1 #include <petsc/private/partitionerimpl.h> /*I "petscpartitioner.h" I*/ 2 3 #if defined(PETSC_HAVE_PARMETIS) 4 #include <parmetis.h> 5 #endif 6 7 PetscBool ParMetisPartitionerCite = PETSC_FALSE; 8 const char ParMetisPartitionerCitation[] = "@article{KarypisKumar98,\n" 9 " author = {George Karypis and Vipin Kumar},\n" 10 " title = {A Parallel Algorithm for Multilevel Graph Partitioning and Sparse Matrix Ordering},\n" 11 " journal = {Journal of Parallel and Distributed Computing},\n" 12 " volume = {48},\n" 13 " pages = {71--85},\n" 14 " year = {1998}\n" 15 " doi = {https://doi.org/10.1006/jpdc.1997.1403}\n" 16 "}\n"; 17 18 typedef struct { 19 MPI_Comm pcomm; 20 PetscInt ptype; 21 PetscReal imbalanceRatio; 22 PetscInt debugFlag; 23 PetscInt randomSeed; 24 } PetscPartitioner_ParMetis; 25 26 static const char *ptypes[] = {"kway", "rb"}; 27 28 static PetscErrorCode PetscPartitionerDestroy_ParMetis(PetscPartitioner part) { 29 PetscPartitioner_ParMetis *p = (PetscPartitioner_ParMetis *)part->data; 30 31 PetscFunctionBegin; 32 PetscCallMPI(MPI_Comm_free(&p->pcomm)); 33 PetscCall(PetscFree(part->data)); 34 PetscFunctionReturn(0); 35 } 36 37 static PetscErrorCode PetscPartitionerView_ParMetis_ASCII(PetscPartitioner part, PetscViewer viewer) { 38 PetscPartitioner_ParMetis *p = (PetscPartitioner_ParMetis *)part->data; 39 40 PetscFunctionBegin; 41 PetscCall(PetscViewerASCIIPushTab(viewer)); 42 PetscCall(PetscViewerASCIIPrintf(viewer, "ParMetis type: %s\n", ptypes[p->ptype])); 43 PetscCall(PetscViewerASCIIPrintf(viewer, "load imbalance ratio %g\n", (double)p->imbalanceRatio)); 44 PetscCall(PetscViewerASCIIPrintf(viewer, "debug flag %" PetscInt_FMT "\n", p->debugFlag)); 45 PetscCall(PetscViewerASCIIPrintf(viewer, "random seed %" PetscInt_FMT "\n", p->randomSeed)); 46 PetscCall(PetscViewerASCIIPopTab(viewer)); 47 PetscFunctionReturn(0); 48 } 49 50 static PetscErrorCode PetscPartitionerView_ParMetis(PetscPartitioner part, PetscViewer viewer) { 51 PetscBool iascii; 52 53 PetscFunctionBegin; 54 PetscValidHeaderSpecific(part, PETSCPARTITIONER_CLASSID, 1); 55 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 56 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERASCII, &iascii)); 57 if (iascii) PetscCall(PetscPartitionerView_ParMetis_ASCII(part, viewer)); 58 PetscFunctionReturn(0); 59 } 60 61 static PetscErrorCode PetscPartitionerSetFromOptions_ParMetis(PetscPartitioner part, PetscOptionItems *PetscOptionsObject) { 62 PetscPartitioner_ParMetis *p = (PetscPartitioner_ParMetis *)part->data; 63 64 PetscFunctionBegin; 65 PetscOptionsHeadBegin(PetscOptionsObject, "PetscPartitioner ParMetis Options"); 66 PetscCall(PetscOptionsEList("-petscpartitioner_parmetis_type", "Partitioning method", "", ptypes, 2, ptypes[p->ptype], &p->ptype, NULL)); 67 PetscCall(PetscOptionsReal("-petscpartitioner_parmetis_imbalance_ratio", "Load imbalance ratio limit", "", p->imbalanceRatio, &p->imbalanceRatio, NULL)); 68 PetscCall(PetscOptionsInt("-petscpartitioner_parmetis_debug", "Debugging flag", "", p->debugFlag, &p->debugFlag, NULL)); 69 PetscCall(PetscOptionsInt("-petscpartitioner_parmetis_seed", "Random seed", "", p->randomSeed, &p->randomSeed, NULL)); 70 PetscOptionsHeadEnd(); 71 PetscFunctionReturn(0); 72 } 73 74 static PetscErrorCode PetscPartitionerPartition_ParMetis(PetscPartitioner part, PetscInt nparts, PetscInt numVertices, PetscInt start[], PetscInt adjacency[], PetscSection vertSection, PetscSection targetSection, PetscSection partSection, IS *partition) { 75 #if defined(PETSC_HAVE_PARMETIS) 76 PetscPartitioner_ParMetis *pm = (PetscPartitioner_ParMetis *)part->data; 77 MPI_Comm comm; 78 PetscInt nvtxs = numVertices; /* The number of vertices in full graph */ 79 PetscInt *vtxdist; /* Distribution of vertices across processes */ 80 PetscInt *xadj = start; /* Start of edge list for each vertex */ 81 PetscInt *adjncy = adjacency; /* Edge lists for all vertices */ 82 PetscInt *vwgt = NULL; /* Vertex weights */ 83 PetscInt *adjwgt = NULL; /* Edge weights */ 84 PetscInt wgtflag = 0; /* Indicates which weights are present */ 85 PetscInt numflag = 0; /* Indicates initial offset (0 or 1) */ 86 PetscInt ncon = 1; /* The number of weights per vertex */ 87 PetscInt metis_ptype = pm->ptype; /* kway or recursive bisection */ 88 real_t *tpwgts; /* The fraction of vertex weights assigned to each partition */ 89 real_t *ubvec; /* The balance intolerance for vertex weights */ 90 PetscInt options[64]; /* Options */ 91 PetscInt v, i, *assignment, *points; 92 PetscMPIInt p, size, rank; 93 PetscBool hasempty = PETSC_FALSE; 94 95 PetscFunctionBegin; 96 PetscCall(PetscObjectGetComm((PetscObject)part, &comm)); 97 PetscCallMPI(MPI_Comm_size(comm, &size)); 98 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 99 /* Calculate vertex distribution */ 100 PetscCall(PetscMalloc4(size + 1, &vtxdist, nparts * ncon, &tpwgts, ncon, &ubvec, nvtxs, &assignment)); 101 vtxdist[0] = 0; 102 PetscCallMPI(MPI_Allgather(&nvtxs, 1, MPIU_INT, &vtxdist[1], 1, MPIU_INT, comm)); 103 for (p = 2; p <= size; ++p) { 104 hasempty = (PetscBool)(hasempty || !vtxdist[p - 1] || !vtxdist[p]); 105 vtxdist[p] += vtxdist[p - 1]; 106 } 107 /* null graph */ 108 if (vtxdist[size] == 0) { 109 PetscCall(PetscFree4(vtxdist, tpwgts, ubvec, assignment)); 110 PetscCall(ISCreateGeneral(comm, 0, NULL, PETSC_OWN_POINTER, partition)); 111 PetscFunctionReturn(0); 112 } 113 /* Calculate partition weights */ 114 if (targetSection) { 115 PetscInt p; 116 real_t sumt = 0.0; 117 118 for (p = 0; p < nparts; ++p) { 119 PetscInt tpd; 120 121 PetscCall(PetscSectionGetDof(targetSection, p, &tpd)); 122 sumt += tpd; 123 tpwgts[p] = tpd; 124 } 125 if (sumt) { /* METIS/ParMETIS do not like exactly zero weight */ 126 for (p = 0, sumt = 0.0; p < nparts; ++p) { 127 tpwgts[p] = PetscMax(tpwgts[p], PETSC_SMALL); 128 sumt += tpwgts[p]; 129 } 130 for (p = 0; p < nparts; ++p) tpwgts[p] /= sumt; 131 for (p = 0, sumt = 0.0; p < nparts - 1; ++p) sumt += tpwgts[p]; 132 tpwgts[nparts - 1] = 1. - sumt; 133 } 134 } else { 135 for (p = 0; p < nparts; ++p) tpwgts[p] = 1.0 / nparts; 136 } 137 ubvec[0] = pm->imbalanceRatio; 138 139 /* Weight cells */ 140 if (vertSection) { 141 PetscCall(PetscMalloc1(nvtxs, &vwgt)); 142 for (v = 0; v < nvtxs; ++v) PetscCall(PetscSectionGetDof(vertSection, v, &vwgt[v])); 143 wgtflag |= 2; /* have weights on graph vertices */ 144 } 145 146 for (p = 0; !vtxdist[p + 1] && p < size; ++p) 147 ; 148 if (vtxdist[p + 1] == vtxdist[size]) { 149 if (rank == p) { 150 int err; 151 err = METIS_SetDefaultOptions(options); /* initialize all defaults */ 152 options[METIS_OPTION_DBGLVL] = pm->debugFlag; 153 options[METIS_OPTION_SEED] = pm->randomSeed; 154 PetscCheck(err == METIS_OK, PETSC_COMM_SELF, PETSC_ERR_LIB, "Error in METIS_SetDefaultOptions()"); 155 if (metis_ptype == 1) { 156 PetscStackPushExternal("METIS_PartGraphRecursive"); 157 err = METIS_PartGraphRecursive(&nvtxs, &ncon, xadj, adjncy, vwgt, NULL, adjwgt, &nparts, tpwgts, ubvec, options, &part->edgeCut, assignment); 158 PetscStackPop; 159 PetscCheck(err == METIS_OK, PETSC_COMM_SELF, PETSC_ERR_LIB, "Error in METIS_PartGraphRecursive()"); 160 } else { 161 /* 162 It would be nice to activate the two options below, but they would need some actual testing. 163 - Turning on these options may exercise path of the METIS code that have bugs and may break production runs. 164 - If CONTIG is set to 1, METIS will exit with error if the graph is disconnected, despite the manual saying the option is ignored in such case. 165 */ 166 /* options[METIS_OPTION_CONTIG] = 1; */ /* try to produce partitions that are contiguous */ 167 /* options[METIS_OPTION_MINCONN] = 1; */ /* minimize the maximum degree of the subdomain graph */ 168 PetscStackPushExternal("METIS_PartGraphKway"); 169 err = METIS_PartGraphKway(&nvtxs, &ncon, xadj, adjncy, vwgt, NULL, adjwgt, &nparts, tpwgts, ubvec, options, &part->edgeCut, assignment); 170 PetscStackPop; 171 PetscCheck(err == METIS_OK, PETSC_COMM_SELF, PETSC_ERR_LIB, "Error in METIS_PartGraphKway()"); 172 } 173 } 174 } else { 175 MPI_Comm pcomm = pm->pcomm; 176 177 options[0] = 1; /*use options */ 178 options[1] = pm->debugFlag; 179 options[2] = (pm->randomSeed == -1) ? 15 : pm->randomSeed; /* default is GLOBAL_SEED=15 from `libparmetis/defs.h` */ 180 181 if (hasempty) { /* parmetis does not support empty graphs on some of the processes */ 182 PetscInt cnt; 183 184 PetscCallMPI(MPI_Comm_split(pm->pcomm, !!nvtxs, rank, &pcomm)); 185 for (p = 0, cnt = 0; p < size; p++) { 186 if (vtxdist[p + 1] != vtxdist[p]) { 187 vtxdist[cnt + 1] = vtxdist[p + 1]; 188 cnt++; 189 } 190 } 191 } 192 if (nvtxs) { 193 int err; 194 PetscStackPushExternal("ParMETIS_V3_PartKway"); 195 err = ParMETIS_V3_PartKway(vtxdist, xadj, adjncy, vwgt, adjwgt, &wgtflag, &numflag, &ncon, &nparts, tpwgts, ubvec, options, &part->edgeCut, assignment, &pcomm); 196 PetscStackPop; 197 PetscCheck(err == METIS_OK, PETSC_COMM_SELF, PETSC_ERR_LIB, "Error %d in ParMETIS_V3_PartKway()", err); 198 } 199 if (hasempty) PetscCallMPI(MPI_Comm_free(&pcomm)); 200 } 201 202 /* Convert to PetscSection+IS */ 203 for (v = 0; v < nvtxs; ++v) PetscCall(PetscSectionAddDof(partSection, assignment[v], 1)); 204 PetscCall(PetscMalloc1(nvtxs, &points)); 205 for (p = 0, i = 0; p < nparts; ++p) { 206 for (v = 0; v < nvtxs; ++v) { 207 if (assignment[v] == p) points[i++] = v; 208 } 209 } 210 PetscCheck(i == nvtxs, comm, PETSC_ERR_PLIB, "Number of points %" PetscInt_FMT " should be %" PetscInt_FMT, i, nvtxs); 211 PetscCall(ISCreateGeneral(comm, nvtxs, points, PETSC_OWN_POINTER, partition)); 212 PetscCall(PetscFree4(vtxdist, tpwgts, ubvec, assignment)); 213 PetscCall(PetscFree(vwgt)); 214 PetscFunctionReturn(0); 215 #else 216 SETERRQ(PetscObjectComm((PetscObject)part), PETSC_ERR_SUP, "Mesh partitioning needs external package support.\nPlease reconfigure with --download-parmetis."); 217 #endif 218 } 219 220 static PetscErrorCode PetscPartitionerInitialize_ParMetis(PetscPartitioner part) { 221 PetscFunctionBegin; 222 part->noGraph = PETSC_FALSE; 223 part->ops->view = PetscPartitionerView_ParMetis; 224 part->ops->setfromoptions = PetscPartitionerSetFromOptions_ParMetis; 225 part->ops->destroy = PetscPartitionerDestroy_ParMetis; 226 part->ops->partition = PetscPartitionerPartition_ParMetis; 227 PetscFunctionReturn(0); 228 } 229 230 /*MC 231 PETSCPARTITIONERPARMETIS = "parmetis" - A PetscPartitioner object using the ParMETIS library 232 233 Level: intermediate 234 235 Options Database Keys: 236 + -petscpartitioner_parmetis_type <string> - ParMETIS partitioning type. Either "kway" or "rb" (recursive bisection) 237 . -petscpartitioner_parmetis_imbalance_ratio <value> - Load imbalance ratio limit 238 . -petscpartitioner_parmetis_debug <int> - Debugging flag passed to ParMETIS/METIS routines 239 - -petscpartitioner_parmetis_seed <int> - Random seed 240 241 Notes: when the graph is on a single process, this partitioner actually calls METIS and not ParMETIS 242 243 .seealso: `PetscPartitionerType`, `PetscPartitionerCreate()`, `PetscPartitionerSetType()` 244 M*/ 245 246 PETSC_EXTERN PetscErrorCode PetscPartitionerCreate_ParMetis(PetscPartitioner part) { 247 PetscPartitioner_ParMetis *p; 248 249 PetscFunctionBegin; 250 PetscValidHeaderSpecific(part, PETSCPARTITIONER_CLASSID, 1); 251 PetscCall(PetscNew(&p)); 252 part->data = p; 253 254 PetscCallMPI(MPI_Comm_dup(PetscObjectComm((PetscObject)part), &p->pcomm)); 255 p->ptype = 0; 256 p->imbalanceRatio = 1.05; 257 p->debugFlag = 0; 258 p->randomSeed = -1; /* defaults to GLOBAL_SEED=15 from `libparmetis/defs.h` */ 259 260 PetscCall(PetscPartitionerInitialize_ParMetis(part)); 261 PetscCall(PetscCitationsRegister(ParMetisPartitionerCitation, &ParMetisPartitionerCite)); 262 PetscFunctionReturn(0); 263 } 264