int main(int argc, char **argv) { Mat mat; MatNullSpace nsp; PetscBool prefix = PETSC_FALSE, flg; PetscErrorCode ierr; PetscInt zero = 0; PetscScalar value = 0; ierr = PetscInitialize(&argc, &argv, NULL, help); if (ierr) return ierr; ierr = PetscOptionsGetBool(NULL, NULL, "-with_prefix",&prefix,NULL);CHKERRQ(ierr); ierr = MatCreateDense(PETSC_COMM_WORLD, 1, 1, 1, 1, NULL, &mat);CHKERRQ(ierr); ierr = MatSetOptionsPrefix(mat, prefix ? "prefix_" : NULL);CHKERRQ(ierr); ierr = MatSetUp(mat);CHKERRQ(ierr); ierr = MatSetValues(mat, 1, &zero, 1, &zero, &value, INSERT_VALUES);CHKERRQ(ierr); ierr = MatAssemblyBegin(mat, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(mat, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatNullSpaceCreate(PETSC_COMM_WORLD, PETSC_TRUE, 0, NULL, &nsp);CHKERRQ(ierr); ierr = MatNullSpaceTest(nsp, mat, &flg);CHKERRQ(ierr); if (!flg) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_PLIB,"Null space test failed!"); ierr = MatNullSpaceDestroy(&nsp);CHKERRQ(ierr); ierr = MatDestroy(&mat);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
PetscErrorCode BVResize_Mat(BV bv,PetscInt m,PetscBool copy) { PetscErrorCode ierr; BV_MAT *ctx = (BV_MAT*)bv->data; PetscScalar *pA,*pnew; Mat A; char str[50]; PetscFunctionBegin; ierr = MatCreateDense(PetscObjectComm((PetscObject)bv->t),bv->n,PETSC_DECIDE,PETSC_DECIDE,m,NULL,&A);CHKERRQ(ierr); ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = PetscLogObjectParent((PetscObject)bv,(PetscObject)A);CHKERRQ(ierr); if (((PetscObject)bv)->name) { ierr = PetscSNPrintf(str,50,"%s_0",((PetscObject)bv)->name);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)A,str);CHKERRQ(ierr); } if (copy) { ierr = MatDenseGetArray(ctx->A,&pA);CHKERRQ(ierr); ierr = MatDenseGetArray(A,&pnew);CHKERRQ(ierr); ierr = PetscMemcpy(pnew,pA,PetscMin(m,bv->m)*bv->n*sizeof(PetscScalar));CHKERRQ(ierr); ierr = MatDenseRestoreArray(ctx->A,&pA);CHKERRQ(ierr); ierr = MatDenseRestoreArray(A,&pnew);CHKERRQ(ierr); } ierr = MatDestroy(&ctx->A);CHKERRQ(ierr); ctx->A = A; PetscFunctionReturn(0); }
PETSC_EXTERN PetscErrorCode BVCreate_Mat(BV bv) { PetscErrorCode ierr; BV_MAT *ctx; PetscInt nloc,bs; PetscBool seq; char str[50]; PetscFunctionBegin; ierr = PetscNewLog(bv,&ctx);CHKERRQ(ierr); bv->data = (void*)ctx; ierr = PetscObjectTypeCompare((PetscObject)bv->t,VECMPI,&ctx->mpi);CHKERRQ(ierr); if (!ctx->mpi) { ierr = PetscObjectTypeCompare((PetscObject)bv->t,VECSEQ,&seq);CHKERRQ(ierr); if (!seq) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot create a BVMAT from a non-standard template vector"); } ierr = VecGetLocalSize(bv->t,&nloc);CHKERRQ(ierr); ierr = VecGetBlockSize(bv->t,&bs);CHKERRQ(ierr); ierr = MatCreateDense(PetscObjectComm((PetscObject)bv->t),nloc,PETSC_DECIDE,PETSC_DECIDE,bv->m,NULL,&ctx->A);CHKERRQ(ierr); ierr = MatAssemblyBegin(ctx->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(ctx->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = PetscLogObjectParent((PetscObject)bv,(PetscObject)ctx->A);CHKERRQ(ierr); if (((PetscObject)bv)->name) { ierr = PetscSNPrintf(str,50,"%s_0",((PetscObject)bv)->name);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)ctx->A,str);CHKERRQ(ierr); } if (ctx->mpi) { ierr = VecCreateMPIWithArray(PetscObjectComm((PetscObject)bv->t),bs,nloc,PETSC_DECIDE,NULL,&bv->cv[0]);CHKERRQ(ierr); ierr = VecCreateMPIWithArray(PetscObjectComm((PetscObject)bv->t),bs,nloc,PETSC_DECIDE,NULL,&bv->cv[1]);CHKERRQ(ierr); } else { ierr = VecCreateSeqWithArray(PetscObjectComm((PetscObject)bv->t),bs,nloc,NULL,&bv->cv[0]);CHKERRQ(ierr); ierr = VecCreateSeqWithArray(PetscObjectComm((PetscObject)bv->t),bs,nloc,NULL,&bv->cv[1]);CHKERRQ(ierr); } bv->ops->mult = BVMult_Mat; bv->ops->multvec = BVMultVec_Mat; bv->ops->multinplace = BVMultInPlace_Mat; bv->ops->multinplacetrans = BVMultInPlaceTranspose_Mat; bv->ops->axpy = BVAXPY_Mat; bv->ops->dot = BVDot_Mat; bv->ops->dotvec = BVDotVec_Mat; bv->ops->scale = BVScale_Mat; bv->ops->norm = BVNorm_Mat; /*bv->ops->orthogonalize = BVOrthogonalize_Mat;*/ bv->ops->matmult = BVMatMult_Mat; bv->ops->copy = BVCopy_Mat; bv->ops->resize = BVResize_Mat; bv->ops->getcolumn = BVGetColumn_Mat; bv->ops->restorecolumn = BVRestoreColumn_Mat; bv->ops->getarray = BVGetArray_Mat; bv->ops->restorearray = BVRestoreArray_Mat; bv->ops->destroy = BVDestroy_Mat; if (!ctx->mpi) bv->ops->view = BVView_Mat; PetscFunctionReturn(0); }
// ------------------------------------------------------------- // MatConvertGAtoDense // ------------------------------------------------------------- PetscErrorCode MatConvertGAToDense(Mat A, Mat *B) { PetscErrorCode ierr = 0; MPI_Comm comm; int nproc; struct MatGACtx *ctx; PetscInt lrows, grows, lcols, gcols, lo, hi; ierr = PetscObjectGetComm((PetscObject)A, &comm); CHKERRQ(ierr); ierr = MPI_Comm_size(comm, &nproc); ierr = MatShellGetContext(A, &ctx); CHKERRQ(ierr); ierr = MatGetSize(A, &grows, &gcols); CHKERRQ(ierr); ierr = MatGetLocalSize(A, &lrows, &lcols); CHKERRQ(ierr); ierr = MatCreateDense(comm, lrows, lcols, grows, gcols, NULL, B); CHKERRQ(ierr); ierr = MatCreate(comm, B); CHKERRXX(ierr); ierr = MatSetSizes(*B, lrows, lcols, grows, gcols); CHKERRXX(ierr); if (nproc == 1) { ierr = MatSetType(*B, MATSEQDENSE); CHKERRXX(ierr); ierr = MatSeqDenseSetPreallocation(*B, PETSC_NULL); CHKERRXX(ierr); } else { ierr = MatSetType(*B, MATDENSE); CHKERRXX(ierr); ierr = MatMPIDenseSetPreallocation(*B, PETSC_NULL); CHKERRXX(ierr); } ierr = MatGetOwnershipRange(*B, &lo, &hi); CHKERRQ(ierr); std::vector<PetscInt> cidx(gcols); for (PetscInt c = 0; c < gcols; ++c) { cidx[c] = c; } std::vector<PetscScalar> rowvals(gcols); for (PetscInt r = lo; r < hi; ++r) { int glo[2] = {r, 0}; int ghi[2] = {r, gcols - 1}; int ld[2] = {1,1}; NGA_Get(ctx->ga, glo, ghi, &rowvals[0], ld); ierr = MatSetValues(*B, 1, &r, gcols, &cidx[0], &rowvals[0], INSERT_VALUES); CHKERRQ(ierr); } ierr = MatAssemblyBegin(*B, MAT_FINAL_ASSEMBLY); CHKERRQ(ierr); ierr = MatAssemblyEnd(*B, MAT_FINAL_ASSEMBLY); CHKERRQ(ierr); return ierr; }
int main(int argc, char **argv) { PetscErrorCode ierr; PetscViewer viewer; Mat A; char filename[PETSC_MAX_PATH_LEN]; PetscBool flg; ierr = PetscInitialize(&argc, &argv, (char*)0, help);if (ierr) return ierr; ierr = PetscOptionsGetString(NULL, NULL, "-f", filename, sizeof(filename), &flg);CHKERRQ(ierr); if (!flg) SETERRQ(PETSC_COMM_WORLD, 1, "Must indicate a filename for input with the -f option"); ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD, filename, FILE_MODE_READ, &viewer);CHKERRQ(ierr); ierr = MatCreateDense(PETSC_COMM_WORLD, PETSC_DECIDE, PETSC_DECIDE, 36, 36, NULL, &A);CHKERRQ(ierr); ierr = MatLoad(A, viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
int main(int argc,char **args) { Mat C,A; PetscInt i,j,m = 3,n = 2,rstart,rend; PetscMPIInt size,rank; PetscErrorCode ierr; PetscScalar v; IS isrow,iscol; PetscBool flg; char type[256]; PetscInitialize(&argc,&args,(char *)0,help); ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); n = 2*size; ierr = PetscStrcpy(type,MATSAME);CHKERRQ(ierr); ierr = PetscOptionsGetString(PETSC_NULL,"-mat_type",type,256,PETSC_NULL);CHKERRQ(ierr); ierr = PetscStrcmp(type,MATMPIDENSE,&flg);CHKERRQ(ierr); if (flg) { ierr = MatCreateDense(PETSC_COMM_WORLD,PETSC_DECIDE,PETSC_DECIDE, m*n,m*n,PETSC_NULL,&C);CHKERRQ(ierr); } else { ierr = MatCreateAIJ(PETSC_COMM_WORLD,PETSC_DECIDE,PETSC_DECIDE, m*n,m*n,PETSC_DECIDE,PETSC_NULL,PETSC_DECIDE,PETSC_NULL,&C);CHKERRQ(ierr); } /* This is JUST to generate a nice test matrix, all processors fill up the entire matrix. This is not something one would ever do in practice. */ for (i=0; i<m*n; i++) { for (j=0; j<m*n; j++) { v = i + j + 1; ierr = MatSetValues(C,1,&i,1,&j,&v,INSERT_VALUES);CHKERRQ(ierr); } } ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = PetscViewerSetFormat(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_ASCII_COMMON);CHKERRQ(ierr); ierr = MatView(C,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); /* Generate a new matrix consisting of every second row and column of the original matrix */ ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); /* Create parallel IS with the rows we want on THIS processor */ ierr = ISCreateStride(PETSC_COMM_WORLD,(rend-rstart)/2,rstart,2,&isrow);CHKERRQ(ierr); /* Create parallel IS with the rows we want on THIS processor (same as rows for now) */ ierr = ISCreateStride(PETSC_COMM_WORLD,(rend-rstart)/2,rstart,2,&iscol);CHKERRQ(ierr); ierr = MatGetSubMatrix(C,isrow,iscol,MAT_INITIAL_MATRIX,&A);CHKERRQ(ierr); ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = MatGetSubMatrix(C,isrow,iscol,MAT_REUSE_MATRIX,&A);CHKERRQ(ierr); ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = ISDestroy(&isrow);CHKERRQ(ierr); ierr = ISDestroy(&iscol);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = MatDestroy(&C);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
int main(int argc,char **args) { Mat A; PetscInt i,j,m = 3,n = 2,rstart,rend; PetscErrorCode ierr; PetscScalar v,*array; PetscViewer view; PetscInitialize(&argc,&args,(char*)0,help); /* Create a parallel dense matrix shared by all processors */ ierr = MatCreateDense(PETSC_COMM_WORLD,PETSC_DECIDE,PETSC_DECIDE,m,n,NULL,&A);CHKERRQ(ierr); /* Set values into the matrix */ for (i=0; i<m; i++) { for (j=0; j<n; j++) { v = 9.0/(i+j+1); ierr = MatSetValues(A,1,&i,1,&j,&v,INSERT_VALUES);CHKERRQ(ierr); } } ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); /* Print the matrix to the screen */ ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); /* Print the local portion of the matrix to the screen */ ierr = MatDenseGetArray(A,&array);CHKERRQ(ierr); ierr = MatGetOwnershipRange(A,&rstart,&rend);CHKERRQ(ierr); for (i=rstart; i<rend; i++) { for (j=0; j<n; j++) { PetscSynchronizedPrintf(PETSC_COMM_WORLD,"%6.4e ",(double)PetscRealPart(array[j*(rend-rstart)+i-rstart])); } PetscSynchronizedPrintf(PETSC_COMM_WORLD,"\n"); } PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT); ierr = MatDenseRestoreArray(A,&array);CHKERRQ(ierr); /* Store the binary matrix to a file */ ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD, "matrix.dat", FILE_MODE_WRITE, &view);CHKERRQ(ierr); ierr = PetscViewerSetFormat(view,PETSC_VIEWER_NATIVE);CHKERRQ(ierr); ierr = MatView(A,view);CHKERRQ(ierr); ierr = PetscViewerDestroy(&view);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); /* Now reload the matrix and view it */ ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"matrix.dat",FILE_MODE_READ,&view);CHKERRQ(ierr); ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr); ierr = MatSetType(A,MATMPIDENSE);CHKERRQ(ierr); ierr = MatLoad(A,view);CHKERRQ(ierr); ierr = PetscViewerDestroy(&view);CHKERRQ(ierr); ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
int main(int argc,char **args) { User user; Mat A,S; PetscScalar *data,diag = 1.3; PetscReal tol = PETSC_SMALL; PetscInt i,j,m = PETSC_DECIDE,n = PETSC_DECIDE,M = 17,N = 15,s1,s2; PetscInt test, ntest = 2; PetscMPIInt rank,size; PetscBool nc = PETSC_FALSE, cong; PetscBool ronl = PETSC_TRUE; PetscBool randomize = PETSC_FALSE; PetscBool keep = PETSC_FALSE; PetscBool testzerorows = PETSC_TRUE, testdiagscale = PETSC_TRUE, testgetdiag = PETSC_TRUE; PetscBool testshift = PETSC_TRUE, testscale = PETSC_TRUE, testdup = PETSC_TRUE, testreset = PETSC_TRUE; PetscErrorCode ierr; ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr; ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-M",&M,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-N",&N,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-ml",&m,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-nl",&n,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,NULL,"-square_nc",&nc,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,NULL,"-rows_only",&ronl,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,NULL,"-randomize",&randomize,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,NULL,"-test_zerorows",&testzerorows,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,NULL,"-test_diagscale",&testdiagscale,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,NULL,"-test_getdiag",&testgetdiag,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,NULL,"-test_shift",&testshift,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,NULL,"-test_scale",&testscale,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,NULL,"-test_dup",&testdup,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,NULL,"-test_reset",&testreset,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-loop",&ntest,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetReal(NULL,NULL,"-tol",&tol,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetScalar(NULL,NULL,"-diag",&diag,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,NULL,"-keep",&keep,NULL);CHKERRQ(ierr); /* This tests square matrices with different row/col layout */ if (nc && size > 1) { M = PetscMax(PetscMax(N,M),1); N = M; m = n = 0; if (rank == 0) { m = M-1; n = 1; } else if (rank == 1) { m = 1; n = N-1; } } ierr = MatCreateDense(PETSC_COMM_WORLD,m,n,M,N,NULL,&A);CHKERRQ(ierr); ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr); ierr = MatGetSize(A,&M,&N);CHKERRQ(ierr); ierr = MatHasCongruentLayouts(A,&cong);CHKERRQ(ierr); ierr = MatGetOwnershipRange(A,&s1,NULL);CHKERRQ(ierr); s2 = 1; while (s2 < M) s2 *= 10; ierr = MatDenseGetArray(A,&data);CHKERRQ(ierr); for (j = 0; j < N; j++) { for (i = 0; i < m; i++) { data[j*m + i] = s2*j + i + s1 + 1; } } ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatConvert(A,MATAIJ,MAT_INPLACE_MATRIX,&A);CHKERRQ(ierr); ierr = MatSetOption(A,MAT_KEEP_NONZERO_PATTERN,keep);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)A,"initial");CHKERRQ(ierr); ierr = MatViewFromOptions(A,NULL,"-view_mat");CHKERRQ(ierr); ierr = PetscNew(&user);CHKERRQ(ierr); ierr = MatCreateShell(PETSC_COMM_WORLD,m,n,M,N,user,&S);CHKERRQ(ierr); ierr = MatShellSetOperation(S,MATOP_MULT,(void (*)(void))MatMult_User);CHKERRQ(ierr); ierr = MatShellSetOperation(S,MATOP_MULT_TRANSPOSE,(void (*)(void))MatMultTranspose_User);CHKERRQ(ierr); if (cong) { ierr = MatShellSetOperation(S,MATOP_GET_DIAGONAL,(void (*)(void))MatGetDiagonal_User);CHKERRQ(ierr); } ierr = MatDuplicate(A,MAT_COPY_VALUES,&user->B);CHKERRQ(ierr); /* Square and rows only scaling */ ronl = cong ? ronl : PETSC_TRUE; for (test = 0; test < ntest; test++) { PetscReal err; if (testzerorows) { Mat ST,B,C,BT,BTT; IS zr; Vec x = NULL, b1 = NULL, b2 = NULL; PetscInt *idxs = NULL, nr = 0; if (rank == (test%size)) { nr = 1; ierr = PetscMalloc1(nr,&idxs);CHKERRQ(ierr); if (test%2) { idxs[0] = (2*M - 1 - test/2)%M; } else { idxs[0] = (test/2)%M; } idxs[0] = PetscMax(idxs[0],0); } ierr = ISCreateGeneral(PETSC_COMM_WORLD,nr,idxs,PETSC_OWN_POINTER,&zr);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)zr,"ZR");CHKERRQ(ierr); ierr = ISViewFromOptions(zr,NULL,"-view_is");CHKERRQ(ierr); ierr = MatCreateVecs(A,&x,&b1);CHKERRQ(ierr); if (randomize) { ierr = VecSetRandom(x,NULL);CHKERRQ(ierr); ierr = VecSetRandom(b1,NULL);CHKERRQ(ierr); } else { ierr = VecSet(x,11.4);CHKERRQ(ierr); ierr = VecSet(b1,-14.2);CHKERRQ(ierr); } ierr = VecDuplicate(b1,&b2);CHKERRQ(ierr); ierr = VecCopy(b1,b2);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)b1,"A_B1");CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)b2,"A_B2");CHKERRQ(ierr); if (size > 1 && !cong) { /* MATMPIAIJ ZeroRows and ZeroRowsColumns are buggy in this case */ ierr = VecDestroy(&b1);CHKERRQ(ierr); } if (ronl) { ierr = MatZeroRowsIS(A,zr,diag,x,b1);CHKERRQ(ierr); ierr = MatZeroRowsIS(S,zr,diag,x,b2);CHKERRQ(ierr); } else { ierr = MatZeroRowsColumnsIS(A,zr,diag,x,b1);CHKERRQ(ierr); ierr = MatZeroRowsColumnsIS(S,zr,diag,x,b2);CHKERRQ(ierr); ierr = ISDestroy(&zr);CHKERRQ(ierr); /* Mix zerorows and zerorowscols */ nr = 0; idxs = NULL; if (!rank) { nr = 1; ierr = PetscMalloc1(nr,&idxs);CHKERRQ(ierr); if (test%2) { idxs[0] = (3*M - 2 - test/2)%M; } else { idxs[0] = (test/2+1)%M; } idxs[0] = PetscMax(idxs[0],0); } ierr = ISCreateGeneral(PETSC_COMM_WORLD,nr,idxs,PETSC_OWN_POINTER,&zr);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)zr,"ZR2");CHKERRQ(ierr); ierr = ISViewFromOptions(zr,NULL,"-view_is");CHKERRQ(ierr); ierr = MatZeroRowsIS(A,zr,diag*2.0+PETSC_SMALL,NULL,NULL);CHKERRQ(ierr); ierr = MatZeroRowsIS(S,zr,diag*2.0+PETSC_SMALL,NULL,NULL);CHKERRQ(ierr); } ierr = ISDestroy(&zr);CHKERRQ(ierr); if (b1) { Vec b; ierr = VecViewFromOptions(b1,NULL,"-view_b");CHKERRQ(ierr); ierr = VecViewFromOptions(b2,NULL,"-view_b");CHKERRQ(ierr); ierr = VecDuplicate(b1,&b);CHKERRQ(ierr); ierr = VecCopy(b1,b);CHKERRQ(ierr); ierr = VecAXPY(b,-1.0,b2);CHKERRQ(ierr); ierr = VecNorm(b,NORM_INFINITY,&err);CHKERRQ(ierr); if (err >= tol) { ierr = PetscPrintf(PETSC_COMM_WORLD,"[test %D] Error b %g\n",test,(double)err);CHKERRQ(ierr); } ierr = VecDestroy(&b);CHKERRQ(ierr); } ierr = VecDestroy(&b1);CHKERRQ(ierr); ierr = VecDestroy(&b2);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = MatConvert(S,MATDENSE,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr); ierr = MatCreateTranspose(S,&ST);CHKERRQ(ierr); ierr = MatComputeOperator(ST,MATDENSE,&BT);CHKERRQ(ierr); ierr = MatTranspose(BT,MAT_INITIAL_MATRIX,&BTT);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)B,"S");CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)BTT,"STT");CHKERRQ(ierr); ierr = MatConvert(A,MATDENSE,MAT_INITIAL_MATRIX,&C);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)C,"A");CHKERRQ(ierr); ierr = MatViewFromOptions(C,NULL,"-view_mat");CHKERRQ(ierr); ierr = MatViewFromOptions(B,NULL,"-view_mat");CHKERRQ(ierr); ierr = MatViewFromOptions(BTT,NULL,"-view_mat");CHKERRQ(ierr); ierr = MatAXPY(C,-1.0,B,SAME_NONZERO_PATTERN);CHKERRQ(ierr); ierr = MatNorm(C,NORM_FROBENIUS,&err);CHKERRQ(ierr); if (err >= tol) { ierr = PetscPrintf(PETSC_COMM_WORLD,"[test %D] Error mat mult %g\n",test,(double)err);CHKERRQ(ierr); } ierr = MatConvert(A,MATDENSE,MAT_REUSE_MATRIX,&C);CHKERRQ(ierr); ierr = MatAXPY(C,-1.0,BTT,SAME_NONZERO_PATTERN);CHKERRQ(ierr); ierr = MatNorm(C,NORM_FROBENIUS,&err);CHKERRQ(ierr); if (err >= tol) { ierr = PetscPrintf(PETSC_COMM_WORLD,"[test %D] Error mat mult transpose %g\n",test,(double)err);CHKERRQ(ierr); } ierr = MatDestroy(&ST);CHKERRQ(ierr); ierr = MatDestroy(&BTT);CHKERRQ(ierr); ierr = MatDestroy(&BT);CHKERRQ(ierr); ierr = MatDestroy(&B);CHKERRQ(ierr); ierr = MatDestroy(&C);CHKERRQ(ierr); } if (testdiagscale) { /* MatDiagonalScale() */ Vec vr,vl; ierr = MatCreateVecs(A,&vr,&vl);CHKERRQ(ierr); if (randomize) { ierr = VecSetRandom(vr,NULL);CHKERRQ(ierr); ierr = VecSetRandom(vl,NULL);CHKERRQ(ierr); } else { ierr = VecSet(vr,test%2 ? 0.15 : 1.0/0.15);CHKERRQ(ierr); ierr = VecSet(vl,test%2 ? -1.2 : 1.0/-1.2);CHKERRQ(ierr); } ierr = MatDiagonalScale(A,vl,vr);CHKERRQ(ierr); ierr = MatDiagonalScale(S,vl,vr);CHKERRQ(ierr); ierr = VecDestroy(&vr);CHKERRQ(ierr); ierr = VecDestroy(&vl);CHKERRQ(ierr); } if (testscale) { /* MatScale() */ ierr = MatScale(A,test%2 ? 1.4 : 1.0/1.4);CHKERRQ(ierr); ierr = MatScale(S,test%2 ? 1.4 : 1.0/1.4);CHKERRQ(ierr); } if (testshift && cong) { /* MatShift() : MATSHELL shift is broken when row/cols layout are not congruent and left/right scaling have been applied */ ierr = MatShift(A,test%2 ? -77.5 : 77.5);CHKERRQ(ierr); ierr = MatShift(S,test%2 ? -77.5 : 77.5);CHKERRQ(ierr); } if (testgetdiag && cong) { /* MatGetDiagonal() */ Vec dA,dS; ierr = MatCreateVecs(A,&dA,NULL);CHKERRQ(ierr); ierr = MatCreateVecs(S,&dS,NULL);CHKERRQ(ierr); ierr = MatGetDiagonal(A,dA);CHKERRQ(ierr); ierr = MatGetDiagonal(S,dS);CHKERRQ(ierr); ierr = VecAXPY(dA,-1.0,dS);CHKERRQ(ierr); ierr = VecNorm(dA,NORM_INFINITY,&err);CHKERRQ(ierr); if (err >= tol) { ierr = PetscPrintf(PETSC_COMM_WORLD,"[test %D] Error diag %g\n",test,(double)err);CHKERRQ(ierr); } ierr = VecDestroy(&dA);CHKERRQ(ierr); ierr = VecDestroy(&dS);CHKERRQ(ierr); } if (testdup && !test) { Mat A2, S2; ierr = MatDuplicate(A,MAT_COPY_VALUES,&A2);CHKERRQ(ierr); ierr = MatDuplicate(S,MAT_COPY_VALUES,&S2);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = MatDestroy(&S);CHKERRQ(ierr); A = A2; S = S2; } if (testreset && (ntest == 1 || test == ntest-2)) { /* reset MATSHELL */ ierr = MatAssemblyBegin(S,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(S,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); /* reset A */ ierr = MatCopy(user->B,A,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr); } } ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = MatDestroy(&user->B);CHKERRQ(ierr); ierr = MatDestroy(&S);CHKERRQ(ierr); ierr = PetscFree(user);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
PETSC_EXTERN void PETSC_STDCALL matcreatedense_(MPI_Comm *comm,PetscInt *m,PetscInt *n,PetscInt *M,PetscInt *N,PetscScalar *data,Mat *newmat,PetscErrorCode *ierr) { CHKFORTRANNULLSCALAR(data); *ierr = MatCreateDense(MPI_Comm_f2c(*(MPI_Fint*)&*comm),*m,*n,*M,*N,data,newmat); }
static void PETScMatvecGenColumnMajor(void *x, PRIMME_INT ldx, void *y, PRIMME_INT ldy, int blockSize, int trans, Mat matrix, MPI_Comm comm) { PetscInt m, n, mLocal, nLocal; PetscErrorCode ierr; Mat X, Y, X0, Y0; int xcompact, ycompact; if (blockSize == 1) { PETScMatvecGenNoBlock(x, ldx, y, ldy, blockSize, trans, matrix, comm); return; } assert(sizeof(PetscScalar) == sizeof(SCALAR)); ierr = MatGetSize(matrix, &m, &n); CHKERRABORT(comm, ierr); ierr = MatGetLocalSize(matrix, &mLocal, &nLocal); CHKERRABORT(comm, ierr); if (trans == 0) { ierr = MatCreateDense(comm,nLocal,PETSC_DECIDE,n,blockSize,x,&X);CHKERRABORT(comm, ierr); ierr = MatCreateDense(comm,mLocal,PETSC_DECIDE,m,blockSize,y,&Y);CHKERRABORT(comm, ierr); xcompact = nLocal == ldx; ycompact = mLocal == ldy; } else { ierr = MatCreateDense(comm,mLocal,PETSC_DECIDE,m,blockSize,x,&X);CHKERRABORT(comm, ierr); ierr = MatCreateDense(comm,nLocal,PETSC_DECIDE,n,blockSize,y,&Y);CHKERRABORT(comm, ierr); xcompact = mLocal == ldx; ycompact = nLocal == ldy; } ierr = MatDenseGetLocalMatrix(X, &X0);CHKERRABORT(comm, ierr); ierr = MatSeqDenseSetLDA(X0, (PetscInt)ldx);CHKERRABORT(comm, ierr); ierr = MatDenseGetLocalMatrix(Y, &Y0);CHKERRABORT(comm, ierr); ierr = MatSeqDenseSetLDA(Y0, (PetscInt)ldy);CHKERRABORT(comm, ierr); /* MatMatMult doesn't support X to be non-contiguous */ if (xcompact) { X0 = X; } else { ierr = MatDuplicate(X, MAT_COPY_VALUES, &X0);CHKERRABORT(comm, ierr); } if (trans == 0) { if (ycompact) { ierr = MatMatMult(matrix, X0, MAT_REUSE_MATRIX, PETSC_DEFAULT, &Y); CHKERRABORT(comm, ierr); } else { ierr = MatMatMult(matrix, X0, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &Y0); CHKERRABORT(comm, ierr); ierr = MatCopy(Y0, Y, SAME_NONZERO_PATTERN); CHKERRABORT(comm, ierr); ierr = MatDestroy(&Y0); CHKERRABORT(comm, ierr); } } else { /* A^H*X is not implemented in PETSc, do instead (A^T*X^c)^c */ ierr = MatConjugate(X0); CHKERRABORT(comm, ierr); if (ycompact) { ierr = MatTransposeMatMult(matrix, X0, MAT_REUSE_MATRIX, PETSC_DEFAULT, &Y); CHKERRABORT(comm, ierr); } else { ierr = MatTransposeMatMult(matrix, X0, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &Y0); CHKERRABORT(comm, ierr); ierr = MatCopy(Y0, Y, SAME_NONZERO_PATTERN); CHKERRABORT(comm, ierr); ierr = MatDestroy(&Y0); CHKERRABORT(comm, ierr); } ierr = MatConjugate(Y); CHKERRABORT(comm, ierr); if (xcompact) { ierr = MatConjugate(X0); CHKERRABORT(comm, ierr); } } if (!xcompact) { ierr = MatDestroy(&X0);CHKERRABORT(comm, ierr); } ierr = MatDestroy(&X);CHKERRABORT(comm, ierr); ierr = MatDestroy(&Y);CHKERRABORT(comm, ierr); }
int main(int argc,char **argv) { TS ts,quadts; /* ODE integrator */ Vec U; /* solution will be stored here */ Mat A; /* Jacobian matrix */ Mat Jacp; /* Jacobian matrix */ Mat DRDU,DRDP; PetscErrorCode ierr; PetscMPIInt size; PetscInt n = 2; AppCtx ctx; PetscScalar *u; PetscReal du[2] = {0.0,0.0}; PetscBool ensemble = PETSC_FALSE,flg1,flg2; PetscReal ftime; PetscInt steps; PetscScalar *x_ptr,*y_ptr; Vec lambda[1],q,mu[1]; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Initialize program - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr; ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); if (size > 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Only for sequential runs"); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create necessary matrix and vectors - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr); ierr = MatSetSizes(A,n,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); ierr = MatSetType(A,MATDENSE);CHKERRQ(ierr); ierr = MatSetFromOptions(A);CHKERRQ(ierr); ierr = MatSetUp(A);CHKERRQ(ierr); ierr = MatCreateVecs(A,&U,NULL);CHKERRQ(ierr); ierr = MatCreate(PETSC_COMM_WORLD,&Jacp);CHKERRQ(ierr); ierr = MatSetSizes(Jacp,PETSC_DECIDE,PETSC_DECIDE,2,1);CHKERRQ(ierr); ierr = MatSetFromOptions(Jacp);CHKERRQ(ierr); ierr = MatSetUp(Jacp);CHKERRQ(ierr); ierr = MatCreateDense(PETSC_COMM_WORLD,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,&DRDP);CHKERRQ(ierr); ierr = MatSetUp(DRDP);CHKERRQ(ierr); ierr = MatCreateDense(PETSC_COMM_WORLD,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,&DRDU);CHKERRQ(ierr); ierr = MatSetUp(DRDU);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set runtime options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Swing equation options","");CHKERRQ(ierr); { ctx.beta = 2; ctx.c = 10000.0; ctx.u_s = 1.0; ctx.omega_s = 1.0; ctx.omega_b = 120.0*PETSC_PI; ctx.H = 5.0; ierr = PetscOptionsScalar("-Inertia","","",ctx.H,&ctx.H,NULL);CHKERRQ(ierr); ctx.D = 5.0; ierr = PetscOptionsScalar("-D","","",ctx.D,&ctx.D,NULL);CHKERRQ(ierr); ctx.E = 1.1378; ctx.V = 1.0; ctx.X = 0.545; ctx.Pmax = ctx.E*ctx.V/ctx.X;; ierr = PetscOptionsScalar("-Pmax","","",ctx.Pmax,&ctx.Pmax,NULL);CHKERRQ(ierr); ctx.Pm = 1.1; ierr = PetscOptionsScalar("-Pm","","",ctx.Pm,&ctx.Pm,NULL);CHKERRQ(ierr); ctx.tf = 0.1; ctx.tcl = 0.2; ierr = PetscOptionsReal("-tf","Time to start fault","",ctx.tf,&ctx.tf,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-tcl","Time to end fault","",ctx.tcl,&ctx.tcl,NULL);CHKERRQ(ierr); ierr = PetscOptionsBool("-ensemble","Run ensemble of different initial conditions","",ensemble,&ensemble,NULL);CHKERRQ(ierr); if (ensemble) { ctx.tf = -1; ctx.tcl = -1; } ierr = VecGetArray(U,&u);CHKERRQ(ierr); u[0] = PetscAsinScalar(ctx.Pm/ctx.Pmax); u[1] = 1.0; ierr = PetscOptionsRealArray("-u","Initial solution","",u,&n,&flg1);CHKERRQ(ierr); n = 2; ierr = PetscOptionsRealArray("-du","Perturbation in initial solution","",du,&n,&flg2);CHKERRQ(ierr); u[0] += du[0]; u[1] += du[1]; ierr = VecRestoreArray(U,&u);CHKERRQ(ierr); if (flg1 || flg2) { ctx.tf = -1; ctx.tcl = -1; } } ierr = PetscOptionsEnd();CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create timestepping solver context - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr); ierr = TSSetType(ts,TSRK);CHKERRQ(ierr); ierr = TSSetRHSFunction(ts,NULL,(TSRHSFunction)RHSFunction,&ctx);CHKERRQ(ierr); ierr = TSSetRHSJacobian(ts,A,A,(TSRHSJacobian)RHSJacobian,&ctx);CHKERRQ(ierr); ierr = TSCreateQuadratureTS(ts,PETSC_TRUE,&quadts);CHKERRQ(ierr); ierr = TSSetRHSFunction(quadts,NULL,(TSRHSFunction)CostIntegrand,&ctx);CHKERRQ(ierr); ierr = TSSetRHSJacobian(quadts,DRDU,DRDU,(TSRHSJacobian)DRDUJacobianTranspose,&ctx);CHKERRQ(ierr); ierr = TSSetRHSJacobianP(quadts,DRDP,(TSRHSJacobianP)DRDPJacobianTranspose,&ctx);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set initial conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetSolution(ts,U);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Save trajectory of solution so that TSAdjointSolve() may be used - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetSaveTrajectory(ts);CHKERRQ(ierr); ierr = MatCreateVecs(A,&lambda[0],NULL);CHKERRQ(ierr); /* Set initial conditions for the adjoint integration */ ierr = VecGetArray(lambda[0],&y_ptr);CHKERRQ(ierr); y_ptr[0] = 0.0; y_ptr[1] = 0.0; ierr = VecRestoreArray(lambda[0],&y_ptr);CHKERRQ(ierr); ierr = MatCreateVecs(Jacp,&mu[0],NULL);CHKERRQ(ierr); ierr = VecGetArray(mu[0],&x_ptr);CHKERRQ(ierr); x_ptr[0] = -1.0; ierr = VecRestoreArray(mu[0],&x_ptr);CHKERRQ(ierr); ierr = TSSetCostGradients(ts,1,lambda,mu);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set solver options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetMaxTime(ts,10.0);CHKERRQ(ierr); ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_MATCHSTEP);CHKERRQ(ierr); ierr = TSSetTimeStep(ts,.01);CHKERRQ(ierr); ierr = TSSetFromOptions(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve nonlinear system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ if (ensemble) { for (du[1] = -2.5; du[1] <= .01; du[1] += .1) { ierr = VecGetArray(U,&u);CHKERRQ(ierr); u[0] = PetscAsinScalar(ctx.Pm/ctx.Pmax); u[1] = ctx.omega_s; u[0] += du[0]; u[1] += du[1]; ierr = VecRestoreArray(U,&u);CHKERRQ(ierr); ierr = TSSetTimeStep(ts,.01);CHKERRQ(ierr); ierr = TSSolve(ts,U);CHKERRQ(ierr); } } else { ierr = TSSolve(ts,U);CHKERRQ(ierr); } ierr = VecView(U,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr); ierr = TSGetStepNumber(ts,&steps);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Adjoint model starts here - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ /* Set initial conditions for the adjoint integration */ ierr = VecGetArray(lambda[0],&y_ptr);CHKERRQ(ierr); y_ptr[0] = 0.0; y_ptr[1] = 0.0; ierr = VecRestoreArray(lambda[0],&y_ptr);CHKERRQ(ierr); ierr = VecGetArray(mu[0],&x_ptr);CHKERRQ(ierr); x_ptr[0] = -1.0; ierr = VecRestoreArray(mu[0],&x_ptr);CHKERRQ(ierr); /* Set RHS JacobianP */ ierr = TSSetRHSJacobianP(ts,Jacp,RHSJacobianP,&ctx);CHKERRQ(ierr); ierr = TSAdjointSolve(ts);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"\n sensitivity wrt initial conditions: d[Psi(tf)]/d[phi0] d[Psi(tf)]/d[omega0]\n");CHKERRQ(ierr); ierr = VecView(lambda[0],PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = VecView(mu[0],PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = TSGetCostIntegral(ts,&q);CHKERRQ(ierr); ierr = VecView(q,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = VecGetArray(q,&x_ptr);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"\n cost function=%g\n",(double)(x_ptr[0]-ctx.Pm));CHKERRQ(ierr); ierr = VecRestoreArray(q,&x_ptr);CHKERRQ(ierr); ierr = ComputeSensiP(lambda[0],mu[0],&ctx);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free work space. All PETSc objects should be destroyed when they are no longer needed. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = MatDestroy(&Jacp);CHKERRQ(ierr); ierr = MatDestroy(&DRDU);CHKERRQ(ierr); ierr = MatDestroy(&DRDP);CHKERRQ(ierr); ierr = VecDestroy(&U);CHKERRQ(ierr); ierr = VecDestroy(&lambda[0]);CHKERRQ(ierr); ierr = VecDestroy(&mu[0]);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }