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/* $Id$ */ |
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|
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/******************************************************* |
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* |
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* Copyright 2003-2007 by ACceSS MNRF |
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* Copyright 2007 by University of Queensland |
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* |
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* http://esscc.uq.edu.au |
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* Primary Business: Queensland, Australia |
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* Licensed under the Open Software License version 3.0 |
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* http://www.opensource.org/licenses/osl-3.0.php |
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* |
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*******************************************************/ |
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|
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/**************************************************************/ |
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/* Finley: Mesh: optimizes the distribution of DOFs across processors */ |
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/* using ParMETIS. On return a new distribution is given and the globalDOF are relabled */ |
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/* accordingly but the mesh has not been redesitributed yet */ |
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|
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/**************************************************************/ |
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|
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#include "Mesh.h" |
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#include "IndexList.h" |
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#ifdef _OPENMP |
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#include <omp.h> |
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#endif |
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#ifdef USE_PARMETIS |
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#include "parmetis.h" |
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#endif |
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|
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/**************************************************************/ |
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|
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void Finley_Mesh_optimizeDOFDistribution(Finley_Mesh* in,dim_t *distribution) { |
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|
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dim_t dim, i,j,k, myNumVertices,p, mpiSize, len, globalNumVertices,*partition_count=NULL, *new_distribution=NULL, *loc_partition_count=NULL; |
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bool_t *setNewDOFId=NULL; |
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index_t myFirstVertex, myLastVertex, firstVertex, lastVertex, *newGlobalDOFID=NULL; |
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size_t mpiSize_size; |
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index_t* partition=NULL; |
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Paso_Pattern *pattern=NULL; |
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Paso_MPI_rank myRank,dest,source,current_rank, rank; |
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Finley_IndexList* index_list=NULL; |
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float *xyz=NULL; |
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int c; |
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|
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#ifdef PASO_MPI |
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MPI_Status status; |
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#endif |
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|
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if (in==NULL) return; |
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if (in->Nodes == NULL) return; |
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|
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myRank=in->MPIInfo->rank; |
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mpiSize=in->MPIInfo->size; |
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mpiSize_size=mpiSize*sizeof(dim_t); |
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dim=in->Nodes->numDim; |
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/* first step is to distribute the elements according to a global X of DOF */ |
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|
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myFirstVertex=distribution[myRank]; |
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myLastVertex=distribution[myRank+1]; |
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myNumVertices=myLastVertex-myFirstVertex; |
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globalNumVertices=distribution[mpiSize]; |
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len=0; |
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for (p=0;p<mpiSize;++p) len=MAX(len,distribution[p+1]-distribution[p]); |
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partition=TMPMEMALLOC(len,index_t); /* len is used for the sending around of partition later on */ |
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xyz=TMPMEMALLOC(myNumVertices*dim,float); |
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partition_count=TMPMEMALLOC(mpiSize+1,dim_t); |
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new_distribution=TMPMEMALLOC(mpiSize+1,dim_t); |
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newGlobalDOFID=TMPMEMALLOC(len,index_t); |
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setNewDOFId=TMPMEMALLOC(in->Nodes->numNodes,bool_t); |
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if (!(Finley_checkPtr(partition) || Finley_checkPtr(xyz) || Finley_checkPtr(partition_count) || Finley_checkPtr(partition_count) || Finley_checkPtr(newGlobalDOFID) || Finley_checkPtr(setNewDOFId))) { |
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dim_t *recvbuf=TMPMEMALLOC(mpiSize*mpiSize,dim_t); |
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|
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/* set the coordinates: *? |
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/* it is assumed that at least one node on this processor provides a coordinate */ |
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#pragma omp parallel for private(i,j,k) |
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for (i=0;i<in->Nodes->numNodes;++i) { |
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k=in->Nodes->globalDegreesOfFreedom[i]-myFirstVertex; |
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if ((k>=0) && (k<myNumVertices)) { |
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for (j=0;j<dim;++j) xyz[k*dim+j]=(float)(in->Nodes->Coordinates[INDEX2(j,i,dim)]); |
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} |
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} |
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|
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index_list=TMPMEMALLOC(myNumVertices,Finley_IndexList); |
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/* ksteube CSR of DOF IDs */ |
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/* create the adjacency structure xadj and adjncy */ |
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if (! Finley_checkPtr(index_list)) { |
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#pragma omp parallel private(i) |
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{ |
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#pragma omp for schedule(static) |
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for(i=0;i<myNumVertices;++i) { |
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index_list[i].extension=NULL; |
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index_list[i].n=0; |
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} |
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/* ksteube build CSR format */ |
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/* insert contributions from element matrices into colums index index_list: */ |
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Finley_IndexList_insertElementsWithRowRange(index_list, myFirstVertex, myLastVertex, |
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in->Elements,in->Nodes->globalDegreesOfFreedom, |
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in->Nodes->globalDegreesOfFreedom); |
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Finley_IndexList_insertElementsWithRowRange(index_list, myFirstVertex, myLastVertex, |
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in->FaceElements,in->Nodes->globalDegreesOfFreedom, |
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in->Nodes->globalDegreesOfFreedom); |
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Finley_IndexList_insertElementsWithRowRange(index_list, myFirstVertex, myLastVertex, |
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in->ContactElements,in->Nodes->globalDegreesOfFreedom, |
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in->Nodes->globalDegreesOfFreedom); |
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Finley_IndexList_insertElementsWithRowRange(index_list, myFirstVertex, myLastVertex, |
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in->Points,in->Nodes->globalDegreesOfFreedom, |
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in->Nodes->globalDegreesOfFreedom); |
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} |
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|
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/* create the local matrix pattern */ |
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pattern=Finley_IndexList_createPattern(0,myNumVertices,index_list,0,globalNumVertices,0); |
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|
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/* clean up index list */ |
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if (index_list!=NULL) { |
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#pragma omp parallel for private(i) |
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for(i=0;i<myNumVertices;++i) Finley_IndexList_free(index_list[i].extension); |
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} |
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|
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if (Finley_noError()) { |
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|
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#ifdef USE_PARMETIS |
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|
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if (in->MPIInfo->size>1) { |
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int i; |
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int wgtflag = 0; |
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int numflag = 0; /* pattern->ptr is C style: starting from 0 instead of 1 */ |
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int ncon = 1; |
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int edgecut; |
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int options[2]; |
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float *tpwgts = TMPMEMALLOC(ncon*mpiSize,float); |
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float *ubvec = TMPMEMALLOC(ncon,float); |
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for (i=0; i<ncon*mpiSize; i++) tpwgts[i] = 1.0/(float)mpiSize; |
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for (i=0; i<ncon; i++) ubvec[i] = 1.05; |
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options[0] = 0; |
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options[1] = 15; |
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ParMETIS_V3_PartGeomKway(distribution, |
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pattern->ptr, |
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pattern->index, |
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NULL, |
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NULL, |
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&wgtflag, |
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&numflag, |
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&dim, |
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xyz, |
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&ncon, |
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&mpiSize, |
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tpwgts, |
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ubvec, |
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options, |
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&edgecut, |
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partition, /* new CPU ownership of elements */ |
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&(in->MPIInfo->comm)); |
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printf("ParMETIS number of edges cut by partitioning: %d\n", edgecut); |
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TMPMEMFREE(ubvec); |
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TMPMEMFREE(tpwgts); |
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} else { |
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for (i=0;i<myNumVertices;++i) partition[i]=0; /* CPU 0 owns it */ |
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} |
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#else |
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for (i=0;i<myNumVertices;++i) partition[i]=myRank; /* CPU 0 owns it */ |
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#endif |
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|
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} |
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|
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Paso_Pattern_free(pattern); |
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/* create a new distributioin and labeling of the DOF */ |
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memset(new_distribution,0,mpiSize_size); |
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#pragma omp parallel private(loc_partition_count) |
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{ |
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loc_partition_count=THREAD_MEMALLOC(mpiSize,dim_t); |
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memset(loc_partition_count,0,mpiSize_size); |
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#pragma omp for private(i) |
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for (i=0;i<myNumVertices;++i) loc_partition_count[partition[i]]++ ; |
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#pragma omp critical |
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{ |
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for (i=0;i<mpiSize;++i) new_distribution[i]+=loc_partition_count[i]; |
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} |
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THREAD_MEMFREE(loc_partition_count); |
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} |
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#ifdef PASO_MPI |
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/* recvbuf will be the concatenation of each CPU's contribution to new_distribution */ |
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MPI_Allgather(new_distribution, mpiSize, MPI_INT, recvbuf, mpiSize, MPI_INT, in->MPIInfo->comm); |
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#else |
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for (i=0;i<mpiSize;++i) recvbuf[i]=new_distribution[i]; |
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#endif |
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new_distribution[0]=0; |
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for (rank=0; rank<mpiSize;rank++) { |
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c=0; |
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for (i=0;i<myRank;++i) c+=recvbuf[rank+mpiSize*i]; |
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for (i=0;i<myNumVertices;++i) { |
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if (rank==partition[i]) { |
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newGlobalDOFID[i]=new_distribution[rank]+c; |
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c++; |
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} |
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} |
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for (i=myRank+1;i<mpiSize;++i) c+=recvbuf[rank+mpiSize*i]; |
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new_distribution[rank+1]=new_distribution[rank]+c; |
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} |
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TMPMEMFREE(recvbuf); |
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/* now the overlap needs to be created by sending the partition around*/ |
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dest=Paso_MPIInfo_mod(mpiSize, myRank + 1); |
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source=Paso_MPIInfo_mod(mpiSize, myRank - 1); |
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current_rank=myRank; |
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#pragma omp parallel for private(i) |
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for (i=0;i<in->Nodes->numNodes;++i) setNewDOFId[i]=TRUE; |
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for (p=0; p< mpiSize; ++p) { |
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firstVertex=distribution[current_rank]; |
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lastVertex=distribution[current_rank+1]; |
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#pragma omp parallel for private(i,j,k) |
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for (i=0;i<in->Nodes->numNodes;++i) { |
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k=in->Nodes->globalDegreesOfFreedom[i]; |
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if (setNewDOFId[i] && (firstVertex<=k) && (k<lastVertex)) { |
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in->Nodes->globalDegreesOfFreedom[i]=newGlobalDOFID[k-firstVertex]; |
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setNewDOFId[i]=FALSE; |
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} |
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} |
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|
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if (p<mpiSize-1) { /* the final send can be skipped */ |
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#ifdef PASO_MPI |
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MPI_Sendrecv_replace(newGlobalDOFID,len, MPI_INT, |
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dest, in->MPIInfo->msg_tag_counter, |
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source, in->MPIInfo->msg_tag_counter, |
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in->MPIInfo->comm,&status); |
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#endif |
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in->MPIInfo->msg_tag_counter++; |
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current_rank=Paso_MPIInfo_mod(mpiSize, current_rank-1); |
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} |
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} |
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for (i=0;i<mpiSize+1;++i) distribution[i]=new_distribution[i]; |
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|
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|
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} |
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TMPMEMFREE(index_list); |
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} |
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TMPMEMFREE(newGlobalDOFID); |
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TMPMEMFREE(setNewDOFId); |
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TMPMEMFREE(new_distribution); |
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TMPMEMFREE(partition_count); |
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TMPMEMFREE(partition); |
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TMPMEMFREE(xyz); |
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return; |
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} |
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