MC
    572:    VECSTANDARD = "standard" - A VECSEQ on one process and VECMPI on more than one process

    574:    Options Database Keys:
    575: . -vec_type standard - sets a vector type to standard on calls to VecSetFromOptions()

    577:   Level: beginner

    579: .seealso: VecCreateSeq(), VecCreateMPI()
    580: M*/

    584: PETSC_EXTERN PetscErrorCode VecCreate_Standard(Vec v)
    585: {
    587:   PetscMPIInt    size;

    590:   MPI_Comm_size(PetscObjectComm((PetscObject)v),&size);
    591:   if (size == 1) {
    592:     VecSetType(v,VECSEQ);
    593:   } else {
    594:     VecSetType(v,VECMPI);
    595:   }
    596:   return(0);
    597: }

    601: /*@C
    602:    VecCreateMPIWithArray - Creates a parallel, array-style vector,
    603:    where the user provides the array space to store the vector values.

    605:    Collective on MPI_Comm

    607:    Input Parameters:
    608: +  comm  - the MPI communicator to use
    609: .  bs    - block size, same meaning as VecSetBlockSize()
    610: .  n     - local vector length, cannot be PETSC_DECIDE
    611: .  N     - global vector length (or PETSC_DECIDE to have calculated)
    612: -  array - the user provided array to store the vector values

    614:    Output Parameter:
    615: .  vv - the vector

    617:    Notes:
    618:    Use VecDuplicate() or VecDuplicateVecs() to form additional vectors of the
    619:    same type as an existing vector.

    621:    If the user-provided array is NULL, then VecPlaceArray() can be used
    622:    at a later stage to SET the array for storing the vector values.

    624:    PETSc does NOT free the array when the vector is destroyed via VecDestroy().
    625:    The user should not free the array until the vector is destroyed.

    627:    Level: intermediate

    629:    Concepts: vectors^creating with array

    631: .seealso: VecCreateSeqWithArray(), VecCreate(), VecDuplicate(), VecDuplicateVecs(), VecCreateGhost(),
    632:           VecCreateMPI(), VecCreateGhostWithArray(), VecPlaceArray()

    634: @*/
    635: PetscErrorCode  VecCreateMPIWithArray(MPI_Comm comm,PetscInt bs,PetscInt n,PetscInt N,const PetscScalar array[],Vec *vv)
    636: {

    640:   if (n == PETSC_DECIDE) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Must set local size of vector");
    641:   PetscSplitOwnership(comm,&n,&N);
    642:   VecCreate(comm,vv);
    643:   VecSetSizes(*vv,n,N);
    644:   VecSetBlockSize(*vv,bs);
    645:   VecCreate_MPI_Private(*vv,PETSC_FALSE,0,array);
    646:   return(0);
    647: }

    651: /*@C
    652:    VecCreateGhostWithArray - Creates a parallel vector with ghost padding on each processor;
    653:    the caller allocates the array space.

    655:    Collective on MPI_Comm

    657:    Input Parameters:
    658: +  comm - the MPI communicator to use
    659: .  n - local vector length
    660: .  N - global vector length (or PETSC_DECIDE to have calculated if n is given)
    661: .  nghost - number of local ghost points
    662: .  ghosts - global indices of ghost points (or NULL if not needed), these do not need to be in increasing order (sorted)
    663: -  array - the space to store the vector values (as long as n + nghost)

    665:    Output Parameter:
    666: .  vv - the global vector representation (without ghost points as part of vector)

    668:    Notes:
    669:    Use VecGhostGetLocalForm() to access the local, ghosted representation
    670:    of the vector.

    672:    This also automatically sets the ISLocalToGlobalMapping() for this vector.

    674:    Level: advanced

    676:    Concepts: vectors^creating with array
    677:    Concepts: vectors^ghosted

    679: .seealso: VecCreate(), VecGhostGetLocalForm(), VecGhostRestoreLocalForm(),
    680:           VecCreateGhost(), VecCreateSeqWithArray(), VecCreateMPIWithArray(),
    681:           VecCreateGhostBlock(), VecCreateGhostBlockWithArray(), VecMPISetGhost()

    683: @*/
    684: PetscErrorCode  VecCreateGhostWithArray(MPI_Comm comm,PetscInt n,PetscInt N,PetscInt nghost,const PetscInt ghosts[],const PetscScalar array[],Vec *vv)
    685: {
    686:   PetscErrorCode         ierr;
    687:   Vec_MPI                *w;
    688:   PetscScalar            *larray;
    689:   IS                     from,to;
    690:   ISLocalToGlobalMapping ltog;
    691:   PetscInt               rstart,i,*indices;

    694:   *vv = 0;

    696:   if (n == PETSC_DECIDE)      SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Must set local size");
    697:   if (nghost == PETSC_DECIDE) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Must set local ghost size");
    698:   if (nghost < 0)             SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Ghost length must be >= 0");
    699:   PetscSplitOwnership(comm,&n,&N);
    700:   /* Create global representation */
    701:   VecCreate(comm,vv);
    702:   VecSetSizes(*vv,n,N);
    703:   VecCreate_MPI_Private(*vv,PETSC_TRUE,nghost,array);
    704:   w    = (Vec_MPI*)(*vv)->data;
    705:   /* Create local representation */
    706:   VecGetArray(*vv,&larray);
    707:   VecCreateSeqWithArray(PETSC_COMM_SELF,1,n+nghost,larray,&w->localrep);
    708:   PetscLogObjectParent((PetscObject)*vv,(PetscObject)w->localrep);
    709:   VecRestoreArray(*vv,&larray);

    711:   /*
    712:        Create scatter context for scattering (updating) ghost values
    713:   */
    714:   ISCreateGeneral(comm,nghost,ghosts,PETSC_COPY_VALUES,&from);
    715:   ISCreateStride(PETSC_COMM_SELF,nghost,n,1,&to);
    716:   VecScatterCreate(*vv,from,w->localrep,to,&w->localupdate);
    717:   PetscLogObjectParent((PetscObject)*vv,(PetscObject)w->localupdate);
    718:   ISDestroy(&to);
    719:   ISDestroy(&from);

    721:   /* set local to global mapping for ghosted vector */
    722:   PetscMalloc1(n+nghost,&indices);
    723:   VecGetOwnershipRange(*vv,&rstart,NULL);
    724:   for (i=0; i<n; i++) {
    725:     indices[i] = rstart + i;
    726:   }
    727:   for (i=0; i<nghost; i++) {
    728:     indices[n+i] = ghosts[i];
    729:   }
    730:   ISLocalToGlobalMappingCreate(comm,1,n+nghost,indices,PETSC_OWN_POINTER,&ltog);
    731:   VecSetLocalToGlobalMapping(*vv,ltog);
    732:   ISLocalToGlobalMappingDestroy(&ltog);
    733:   return(0);
    734: }

    738: /*@
    739:    VecCreateGhost - Creates a parallel vector with ghost padding on each processor.

    741:    Collective on MPI_Comm

    743:    Input Parameters:
    744: +  comm - the MPI communicator to use
    745: .  n - local vector length
    746: .  N - global vector length (or PETSC_DECIDE to have calculated if n is given)
    747: .  nghost - number of local ghost points
    748: -  ghosts - global indices of ghost points, these do not need to be in increasing order (sorted)

    750:    Output Parameter:
    751: .  vv - the global vector representation (without ghost points as part of vector)

    753:    Notes:
    754:    Use VecGhostGetLocalForm() to access the local, ghosted representation
    755:    of the vector.

    757:    This also automatically sets the ISLocalToGlobalMapping() for this vector.

    759:    Level: advanced

    761:    Concepts: vectors^ghosted

    763: .seealso: VecCreateSeq(), VecCreate(), VecDuplicate(), VecDuplicateVecs(), VecCreateMPI(),
    764:           VecGhostGetLocalForm(), VecGhostRestoreLocalForm(), VecGhostUpdateBegin(),
    765:           VecCreateGhostWithArray(), VecCreateMPIWithArray(), VecGhostUpdateEnd(),
    766:           VecCreateGhostBlock(), VecCreateGhostBlockWithArray(), VecMPISetGhost()

    768: @*/
    769: PetscErrorCode  VecCreateGhost(MPI_Comm comm,PetscInt n,PetscInt N,PetscInt nghost,const PetscInt ghosts[],Vec *vv)
    770: {

    774:   VecCreateGhostWithArray(comm,n,N,nghost,ghosts,0,vv);
    775:   return(0);
    776: }

    780: /*@
    781:    VecMPISetGhost - Sets the ghost points for an MPI ghost vector

    783:    Collective on Vec

    785:    Input Parameters:
    786: +  vv - the MPI vector
    787: .  nghost - number of local ghost points
    788: -  ghosts - global indices of ghost points, these do not need to be in increasing order (sorted)

    791:    Notes:
    792:    Use VecGhostGetLocalForm() to access the local, ghosted representation
    793:    of the vector.

    795:    This also automatically sets the ISLocalToGlobalMapping() for this vector.

    797:    You must call this AFTER you have set the type of the vector (with VecSetType()) and the size (with VecSetSizes()).

    799:    Level: advanced

    801:    Concepts: vectors^ghosted

    803: .seealso: VecCreateSeq(), VecCreate(), VecDuplicate(), VecDuplicateVecs(), VecCreateMPI(),
    804:           VecGhostGetLocalForm(), VecGhostRestoreLocalForm(), VecGhostUpdateBegin(),
    805:           VecCreateGhostWithArray(), VecCreateMPIWithArray(), VecGhostUpdateEnd(),
    806:           VecCreateGhostBlock(), VecCreateGhostBlockWithArray()

    808: @*/
    809: PetscErrorCode  VecMPISetGhost(Vec vv,PetscInt nghost,const PetscInt ghosts[])
    810: {
    812:   PetscBool      flg;

    815:   PetscObjectTypeCompare((PetscObject)vv,VECMPI,&flg);
    816:   /* if already fully existant VECMPI then basically destroy it and rebuild with ghosting */
    817:   if (flg) {
    818:     PetscInt               n,N;
    819:     Vec_MPI                *w;
    820:     PetscScalar            *larray;
    821:     IS                     from,to;
    822:     ISLocalToGlobalMapping ltog;
    823:     PetscInt               rstart,i,*indices;
    824:     MPI_Comm               comm;

    826:     PetscObjectGetComm((PetscObject)vv,&comm);
    827:     n    = vv->map->n;
    828:     N    = vv->map->N;
    829:     (*vv->ops->destroy)(vv);
    830:     VecSetSizes(vv,n,N);
    831:     VecCreate_MPI_Private(vv,PETSC_TRUE,nghost,NULL);
    832:     w    = (Vec_MPI*)(vv)->data;
    833:     /* Create local representation */
    834:     VecGetArray(vv,&larray);
    835:     VecCreateSeqWithArray(PETSC_COMM_SELF,1,n+nghost,larray,&w->localrep);
    836:     PetscLogObjectParent((PetscObject)vv,(PetscObject)w->localrep);
    837:     VecRestoreArray(vv,&larray);

    839:     /*
    840:      Create scatter context for scattering (updating) ghost values
    841:      */
    842:     ISCreateGeneral(comm,nghost,ghosts,PETSC_COPY_VALUES,&from);
    843:     ISCreateStride(PETSC_COMM_SELF,nghost,n,1,&to);
    844:     VecScatterCreate(vv,from,w->localrep,to,&w->localupdate);
    845:     PetscLogObjectParent((PetscObject)vv,(PetscObject)w->localupdate);
    846:     ISDestroy(&to);
    847:     ISDestroy(&from);

    849:     /* set local to global mapping for ghosted vector */
    850:     PetscMalloc1(n+nghost,&indices);
    851:     VecGetOwnershipRange(vv,&rstart,NULL);

    853:     for (i=0; i<n; i++)      indices[i]   = rstart + i;
    854:     for (i=0; i<nghost; i++) indices[n+i] = ghosts[i];

    856:     ISLocalToGlobalMappingCreate(comm,1,n+nghost,indices,PETSC_OWN_POINTER,&ltog);
    857:     VecSetLocalToGlobalMapping(vv,ltog);
    858:     ISLocalToGlobalMappingDestroy(&ltog);
    859:   } else if (vv->ops->create == VecCreate_MPI) SETERRQ(PetscObjectComm((PetscObject)vv),PETSC_ERR_ARG_WRONGSTATE,"Must set local or global size before setting ghosting");
    860:   else if (!((PetscObject)vv)->type_name) SETERRQ(PetscObjectComm((PetscObject)vv),PETSC_ERR_ARG_WRONGSTATE,"Must set type to VECMPI before ghosting");
    861:   return(0);
    862: }

    865: /* ------------------------------------------------------------------------------------------*/
    868: /*@C
    869:    VecCreateGhostBlockWithArray - Creates a parallel vector with ghost padding on each processor;
    870:    the caller allocates the array space. Indices in the ghost region are based on blocks.

    872:    Collective on MPI_Comm

    874:    Input Parameters:
    875: +  comm - the MPI communicator to use
    876: .  bs - block size
    877: .  n - local vector length
    878: .  N - global vector length (or PETSC_DECIDE to have calculated if n is given)
    879: .  nghost - number of local ghost blocks
    880: .  ghosts - global indices of ghost blocks (or NULL if not needed), counts are by block not by index, these do not need to be in increasing order (sorted)
    881: -  array - the space to store the vector values (as long as n + nghost*bs)

    883:    Output Parameter:
    884: .  vv - the global vector representation (without ghost points as part of vector)

    886:    Notes:
    887:    Use VecGhostGetLocalForm() to access the local, ghosted representation
    888:    of the vector.

    890:    n is the local vector size (total local size not the number of blocks) while nghost
    891:    is the number of blocks in the ghost portion, i.e. the number of elements in the ghost
    892:    portion is bs*nghost

    894:    Level: advanced

    896:    Concepts: vectors^creating ghosted
    897:    Concepts: vectors^creating with array

    899: .seealso: VecCreate(), VecGhostGetLocalForm(), VecGhostRestoreLocalForm(),
    900:           VecCreateGhost(), VecCreateSeqWithArray(), VecCreateMPIWithArray(),
    901:           VecCreateGhostWithArray(), VecCreateGhostBlock()

    903: @*/
    904: PetscErrorCode  VecCreateGhostBlockWithArray(MPI_Comm comm,PetscInt bs,PetscInt n,PetscInt N,PetscInt nghost,const PetscInt ghosts[],const PetscScalar array[],Vec *vv)
    905: {
    906:   PetscErrorCode         ierr;
    907:   Vec_MPI                *w;
    908:   PetscScalar            *larray;
    909:   IS                     from,to;
    910:   ISLocalToGlobalMapping ltog;
    911:   PetscInt               rstart,i,nb,*indices;

    914:   *vv = 0;

    916:   if (n == PETSC_DECIDE)      SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Must set local size");
    917:   if (nghost == PETSC_DECIDE) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Must set local ghost size");
    918:   if (nghost < 0)             SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Ghost length must be >= 0");
    919:   if (n % bs)                 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Local size must be a multiple of block size");
    920:   PetscSplitOwnership(comm,&n,&N);
    921:   /* Create global representation */
    922:   VecCreate(comm,vv);
    923:   VecSetSizes(*vv,n,N);
    924:   VecSetBlockSize(*vv,bs);
    925:   VecCreate_MPI_Private(*vv,PETSC_TRUE,nghost*bs,array);
    926:   w    = (Vec_MPI*)(*vv)->data;
    927:   /* Create local representation */
    928:   VecGetArray(*vv,&larray);
    929:   VecCreateSeqWithArray(PETSC_COMM_SELF,bs,n+bs*nghost,larray,&w->localrep);
    930:   PetscLogObjectParent((PetscObject)*vv,(PetscObject)w->localrep);
    931:   VecRestoreArray(*vv,&larray);

    933:   /*
    934:        Create scatter context for scattering (updating) ghost values
    935:   */
    936:   ISCreateBlock(comm,bs,nghost,ghosts,PETSC_COPY_VALUES,&from);
    937:   ISCreateStride(PETSC_COMM_SELF,bs*nghost,n,1,&to);
    938:   VecScatterCreate(*vv,from,w->localrep,to,&w->localupdate);
    939:   PetscLogObjectParent((PetscObject)*vv,(PetscObject)w->localupdate);
    940:   ISDestroy(&to);
    941:   ISDestroy(&from);

    943:   /* set local to global mapping for ghosted vector */
    944:   nb   = n/bs;
    945:   PetscMalloc1(nb+nghost,&indices);
    946:   VecGetOwnershipRange(*vv,&rstart,NULL);

    948:   for (i=0; i<nb; i++)      indices[i]    = rstart + i;
    949:   for (i=0; i<nghost; i++)  indices[nb+i] = ghosts[i];

    951:   ISLocalToGlobalMappingCreate(comm,bs,nb+nghost,indices,PETSC_OWN_POINTER,&ltog);
    952:   VecSetLocalToGlobalMapping(*vv,ltog);
    953:   ISLocalToGlobalMappingDestroy(&ltog);
    954:   return(0);
    955: }

    959: /*@
    960:    VecCreateGhostBlock - Creates a parallel vector with ghost padding on each processor.
    961:         The indicing of the ghost points is done with blocks.

    963:    Collective on MPI_Comm

    965:    Input Parameters:
    966: +  comm - the MPI communicator to use
    967: .  bs - the block size
    968: .  n - local vector length
    969: .  N - global vector length (or PETSC_DECIDE to have calculated if n is given)
    970: .  nghost - number of local ghost blocks
    971: -  ghosts - global indices of ghost blocks, counts are by block, not by individual index, these do not need to be in increasing order (sorted)

    973:    Output Parameter:
    974: .  vv - the global vector representation (without ghost points as part of vector)

    976:    Notes:
    977:    Use VecGhostGetLocalForm() to access the local, ghosted representation
    978:    of the vector.

    980:    n is the local vector size (total local size not the number of blocks) while nghost
    981:    is the number of blocks in the ghost portion, i.e. the number of elements in the ghost
    982:    portion is bs*nghost

    984:    Level: advanced

    986:    Concepts: vectors^ghosted

    988: .seealso: VecCreateSeq(), VecCreate(), VecDuplicate(), VecDuplicateVecs(), VecCreateMPI(),
    989:           VecGhostGetLocalForm(), VecGhostRestoreLocalForm(),
    990:           VecCreateGhostWithArray(), VecCreateMPIWithArray(), VecCreateGhostBlockWithArray()

    992: @*/
    993: PetscErrorCode  VecCreateGhostBlock(MPI_Comm comm,PetscInt bs,PetscInt n,PetscInt N,PetscInt nghost,const PetscInt ghosts[],Vec *vv)
    994: {

    998:   VecCreateGhostBlockWithArray(comm,bs,n,N,nghost,ghosts,0,vv);
    999:   return(0);
    1000: }