Date: 2013-07-02T14:47:21+00:00

Actual source code: redistribute.c
petsc-3.4.2 2013-07-02

      2: /*
      3:   This file defines a "solve the problem redistributely on each subgroup of processor" preconditioner.
      4: */
      5: #include <petsc-private/pcimpl.h>     /*I "petscksp.h" I*/
      6: #include <petscksp.h>

      8: typedef struct {
      9:   KSP         ksp;
     10:   Vec         x,b;
     11:   VecScatter  scatter;
     12:   IS          is;
     13:   PetscInt    dcnt,*drows;    /* these are the local rows that have only diagonal entry */
     14:   PetscScalar *diag;
     15:   Vec         work;
     16: } PC_Redistribute;

     20: static PetscErrorCode PCView_Redistribute(PC pc,PetscViewer viewer)
     21: {
     22:   PC_Redistribute *red = (PC_Redistribute*)pc->data;
     23:   PetscErrorCode  ierr;
     24:   PetscBool       iascii,isstring;
     25:   PetscInt        ncnt,N;

     28:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);
     29:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERSTRING,&isstring);
     30:   if (iascii) {
     31:     MPI_Allreduce(&red->dcnt,&ncnt,1,MPIU_INT,MPI_SUM,PetscObjectComm((PetscObject)pc));
     32:     MatGetSize(pc->pmat,&N,NULL);
     33:     PetscViewerASCIIPrintf(viewer,"    Number rows eliminated %D Percentage rows eliminated %g\n",ncnt,100.0*((PetscReal)ncnt)/((PetscReal)N));
     34:     PetscViewerASCIIPrintf(viewer,"  Redistribute preconditioner: \n");
     35:     KSPView(red->ksp,viewer);
     36:   } else if (isstring) {
     37:     PetscViewerStringSPrintf(viewer," Redistribute preconditioner");
     38:     KSPView(red->ksp,viewer);
     39:   }
     40:   return(0);
     41: }

     45: static PetscErrorCode PCSetUp_Redistribute(PC pc)
     46: {
     47:   PC_Redistribute   *red = (PC_Redistribute*)pc->data;
     48:   PetscErrorCode    ierr;
     49:   MPI_Comm          comm;
     50:   PetscInt          rstart,rend,i,nz,cnt,*rows,ncnt,dcnt,*drows;
     51:   PetscLayout       map,nmap;
     52:   PetscMPIInt       size,imdex,tag,n;
     53:   PetscInt          *source = NULL;
     54:   PetscMPIInt       *nprocs = NULL,nrecvs;
     55:   PetscInt          j,nsends;
     56:   PetscInt          *owner = NULL,*starts = NULL,count,slen;
     57:   PetscInt          *rvalues,*svalues,recvtotal;
     58:   PetscMPIInt       *onodes1,*olengths1;
     59:   MPI_Request       *send_waits = NULL,*recv_waits = NULL;
     60:   MPI_Status        recv_status,*send_status;
     61:   Vec               tvec,diag;
     62:   Mat               tmat;
     63:   const PetscScalar *d;

     66:   if (pc->setupcalled) {
     67:     KSPGetOperators(red->ksp,NULL,&tmat,NULL);
     68:     MatGetSubMatrix(pc->pmat,red->is,red->is,MAT_REUSE_MATRIX,&tmat);
     69:     KSPSetOperators(red->ksp,tmat,tmat,SAME_NONZERO_PATTERN);
     70:   } else {
     71:     PetscInt NN;

     73:     PetscObjectGetComm((PetscObject)pc,&comm);
     74:     MPI_Comm_size(comm,&size);
     75:     PetscObjectGetNewTag((PetscObject)pc,&tag);

     77:     /* count non-diagonal rows on process */
     78:     MatGetOwnershipRange(pc->mat,&rstart,&rend);
     79:     cnt  = 0;
     80:     for (i=rstart; i<rend; i++) {
     81:       MatGetRow(pc->mat,i,&nz,NULL,NULL);
     82:       if (nz > 1) cnt++;
     83:       MatRestoreRow(pc->mat,i,&nz,NULL,NULL);
     84:     }
     85:     PetscMalloc(cnt*sizeof(PetscInt),&rows);
     86:     PetscMalloc((rend - rstart - cnt)*sizeof(PetscInt),&drows);

     88:     /* list non-diagonal rows on process */
     89:     cnt = 0; dcnt = 0;
     90:     for (i=rstart; i<rend; i++) {
     91:       MatGetRow(pc->mat,i,&nz,NULL,NULL);
     92:       if (nz > 1) rows[cnt++] = i;
     93:       else drows[dcnt++] = i - rstart;
     94:       MatRestoreRow(pc->mat,i,&nz,NULL,NULL);
     95:     }

     97:     /* create PetscLayout for non-diagonal rows on each process */
     98:     PetscLayoutCreate(comm,&map);
     99:     PetscLayoutSetLocalSize(map,cnt);
    100:     PetscLayoutSetBlockSize(map,1);
    101:     PetscLayoutSetUp(map);
    102:     rstart = map->rstart;
    103:     rend   = map->rend;

    105:     /* create PetscLayout for load-balanced non-diagonal rows on each process */
    106:     PetscLayoutCreate(comm,&nmap);
    107:     MPI_Allreduce(&cnt,&ncnt,1,MPIU_INT,MPI_SUM,comm);
    108:     PetscLayoutSetSize(nmap,ncnt);
    109:     PetscLayoutSetBlockSize(nmap,1);
    110:     PetscLayoutSetUp(nmap);

    112:     MatGetSize(pc->pmat,&NN,NULL);
    113:     PetscInfo2(pc,"Number of diagonal rows eliminated %d, percentage eliminated %g\n",NN-ncnt,((PetscReal)(NN-ncnt))/((PetscReal)(NN)));
    114:     /*
    115:         this code is taken from VecScatterCreate_PtoS()
    116:         Determines what rows need to be moved where to
    117:         load balance the non-diagonal rows
    118:     */
    119:     /*  count number of contributors to each processor */
    120:     PetscMalloc2(size,PetscMPIInt,&nprocs,cnt,PetscInt,&owner);
    121:     PetscMemzero(nprocs,size*sizeof(PetscMPIInt));
    122:     j      = 0;
    123:     nsends = 0;
    124:     for (i=rstart; i<rend; i++) {
    125:       if (i < nmap->range[j]) j = 0;
    126:       for (; j<size; j++) {
    127:         if (i < nmap->range[j+1]) {
    128:           if (!nprocs[j]++) nsends++;
    129:           owner[i-rstart] = j;
    130:           break;
    131:         }
    132:       }
    133:     }
    134:     /* inform other processors of number of messages and max length*/
    135:     PetscGatherNumberOfMessages(comm,NULL,nprocs,&nrecvs);
    136:     PetscGatherMessageLengths(comm,nsends,nrecvs,nprocs,&onodes1,&olengths1);
    137:     PetscSortMPIIntWithArray(nrecvs,onodes1,olengths1);
    138:     recvtotal = 0; for (i=0; i<nrecvs; i++) recvtotal += olengths1[i];

    140:     /* post receives:  rvalues - rows I will own; count - nu */
    141:     PetscMalloc3(recvtotal,PetscInt,&rvalues,nrecvs,PetscInt,&source,nrecvs,MPI_Request,&recv_waits);
    142:     count = 0;
    143:     for (i=0; i<nrecvs; i++) {
    144:       MPI_Irecv((rvalues+count),olengths1[i],MPIU_INT,onodes1[i],tag,comm,recv_waits+i);
    145:       count += olengths1[i];
    146:     }

    148:     /* do sends:
    149:        1) starts[i] gives the starting index in svalues for stuff going to
    150:        the ith processor
    151:     */
    152:     PetscMalloc3(cnt,PetscInt,&svalues,nsends,MPI_Request,&send_waits,size,PetscInt,&starts);
    153:     starts[0] = 0;
    154:     for (i=1; i<size; i++) starts[i] = starts[i-1] + nprocs[i-1];
    155:     for (i=0; i<cnt; i++)  svalues[starts[owner[i]]++] = rows[i];
    156:     for (i=0; i<cnt; i++)  rows[i] = rows[i] - rstart;
    157:     red->drows = drows;
    158:     red->dcnt  = dcnt;
    159:     PetscFree(rows);

    161:     starts[0] = 0;
    162:     for (i=1; i<size; i++) starts[i] = starts[i-1] + nprocs[i-1];
    163:     count = 0;
    164:     for (i=0; i<size; i++) {
    165:       if (nprocs[i]) {
    166:         MPI_Isend(svalues+starts[i],nprocs[i],MPIU_INT,i,tag,comm,send_waits+count++);
    167:       }
    168:     }

    170:     /*  wait on receives */
    171:     count = nrecvs;
    172:     slen  = 0;
    173:     while (count) {
    174:       MPI_Waitany(nrecvs,recv_waits,&imdex,&recv_status);
    175:       /* unpack receives into our local space */
    176:       MPI_Get_count(&recv_status,MPIU_INT,&n);
    177:       slen += n;
    178:       count--;
    179:     }
    180:     if (slen != recvtotal) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Total message lengths %D not expected %D",slen,recvtotal);

    182:     ISCreateGeneral(comm,slen,rvalues,PETSC_COPY_VALUES,&red->is);

    184:     /* free up all work space */
    185:     PetscFree(olengths1);
    186:     PetscFree(onodes1);
    187:     PetscFree3(rvalues,source,recv_waits);
    188:     PetscFree2(nprocs,owner);
    189:     if (nsends) {   /* wait on sends */
    190:       PetscMalloc(nsends*sizeof(MPI_Status),&send_status);
    191:       MPI_Waitall(nsends,send_waits,send_status);
    192:       PetscFree(send_status);
    193:     }
    194:     PetscFree3(svalues,send_waits,starts);
    195:     PetscLayoutDestroy(&map);
    196:     PetscLayoutDestroy(&nmap);

    198:     VecCreateMPI(comm,slen,PETSC_DETERMINE,&red->b);
    199:     VecDuplicate(red->b,&red->x);
    200:     MatGetVecs(pc->pmat,&tvec,NULL);
    201:     VecScatterCreate(tvec,red->is,red->b,NULL,&red->scatter);
    202:     VecDestroy(&tvec);
    203:     MatGetSubMatrix(pc->pmat,red->is,red->is,MAT_INITIAL_MATRIX,&tmat);
    204:     KSPSetOperators(red->ksp,tmat,tmat,SAME_NONZERO_PATTERN);
    205:     MatDestroy(&tmat);
    206:   }

    208:   /* get diagonal portion of matrix */
    209:   PetscMalloc(red->dcnt*sizeof(PetscScalar),&red->diag);
    210:   MatGetVecs(pc->pmat,&diag,NULL);
    211:   MatGetDiagonal(pc->pmat,diag);
    212:   VecGetArrayRead(diag,&d);
    213:   for (i=0; i<red->dcnt; i++) red->diag[i] = 1.0/d[red->drows[i]];
    214:   VecRestoreArrayRead(diag,&d);
    215:   VecDestroy(&diag);
    216:   KSPSetUp(red->ksp);
    217:   return(0);
    218: }

    222: static PetscErrorCode PCApply_Redistribute(PC pc,Vec b,Vec x)
    223: {
    224:   PC_Redistribute   *red = (PC_Redistribute*)pc->data;
    225:   PetscErrorCode    ierr;
    226:   PetscInt          dcnt   = red->dcnt,i;
    227:   const PetscInt    *drows = red->drows;
    228:   PetscScalar       *xwork;
    229:   const PetscScalar *bwork,*diag = red->diag;

    232:   if (!red->work) {
    233:     VecDuplicate(b,&red->work);
    234:   }
    235:   /* compute the rows of solution that have diagonal entries only */
    236:   VecSet(x,0.0);         /* x = diag(A)^{-1} b */
    237:   VecGetArray(x,&xwork);
    238:   VecGetArrayRead(b,&bwork);
    239:   for (i=0; i<dcnt; i++) xwork[drows[i]] = diag[i]*bwork[drows[i]];
    240:   PetscLogFlops(dcnt);
    241:   VecRestoreArray(red->work,&xwork);
    242:   VecRestoreArrayRead(b,&bwork);
    243:   /* update the right hand side for the reduced system with diagonal rows (and corresponding columns) removed */
    244:   MatMult(pc->pmat,x,red->work);
    245:   VecAYPX(red->work,-1.0,b);   /* red->work = b - A x */

    247:   VecScatterBegin(red->scatter,red->work,red->b,INSERT_VALUES,SCATTER_FORWARD);
    248:   VecScatterEnd(red->scatter,red->work,red->b,INSERT_VALUES,SCATTER_FORWARD);
    249:   KSPSolve(red->ksp,red->b,red->x);
    250:   VecScatterBegin(red->scatter,red->x,x,INSERT_VALUES,SCATTER_REVERSE);
    251:   VecScatterEnd(red->scatter,red->x,x,INSERT_VALUES,SCATTER_REVERSE);
    252:   return(0);
    253: }

    257: static PetscErrorCode PCDestroy_Redistribute(PC pc)
    258: {
    259:   PC_Redistribute *red = (PC_Redistribute*)pc->data;
    260:   PetscErrorCode  ierr;

    263:   VecScatterDestroy(&red->scatter);
    264:   ISDestroy(&red->is);
    265:   VecDestroy(&red->b);
    266:   VecDestroy(&red->x);
    267:   KSPDestroy(&red->ksp);
    268:   VecDestroy(&red->work);
    269:   PetscFree(red->drows);
    270:   PetscFree(red->diag);
    271:   PetscFree(pc->data);
    272:   return(0);
    273: }

    277: static PetscErrorCode PCSetFromOptions_Redistribute(PC pc)
    278: {
    279:   PetscErrorCode  ierr;
    280:   PC_Redistribute *red = (PC_Redistribute*)pc->data;

    283:   KSPSetFromOptions(red->ksp);
    284:   return(0);
    285: }

    289: /*@
    290:    PCRedistributeGetKSP - Gets the KSP created by the PCREDISTRIBUTE

    292:    Not Collective

    294:    Input Parameter:
    295: .  pc - the preconditioner context

    297:    Output Parameter:
    298: .  innerksp - the inner KSP

    300:    Level: advanced

    302: .keywords: PC, redistribute solve
    303: @*/
    304: PetscErrorCode  PCRedistributeGetKSP(PC pc,KSP *innerksp)
    305: {
    306:   PC_Redistribute *red = (PC_Redistribute*)pc->data;

    311:   *innerksp = red->ksp;
    312:   return(0);
    313: }

    315: /* -------------------------------------------------------------------------------------*/
    316: /*MC
    317:      PCREDISTRIBUTE - Redistributes a matrix for load balancing, removing the rows that only have a diagonal entry and then applys a KSP to that new matrix

    319:      Options for the redistribute preconditioners can be set with -redistribute_ksp_xxx <values> and -redistribute_pc_xxx <values>

    321:      Notes:  Usually run this with -ksp_type preonly

    323:      If you have used MatZeroRows() to eliminate (for example, Dirichlet) boundary conditions for a symmetric problem then you can use, for example, -ksp_type preonly
    324:      -pc_type redistribute -redistribute_ksp_type cg -redistribute_pc_type bjacobi -redistribute_sub_pc_type icc to take advantage of the symmetry.

    326:      This does NOT call a partitioner to reorder rows to lower communication; the ordering of the rows in the original matrix and redistributed matrix is the same.

    328:      Developer Notes: Should add an option to this preconditioner to use a partitioner to redistribute the rows to lower communication.

    330:    Level: intermediate

    332: .seealso:  PCCreate(), PCSetType(), PCType (for list of available types), PCRedistributeGetKSP()
    333: M*/

    337: PETSC_EXTERN PetscErrorCode PCCreate_Redistribute(PC pc)
    338: {
    339:   PetscErrorCode  ierr;
    340:   PC_Redistribute *red;
    341:   const char      *prefix;

    344:   PetscNewLog(pc,PC_Redistribute,&red);
    345:   pc->data = (void*)red;

    347:   pc->ops->apply          = PCApply_Redistribute;
    348:   pc->ops->applytranspose = 0;
    349:   pc->ops->setup          = PCSetUp_Redistribute;
    350:   pc->ops->destroy        = PCDestroy_Redistribute;
    351:   pc->ops->setfromoptions = PCSetFromOptions_Redistribute;
    352:   pc->ops->view           = PCView_Redistribute;

    354:   KSPCreate(PetscObjectComm((PetscObject)pc),&red->ksp);
    355:   PetscObjectIncrementTabLevel((PetscObject)red->ksp,(PetscObject)pc,1);
    356:   PetscLogObjectParent(pc,red->ksp);
    357:   PCGetOptionsPrefix(pc,&prefix);
    358:   KSPSetOptionsPrefix(red->ksp,prefix);
    359:   KSPAppendOptionsPrefix(red->ksp,"redistribute_");
    360:   return(0);
    361: }