1 2 static char help[] = "Reads a PETSc matrix from a file partitions it\n\n"; 3 4 /* 5 Include "petscmat.h" so that we can use matrices. Note that this file 6 automatically includes: 7 petscsys.h - base PETSc routines petscvec.h - vectors 8 petscmat.h - matrices 9 petscis.h - index sets 10 petscviewer.h - viewers 11 12 Example of usage: 13 mpiexec -n 3 ex73 -f <matfile> -mat_partitioning_type parmetis/scotch -viewer_binary_skip_info -nox 14 */ 15 #include <petscmat.h> 16 17 int main(int argc,char **args) 18 { 19 MatType mtype = MATMPIAIJ; /* matrix format */ 20 Mat A,B; /* matrix */ 21 PetscViewer fd; /* viewer */ 22 char file[PETSC_MAX_PATH_LEN]; /* input file name */ 23 PetscBool flg,viewMats,viewIS,viewVecs,useND,noVecLoad = PETSC_FALSE; 24 PetscInt *nlocal,m,n; 25 PetscMPIInt rank,size; 26 MatPartitioning part; 27 IS is,isn; 28 Vec xin, xout; 29 VecScatter scat; 30 31 PetscFunctionBeginUser; 32 PetscCall(PetscInitialize(&argc,&args,(char*)0,help)); 33 PetscCallMPI(MPI_Comm_size(PETSC_COMM_WORLD,&size)); 34 PetscCallMPI(MPI_Comm_rank(PETSC_COMM_WORLD,&rank)); 35 PetscCall(PetscOptionsHasName(NULL,NULL, "-view_mats", &viewMats)); 36 PetscCall(PetscOptionsHasName(NULL,NULL, "-view_is", &viewIS)); 37 PetscCall(PetscOptionsHasName(NULL,NULL, "-view_vecs", &viewVecs)); 38 PetscCall(PetscOptionsHasName(NULL,NULL, "-use_nd", &useND)); 39 PetscCall(PetscOptionsHasName(NULL,NULL, "-novec_load", &noVecLoad)); 40 41 /* 42 Determine file from which we read the matrix 43 */ 44 PetscCall(PetscOptionsGetString(NULL,NULL,"-f",file,sizeof(file),&flg)); 45 46 /* 47 Open binary file. Note that we use FILE_MODE_READ to indicate 48 reading from this file. 49 */ 50 PetscCall(PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd)); 51 52 /* 53 Load the matrix and vector; then destroy the viewer. 54 */ 55 PetscCall(MatCreate(PETSC_COMM_WORLD,&A)); 56 PetscCall(MatSetType(A,mtype)); 57 PetscCall(MatLoad(A,fd)); 58 if (!noVecLoad) { 59 PetscCall(VecCreate(PETSC_COMM_WORLD,&xin)); 60 PetscCall(VecLoad(xin,fd)); 61 } else { 62 PetscCall(MatCreateVecs(A,&xin,NULL)); 63 PetscCall(VecSetRandom(xin,NULL)); 64 } 65 PetscCall(PetscViewerDestroy(&fd)); 66 if (viewMats) { 67 PetscCall(PetscPrintf(PETSC_COMM_WORLD,"Original matrix:\n")); 68 PetscCall(MatView(A,PETSC_VIEWER_DRAW_WORLD)); 69 } 70 if (viewVecs) { 71 PetscCall(PetscPrintf(PETSC_COMM_WORLD,"Original vector:\n")); 72 PetscCall(VecView(xin,PETSC_VIEWER_STDOUT_WORLD)); 73 } 74 75 /* Partition the graph of the matrix */ 76 PetscCall(MatPartitioningCreate(PETSC_COMM_WORLD,&part)); 77 PetscCall(MatPartitioningSetAdjacency(part,A)); 78 PetscCall(MatPartitioningSetFromOptions(part)); 79 80 /* get new processor owner number of each vertex */ 81 if (useND) { 82 PetscCall(MatPartitioningApplyND(part,&is)); 83 } else { 84 PetscCall(MatPartitioningApply(part,&is)); 85 } 86 if (viewIS) { 87 PetscCall(PetscPrintf(PETSC_COMM_WORLD,"IS1 - new processor ownership:\n")); 88 PetscCall(ISView(is,PETSC_VIEWER_STDOUT_WORLD)); 89 } 90 91 /* get new global number of each old global number */ 92 PetscCall(ISPartitioningToNumbering(is,&isn)); 93 if (viewIS) { 94 PetscCall(PetscPrintf(PETSC_COMM_WORLD,"IS2 - new global numbering:\n")); 95 PetscCall(ISView(isn,PETSC_VIEWER_STDOUT_WORLD)); 96 } 97 98 /* get number of new vertices for each processor */ 99 PetscCall(PetscMalloc1(size,&nlocal)); 100 PetscCall(ISPartitioningCount(is,size,nlocal)); 101 PetscCall(ISDestroy(&is)); 102 103 /* get old global number of each new global number */ 104 PetscCall(ISInvertPermutation(isn,useND ? PETSC_DECIDE : nlocal[rank],&is)); 105 if (viewIS) { 106 PetscCall(PetscPrintf(PETSC_COMM_WORLD,"IS3=inv(IS2) - old global number of each new global number:\n")); 107 PetscCall(ISView(is,PETSC_VIEWER_STDOUT_WORLD)); 108 } 109 110 /* move the matrix rows to the new processes they have been assigned to by the permutation */ 111 PetscCall(MatCreateSubMatrix(A,is,is,MAT_INITIAL_MATRIX,&B)); 112 PetscCall(PetscFree(nlocal)); 113 PetscCall(ISDestroy(&isn)); 114 PetscCall(MatDestroy(&A)); 115 PetscCall(MatPartitioningDestroy(&part)); 116 if (viewMats) { 117 PetscCall(PetscPrintf(PETSC_COMM_WORLD,"Partitioned matrix:\n")); 118 PetscCall(MatView(B,PETSC_VIEWER_DRAW_WORLD)); 119 } 120 121 /* move the vector rows to the new processes they have been assigned to */ 122 PetscCall(MatGetLocalSize(B,&m,&n)); 123 PetscCall(VecCreateMPI(PETSC_COMM_WORLD,m,PETSC_DECIDE,&xout)); 124 PetscCall(VecScatterCreate(xin,is,xout,NULL,&scat)); 125 PetscCall(VecScatterBegin(scat,xin,xout,INSERT_VALUES,SCATTER_FORWARD)); 126 PetscCall(VecScatterEnd(scat,xin,xout,INSERT_VALUES,SCATTER_FORWARD)); 127 PetscCall(VecScatterDestroy(&scat)); 128 if (viewVecs) { 129 PetscCall(PetscPrintf(PETSC_COMM_WORLD,"Mapped vector:\n")); 130 PetscCall(VecView(xout,PETSC_VIEWER_STDOUT_WORLD)); 131 } 132 PetscCall(VecDestroy(&xout)); 133 PetscCall(ISDestroy(&is)); 134 135 { 136 PetscInt rstart,i,*nzd,*nzo,nzl,nzmax = 0,*ncols,nrow,j; 137 Mat J; 138 const PetscInt *cols; 139 const PetscScalar *vals; 140 PetscScalar *nvals; 141 142 PetscCall(MatGetOwnershipRange(B,&rstart,NULL)); 143 PetscCall(PetscCalloc2(2*m,&nzd,2*m,&nzo)); 144 for (i=0; i<m; i++) { 145 PetscCall(MatGetRow(B,i+rstart,&nzl,&cols,NULL)); 146 for (j=0; j<nzl; j++) { 147 if (cols[j] >= rstart && cols[j] < rstart+n) { 148 nzd[2*i] += 2; 149 nzd[2*i+1] += 2; 150 } else { 151 nzo[2*i] += 2; 152 nzo[2*i+1] += 2; 153 } 154 } 155 nzmax = PetscMax(nzmax,nzd[2*i]+nzo[2*i]); 156 PetscCall(MatRestoreRow(B,i+rstart,&nzl,&cols,NULL)); 157 } 158 PetscCall(MatCreateAIJ(PETSC_COMM_WORLD,2*m,2*m,PETSC_DECIDE,PETSC_DECIDE,0,nzd,0,nzo,&J)); 159 PetscCall(PetscInfo(0,"Created empty Jacobian matrix\n")); 160 PetscCall(PetscFree2(nzd,nzo)); 161 PetscCall(PetscMalloc2(nzmax,&ncols,nzmax,&nvals)); 162 PetscCall(PetscArrayzero(nvals,nzmax)); 163 for (i=0; i<m; i++) { 164 PetscCall(MatGetRow(B,i+rstart,&nzl,&cols,&vals)); 165 for (j=0; j<nzl; j++) { 166 ncols[2*j] = 2*cols[j]; 167 ncols[2*j+1] = 2*cols[j]+1; 168 } 169 nrow = 2*(i+rstart); 170 PetscCall(MatSetValues(J,1,&nrow,2*nzl,ncols,nvals,INSERT_VALUES)); 171 nrow = 2*(i+rstart) + 1; 172 PetscCall(MatSetValues(J,1,&nrow,2*nzl,ncols,nvals,INSERT_VALUES)); 173 PetscCall(MatRestoreRow(B,i+rstart,&nzl,&cols,&vals)); 174 } 175 PetscCall(MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY)); 176 PetscCall(MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY)); 177 if (viewMats) { 178 PetscCall(PetscPrintf(PETSC_COMM_WORLD,"Jacobian matrix structure:\n")); 179 PetscCall(MatView(J,PETSC_VIEWER_DRAW_WORLD)); 180 } 181 PetscCall(MatDestroy(&J)); 182 PetscCall(PetscFree2(ncols,nvals)); 183 } 184 185 /* 186 Free work space. All PETSc objects should be destroyed when they 187 are no longer needed. 188 */ 189 PetscCall(MatDestroy(&B)); 190 PetscCall(VecDestroy(&xin)); 191 PetscCall(PetscFinalize()); 192 return 0; 193 } 194 195 /*TEST 196 197 test: 198 nsize: 3 199 requires: parmetis datafilespath !complex double !defined(PETSC_USE_64BIT_INDICES) 200 args: -nox -f ${DATAFILESPATH}/matrices/arco1 -mat_partitioning_type parmetis -viewer_binary_skip_info -novec_load 201 202 test: 203 requires: parmetis !complex double !defined(PETSC_USE_64BIT_INDICES) 204 output_file: output/ex73_1.out 205 suffix: parmetis_nd_32 206 nsize: 3 207 args: -nox -f ${wPETSC_DIR}/share/petsc/datafiles/matrices/spd-real-int32-float64 -mat_partitioning_type parmetis -viewer_binary_skip_info -use_nd -novec_load 208 209 test: 210 requires: parmetis !complex double defined(PETSC_USE_64BIT_INDICES) 211 output_file: output/ex73_1.out 212 suffix: parmetis_nd_64 213 nsize: 3 214 args: -nox -f ${wPETSC_DIR}/share/petsc/datafiles/matrices/spd-real-int64-float64 -mat_partitioning_type parmetis -viewer_binary_skip_info -use_nd -novec_load 215 216 test: 217 requires: ptscotch !complex double !defined(PETSC_USE_64BIT_INDICES) defined(PETSC_HAVE_SCOTCH_PARMETIS_V3_NODEND) 218 output_file: output/ex73_1.out 219 suffix: ptscotch_nd_32 220 nsize: 4 221 args: -nox -f ${wPETSC_DIR}/share/petsc/datafiles/matrices/spd-real-int32-float64 -mat_partitioning_type ptscotch -viewer_binary_skip_info -use_nd -novec_load 222 223 test: 224 requires: ptscotch !complex double defined(PETSC_USE_64BIT_INDICES) defined(PETSC_HAVE_SCOTCH_PARMETIS_V3_NODEND) 225 output_file: output/ex73_1.out 226 suffix: ptscotch_nd_64 227 nsize: 4 228 args: -nox -f ${wPETSC_DIR}/share/petsc/datafiles/matrices/spd-real-int64-float64 -mat_partitioning_type ptscotch -viewer_binary_skip_info -use_nd -novec_load 229 230 TEST*/ 231