1 #define PETSCMAT_DLL 2 3 /* 4 Defines a matrix-vector product for the MATMPIAIJCRL matrix class. 5 This class is derived from the MATMPIAIJ class and retains the 6 compressed row storage (aka Yale sparse matrix format) but augments 7 it with a column oriented storage that is more efficient for 8 matrix vector products on Vector machines. 9 10 CRL stands for constant row length (that is the same number of columns 11 is kept (padded with zeros) for each row of the sparse matrix. 12 13 See src/mat/impls/aij/seq/crl/crl.c for the sequential version 14 */ 15 16 #include "../src/mat/impls/aij/mpi/mpiaij.h" 17 #include "../src/mat/impls/aij/seq/crl/crl.h" 18 19 #undef __FUNCT__ 20 #define __FUNCT__ "MatDestroy_MPICRL" 21 PetscErrorCode MatDestroy_MPICRL(Mat A) 22 { 23 PetscErrorCode ierr; 24 Mat_CRL *crl = (Mat_CRL *) A->spptr; 25 26 /* We are going to convert A back into a MPIAIJ matrix, since we are 27 * eventually going to use MatDestroy_MPIAIJ() to destroy everything 28 * that is not specific to CRL. 29 * In preparation for this, reset the operations pointers in A to 30 * their MPIAIJ versions. */ 31 A->ops->assemblyend = crl->AssemblyEnd; 32 A->ops->destroy = crl->MatDestroy; 33 A->ops->duplicate = crl->MatDuplicate; 34 35 /* Free everything in the Mat_CRL data structure. */ 36 ierr = PetscFree2(crl->acols,crl->icols);CHKERRQ(ierr); 37 if (crl->fwork) { 38 ierr = VecDestroy(crl->fwork);CHKERRQ(ierr); 39 } 40 if (crl->xwork) { 41 ierr = VecDestroy(crl->xwork);CHKERRQ(ierr); 42 } 43 ierr = PetscFree(crl->array);CHKERRQ(ierr); 44 ierr = PetscFree(crl);CHKERRQ(ierr); 45 A->spptr = 0; 46 47 /* Change the type of A back to MPIAIJ and use MatDestroy_MPIAIJ() 48 * to destroy everything that remains. */ 49 ierr = PetscObjectChangeTypeName( (PetscObject)A, MATMPIAIJ);CHKERRQ(ierr); 50 /* Note that I don't call MatSetType(). I believe this is because that 51 * is only to be called when *building* a matrix. */ 52 ierr = (*A->ops->destroy)(A);CHKERRQ(ierr); 53 PetscFunctionReturn(0); 54 } 55 56 #undef __FUNCT__ 57 #define __FUNCT__ "MPICRL_create_crl" 58 PetscErrorCode MPICRL_create_crl(Mat A) 59 { 60 Mat_MPIAIJ *a = (Mat_MPIAIJ *)(A)->data; 61 Mat_SeqAIJ *Aij = (Mat_SeqAIJ*)(a->A->data), *Bij = (Mat_SeqAIJ*)(a->B->data); 62 Mat_CRL *crl = (Mat_CRL*) A->spptr; 63 PetscInt m = A->rmap->n; /* Number of rows in the matrix. */ 64 PetscInt nd = a->A->cmap->n; /* number of columns in diagonal portion */ 65 PetscInt *aj = Aij->j,*bj = Bij->j; /* From the CSR representation; points to the beginning of each row. */ 66 PetscInt i, j,rmax = 0,*icols, *ailen = Aij->ilen, *bilen = Bij->ilen; 67 PetscScalar *aa = Aij->a,*ba = Bij->a,*acols,*array; 68 PetscErrorCode ierr; 69 70 PetscFunctionBegin; 71 /* determine the row with the most columns */ 72 for (i=0; i<m; i++) { 73 rmax = PetscMax(rmax,ailen[i]+bilen[i]); 74 } 75 crl->nz = Aij->nz+Bij->nz; 76 crl->m = A->rmap->n; 77 crl->rmax = rmax; 78 ierr = PetscMalloc2(rmax*m,PetscScalar,&crl->acols,rmax*m,PetscInt,&crl->icols);CHKERRQ(ierr); 79 acols = crl->acols; 80 icols = crl->icols; 81 for (i=0; i<m; i++) { 82 for (j=0; j<ailen[i]; j++) { 83 acols[j*m+i] = *aa++; 84 icols[j*m+i] = *aj++; 85 } 86 for (;j<ailen[i]+bilen[i]; j++) { 87 acols[j*m+i] = *ba++; 88 icols[j*m+i] = nd + *bj++; 89 } 90 for (;j<rmax; j++) { /* empty column entries */ 91 acols[j*m+i] = 0.0; 92 icols[j*m+i] = (j) ? icols[(j-1)*m+i] : 0; /* handle case where row is EMPTY */ 93 } 94 } 95 ierr = PetscInfo1(A,"Percentage of 0's introduced for vectorized multiply %g\n",1.0-((double)(crl->nz))/((double)(rmax*m))); 96 97 ierr = PetscMalloc((a->B->cmap->n+nd)*sizeof(PetscScalar),&array);CHKERRQ(ierr); 98 /* xwork array is actually B->n+nd long, but we define xwork this length so can copy into it */ 99 ierr = VecCreateMPIWithArray(((PetscObject)A)->comm,nd,PETSC_DECIDE,array,&crl->xwork);CHKERRQ(ierr); 100 ierr = VecCreateSeqWithArray(PETSC_COMM_SELF,a->B->cmap->n,array+nd,&crl->fwork);CHKERRQ(ierr); 101 crl->array = array; 102 crl->xscat = a->Mvctx; 103 PetscFunctionReturn(0); 104 } 105 106 #undef __FUNCT__ 107 #define __FUNCT__ "MatAssemblyEnd_MPICRL" 108 PetscErrorCode MatAssemblyEnd_MPICRL(Mat A, MatAssemblyType mode) 109 { 110 PetscErrorCode ierr; 111 Mat_CRL *crl = (Mat_CRL*) A->spptr; 112 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 113 Mat_SeqAIJ *Aij = (Mat_SeqAIJ*)(a->A->data), *Bij = (Mat_SeqAIJ*)(a->A->data); 114 115 PetscFunctionBegin; 116 if (mode == MAT_FLUSH_ASSEMBLY) PetscFunctionReturn(0); 117 118 /* Since a MATMPICRL matrix is really just a MATMPIAIJ with some 119 * extra information, call the AssemblyEnd routine for a MATMPIAIJ. 120 * I'm not sure if this is the best way to do this, but it avoids 121 * a lot of code duplication. 122 * I also note that currently MATMPICRL doesn't know anything about 123 * the Mat_CompressedRow data structure that MPIAIJ now uses when there 124 * are many zero rows. If the MPIAIJ assembly end routine decides to use 125 * this, this may break things. (Don't know... haven't looked at it.) */ 126 Aij->inode.use = PETSC_FALSE; 127 Bij->inode.use = PETSC_FALSE; 128 (*crl->AssemblyEnd)(A, mode); 129 130 /* Now calculate the permutation and grouping information. */ 131 ierr = MPICRL_create_crl(A);CHKERRQ(ierr); 132 PetscFunctionReturn(0); 133 } 134 135 extern PetscErrorCode MatMult_CRL(Mat,Vec,Vec); 136 extern PetscErrorCode MatDuplicate_CRL(Mat,MatDuplicateOption,Mat*); 137 138 /* MatConvert_MPIAIJ_MPICRL converts a MPIAIJ matrix into a 139 * MPICRL matrix. This routine is called by the MatCreate_MPICRL() 140 * routine, but can also be used to convert an assembled MPIAIJ matrix 141 * into a MPICRL one. */ 142 EXTERN_C_BEGIN 143 #undef __FUNCT__ 144 #define __FUNCT__ "MatConvert_MPIAIJ_MPICRL" 145 PetscErrorCode PETSCMAT_DLLEXPORT MatConvert_MPIAIJ_MPICRL(Mat A,const MatType type,MatReuse reuse,Mat *newmat) 146 { 147 PetscErrorCode ierr; 148 Mat B = *newmat; 149 Mat_CRL *crl; 150 151 PetscFunctionBegin; 152 if (reuse == MAT_INITIAL_MATRIX) { 153 ierr = MatDuplicate(A,MAT_COPY_VALUES,&B);CHKERRQ(ierr); 154 } 155 156 ierr = PetscNewLog(B,Mat_CRL,&crl);CHKERRQ(ierr); 157 B->spptr = (void *) crl; 158 159 crl->AssemblyEnd = A->ops->assemblyend; 160 crl->MatDestroy = A->ops->destroy; 161 crl->MatDuplicate = A->ops->duplicate; 162 163 /* Set function pointers for methods that we inherit from AIJ but override. */ 164 B->ops->duplicate = MatDuplicate_CRL; 165 B->ops->assemblyend = MatAssemblyEnd_MPICRL; 166 B->ops->destroy = MatDestroy_MPICRL; 167 B->ops->mult = MatMult_CRL; 168 169 /* If A has already been assembled, compute the permutation. */ 170 if (A->assembled) { 171 ierr = MPICRL_create_crl(B);CHKERRQ(ierr); 172 } 173 ierr = PetscObjectChangeTypeName((PetscObject)B,MATMPICRL);CHKERRQ(ierr); 174 *newmat = B; 175 PetscFunctionReturn(0); 176 } 177 EXTERN_C_END 178 179 180 #undef __FUNCT__ 181 #define __FUNCT__ "MatCreateMPICRL" 182 /*@C 183 MatCreateMPICRL - Creates a sparse matrix of type MPICRL. 184 This type inherits from AIJ, but stores some additional 185 information that is used to allow better vectorization of 186 the matrix-vector product. At the cost of increased storage, the AIJ formatted 187 matrix can be copied to a format in which pieces of the matrix are 188 stored in ELLPACK format, allowing the vectorized matrix multiply 189 routine to use stride-1 memory accesses. As with the AIJ type, it is 190 important to preallocate matrix storage in order to get good assembly 191 performance. 192 193 Collective on MPI_Comm 194 195 Input Parameters: 196 + comm - MPI communicator, set to PETSC_COMM_SELF 197 . m - number of rows 198 . n - number of columns 199 . nz - number of nonzeros per row (same for all rows) 200 - nnz - array containing the number of nonzeros in the various rows 201 (possibly different for each row) or PETSC_NULL 202 203 Output Parameter: 204 . A - the matrix 205 206 Notes: 207 If nnz is given then nz is ignored 208 209 Level: intermediate 210 211 .keywords: matrix, cray, sparse, parallel 212 213 .seealso: MatCreate(), MatCreateMPICSRPERM(), MatSetValues() 214 @*/ 215 PetscErrorCode PETSCMAT_DLLEXPORT MatCreateMPICRL(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt nz,const PetscInt nnz[],PetscInt onz,const PetscInt onnz[],Mat *A) 216 { 217 PetscErrorCode ierr; 218 219 PetscFunctionBegin; 220 ierr = MatCreate(comm,A);CHKERRQ(ierr); 221 ierr = MatSetSizes(*A,m,n,m,n);CHKERRQ(ierr); 222 ierr = MatSetType(*A,MATMPICRL);CHKERRQ(ierr); 223 ierr = MatMPIAIJSetPreallocation_MPIAIJ(*A,nz,(PetscInt*)nnz,onz,(PetscInt*)onnz);CHKERRQ(ierr); 224 PetscFunctionReturn(0); 225 } 226 227 228 EXTERN_C_BEGIN 229 #undef __FUNCT__ 230 #define __FUNCT__ "MatCreate_MPICRL" 231 PetscErrorCode PETSCMAT_DLLEXPORT MatCreate_MPICRL(Mat A) 232 { 233 PetscErrorCode ierr; 234 235 PetscFunctionBegin; 236 ierr = MatSetType(A,MATMPIAIJ);CHKERRQ(ierr); 237 ierr = MatConvert_MPIAIJ_MPICRL(A,MATMPICRL,MAT_REUSE_MATRIX,&A);CHKERRQ(ierr); 238 PetscFunctionReturn(0); 239 } 240 EXTERN_C_END 241 242