Date: 2016-07-24T16:58:24+00:00

Actual source code: hierarchical.c
petsc-3.7.3 2016-07-24
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      2: #include <../src/mat/impls/adj/mpi/mpiadj.h>    /*I "petscmat.h" I*/
      3: #include <petscsf.h>
      4: #include <petsc/private/matimpl.h>

      6: /*
      7:   It is a hierarchical partitioning. The partitioner has two goals:
      8:   (1) Most of current partitioners fail at a large scale. The hierarchical partitioning
      9:   strategy is trying to produce large number of subdomains when number of processor cores is large.
     10:   (2) PCGASM needs one 'big' subdomain across multi-cores. The partitioner provides two
     11:   consistent partitions, coarse parts and fine parts. A coarse part is a 'big' subdomain consisting
     12:   of several small subdomains.
     13: */

     15: PetscErrorCode MatPartitioningHierarchical_DetermineDestination(MatPartitioning part, IS partitioning, PetscInt pstart, PetscInt pend, IS *destination);
     16: PetscErrorCode MatPartitioningHierarchical_AssembleSubdomain(Mat adj,IS destination,Mat *sadj, ISLocalToGlobalMapping *mapping);
     17: PetscErrorCode MatPartitioningHierarchical_ReassembleFineparts(Mat adj, IS fineparts, ISLocalToGlobalMapping mapping, IS *sfineparts);

     19: typedef struct {
     20:   char*                fineparttype; /* partitioner on fine level */
     21:   char*                coarseparttype; /* partitioner on coarse level */
     22:   PetscInt             Nfineparts; /* number of fine parts on each coarse subdomain */
     23:   PetscInt             Ncoarseparts; /* number of coarse parts */
     24:   IS                   coarseparts; /* partitioning on coarse level */
     25:   IS                   fineparts; /* partitioning on fine level */
     26: } MatPartitioning_Hierarchical;

     28: /*
     29:    Uses a hierarchical partitioning strategy to partition the matrix in parallel.
     30:    Use this interface to make the partitioner consistent with others
     31: */
     34: static PetscErrorCode MatPartitioningApply_Hierarchical(MatPartitioning part,IS *partitioning)
     35: {
     36:   MatPartitioning_Hierarchical *hpart  = (MatPartitioning_Hierarchical*)part->data;
     37:   const PetscInt               *fineparts_indices, *coarseparts_indices;
     38:   PetscInt                     *parts_indices,i,j,mat_localsize;
     39:   Mat                           mat    = part->adj,adj,sadj;
     40:   PetscBool                     flg;
     41:   PetscInt                      bs     = 1;
     42:   MatPartitioning               finePart, coarsePart;
     43:   PetscInt                     *coarse_vertex_weights = 0;
     44:   PetscMPIInt                   size,rank;
     45:   MPI_Comm                      comm,scomm;
     46:   IS                            destination,fineparts_temp;
     47:   ISLocalToGlobalMapping        mapping;
     48:   PetscErrorCode                ierr;

     51:   PetscObjectGetComm((PetscObject)part,&comm);
     52:   MPI_Comm_size(comm,&size);
     53:   MPI_Comm_rank(comm,&rank);
     54:   PetscObjectTypeCompare((PetscObject)mat,MATMPIADJ,&flg);
     55:   if (flg) {
     56:     adj = mat;
     57:     PetscObjectReference((PetscObject)adj);
     58:   }else {
     59:     /* bs indicates if the converted matrix is "reduced" from the original and hence the
     60:        resulting partition results need to be stretched to match the original matrix */
     61:    MatConvert(mat,MATMPIADJ,MAT_INITIAL_MATRIX,&adj);
     62:    if (adj->rmap->n > 0) bs = mat->rmap->n/adj->rmap->n;
     63:   }
     64:   /* local size of mat */
     65:   mat_localsize = adj->rmap->n;
     66:   /* check parameters */
     67:   /* how many small subdomains we want from a given 'big' suddomain */
     68:   if(!hpart->Nfineparts) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG," must set number of small subdomains for each big subdomain \n");
     69:   if(!hpart->Ncoarseparts && !part->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE," did not either set number of coarse parts or total number of parts \n");
     70:   if(part->n && part->n%hpart->Nfineparts!=0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,
     71:                    " total number of parts %D can not be divided by number of fine parts %D\n",part->n,hpart->Nfineparts);
     72:   if(part->n){
     73:     hpart->Ncoarseparts = part->n/hpart->Nfineparts;
     74:   }else{
     75:         part->n = hpart->Ncoarseparts*hpart->Nfineparts;
     76:   }
     77:    /* we do not support this case currently, but this restriction should be
     78:      * removed in the further
     79:      * */
     80:   if(hpart->Ncoarseparts>size) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_SUP," we do not support number of coarse parts %D > size %D \n",hpart->Ncoarseparts,size);
     81:   MatPartitioningCreate(comm,&coarsePart);
     82:     /* if did not set partitioning type yet, use parmetis by default */
     83:   if(!hpart->coarseparttype){
     84:         MatPartitioningSetType(coarsePart,MATPARTITIONINGPARMETIS);
     85:   }else{
     86:         MatPartitioningSetType(coarsePart,hpart->coarseparttype);
     87:   }
     88:   MatPartitioningSetAdjacency(coarsePart,adj);
     89:   MatPartitioningSetNParts(coarsePart, hpart->Ncoarseparts);
     90:   /* copy over vertex weights */
     91:   if(part->vertex_weights){
     92:    PetscMalloc(sizeof(PetscInt)*mat_localsize,&coarse_vertex_weights);
     93:    PetscMemcpy(coarse_vertex_weights,part->vertex_weights,sizeof(PetscInt)*mat_localsize);
     94:    MatPartitioningSetVertexWeights(coarsePart,coarse_vertex_weights);
     95:   }
     96:   /* It looks nontrivial to support part weights,
     97:    * I will return back to implement it when have
     98:    * an idea.
     99:    *  */
    100:   MatPartitioningApply(coarsePart,&hpart->coarseparts);
    101:   MatPartitioningDestroy(&coarsePart);
    102:   /* In the current implementation, destination should be the same as hpart->coarseparts,
    103:    * and this interface is preserved to deal with the case hpart->coarseparts>size in the
    104:    * future.
    105:    * */
    106:   MatPartitioningHierarchical_DetermineDestination(part,hpart->coarseparts,0,hpart->Ncoarseparts,&destination);
    107:   /* assemble a submatrix for partitioning subdomains  */
    108:   MatPartitioningHierarchical_AssembleSubdomain(adj,destination,&sadj,&mapping);
    109:   ISDestroy(&destination);
    110:   PetscObjectGetComm((PetscObject)sadj,&scomm);
    111:   /* create a fine partitioner */
    112:   MatPartitioningCreate(scomm,&finePart);
    113:   /* if do not set partitioning type, use parmetis by default */
    114:   if(!hpart->fineparttype){
    115:     MatPartitioningSetType(finePart,MATPARTITIONINGPARMETIS);
    116:   }else{
    117:     MatPartitioningSetType(finePart,hpart->fineparttype);
    118:   }
    119:   MatPartitioningSetAdjacency(finePart,sadj);
    120:   MatPartitioningSetNParts(finePart, hpart->Nfineparts);
    121:   MatPartitioningApply(finePart,&fineparts_temp);
    122:   MatDestroy(&sadj);
    123:   MatPartitioningDestroy(&finePart);
    124:   MatPartitioningHierarchical_ReassembleFineparts(adj,fineparts_temp,mapping,&hpart->fineparts);
    125:   ISDestroy(&fineparts_temp);
    126:   ISLocalToGlobalMappingDestroy(&mapping);

    128:   ISGetIndices(hpart->fineparts,&fineparts_indices);
    129:   ISGetIndices(hpart->coarseparts,&coarseparts_indices);
    130:   PetscMalloc1(bs*adj->rmap->n,&parts_indices);
    131:   for(i=0; i<adj->rmap->n; i++){
    132:     for(j=0; j<bs; j++){
    133:       parts_indices[bs*i+j] = fineparts_indices[i]+coarseparts_indices[i]*hpart->Nfineparts;
    134:     }
    135:   }
    136:   ISCreateGeneral(comm,bs*adj->rmap->n,parts_indices,PETSC_OWN_POINTER,partitioning);
    137:   MatDestroy(&adj);
    138:   return(0);
    139: }

    144: PetscErrorCode MatPartitioningHierarchical_ReassembleFineparts(Mat adj, IS fineparts, ISLocalToGlobalMapping mapping, IS *sfineparts)
    145: {
    146:   PetscInt            *local_indices, *global_indices,*owners,*sfineparts_indices,localsize,i;
    147:   const PetscInt      *ranges,*fineparts_indices;
    148:   PetscMPIInt         rank;
    149:   MPI_Comm            comm;
    150:   PetscLayout         rmap;
    151:   PetscSFNode        *remote;
    152:   PetscSF             sf;
    153:   PetscErrorCode      ierr;

    156:   PetscObjectGetComm((PetscObject)adj,&comm);
    157:   MPI_Comm_rank(comm,&rank);
    158:   MatGetLayouts(adj,&rmap,PETSC_NULL);
    159:   ISGetLocalSize(fineparts,&localsize);
    160:   PetscCalloc2(localsize,&global_indices,localsize,&local_indices);
    161:   for(i=0; i<localsize; i++){
    162:         local_indices[i] = i;
    163:   }
    164:   /* map local indices back to global so that we can permulate data globally */
    165:   ISLocalToGlobalMappingApply(mapping,localsize,local_indices,global_indices);
    166:   PetscCalloc1(localsize,&owners);
    167:   /* find owners for global indices */
    168:   for(i=0; i<localsize; i++){
    169:         PetscLayoutFindOwner(rmap,global_indices[i],&owners[i]);
    170:   }
    171:   PetscLayoutGetRanges(rmap,&ranges);
    172:   PetscCalloc1(ranges[rank+1]-ranges[rank],&sfineparts_indices);
    173:   ISGetIndices(fineparts,&fineparts_indices);
    174:   PetscSFCreate(comm,&sf);
    175:   PetscCalloc1(localsize,&remote);
    176:   for(i=0; i<localsize; i++){
    177:         remote[i].rank  = owners[i];
    178:         remote[i].index = global_indices[i]-ranges[owners[i]];
    179:   }
    180:   PetscSFSetType(sf,PETSCSFBASIC);
    181:   /* not sure how to add prefix to sf */
    182:   PetscSFSetFromOptions(sf);
    183:   PetscSFSetGraph(sf,localsize,localsize,PETSC_NULL,PETSC_OWN_POINTER,remote,PETSC_OWN_POINTER);
    184:   PetscSFReduceBegin(sf,MPIU_INT,fineparts_indices,sfineparts_indices,MPIU_REPLACE);
    185:   PetscSFReduceEnd(sf,MPIU_INT,fineparts_indices,sfineparts_indices,MPIU_REPLACE);
    186:   PetscSFDestroy(&sf);
    187:   ISRestoreIndices(fineparts,&fineparts_indices);
    188:   ISCreateGeneral(comm,ranges[rank+1]-ranges[rank],sfineparts_indices,PETSC_OWN_POINTER,sfineparts);
    189:   PetscFree2(global_indices,local_indices);
    190:   PetscFree(owners);
    191:   return(0);
    192: }

    197: PetscErrorCode MatPartitioningHierarchical_AssembleSubdomain(Mat adj,IS destination,Mat *sadj, ISLocalToGlobalMapping *mapping)
    198: {
    199:   IS              irows,icols;
    200:   PetscInt        irows_ln;
    201:   PetscMPIInt     rank;
    202:   const PetscInt *irows_indices;
    203:   MPI_Comm        comm;
    204:   PetscErrorCode  ierr;

    207:   PetscObjectGetComm((PetscObject)adj,&comm);
    208:   MPI_Comm_rank(comm,&rank);
    209:   /* figure out where data comes from  */
    210:   ISBuildTwoSided(destination,NULL,&irows);
    211:   ISDuplicate(irows,&icols);
    212:   ISGetLocalSize(irows,&irows_ln);
    213:   ISGetIndices(irows,&irows_indices);
    214:   ISLocalToGlobalMappingCreate(comm,1,irows_ln,irows_indices,PETSC_COPY_VALUES,mapping);
    215:   ISRestoreIndices(irows,&irows_indices);
    216:   MatGetSubMatrices(adj,1,&irows,&icols,MAT_INITIAL_MATRIX,&sadj);
    217:   ISDestroy(&irows);
    218:   ISDestroy(&icols);
    219:   return(0);
    220: }

    225: PetscErrorCode MatPartitioningHierarchical_DetermineDestination(MatPartitioning part, IS partitioning, PetscInt pstart, PetscInt pend, IS *destination)
    226: {
    227:   MPI_Comm            comm;
    228:   PetscMPIInt         rank,size,target;
    229:   PetscInt            plocalsize,*dest_indices,i;
    230:   const PetscInt     *part_indices;
    231:   PetscErrorCode      ierr;

    234:   PetscObjectGetComm((PetscObject)part,&comm);
    235:   MPI_Comm_rank(comm,&rank);
    236:   MPI_Comm_size(comm,&size);
    237:   if((pend-pstart)>size) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"range [%D, %D] should be smaller than or equal to size %D",pstart,pend,size);
    238:   if(pstart>pend) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP," pstart %D should be smaller than pend %D",pstart,pend);
    239:   ISGetLocalSize(partitioning,&plocalsize);
    240:   PetscCalloc1(plocalsize,&dest_indices);
    241:   ISGetIndices(partitioning,&part_indices);
    242:   for(i=0; i<plocalsize; i++){
    243:         /* compute target */
    244:     target = part_indices[i]-pstart;
    245:     /* mark out of range entity as -1 */
    246:     if(part_indices[i]<pstart || part_indices[i]>pend) target = -1;
    247:         dest_indices[i] = target;
    248:   }
    249:   ISCreateGeneral(comm,plocalsize,dest_indices,PETSC_OWN_POINTER,destination);
    250:   return(0);
    251: }

    256: PetscErrorCode MatPartitioningView_Hierarchical(MatPartitioning part,PetscViewer viewer)
    257: {
    258:   MatPartitioning_Hierarchical *hpart = (MatPartitioning_Hierarchical*)part->data;
    259:   PetscErrorCode           ierr;
    260:   PetscMPIInt              rank;
    261:   PetscBool                iascii;

    264:   MPI_Comm_rank(PetscObjectComm((PetscObject)part),&rank);
    265:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);
    266:   if(iascii){
    267:          PetscViewerASCIIPrintf(viewer," Fine partitioner %s \n",hpart->fineparttype);
    268:          PetscViewerASCIIPrintf(viewer," Coarse partitioner %s \n",hpart->coarseparttype);
    269:          PetscViewerASCIIPrintf(viewer," Number of coarse parts %D \n",hpart->Ncoarseparts);
    270:          PetscViewerASCIIPrintf(viewer," Number of fine parts %D \n",hpart->Nfineparts);
    271:   }
    272:   return(0);
    273: }

    278: PetscErrorCode MatPartitioningHierarchicalGetFineparts(MatPartitioning part,IS *fineparts)
    279: {
    280:   MatPartitioning_Hierarchical *hpart = (MatPartitioning_Hierarchical*)part->data;
    281:   PetscErrorCode                ierr;

    284:   *fineparts = hpart->fineparts;
    285:   PetscObjectReference((PetscObject)hpart->fineparts);
    286:   return(0);
    287: }

    291: PetscErrorCode MatPartitioningHierarchicalGetCoarseparts(MatPartitioning part,IS *coarseparts)
    292: {
    293:   MatPartitioning_Hierarchical *hpart = (MatPartitioning_Hierarchical*)part->data;
    294:   PetscErrorCode                ierr;

    297:   *coarseparts = hpart->coarseparts;
    298:   PetscObjectReference((PetscObject)hpart->coarseparts);
    299:   return(0);
    300: }

    304: PetscErrorCode MatPartitioningHierarchicalSetNcoarseparts(MatPartitioning part, PetscInt Ncoarseparts)
    305: {
    306:   MatPartitioning_Hierarchical *hpart = (MatPartitioning_Hierarchical*)part->data;

    309:   hpart->Ncoarseparts = Ncoarseparts;
    310:   return(0);
    311: }

    315: PetscErrorCode MatPartitioningHierarchicalSetNfineparts(MatPartitioning part, PetscInt Nfineparts)
    316: {
    317:   MatPartitioning_Hierarchical *hpart = (MatPartitioning_Hierarchical*)part->data;

    320:   hpart->Nfineparts = Nfineparts;
    321:   return(0);
    322: }

    326: PetscErrorCode MatPartitioningSetFromOptions_Hierarchical(PetscOptionItems *PetscOptionsObject,MatPartitioning part)
    327: {
    328:   MatPartitioning_Hierarchical *hpart = (MatPartitioning_Hierarchical*)part->data;
    330:   char           value[1024];
    331:   PetscBool      flag = PETSC_FALSE;

    334:   PetscOptionsHead(PetscOptionsObject,"Set hierarchical partitioning options");
    335:   PetscOptionsString("-mat_partitioning_hierarchical_coarseparttype","coarse part type",PETSC_NULL,PETSC_NULL,value,1024,&flag);
    336:   if(flag){
    337:    PetscCalloc1(1024,&hpart->coarseparttype);
    338:    PetscStrcpy(hpart->coarseparttype,value);
    339:   }
    340:   PetscOptionsString("-mat_partitioning_hierarchical_fineparttype","fine part type",PETSC_NULL,PETSC_NULL,value,1024,&flag);
    341:   if(flag){
    342:     PetscCalloc1(1024,&hpart->fineparttype);
    343:     PetscStrcpy(hpart->fineparttype,value);
    344:   }
    345:   PetscOptionsInt("-mat_partitioning_hierarchical_Ncoarseparts","number of coarse parts",PETSC_NULL,0,&hpart->Ncoarseparts,&flag);
    346:   PetscOptionsInt("-mat_partitioning_hierarchical_Nfineparts","number of fine parts",PETSC_NULL,1,&hpart->Nfineparts,&flag);
    347:   PetscOptionsTail();
    348:   return(0);
    349: }

    354: PetscErrorCode MatPartitioningDestroy_Hierarchical(MatPartitioning part)
    355: {
    356:   MatPartitioning_Hierarchical *hpart = (MatPartitioning_Hierarchical*)part->data;
    357:   PetscErrorCode           ierr;

    360:   if(hpart->coarseparttype) {PetscFree(hpart->coarseparttype);}
    361:   if(hpart->fineparttype) {PetscFree(hpart->fineparttype);}
    362:   ISDestroy(&hpart->fineparts);
    363:   ISDestroy(&hpart->coarseparts);
    364:   PetscFree(hpart);
    365:   return(0);
    366: }

    369: /*MC
    370:    MATPARTITIONINGHIERARCHPART - Creates a partitioning context via hierarchical partitioning strategy.

    372:    Collective on MPI_Comm

    374:    Input Parameter:
    375: .  part - the partitioning context

    377:    Options Database Keys:

    379:    Level: beginner

    381: .keywords: Partitioning, create, context

    383: .seealso: MatPartitioningSetType(), MatPartitioningType

    385: M*/

    389: PETSC_EXTERN PetscErrorCode MatPartitioningCreate_Hierarchical(MatPartitioning part)
    390: {
    391:   PetscErrorCode                ierr;
    392:   MatPartitioning_Hierarchical *hpart;

    395:   PetscNewLog(part,&hpart);
    396:   part->data = (void*)hpart;

    398:   hpart->fineparttype       = 0; /* fine level partitioner */
    399:   hpart->coarseparttype     = 0; /* coarse level partitioner */
    400:   hpart->Nfineparts         = 1; /* we do not further partition coarse partition any more by default */
    401:   hpart->Ncoarseparts       = 0; /* number of coarse parts (first level) */
    402:   hpart->coarseparts        = 0;
    403:   hpart->fineparts          = 0;

    405:   part->ops->apply          = MatPartitioningApply_Hierarchical;
    406:   part->ops->view           = MatPartitioningView_Hierarchical;
    407:   part->ops->destroy        = MatPartitioningDestroy_Hierarchical;
    408:   part->ops->setfromoptions = MatPartitioningSetFromOptions_Hierarchical;
    409:   return(0);
    410: }