Date: 2015-10-02T22:07:34+00:00

Actual source code: clique.cxx
petsc-3.6.2 2015-10-02
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      1: #include <../src/mat/impls/aij/mpi/clique/matcliqueimpl.h> /*I "petscmat.h" I*/
      2: /*
      3:  Provides an interface to the Clique sparse solver (http://poulson.github.com/Clique/)
      4: */

      8: PetscErrorCode PetscCliqueFinalizePackage(void)
      9: {
     11:   cliq::Finalize();
     12:   return(0);
     13: }

     17: PetscErrorCode PetscCliqueInitializePackage(void)
     18: {

     22:   if (cliq::Initialized()) return(0);
     23:   { /* We have already initialized MPI, so this song and dance is just to pass these variables (which won't be used by Clique) through the interface that needs references */
     24:     int zero = 0;
     25:     char **nothing = 0;
     26:     cliq::Initialize(zero,nothing);
     27:   }
     28:   PetscRegisterFinalize(PetscCliqueFinalizePackage);
     29:   return(0);
     30: }

     32: /*
     33:   MatConvertToClique: Convert Petsc aij matrix to Clique matrix

     35:   input:
     36: +   A     - matrix in seqaij or mpiaij format
     37: -   reuse - denotes if the destination matrix is to be created or reused. Currently
     38:             MAT_REUSE_MATRIX is only supported for inplace conversion, otherwise use MAT_INITIAL_MATRIX.

     40:   output:
     41: .   cliq - Clique context
     42: */
     45: PetscErrorCode MatConvertToClique(Mat A,MatReuse reuse,Mat_Clique *cliq)
     46: {
     47:   PetscErrorCode        ierr;
     48:   PetscInt              i,j,rstart,rend,ncols;
     49:   const PetscInt        *cols;
     50:   const PetscCliqScalar *vals;
     51:   cliq::DistSparseMatrix<PetscCliqScalar> *cmat;

     54:   if (reuse == MAT_INITIAL_MATRIX){
     55:     /* create Clique matrix */
     56:     cmat = new cliq::DistSparseMatrix<PetscCliqScalar>(A->rmap->N,cliq->cliq_comm);
     57:     cliq->cmat = cmat;
     58:   } else {
     59:     cmat = cliq->cmat;
     60:   }
     61:   /* fill matrix values */
     62:   MatGetOwnershipRange(A,&rstart,&rend);
     63:   const int firstLocalRow = cmat->FirstLocalRow();
     64:   const int localHeight = cmat->LocalHeight();
     65:   if (rstart != firstLocalRow || rend-rstart != localHeight) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"matrix rowblock distribution does not match");

     67:   cmat->StartAssembly();
     68:   //cmat->Reserve( 7*localHeight ); ???
     69:   for (i=rstart; i<rend; i++){
     70:     MatGetRow(A,i,&ncols,&cols,&vals);
     71:     for (j=0; j<ncols; j++){
     72:       cmat->Update(i,cols[j],vals[j]);
     73:     }
     74:     MatRestoreRow(A,i,&ncols,&cols,&vals);
     75:   }
     76:   cmat->StopAssembly();
     77:   return(0);
     78: }

     82: static PetscErrorCode MatMult_Clique(Mat A,Vec X,Vec Y)
     83: {
     84:   PetscErrorCode        ierr;
     85:   PetscInt              i;
     86:   const PetscCliqScalar *x;
     87:   Mat_Clique            *cliq=(Mat_Clique*)A->spptr;
     88:   cliq::DistSparseMatrix<PetscCliqScalar> *cmat=cliq->cmat;
     89:   cliq::mpi::Comm cxxcomm(PetscObjectComm((PetscObject)A));

     92:   if (!cmat) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NULL,"Clique matrix cmat is not created yet");
     93:   VecGetArrayRead(X,(const PetscScalar **)&x);

     95:   cliq::DistMultiVec<PetscCliqScalar> xc(A->cmap->N,1,cxxcomm);
     96:   cliq::DistMultiVec<PetscCliqScalar> yc(A->rmap->N,1,cxxcomm);
     97:   for (i=0; i<A->cmap->n; i++) {
     98:     xc.SetLocal(i,0,x[i]);
     99:   }
    100:   cliq::Multiply(1.0,*cmat,xc,0.0,yc);
    101:   VecRestoreArrayRead(X,(const PetscScalar **)&x);

    103:   for (i=0; i<A->cmap->n; i++) {
    104:     VecSetValueLocal(Y,i,yc.GetLocal(i,0),INSERT_VALUES);
    105:   }
    106:   VecAssemblyBegin(Y);
    107:   VecAssemblyEnd(Y);
    108:   return(0);
    109: }

    113: PetscErrorCode MatView_Clique(Mat A,PetscViewer viewer)
    114: {
    116:   PetscBool      iascii;

    119:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);
    120:   if (iascii) {
    121:     PetscViewerFormat format;
    122:     PetscViewerGetFormat(viewer,&format);
    123:     if (format == PETSC_VIEWER_ASCII_INFO) {
    124:       PetscViewerASCIIPrintf(viewer,"Clique run parameters:\n");
    125:     } else if (format == PETSC_VIEWER_DEFAULT) { /* matrix A is factored matrix, remove this block */
    126:       Mat Aaij;
    127:       PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
    128:       PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
    129:       PetscPrintf(PetscObjectComm((PetscObject)viewer),"Clique matrix\n");
    130:       MatComputeExplicitOperator(A,&Aaij);
    131:       MatView(Aaij,PETSC_VIEWER_STDOUT_WORLD);
    132:       MatDestroy(&Aaij);
    133:     }
    134:   }
    135:   return(0);
    136: }

    140: PetscErrorCode MatDestroy_Clique(Mat A)
    141: {
    143:   Mat_Clique     *cliq=(Mat_Clique*)A->spptr;

    146:   printf("MatDestroy_Clique ...\n");
    147:   if (cliq && cliq->CleanUpClique) {
    148:     /* Terminate instance, deallocate memories */
    149:     printf("MatDestroy_Clique ... destroy clique struct \n");
    150:     PetscCommDestroy(&(cliq->cliq_comm));
    151:     // free cmat here
    152:     delete cliq->cmat;
    153:     delete cliq->frontTree;
    154:     delete cliq->rhs;
    155:     delete cliq->xNodal;
    156:     delete cliq->info;
    157:     delete cliq->inverseMap;
    158:   }
    159:   if (cliq && cliq->Destroy) {
    160:     cliq->Destroy(A);
    161:   }
    162:   PetscFree(A->spptr);

    164:   /* clear composed functions */
    165:   PetscObjectComposeFunction((PetscObject)A,"MatFactorGetSolverPackage_C",NULL);

    167:   return(0);
    168: }

    172: PetscErrorCode MatSolve_Clique(Mat A,Vec B,Vec X)
    173: {
    174:   PetscErrorCode        ierr;
    175:   PetscInt              i,rank;
    176:   const PetscCliqScalar *b;
    177:   Mat_Clique            *cliq=(Mat_Clique*)A->spptr;
    178:   cliq::DistMultiVec<PetscCliqScalar> *bc=cliq->rhs;
    179:   cliq::DistNodalMultiVec<PetscCliqScalar> *xNodal=cliq->xNodal;

    182:   VecGetArrayRead(B,(const PetscScalar **)&b);
    183:   for (i=0; i<A->rmap->n; i++) {
    184:     bc->SetLocal(i,0,b[i]);
    185:   }
    186:   VecRestoreArrayRead(B,(const PetscScalar **)&b);

    188:   xNodal->Pull( *cliq->inverseMap, *cliq->info, *bc );
    189:   cliq::Solve( *cliq->info, *cliq->frontTree, *xNodal);
    190:   xNodal->Push( *cliq->inverseMap, *cliq->info, *bc );

    192:   MPI_Comm_rank(cliq->cliq_comm,&rank);
    193:   for (i=0; i<bc->LocalHeight(); i++) {
    194:     VecSetValue(X,rank*bc->Blocksize()+i,bc->GetLocal(i,0),INSERT_VALUES);
    195:   }
    196:   VecAssemblyBegin(X);
    197:   VecAssemblyEnd(X);
    198:   return(0);
    199: }

    203: PetscErrorCode MatCholeskyFactorNumeric_Clique(Mat F,Mat A,const MatFactorInfo *info)
    204: {
    205:   PetscErrorCode    ierr;
    206:   Mat_Clique        *cliq=(Mat_Clique*)F->spptr;
    207:   PETSC_UNUSED
    208:   cliq::DistSparseMatrix<PetscCliqScalar> *cmat;

    211:   cmat = cliq->cmat;
    212:   if (cliq->matstruc == SAME_NONZERO_PATTERN){ /* successing numerical factorization */
    213:     /* Update cmat */
    214:     MatConvertToClique(A,MAT_REUSE_MATRIX,cliq);
    215:   }

    217:   /* Numeric factorization */
    218:   cliq::LDL( *cliq->info, *cliq->frontTree, cliq::LDL_1D);
    219:   //L.frontType = cliq::SYMM_2D;

    221:   // refactor
    222:   //cliq::ChangeFrontType( *cliq->frontTree, cliq::LDL_2D );
    223:   //*(cliq->frontTree.frontType) = cliq::LDL_2D;
    224:   //cliq::LDL( *cliq->info, *cliq->frontTree, cliq::LDL_2D );

    226:   cliq->matstruc = SAME_NONZERO_PATTERN;
    227:   F->assembled   = PETSC_TRUE;
    228:   return(0);
    229: }

    233: PetscErrorCode MatCholeskyFactorSymbolic_Clique(Mat F,Mat A,IS r,const MatFactorInfo *info)
    234: {
    235:   PetscErrorCode    ierr;
    236:   Mat_Clique        *Acliq=(Mat_Clique*)F->spptr;
    237:   cliq::DistSparseMatrix<PetscCliqScalar> *cmat;
    238:   cliq::DistSeparatorTree                 sepTree;
    239:   cliq::DistMap                           map;

    242:   /* Convert A to Aclique */
    243:   MatConvertToClique(A,MAT_INITIAL_MATRIX,Acliq);
    244:   cmat = Acliq->cmat;

    246:   cliq::NestedDissection( cmat->DistGraph(), map, sepTree, *Acliq->info, PETSC_TRUE, Acliq->numDistSeps, Acliq->numSeqSeps, Acliq->cutoff);
    247:   map.FormInverse( *Acliq->inverseMap );
    248:   Acliq->frontTree = new cliq::DistSymmFrontTree<PetscCliqScalar>( cliq::TRANSPOSE, *cmat, map, sepTree, *Acliq->info );

    250:   Acliq->matstruc      = DIFFERENT_NONZERO_PATTERN;
    251:   Acliq->CleanUpClique = PETSC_TRUE;
    252:   return(0);
    253: }

    255: /*MC
    256:      MATSOLVERCLIQUE  - A solver package providing direct solvers for distributed
    257:   and sequential matrices via the external package Clique.

    259:   Use ./configure --download-clique to have PETSc installed with Clique

    261:   Use -pc_type lu -pc_factor_mat_solver_package clique to us this direct solver

    263:   Options Database Keys:
    264: + -mat_clique_    -
    265: - -mat_clique_ <integer> -

    267:   Level: beginner

    269: .seealso: PCFactorSetMatSolverPackage(), MatSolverPackage

    271: M*/

    275: PetscErrorCode MatFactorGetSolverPackage_Clique(Mat A,const MatSolverPackage *type)
    276: {
    278:   *type = MATSOLVERCLIQUE;
    279:   return(0);
    280: }

    284: PETSC_EXTERN PetscErrorCode MatGetFactor_aij_clique(Mat A,MatFactorType ftype,Mat *F)
    285: {
    286:   Mat            B;
    287:   Mat_Clique     *cliq;

    291:   PetscCliqueInitializePackage();
    292:   MatCreate(PetscObjectComm((PetscObject)A),&B);
    293:   MatSetSizes(B,A->rmap->n,A->cmap->n,PETSC_DETERMINE,PETSC_DETERMINE);
    294:   MatSetType(B,((PetscObject)A)->type_name);
    295:   MatSetUp(B);

    297:   if (ftype == MAT_FACTOR_CHOLESKY){
    298:     B->ops->choleskyfactorsymbolic = MatCholeskyFactorSymbolic_Clique;
    299:     B->ops->choleskyfactornumeric  = MatCholeskyFactorNumeric_Clique;
    300:   } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Factor type not supported");

    302:   PetscNewLog(B,&cliq);
    303:   B->spptr            = (void*)cliq;
    304:   cliq::mpi::Comm cxxcomm(PetscObjectComm((PetscObject)A));
    305:   PetscCommDuplicate(cxxcomm,&(cliq->cliq_comm),NULL);
    306:   cliq->rhs           = new cliq::DistMultiVec<PetscCliqScalar>(A->rmap->N,1,cliq->cliq_comm);
    307:   cliq->xNodal        = new cliq::DistNodalMultiVec<PetscCliqScalar>();
    308:   cliq->info          = new cliq::DistSymmInfo;
    309:   cliq->inverseMap    = new cliq::DistMap;
    310:   cliq->CleanUpClique = PETSC_FALSE;
    311:   cliq->Destroy       = B->ops->destroy;

    313:   B->ops->view    = MatView_Clique;
    314:   B->ops->mult    = MatMult_Clique; /* for cliq->cmat */
    315:   B->ops->solve   = MatSolve_Clique;

    317:   B->ops->destroy = MatDestroy_Clique;
    318:   B->factortype   = ftype;
    319:   B->assembled    = PETSC_FALSE;

    321:   /* Set Clique options */
    322:   PetscOptionsBegin(PetscObjectComm((PetscObject)A),((PetscObject)A)->prefix,"Clique Options","Mat");
    323:   cliq->cutoff      = 128;  /* maximum size of leaf node */
    324:   cliq->numDistSeps = 1;    /* number of distributed separators to try */
    325:   cliq->numSeqSeps  = 1;    /* number of sequential separators to try */
    326:   PetscOptionsEnd();

    328:   *F = B;
    329:   return(0);
    330: }

    334: PETSC_EXTERN PetscErrorCode MatSolverPackageRegister_Clique(void)
    335: {

    339:   MatSolverPackageRegister(MATSOLVERCLIQUE,MATMPIAIJ,        MAT_FACTOR_LU,MatGetFactor_aij_clique);
    340:   return(0);
    341: }