1 #include <petscsf.h> 2 #include <petsc/private/matimpl.h> 3 4 5 #undef __FUNCT__ 6 #define __FUNCT__ "MatIncreaseOverlapSplit_Single" 7 8 /* 9 * Increase overlap for the sub-matrix across sub communicator 10 * sub-matrix could be a graph or numerical matrix 11 * */ 12 PetscErrorCode MatIncreaseOverlapSplit_Single(Mat mat,IS *is,PetscInt ov) 13 { 14 PetscInt i,nindx,*indices_sc,*indices_ov,localsize,*localsizes_sc,localsize_tmp; 15 PetscInt *indices_ov_rd,nroots,nleaves,*localoffsets,*indices_recv,*sources_sc,*sources_sc_rd; 16 const PetscInt *indices; 17 PetscMPIInt srank,ssize,issamecomm,k; 18 IS is_sc,allis_sc,partitioning; 19 MPI_Comm gcomm,scomm; 20 PetscSF sf; 21 PetscSFNode *remote; 22 Mat *smat; 23 MatPartitioning part; 24 PetscErrorCode ierr; 25 26 PetscFunctionBegin; 27 /* get a sub communicator before call individual MatIncreaseOverlap 28 * since the sub communicator may be changed. 29 * */ 30 ierr = PetscObjectGetComm((PetscObject)*is,&scomm);CHKERRQ(ierr); 31 /*get a global communicator, where mat should be a global matrix */ 32 ierr = PetscObjectGetComm((PetscObject)mat,&gcomm);CHKERRQ(ierr); 33 #if 1 34 ierr = PetscPrintf(gcomm,"before mat->ops->increaseoverlap\n");CHKERRQ(ierr); 35 #endif 36 /*increase overlap on each individual subdomain*/ 37 ierr = (*mat->ops->increaseoverlap)(mat,1,is,ov);CHKERRQ(ierr); 38 #if 1 39 ierr = PetscPrintf(gcomm,"after mat->ops->increaseoverlap \n");CHKERRQ(ierr); 40 ierr = ISView(*is,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 41 #endif 42 /*compare communicators */ 43 ierr = MPI_Comm_compare(gcomm,scomm,&issamecomm);CHKERRQ(ierr); 44 /* if the sub-communicator is the same as the global communicator, 45 * user does not want to use a sub-communicator 46 * */ 47 if(issamecomm == MPI_IDENT) PetscFunctionReturn(0); 48 /* if the sub-communicator is petsc_comm_self, 49 * user also does not care the sub-communicator 50 * */ 51 ierr = MPI_Comm_compare(scomm,PETSC_COMM_SELF,&issamecomm);CHKERRQ(ierr); 52 if(issamecomm == MPI_IDENT) PetscFunctionReturn(0); 53 /*local rank, size in a sub-communicator */ 54 ierr = MPI_Comm_rank(scomm,&srank);CHKERRQ(ierr); 55 ierr = MPI_Comm_size(scomm,&ssize);CHKERRQ(ierr); 56 /*create a new IS based on sub-communicator 57 * since the old IS is often based on petsc_comm_self 58 * */ 59 ierr = ISGetLocalSize(*is,&nindx);CHKERRQ(ierr); 60 ierr = PetscCalloc1(nindx,&indices_sc);CHKERRQ(ierr); 61 ierr = ISGetIndices(*is,&indices);CHKERRQ(ierr); 62 ierr = PetscMemcpy(indices_sc,indices,sizeof(PetscInt)*nindx);CHKERRQ(ierr); 63 ierr = ISRestoreIndices(*is,&indices);CHKERRQ(ierr); 64 /*we do not need any more*/ 65 ierr = ISDestroy(is);CHKERRQ(ierr); 66 /*create a index set based on the sub communicator */ 67 ierr = ISCreateGeneral(scomm,nindx,indices_sc,PETSC_OWN_POINTER,&is_sc);CHKERRQ(ierr); 68 /*gather all indices within the sub communicator*/ 69 ierr = ISAllGather(is_sc,&allis_sc);CHKERRQ(ierr); 70 ierr = ISDestroy(&is_sc);CHKERRQ(ierr); 71 /* gather local sizes */ 72 ierr = PetscMalloc1(ssize,&localsizes_sc);CHKERRQ(ierr); 73 /*get individual local sizes for all index sets*/ 74 ierr = MPI_Gather(&nindx,1,MPIU_INT,localsizes_sc,1,MPIU_INT,0,scomm);CHKERRQ(ierr); 75 /*only root does these computations */ 76 if(!srank){ 77 /*get local size for the big index set*/ 78 ierr = ISGetLocalSize(allis_sc,&localsize);CHKERRQ(ierr); 79 ierr = PetscCalloc2(localsize,&indices_ov,localsize,&sources_sc);CHKERRQ(ierr); 80 ierr = PetscCalloc2(localsize,&indices_ov_rd,localsize,&sources_sc_rd);CHKERRQ(ierr); 81 ierr = ISGetIndices(allis_sc,&indices);CHKERRQ(ierr); 82 ierr = PetscMemcpy(indices_ov,indices,sizeof(PetscInt)*localsize);CHKERRQ(ierr); 83 ierr = ISRestoreIndices(allis_sc,&indices);CHKERRQ(ierr); 84 /*we do not need it any more */ 85 ierr = ISDestroy(&allis_sc);CHKERRQ(ierr); 86 /*assign corresponding sources */ 87 localsize_tmp = 0; 88 for(k=0; k<ssize; k++){ 89 for(i=0; i<localsizes_sc[k]; i++){ 90 sources_sc[localsize_tmp++] = k; 91 } 92 } 93 /*record where indices come from */ 94 ierr = PetscSortIntWithArray(localsize,indices_ov,sources_sc);CHKERRQ(ierr); 95 /*count local sizes for reduced indices */ 96 ierr = PetscMemzero(localsizes_sc,sizeof(PetscInt)*ssize);CHKERRQ(ierr); 97 /*initialize the first entity*/ 98 if(localsize){ 99 indices_ov_rd[0] = indices_ov[0]; 100 sources_sc_rd[0] = sources_sc[0]; 101 localsizes_sc[sources_sc[0]]++; 102 } 103 localsize_tmp = 1; 104 /*remove duplicate integers */ 105 for(i=1; i<localsize; i++){ 106 if(indices_ov[i] != indices_ov[i-1]){ 107 indices_ov_rd[localsize_tmp] = indices_ov[i]; 108 sources_sc_rd[localsize_tmp++] = sources_sc[i]; 109 localsizes_sc[sources_sc[i]]++; 110 } 111 } 112 ierr = PetscFree2(indices_ov,sources_sc);CHKERRQ(ierr); 113 ierr = PetscCalloc1(ssize+1,&localoffsets);CHKERRQ(ierr); 114 for(k=0; k<ssize; k++){ 115 localoffsets[k+1] = localoffsets[k] + localsizes_sc[i]; 116 } 117 /*construct a star forest to send data back */ 118 nleaves = localoffsets[ssize]; 119 ierr = PetscMemzero(localoffsets,(ssize+1)*sizeof(PetscInt));CHKERRQ(ierr); 120 nroots = localsizes_sc[srank]; 121 ierr = PetscCalloc1(nleaves,&remote);CHKERRQ(ierr); 122 for(i=0; i<nleaves; i++){ 123 remote[i].rank = sources_sc_rd[i]; 124 remote[i].index = localoffsets[sources_sc_rd[i]]++; 125 } 126 ierr = PetscFree(localoffsets);CHKERRQ(ierr); 127 }else{ 128 ierr = ISDestroy(&allis_sc);CHKERRQ(ierr); 129 nleaves = 0; 130 indices_ov_rd = 0; 131 sources_sc_rd = 0; 132 } 133 /*scatter sizes to everybody */ 134 ierr = MPI_Scatter(localsizes_sc,1, MPIU_INT,&nroots,1, MPIU_INT,0,scomm);CHKERRQ(ierr); 135 /*free memory */ 136 ierr = PetscFree(localsizes_sc);CHKERRQ(ierr); 137 ierr = PetscCalloc1(nroots,&indices_recv);CHKERRQ(ierr); 138 /*set data back to every body */ 139 ierr = PetscSFCreate(scomm,&sf);CHKERRQ(ierr); 140 ierr = PetscSFSetType(sf,PETSCSFBASIC);CHKERRQ(ierr); 141 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 142 ierr = PetscSFSetGraph(sf,nroots,nleaves,PETSC_NULL,PETSC_OWN_POINTER,remote,PETSC_OWN_POINTER);CHKERRQ(ierr); 143 ierr = PetscSFReduceBegin(sf,MPIU_INT,&indices_ov_rd,indices_recv,MPIU_REPLACE);CHKERRQ(ierr); 144 ierr = PetscSFReduceEnd(sf,MPIU_INT,&indices_ov_rd,indices_recv,MPIU_REPLACE);CHKERRQ(ierr); 145 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 146 /* free memory */ 147 ierr = PetscFree2(indices_ov_rd,sources_sc_rd);CHKERRQ(ierr); 148 /*create a index set*/ 149 ierr = ISCreateGeneral(scomm,nroots,indices_recv,PETSC_OWN_POINTER,&is_sc);CHKERRQ(ierr); 150 /*create a index set for cols */ 151 ierr = ISAllGather(is_sc,&allis_sc);CHKERRQ(ierr); 152 /*construct a parallel submatrix */ 153 ierr = PetscCalloc1(1,&smat);CHKERRQ(ierr); 154 ierr = MatGetSubMatricesMPI(mat,1,&is_sc,&allis_sc,MAT_INITIAL_MATRIX,&smat);CHKERRQ(ierr); 155 /* we do not need them any more */ 156 ierr = ISDestroy(&is_sc);CHKERRQ(ierr); 157 ierr = ISDestroy(&allis_sc);CHKERRQ(ierr); 158 /*create a partitioner to repartition the sub-matrix*/ 159 ierr = MatPartitioningCreate(scomm,&part);CHKERRQ(ierr); 160 ierr = MatPartitioningSetAdjacency(part,smat[0]);CHKERRQ(ierr); 161 #if PETSC_HAVE_PARMETIS 162 /* if there exists a ParMETIS installation, we try to use ParMETIS 163 * because a repartition routine possibly work better 164 * */ 165 ierr = MatPartitioningSetType(part,MATPARTITIONINGPARMETIS);CHKERRQ(ierr); 166 /*try to use reparition function, instead of partition function */ 167 ierr = MatPartitioningParmetisSetRepartition(part);CHKERRQ(ierr); 168 #else 169 /*we at least provide a default partitioner to rebalance the computation */ 170 ierr = MatPartitioningSetType(part,MATPARTITIONINGAVERAGE);CHKERRQ(ierr); 171 #endif 172 /*user can pick up any partitioner by using an option*/ 173 ierr = MatPartitioningSetFromOptions(part);CHKERRQ(ierr); 174 /* apply partition */ 175 ierr = MatPartitioningApply(part,&partitioning);CHKERRQ(ierr); 176 ierr = MatPartitioningDestroy(&part);CHKERRQ(ierr); 177 ierr = MatDestroy(&(smat[0]));CHKERRQ(ierr); 178 ierr = PetscFree(smat);CHKERRQ(ierr); 179 /* get local rows including overlap */ 180 ierr = ISBuildTwoSided(partitioning,is);CHKERRQ(ierr); 181 PetscFunctionReturn(0); 182 } 183 184 185