Date: 2016-07-24T16:54:14+00:00

Actual source code: mcrl.c
petsc-3.7.3 2016-07-24
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      2: /*
      3:   Defines a matrix-vector product for the MATMPIAIJCRL matrix class.
      4:   This class is derived from the MATMPIAIJ class and retains the
      5:   compressed row storage (aka Yale sparse matrix format) but augments
      6:   it with a column oriented storage that is more efficient for
      7:   matrix vector products on Vector machines.

      9:   CRL stands for constant row length (that is the same number of columns
     10:   is kept (padded with zeros) for each row of the sparse matrix.

     12:    See src/mat/impls/aij/seq/crl/crl.c for the sequential version
     13: */

     15: #include <../src/mat/impls/aij/mpi/mpiaij.h>
     16: #include <../src/mat/impls/aij/seq/crl/crl.h>

     18: extern PetscErrorCode MatDestroy_MPIAIJ(Mat);

     22: PetscErrorCode MatDestroy_MPIAIJCRL(Mat A)
     23: {
     25:   Mat_AIJCRL     *aijcrl = (Mat_AIJCRL*) A->spptr;

     27:   /* Free everything in the Mat_AIJCRL data structure. */
     28:   if (aijcrl) {
     29:     PetscFree2(aijcrl->acols,aijcrl->icols);
     30:     VecDestroy(&aijcrl->fwork);
     31:     VecDestroy(&aijcrl->xwork);
     32:     PetscFree(aijcrl->array);
     33:   }
     34:   PetscFree(A->spptr);

     36:   PetscObjectChangeTypeName((PetscObject)A, MATMPIAIJ);
     37:   MatDestroy_MPIAIJ(A);
     38:   return(0);
     39: }

     43: PetscErrorCode MatMPIAIJCRL_create_aijcrl(Mat A)
     44: {
     45:   Mat_MPIAIJ     *a      = (Mat_MPIAIJ*)(A)->data;
     46:   Mat_SeqAIJ     *Aij    = (Mat_SeqAIJ*)(a->A->data), *Bij = (Mat_SeqAIJ*)(a->B->data);
     47:   Mat_AIJCRL     *aijcrl = (Mat_AIJCRL*) A->spptr;
     48:   PetscInt       m       = A->rmap->n; /* Number of rows in the matrix. */
     49:   PetscInt       nd      = a->A->cmap->n; /* number of columns in diagonal portion */
     50:   PetscInt       *aj     = Aij->j,*bj = Bij->j; /* From the CSR representation; points to the beginning  of each row. */
     51:   PetscInt       i, j,rmax = 0,*icols, *ailen = Aij->ilen, *bilen = Bij->ilen;
     52:   PetscScalar    *aa = Aij->a,*ba = Bij->a,*acols,*array;

     56:   /* determine the row with the most columns */
     57:   for (i=0; i<m; i++) {
     58:     rmax = PetscMax(rmax,ailen[i]+bilen[i]);
     59:   }
     60:   aijcrl->nz   = Aij->nz+Bij->nz;
     61:   aijcrl->m    = A->rmap->n;
     62:   aijcrl->rmax = rmax;

     64:   PetscFree2(aijcrl->acols,aijcrl->icols);
     65:   PetscMalloc2(rmax*m,&aijcrl->acols,rmax*m,&aijcrl->icols);
     66:   acols = aijcrl->acols;
     67:   icols = aijcrl->icols;
     68:   for (i=0; i<m; i++) {
     69:     for (j=0; j<ailen[i]; j++) {
     70:       acols[j*m+i] = *aa++;
     71:       icols[j*m+i] = *aj++;
     72:     }
     73:     for (; j<ailen[i]+bilen[i]; j++) {
     74:       acols[j*m+i] = *ba++;
     75:       icols[j*m+i] = nd + *bj++;
     76:     }
     77:     for (; j<rmax; j++) { /* empty column entries */
     78:       acols[j*m+i] = 0.0;
     79:       icols[j*m+i] = (j) ? icols[(j-1)*m+i] : 0;  /* handle case where row is EMPTY */
     80:     }
     81:   }
     82:   PetscInfo1(A,"Percentage of 0's introduced for vectorized multiply %g\n",1.0-((double)(aijcrl->nz))/((double)(rmax*m)));

     84:   PetscFree(aijcrl->array);
     85:   PetscMalloc1(a->B->cmap->n+nd,&array);
     86:   /* xwork array is actually B->n+nd long, but we define xwork this length so can copy into it */
     87:   VecDestroy(&aijcrl->xwork);
     88:   VecCreateMPIWithArray(PetscObjectComm((PetscObject)A),1,nd,PETSC_DECIDE,array,&aijcrl->xwork);
     89:   VecDestroy(&aijcrl->fwork);
     90:   VecCreateSeqWithArray(PETSC_COMM_SELF,1,a->B->cmap->n,array+nd,&aijcrl->fwork);

     92:   aijcrl->array = array;
     93:   aijcrl->xscat = a->Mvctx;
     94:   return(0);
     95: }

     97: extern PetscErrorCode MatAssemblyEnd_MPIAIJ(Mat,MatAssemblyType);

    101: PetscErrorCode MatAssemblyEnd_MPIAIJCRL(Mat A, MatAssemblyType mode)
    102: {
    104:   Mat_MPIAIJ     *a   = (Mat_MPIAIJ*)A->data;
    105:   Mat_SeqAIJ     *Aij = (Mat_SeqAIJ*)(a->A->data), *Bij = (Mat_SeqAIJ*)(a->A->data);

    108:   Aij->inode.use = PETSC_FALSE;
    109:   Bij->inode.use = PETSC_FALSE;

    111:   MatAssemblyEnd_MPIAIJ(A,mode);
    112:   if (mode == MAT_FLUSH_ASSEMBLY) return(0);

    114:   /* Now calculate the permutation and grouping information. */
    115:   MatMPIAIJCRL_create_aijcrl(A);
    116:   return(0);
    117: }

    119: extern PetscErrorCode MatMult_AIJCRL(Mat,Vec,Vec);
    120: extern PetscErrorCode MatDuplicate_AIJCRL(Mat,MatDuplicateOption,Mat*);

    122: /* MatConvert_MPIAIJ_MPIAIJCRL converts a MPIAIJ matrix into a
    123:  * MPIAIJCRL matrix.  This routine is called by the MatCreate_MPIAIJCRL()
    124:  * routine, but can also be used to convert an assembled MPIAIJ matrix
    125:  * into a MPIAIJCRL one. */

    129: PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJCRL(Mat A,MatType type,MatReuse reuse,Mat *newmat)
    130: {
    132:   Mat            B = *newmat;
    133:   Mat_AIJCRL     *aijcrl;

    136:   if (reuse == MAT_INITIAL_MATRIX) {
    137:     MatDuplicate(A,MAT_COPY_VALUES,&B);
    138:   }

    140:   PetscNewLog(B,&aijcrl);
    141:   B->spptr = (void*) aijcrl;

    143:   /* Set function pointers for methods that we inherit from AIJ but override. */
    144:   B->ops->duplicate   = MatDuplicate_AIJCRL;
    145:   B->ops->assemblyend = MatAssemblyEnd_MPIAIJCRL;
    146:   B->ops->destroy     = MatDestroy_MPIAIJCRL;
    147:   B->ops->mult        = MatMult_AIJCRL;

    149:   /* If A has already been assembled, compute the permutation. */
    150:   if (A->assembled) {
    151:     MatMPIAIJCRL_create_aijcrl(B);
    152:   }
    153:   PetscObjectChangeTypeName((PetscObject)B,MATMPIAIJCRL);
    154:   *newmat = B;
    155:   return(0);
    156: }

    160: /*@C
    161:    MatCreateMPIAIJCRL - Creates a sparse matrix of type MPIAIJCRL.
    162:    This type inherits from AIJ, but stores some additional
    163:    information that is used to allow better vectorization of
    164:    the matrix-vector product. At the cost of increased storage, the AIJ formatted
    165:    matrix can be copied to a format in which pieces of the matrix are
    166:    stored in ELLPACK format, allowing the vectorized matrix multiply
    167:    routine to use stride-1 memory accesses.  As with the AIJ type, it is
    168:    important to preallocate matrix storage in order to get good assembly
    169:    performance.

    171:    Collective on MPI_Comm

    173:    Input Parameters:
    174: +  comm - MPI communicator, set to PETSC_COMM_SELF
    175: .  m - number of rows
    176: .  n - number of columns
    177: .  nz - number of nonzeros per row (same for all rows)
    178: -  nnz - array containing the number of nonzeros in the various rows
    179:          (possibly different for each row) or NULL

    181:    Output Parameter:
    182: .  A - the matrix

    184:    Notes:
    185:    If nnz is given then nz is ignored

    187:    Level: intermediate

    189: .keywords: matrix, cray, sparse, parallel

    191: .seealso: MatCreate(), MatCreateMPIAIJPERM(), MatSetValues()
    192: @*/
    193: PetscErrorCode  MatCreateMPIAIJCRL(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt nz,const PetscInt nnz[],PetscInt onz,const PetscInt onnz[],Mat *A)
    194: {

    198:   MatCreate(comm,A);
    199:   MatSetSizes(*A,m,n,m,n);
    200:   MatSetType(*A,MATMPIAIJCRL);
    201:   MatMPIAIJSetPreallocation_MPIAIJ(*A,nz,(PetscInt*)nnz,onz,(PetscInt*)onnz);
    202:   return(0);
    203: }

    207: PETSC_EXTERN PetscErrorCode MatCreate_MPIAIJCRL(Mat A)
    208: {

    212:   MatSetType(A,MATMPIAIJ);
    213:   MatConvert_MPIAIJ_MPIAIJCRL(A,MATMPIAIJCRL,MAT_INPLACE_MATRIX,&A);
    214:   return(0);
    215: }