1 2 static char help[] = "Reads a PETSc matrix from a file partitions it\n\n"; 3 4 /*T 5 Concepts: partitioning 6 Processors: n 7 T*/ 8 9 /* 10 Include "petscmat.h" so that we can use matrices. Note that this file 11 automatically includes: 12 petscsys.h - base PETSc routines petscvec.h - vectors 13 petscmat.h - matrices 14 petscis.h - index sets 15 petscviewer.h - viewers 16 17 Example of usage: 18 mpiexec -n 3 ex73 -f <matfile> -mat_partitioning_type parmetis/scotch -viewer_binary_skip_info -nox 19 */ 20 #include <petscmat.h> 21 22 int main(int argc,char **args) 23 { 24 MatType mtype = MATMPIAIJ; /* matrix format */ 25 Mat A,B; /* matrix */ 26 PetscViewer fd; /* viewer */ 27 char file[PETSC_MAX_PATH_LEN]; /* input file name */ 28 PetscBool flg,viewMats,viewIS,viewVecs,useND,noVecLoad = PETSC_FALSE; 29 PetscInt ierr,*nlocal,m,n; 30 PetscMPIInt rank,size; 31 MatPartitioning part; 32 IS is,isn; 33 Vec xin, xout; 34 VecScatter scat; 35 36 ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr; 37 ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRMPI(ierr); 38 ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRMPI(ierr); 39 ierr = PetscOptionsHasName(NULL,NULL, "-view_mats", &viewMats);CHKERRQ(ierr); 40 ierr = PetscOptionsHasName(NULL,NULL, "-view_is", &viewIS);CHKERRQ(ierr); 41 ierr = PetscOptionsHasName(NULL,NULL, "-view_vecs", &viewVecs);CHKERRQ(ierr); 42 ierr = PetscOptionsHasName(NULL,NULL, "-use_nd", &useND);CHKERRQ(ierr); 43 ierr = PetscOptionsHasName(NULL,NULL, "-novec_load", &noVecLoad);CHKERRQ(ierr); 44 45 /* 46 Determine file from which we read the matrix 47 */ 48 ierr = PetscOptionsGetString(NULL,NULL,"-f",file,sizeof(file),&flg);CHKERRQ(ierr); 49 50 /* 51 Open binary file. Note that we use FILE_MODE_READ to indicate 52 reading from this file. 53 */ 54 ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr); 55 56 /* 57 Load the matrix and vector; then destroy the viewer. 58 */ 59 ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr); 60 ierr = MatSetType(A,mtype);CHKERRQ(ierr); 61 ierr = MatLoad(A,fd);CHKERRQ(ierr); 62 if (!noVecLoad) { 63 ierr = VecCreate(PETSC_COMM_WORLD,&xin);CHKERRQ(ierr); 64 ierr = VecLoad(xin,fd);CHKERRQ(ierr); 65 } else { 66 ierr = MatCreateVecs(A,&xin,NULL);CHKERRQ(ierr); 67 ierr = VecSetRandom(xin,NULL);CHKERRQ(ierr); 68 } 69 ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr); 70 if (viewMats) { 71 ierr = PetscPrintf(PETSC_COMM_WORLD,"Original matrix:\n");CHKERRQ(ierr); 72 ierr = MatView(A,PETSC_VIEWER_DRAW_WORLD);CHKERRQ(ierr); 73 } 74 if (viewVecs) { 75 ierr = PetscPrintf(PETSC_COMM_WORLD,"Original vector:\n");CHKERRQ(ierr); 76 ierr = VecView(xin,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 77 } 78 79 /* Partition the graph of the matrix */ 80 ierr = MatPartitioningCreate(PETSC_COMM_WORLD,&part);CHKERRQ(ierr); 81 ierr = MatPartitioningSetAdjacency(part,A);CHKERRQ(ierr); 82 ierr = MatPartitioningSetFromOptions(part);CHKERRQ(ierr); 83 84 /* get new processor owner number of each vertex */ 85 if (useND) { 86 ierr = MatPartitioningApplyND(part,&is);CHKERRQ(ierr); 87 } else { 88 ierr = MatPartitioningApply(part,&is);CHKERRQ(ierr); 89 } 90 if (viewIS) { 91 ierr = PetscPrintf(PETSC_COMM_WORLD,"IS1 - new processor ownership:\n");CHKERRQ(ierr); 92 ierr = ISView(is,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 93 } 94 95 /* get new global number of each old global number */ 96 ierr = ISPartitioningToNumbering(is,&isn);CHKERRQ(ierr); 97 if (viewIS) { 98 ierr = PetscPrintf(PETSC_COMM_WORLD,"IS2 - new global numbering:\n");CHKERRQ(ierr); 99 ierr = ISView(isn,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 100 } 101 102 /* get number of new vertices for each processor */ 103 ierr = PetscMalloc1(size,&nlocal);CHKERRQ(ierr); 104 ierr = ISPartitioningCount(is,size,nlocal);CHKERRQ(ierr); 105 ierr = ISDestroy(&is);CHKERRQ(ierr); 106 107 /* get old global number of each new global number */ 108 ierr = ISInvertPermutation(isn,useND ? PETSC_DECIDE : nlocal[rank],&is);CHKERRQ(ierr); 109 if (viewIS) { 110 ierr = PetscPrintf(PETSC_COMM_WORLD,"IS3=inv(IS2) - old global number of each new global number:\n");CHKERRQ(ierr); 111 ierr = ISView(is,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 112 } 113 114 /* move the matrix rows to the new processes they have been assigned to by the permutation */ 115 ierr = MatCreateSubMatrix(A,is,is,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr); 116 ierr = PetscFree(nlocal);CHKERRQ(ierr); 117 ierr = ISDestroy(&isn);CHKERRQ(ierr); 118 ierr = MatDestroy(&A);CHKERRQ(ierr); 119 ierr = MatPartitioningDestroy(&part);CHKERRQ(ierr); 120 if (viewMats) { 121 ierr = PetscPrintf(PETSC_COMM_WORLD,"Partitioned matrix:\n");CHKERRQ(ierr); 122 ierr = MatView(B,PETSC_VIEWER_DRAW_WORLD);CHKERRQ(ierr); 123 } 124 125 /* move the vector rows to the new processes they have been assigned to */ 126 ierr = MatGetLocalSize(B,&m,&n);CHKERRQ(ierr); 127 ierr = VecCreateMPI(PETSC_COMM_WORLD,m,PETSC_DECIDE,&xout);CHKERRQ(ierr); 128 ierr = VecScatterCreate(xin,is,xout,NULL,&scat);CHKERRQ(ierr); 129 ierr = VecScatterBegin(scat,xin,xout,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 130 ierr = VecScatterEnd(scat,xin,xout,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 131 ierr = VecScatterDestroy(&scat);CHKERRQ(ierr); 132 if (viewVecs) { 133 ierr = PetscPrintf(PETSC_COMM_WORLD,"Mapped vector:\n");CHKERRQ(ierr); 134 ierr = VecView(xout,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 135 } 136 ierr = VecDestroy(&xout);CHKERRQ(ierr); 137 ierr = ISDestroy(&is);CHKERRQ(ierr); 138 139 { 140 PetscInt rstart,i,*nzd,*nzo,nzl,nzmax = 0,*ncols,nrow,j; 141 Mat J; 142 const PetscInt *cols; 143 const PetscScalar *vals; 144 PetscScalar *nvals; 145 146 ierr = MatGetOwnershipRange(B,&rstart,NULL);CHKERRQ(ierr); 147 ierr = PetscCalloc2(2*m,&nzd,2*m,&nzo);CHKERRQ(ierr); 148 for (i=0; i<m; i++) { 149 ierr = MatGetRow(B,i+rstart,&nzl,&cols,NULL);CHKERRQ(ierr); 150 for (j=0; j<nzl; j++) { 151 if (cols[j] >= rstart && cols[j] < rstart+n) { 152 nzd[2*i] += 2; 153 nzd[2*i+1] += 2; 154 } else { 155 nzo[2*i] += 2; 156 nzo[2*i+1] += 2; 157 } 158 } 159 nzmax = PetscMax(nzmax,nzd[2*i]+nzo[2*i]); 160 ierr = MatRestoreRow(B,i+rstart,&nzl,&cols,NULL);CHKERRQ(ierr); 161 } 162 ierr = MatCreateAIJ(PETSC_COMM_WORLD,2*m,2*m,PETSC_DECIDE,PETSC_DECIDE,0,nzd,0,nzo,&J);CHKERRQ(ierr); 163 ierr = PetscInfo(0,"Created empty Jacobian matrix\n");CHKERRQ(ierr); 164 ierr = PetscFree2(nzd,nzo);CHKERRQ(ierr); 165 ierr = PetscMalloc2(nzmax,&ncols,nzmax,&nvals);CHKERRQ(ierr); 166 ierr = PetscArrayzero(nvals,nzmax);CHKERRQ(ierr); 167 for (i=0; i<m; i++) { 168 ierr = MatGetRow(B,i+rstart,&nzl,&cols,&vals);CHKERRQ(ierr); 169 for (j=0; j<nzl; j++) { 170 ncols[2*j] = 2*cols[j]; 171 ncols[2*j+1] = 2*cols[j]+1; 172 } 173 nrow = 2*(i+rstart); 174 ierr = MatSetValues(J,1,&nrow,2*nzl,ncols,nvals,INSERT_VALUES);CHKERRQ(ierr); 175 nrow = 2*(i+rstart) + 1; 176 ierr = MatSetValues(J,1,&nrow,2*nzl,ncols,nvals,INSERT_VALUES);CHKERRQ(ierr); 177 ierr = MatRestoreRow(B,i+rstart,&nzl,&cols,&vals);CHKERRQ(ierr); 178 } 179 ierr = MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 180 ierr = MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 181 if (viewMats) { 182 ierr = PetscPrintf(PETSC_COMM_WORLD,"Jacobian matrix structure:\n");CHKERRQ(ierr); 183 ierr = MatView(J,PETSC_VIEWER_DRAW_WORLD);CHKERRQ(ierr); 184 } 185 ierr = MatDestroy(&J);CHKERRQ(ierr); 186 ierr = PetscFree2(ncols,nvals);CHKERRQ(ierr); 187 } 188 189 /* 190 Free work space. All PETSc objects should be destroyed when they 191 are no longer needed. 192 */ 193 ierr = MatDestroy(&B);CHKERRQ(ierr); 194 ierr = VecDestroy(&xin);CHKERRQ(ierr); 195 ierr = PetscFinalize(); 196 return ierr; 197 } 198 199 /*TEST 200 201 test: 202 nsize: 3 203 requires: parmetis datafilespath !complex double !define(PETSC_USE_64BIT_INDICES) 204 args: -nox -f ${DATAFILESPATH}/matrices/arco1 -mat_partitioning_type parmetis -viewer_binary_skip_info -novec_load 205 206 test: 207 requires: parmetis !complex double !define(PETSC_USE_64BIT_INDICES) 208 output_file: output/ex73_1.out 209 suffix: parmetis_nd_32 210 nsize: 3 211 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 212 213 test: 214 requires: parmetis !complex double define(PETSC_USE_64BIT_INDICES) 215 output_file: output/ex73_1.out 216 suffix: parmetis_nd_64 217 nsize: 3 218 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 219 220 test: 221 requires: ptscotch !complex double !define(PETSC_USE_64BIT_INDICES) define(PETSC_HAVE_SCOTCH_PARMETIS_V3_NODEND) 222 output_file: output/ex73_1.out 223 suffix: ptscotch_nd_32 224 nsize: 4 225 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 226 227 test: 228 requires: ptscotch !complex double define(PETSC_USE_64BIT_INDICES) define(PETSC_HAVE_SCOTCH_PARMETIS_V3_NODEND) 229 output_file: output/ex73_1.out 230 suffix: ptscotch_nd_64 231 nsize: 4 232 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 233 234 TEST*/ 235