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