int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscInt i,blocks[2],nlocal;
PetscMPIInt size,rank;
PetscScalar value;
Vec x,y;
IS is1,is2;
VecScatter ctx = 0;
PetscViewer subviewer;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
if (size != 2) SETERRQ(PETSC_COMM_SELF,1,"Must run with 2 processors");
/* create two vectors */
if (!rank) nlocal = 8;
else nlocal = 4;
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,nlocal,12);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_SELF,&y);CHKERRQ(ierr);
ierr = VecSetSizes(y,8,PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetFromOptions(y);CHKERRQ(ierr);
/* create two index sets */
if (!rank) {
blocks[0] = 0; blocks[1] = 2;
} else {
blocks[0] = 1; blocks[1] = 2;
}
ierr = ISCreateBlock(PETSC_COMM_SELF,4,2,blocks,PETSC_COPY_VALUES,&is1);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_SELF,8,0,1,&is2);CHKERRQ(ierr);
for (i=0; i<12; i++) {
value = i;
ierr = VecSetValues(x,1,&i,&value,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = VecAssemblyBegin(x);CHKERRQ(ierr);
ierr = VecAssemblyEnd(x);CHKERRQ(ierr);
ierr = VecScatterCreateWithData(x,is1,y,is2,&ctx);CHKERRQ(ierr);
ierr = VecScatterBegin(ctx,x,y,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterEnd(ctx,x,y,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterDestroy(&ctx);CHKERRQ(ierr);
ierr = PetscViewerGetSubViewer(PETSC_VIEWER_STDOUT_WORLD,PETSC_COMM_SELF,&subviewer);CHKERRQ(ierr);
ierr = VecView(y,subviewer);CHKERRQ(ierr);
ierr = PetscViewerRestoreSubViewer(PETSC_VIEWER_STDOUT_WORLD,PETSC_COMM_SELF,&subviewer);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&y);CHKERRQ(ierr);
ierr = ISDestroy(&is1);CHKERRQ(ierr);
ierr = ISDestroy(&is2);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
void PETSc::Create(
MPI_Comm Comm,
int ilower,
int iupper,
int d_nz,
int o_nz)
{
int n = iupper - ilower +1;
comm = Comm;
iLower = ilower;
iUpper = iupper;
MatCreateAIJ(PETSC_COMM_WORLD,n,n,PETSC_DECIDE,PETSC_DECIDE,
d_nz,PETSC_NULL,o_nz,PETSC_NULL,&A);
ierr = PetscObjectSetName((PetscObject) A, "A");
ierr = MatSetFromOptions(A);
// b
ierr = VecCreate(PETSC_COMM_WORLD, &b);
ierr = PetscObjectSetName((PetscObject) b, "b");
ierr = VecSetSizes(b, n, PETSC_DECIDE);
ierr = VecSetFromOptions(b);
ierr = VecCreate(PETSC_COMM_WORLD,&x);
ierr = PetscObjectSetName((PetscObject) x, "X");
ierr = VecSetSizes(x, n, PETSC_DECIDE);
ierr = VecSetFromOptions(x);
}
int main(int argc,char **argv)
{
Vec v,s,r,vecs[2]; /* vectors */
PetscInt i,start,end,n = 20;
PetscErrorCode ierr;
PetscScalar value;
PetscInitialize(&argc,&argv,(char*)0,help);
ierr = PetscOptionsGetInt(PETSC_NULL,"-n",&n,PETSC_NULL);CHKERRQ(ierr);
/*
Create multi-component vector with 2 components
*/
ierr = VecCreate(PETSC_COMM_WORLD,&v);CHKERRQ(ierr);
ierr = VecSetSizes(v,PETSC_DECIDE,n);CHKERRQ(ierr);
ierr = VecSetBlockSize(v,4);CHKERRQ(ierr);
ierr = VecSetFromOptions(v);CHKERRQ(ierr);
/*
Create double-component vectors
*/
ierr = VecCreate(PETSC_COMM_WORLD,&s);CHKERRQ(ierr);
ierr = VecSetSizes(s,PETSC_DECIDE,n/2);CHKERRQ(ierr);
ierr = VecSetBlockSize(s,2);CHKERRQ(ierr);
ierr = VecSetFromOptions(s);CHKERRQ(ierr);
ierr = VecDuplicate(s,&r);CHKERRQ(ierr);
vecs[0] = s;
vecs[1] = r;
/*
Set the vector values
*/
ierr = VecGetOwnershipRange(v,&start,&end);CHKERRQ(ierr);
for (i=start; i<end; i++) {
value = i;
ierr = VecSetValues(v,1,&i,&value,INSERT_VALUES);CHKERRQ(ierr);
}
/*
Get the components from the multi-component vector to the other vectors
*/
ierr = VecStrideGatherAll(v,vecs,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecView(s,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecView(r,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecStrideScatterAll(vecs,v,ADD_VALUES);CHKERRQ(ierr);
ierr = VecView(v,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/*
Free work space. All PETSc objects should be destroyed when they
are no longer needed.
*/
ierr = VecDestroy(&v);CHKERRQ(ierr);
ierr = VecDestroy(&s);CHKERRQ(ierr);
ierr = VecDestroy(&r);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
void FETI_Operations::export_ext_solver_rhs(Vec vec_in)
{
homemade_assert_msg(m_bScratchFolderSet,"Scratch folder not set yet!");
Vec vec_C_micro_t_p_kkk_PETSc;
VecCreate(m_comm.get(),&vec_C_micro_t_p_kkk_PETSc);
VecSetSizes(vec_C_micro_t_p_kkk_PETSc,m_C_R_micro_N_local,m_C_R_micro_N);
VecSetFromOptions(vec_C_micro_t_p_kkk_PETSc);
Vec vec_C_BIG_t_p_kkk_PETSc;
VecCreate(m_comm.get(),&vec_C_BIG_t_p_kkk_PETSc);
VecSetSizes(vec_C_BIG_t_p_kkk_PETSc,m_C_R_BIG_N_local,m_C_R_BIG_N);
VecSetFromOptions(vec_C_BIG_t_p_kkk_PETSc);
MatMultTranspose(m_C_R_micro,vec_in,vec_C_micro_t_p_kkk_PETSc);
MatMultTranspose(m_C_R_BIG,vec_in,vec_C_BIG_t_p_kkk_PETSc);
write_PETSC_vector(vec_C_BIG_t_p_kkk_PETSc,m_scratch_folder_path + "/ext_solver_A_rhs.petscvec",m_comm.rank(),m_comm.get());
write_PETSC_vector(vec_C_micro_t_p_kkk_PETSc,m_scratch_folder_path + "/ext_solver_B_rhs.petscvec",m_comm.rank(),m_comm.get());
// Print MatLab debugging output? Variable defined at "carl_headers.h"
#ifdef PRINT_MATLAB_DEBUG
write_PETSC_vector_MATLAB(vec_C_micro_t_p_kkk_PETSc,m_scratch_folder_path + "/ext_solver_B_rhs.m",m_comm.get());
write_PETSC_vector_MATLAB(vec_C_BIG_t_p_kkk_PETSc,m_scratch_folder_path + "/ext_solver_A_rhs.m",m_comm.get());
#endif
VecDestroy(&vec_C_micro_t_p_kkk_PETSc);
VecDestroy(&vec_C_BIG_t_p_kkk_PETSc);
}
/*@
MatMultEqual - Compares matrix-vector products of two matrices.
Collective on Mat
Input Parameters:
+ A - the first matrix
- B - the second matrix
- n - number of random vectors to be tested
Output Parameter:
. flg - PETSC_TRUE if the products are equal; PETSC_FALSE otherwise.
Level: intermediate
Concepts: matrices^equality between
@*/
PetscErrorCode MatMultEqual(Mat A,Mat B,PetscInt n,PetscBool *flg)
{
PetscErrorCode ierr;
Vec x,s1,s2;
PetscRandom rctx;
PetscReal r1,r2,tol=1.e-10;
PetscInt am,an,bm,bn,k;
PetscScalar none = -1.0;
PetscFunctionBegin;
PetscValidHeaderSpecific(A,MAT_CLASSID,1);
PetscValidHeaderSpecific(B,MAT_CLASSID,2);
ierr = MatGetLocalSize(A,&am,&an);CHKERRQ(ierr);
ierr = MatGetLocalSize(B,&bm,&bn);CHKERRQ(ierr);
if (am != bm || an != bn) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Mat A,Mat B: local dim %D %D %D %D",am,bm,an,bn);
PetscCheckSameComm(A,1,B,2);
#if defined(PETSC_USE_REAL_SINGLE)
tol = 1.e-5;
#endif
ierr = PetscRandomCreate(((PetscObject)A)->comm,&rctx);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rctx);CHKERRQ(ierr);
ierr = VecCreate(((PetscObject)A)->comm,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,an,PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
ierr = VecCreate(((PetscObject)A)->comm,&s1);CHKERRQ(ierr);
ierr = VecSetSizes(s1,am,PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetFromOptions(s1);CHKERRQ(ierr);
ierr = VecDuplicate(s1,&s2);CHKERRQ(ierr);
*flg = PETSC_TRUE;
for (k=0; k<n; k++) {
ierr = VecSetRandom(x,rctx);CHKERRQ(ierr);
ierr = MatMult(A,x,s1);CHKERRQ(ierr);
ierr = MatMult(B,x,s2);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_INFINITY,&r2);CHKERRQ(ierr);
if (r2 < tol){
ierr = VecNorm(s1,NORM_INFINITY,&r1);CHKERRQ(ierr);
} else {
ierr = VecAXPY(s2,none,s1);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_INFINITY,&r1);CHKERRQ(ierr);
r1 /= r2;
}
if (r1 > tol) {
*flg = PETSC_FALSE;
ierr = PetscInfo2(A,"Error: %D-th MatMult() %G\n",k,r1);CHKERRQ(ierr);
break;
}
}
ierr = PetscRandomDestroy(&rctx);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&s1);CHKERRQ(ierr);
ierr = VecDestroy(&s2);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
void MultigridSolver_UpdateWorkVectors( MultigridSolver* self ) {
MultigridSolver_Level* level;
//unsigned rowSize, colSize;
PetscInt rowSize, colSize, vecSize;
unsigned l_i;
assert( self && Stg_CheckType( self, MultigridSolver ) );
for( l_i = 0; l_i < self->nLevels - 1; l_i++ ) {
level = self->levels + l_i;
//Matrix_GetLocalSize( MatrixSolver_GetMatrix( level->downSolver ), &rowSize, &colSize );
MatGetLocalSize( level->downSolver->matrix, &rowSize, &colSize );
VecGetLocalSize( level->workSol, &vecSize );
//if( !level->workSol || Vector_GetLocalSize( level->workSol ) != rowSize ) {
if( !level->workSol || vecSize != rowSize ) {
//if( level->workSol )
// Stg_Class_RemoveRef( level->workSol );
//Vector_Duplicate( self->curSolution, (void**)&level->workSol );
//Vector_SetLocalSize( level->workSol, rowSize );
if( level->workSol != PETSC_NULL )
Stg_VecDestroy(&level->workSol );
VecCreate( self->mgData->comm, &level->workSol );
VecSetSizes( level->workSol, rowSize, PETSC_DECIDE );
VecSetFromOptions( level->workSol );
#if( PETSC_VERSION_MAJOR <= 2 && PETSC_VERSION_MINOR >= 3 && PETSC_VERSION_SUBMINOR >= 3 )
VecSetOption( level->workSol, VEC_IGNORE_NEGATIVE_INDICES );
#elif( PETSC_VERSION_MAJOR >= 3 )
VecSetOption( level->workSol, VEC_IGNORE_NEGATIVE_INDICES, PETSC_TRUE );
#endif
}
VecGetLocalSize( level->workRHS, &vecSize );
if( !level->workRHS || /*Vector_GetLocalSize( level->workRHS )*/vecSize != rowSize ) {
//if( level->workRHS )
// Stg_Class_RemoveRef( level->workRHS );
//Vector_Duplicate( self->curSolution, (void**)&level->workRHS );
//Vector_SetLocalSize( level->workRHS, rowSize );
if( level->workRHS != PETSC_NULL )
Stg_VecDestroy(&level->workRHS );
VecCreate( self->mgData->comm, &level->workRHS );
VecSetSizes( level->workRHS, rowSize, PETSC_DECIDE );
VecSetFromOptions( level->workRHS );
#if( PETSC_VERSION_MAJOR <= 2 && PETSC_VERSION_MINOR >= 3 && PETSC_VERSION_SUBMINOR >= 3 )
VecSetOption( level->workRHS, VEC_IGNORE_NEGATIVE_INDICES );
#elif( PETSC_VERSION_MAJOR >= 3 )
VecSetOption( level->workRHS, VEC_IGNORE_NEGATIVE_INDICES, PETSC_TRUE );
#endif
}
}
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
Vec v,s; /* vectors */
PetscInt n = 20;
PetscScalar one = 1.0;
PetscInitialize(&argc,&argv,(char*)0,help);
ierr = PetscOptionsGetInt(PETSC_NULL,"-n",&n,PETSC_NULL);CHKERRQ(ierr);
/*
Create multi-component vector with 2 components
*/
ierr = VecCreate(PETSC_COMM_WORLD,&v);CHKERRQ(ierr);
ierr = VecSetSizes(v,PETSC_DECIDE,n);CHKERRQ(ierr);
ierr = VecSetBlockSize(v,2);CHKERRQ(ierr);
ierr = VecSetFromOptions(v);CHKERRQ(ierr);
/*
Create single-component vector
*/
ierr = VecCreate(PETSC_COMM_WORLD,&s);CHKERRQ(ierr);
ierr = VecSetSizes(s,PETSC_DECIDE,n/2);CHKERRQ(ierr);
ierr = VecSetFromOptions(s);CHKERRQ(ierr);
/*
Set the vectors to entries to a constant value.
*/
ierr = VecSet(v,one);CHKERRQ(ierr);
/*
Get the first component from the multi-component vector to the single vector
*/
ierr = VecStrideGather(v,0,s,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecView(s,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/*
Put the values back into the second component
*/
ierr = VecStrideScatter(s,1,v,ADD_VALUES);CHKERRQ(ierr);
ierr = VecView(v,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/*
Free work space. All PETSc objects should be destroyed when they
are no longer needed.
*/
ierr = VecDestroy(&v);CHKERRQ(ierr);
ierr = VecDestroy(&s);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscInt n = 5,N,i;
PetscMPIInt size,rank;
PetscScalar value,zero = 0.0;
Vec x,y;
IS is1,is2;
VecScatter ctx = 0;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
/* create two vectors */
N = size*n;
ierr = VecCreate(PETSC_COMM_WORLD,&y);CHKERRQ(ierr);
ierr = VecSetSizes(y,n,PETSC_DECIDE);CHKERRQ(ierr)
ierr = VecSetFromOptions(y);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,n,PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
/* create two index sets */
ierr = ISCreateStride(PETSC_COMM_WORLD,n,n*rank,1,&is1);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_WORLD,n,(n*(rank+1))%N,1,&is2);CHKERRQ(ierr);
/* fill local part of parallel vector x */
value = (PetscScalar)(rank+1);
for (i=n*rank; i<n*(rank+1); i++) {
ierr = VecSetValues(x,1,&i,&value,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = VecAssemblyBegin(x);CHKERRQ(ierr);
ierr = VecAssemblyEnd(x);CHKERRQ(ierr);
ierr = VecSet(y,zero);CHKERRQ(ierr);
ierr = VecScatterCreate(x,is1,y,is2,&ctx);CHKERRQ(ierr);
ierr = VecScatterBegin(ctx,x,y,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterEnd(ctx,x,y,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterDestroy(ctx);CHKERRQ(ierr);
ierr = VecView(y,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecDestroy(x);CHKERRQ(ierr);
ierr = VecDestroy(y);CHKERRQ(ierr);
ierr = ISDestroy(is1);CHKERRQ(ierr);
ierr = ISDestroy(is2);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
int main(int argc,char **args)
{
KSP ksp; /* linear solver context */
Mat A; /* linear system matrix */
Vec x,b; /* approx solution, RHS */
PetscInt Ii,Istart,Iend;
PetscErrorCode ierr;
PetscScalar v[3] = {-1./2., 1., -1./2.};
PetscInt j[3];
PetscInt k=15;
PetscInt M,m=420;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
ierr = PetscOptionsGetInt(NULL,NULL,"-k",&k,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-m",&m,NULL);CHKERRQ(ierr);
ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr);
ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
ierr = KSPGetOperators(ksp,&A,NULL);CHKERRQ(ierr);
ierr = MatSetSizes(A,m,m,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(A,&Istart,&Iend);CHKERRQ(ierr);
ierr = MatGetSize(A,&M,NULL);CHKERRQ(ierr);
for (Ii=Istart; Ii<Iend; Ii++) {
j[0] = Ii - k;
j[1] = Ii;
j[2] = (Ii + k) < M ? (Ii + k) : -1;
ierr = MatSetValues(A,1,&Ii,3,j,v,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatCreateVecs(A,&x,&b);CHKERRQ(ierr);
ierr = VecSetFromOptions(b);CHKERRQ(ierr);
ierr = VecSet(b,1.0);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
ierr = VecSet(x,2.0);CHKERRQ(ierr);
ierr = KSPSolve(ksp,b,x);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
void operator| (PUP::er& p, Vec& v) {
PetscInt sz;
if (!p.isUnpacking()) {
VecGetSize(v, &sz);
}
p | sz;
if(p.isUnpacking()) {
VecCreateSeq(PETSC_COMM_WORLD, sz, &v);
VecSetFromOptions(v);
VecGetSize(v, &sz);
for (int i = 0; i < sz; i++) {
PetscScalar d;
p | d;
VecSetValue(v, i, d, INSERT_VALUES);
}
VecAssemblyBegin(v);
VecAssemblyEnd(v);
}
else {
for (int i = 0; i < sz; i++) {
PetscScalar d;
VecGetValues(v, 1, &i, &d);
p | d;
}
}
}
int main(int argc,char **args)
{
PetscErrorCode ierr;
PetscInt m = 10;
int fcomm;
Vec vec;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
/* This function should be called to be able to use PETSc routines
from the FORTRAN subroutines needed by this program */
PetscInitializeFortran();
ierr = VecCreate(PETSC_COMM_WORLD,&vec);CHKERRQ(ierr);
ierr = VecSetSizes(vec,PETSC_DECIDE,m);CHKERRQ(ierr);
ierr = VecSetFromOptions(vec);CHKERRQ(ierr);
/*
Call Fortran routine - the use of MPI_Comm_c2f() allows
translation of the MPI_Comm from C so that it can be properly
interpreted from Fortran.
*/
fcomm = MPI_Comm_c2f(PETSC_COMM_WORLD);
ex7f_(&vec,&fcomm);
ierr = VecView(vec,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecDestroy(&vec);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc,char **argv) {
PetscErrorCode ierr;
SNES snes; // nonlinear solver context
Vec x, r; // solution, residual vectors
PetscReal x0 = 2.0;
PetscInitialize(&argc,&argv,(char*)0,help);
ierr = PetscOptionsBegin(PETSC_COMM_WORLD,"","options to atan","");CHKERRQ(ierr);
ierr = PetscOptionsReal("-x0","initial value","atan.c",x0,&x0,NULL); CHKERRQ(ierr);
ierr = PetscOptionsEnd();CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&x); CHKERRQ(ierr);
ierr = VecSetSizes(x,PETSC_DECIDE,1); CHKERRQ(ierr);
ierr = VecSetFromOptions(x); CHKERRQ(ierr);
ierr = VecSet(x,x0); CHKERRQ(ierr);
ierr = VecDuplicate(x,&r); CHKERRQ(ierr);
ierr = SNESCreate(PETSC_COMM_WORLD,&snes); CHKERRQ(ierr);
ierr = SNESSetFunction(snes,r,FormFunction,NULL); CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes); CHKERRQ(ierr);
ierr = SNESSolve(snes,NULL,x); CHKERRQ(ierr);
ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD); CHKERRQ(ierr);
VecDestroy(&x); VecDestroy(&r); SNESDestroy(&snes);
PetscFinalize();
return 0;
}
PetscErrorCode DistributeCoordinates(DM dm, PetscSF pointSF, DM parallelDM)
{
PetscSF coordSF;
PetscSection originalCoordSection, newCoordSection;
Vec coordinates, newCoordinates;
PetscScalar *coords, *newCoords;
PetscInt *remoteOffsets, coordSize;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMMeshGetCoordinateSection(dm, &originalCoordSection);CHKERRQ(ierr);
ierr = DMMeshGetCoordinateSection(parallelDM, &newCoordSection);CHKERRQ(ierr);
ierr = PetscSFDistributeSection(pointSF, originalCoordSection, &remoteOffsets, newCoordSection);CHKERRQ(ierr);
ierr = DMMeshGetCoordinateVec(dm, &coordinates);CHKERRQ(ierr);
ierr = DMMeshGetCoordinateVec(parallelDM, &newCoordinates);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(newCoordSection, &coordSize);CHKERRQ(ierr);
ierr = VecSetSizes(newCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetFromOptions(newCoordinates);CHKERRQ(ierr);
ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
ierr = VecGetArray(newCoordinates, &newCoords);CHKERRQ(ierr);
ierr = PetscSFCreateSectionSF(pointSF, originalCoordSection, remoteOffsets, newCoordSection, &coordSF);CHKERRQ(ierr);
ierr = PetscSFBcastBegin(coordSF, MPIU_SCALAR, coords, newCoords);CHKERRQ(ierr);
ierr = PetscSFBcastEnd(coordSF, MPIU_SCALAR, coords, newCoords);CHKERRQ(ierr);
ierr = PetscSFDestroy(&coordSF);CHKERRQ(ierr);
ierr = VecRestoreArray(newCoordinates, &newCoords);CHKERRQ(ierr);
ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
SparseGp *
SparseGp_create (AcfrKern *kern, int rank, gsl_matrix *trainObs,
gsl_vector *trainLabels, gsl_matrix *testObs,
gsl_vector *testLabels)
{
PetscErrorCode ierr; /* not used here - not returning int */
(void) ierr;
SparseGp *gp = calloc (1, sizeof (*gp));
gp->kern = kern;
gp->trainObs = trainObs;
gp->trainLabels = trainLabels;
gp->testObs = testObs;
gp->testLabels = testLabels;
PetscInt N = gp->trainLabels->size;
ierr = VecCreate (PETSC_COMM_WORLD, &(gp->_trainLabels)); /* CHKERRQ (ierr); */
ierr = VecSetSizes (gp->_trainLabels, PETSC_DECIDE, N); /* CHKERRQ (ierr); */
ierr = VecSetFromOptions (gp->_trainLabels); /* CHKERRQ (ierr); */
ierr = VecGetOwnershipRange (gp->_trainLabels, &(gp->rstart), &(gp->rend)); /* CHKERRQ (ierr); */
ierr = VecGetLocalSize (gp->_trainLabels, &(gp->nlocal)); /* CHKERRQ (ierr); */
petsc_util_fillVec (gp->trainLabels, &gp->_trainLabels, gp->rstart, gp->rend);
gp->rank = rank;
return gp;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscMPIInt rank;
PetscInt n = 5;
char *output;
Vec x;
PetscInitialize(&argc,&argv,(char *)0,0);
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,PETSC_DECIDE,n);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);
ierr = PetscMatlabEngineGetOutput(PETSC_MATLAB_ENGINE_WORLD,&output);
ierr = PetscMatlabEngineEvaluate(PETSC_MATLAB_ENGINE_WORLD,"MPI_Comm_rank");
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d]Processor rank is %s",rank,output);CHKERRQ(ierr);
ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)x,"x");CHKERRQ(ierr);
ierr = PetscMatlabEnginePut(PETSC_MATLAB_ENGINE_WORLD,(PetscObject)x);CHKERRQ(ierr);
ierr = PetscMatlabEngineEvaluate(PETSC_MATLAB_ENGINE_WORLD,"x = x + MPI_Comm_rank;\n");
ierr = PetscMatlabEngineGet(PETSC_MATLAB_ENGINE_WORLD,(PetscObject)x);CHKERRQ(ierr);
ierr = PetscMatlabEngineEvaluate(PETSC_MATLAB_ENGINE_WORLD,"whos\n");
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d]The result is %s",rank,output);CHKERRQ(ierr);
ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD);CHKERRQ(ierr);
ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecDestroy(x);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscInt n = 5,N,low,high,iglobal,i;
PetscMPIInt size,rank;
PetscScalar value,zero = 0.0;
Vec x,y;
IS is1,is2;
VecScatter ctx;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
/* create two vectors */
N = size*n;
ierr = VecCreate(PETSC_COMM_WORLD,&y);CHKERRQ(ierr);
ierr = VecSetSizes(y,PETSC_DECIDE,N);CHKERRQ(ierr);
ierr = VecSetFromOptions(y);CHKERRQ(ierr);
if (!rank) {
ierr = VecCreateSeq(PETSC_COMM_SELF,N,&x);CHKERRQ(ierr);
} else {
ierr = VecCreateSeq(PETSC_COMM_SELF,0,&x);CHKERRQ(ierr);
}
/* create two index sets */
if (!rank) {
ierr = ISCreateStride(PETSC_COMM_SELF,N,0,1,&is1);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_SELF,N,0,1,&is2);CHKERRQ(ierr);
} else {
ierr = ISCreateStride(PETSC_COMM_SELF,0,0,1,&is1);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_SELF,0,0,1,&is2);CHKERRQ(ierr);
}
ierr = VecSet(x,zero);CHKERRQ(ierr);
ierr = VecGetOwnershipRange(y,&low,&high);CHKERRQ(ierr);
for (i=0; i<n; i++) {
iglobal = i + low; value = (PetscScalar) (i + 10*rank);
ierr = VecSetValues(y,1,&iglobal,&value,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = VecAssemblyBegin(y);CHKERRQ(ierr);
ierr = VecAssemblyEnd(y);CHKERRQ(ierr);
ierr = VecView(y,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecScatterCreate(y,is2,x,is1,&ctx);CHKERRQ(ierr);
ierr = VecScatterBegin(ctx,y,x,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterEnd(ctx,y,x,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterDestroy(&ctx);CHKERRQ(ierr);
if (!rank)
{printf("----\n"); ierr = VecView(x,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);}
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&y);CHKERRQ(ierr);
ierr = ISDestroy(&is1);CHKERRQ(ierr);
ierr = ISDestroy(&is2);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
/*
This takes as input the coordinates for each vertex
*/
PetscErrorCode DMPlexBuildCoordinates_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[])
{
PetscSection coordSection;
Vec coordinates;
PetscScalar *coords;
PetscInt coordSize, v, d;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr);
ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr);
ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr);
for (v = numCells; v < numCells+numVertices; ++v) {
ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr);
ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr);
ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetFromOptions(coordinates);CHKERRQ(ierr);
ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
for (v = 0; v < numVertices; ++v) {
for (d = 0; d < spaceDim; ++d) {
coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d];
}
}
ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr);
ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode MatSetLocalToGlobalMapping_IS(Mat A,ISLocalToGlobalMapping rmapping,ISLocalToGlobalMapping cmapping)
{
PetscErrorCode ierr;
PetscInt n,bs;
Mat_IS *is = (Mat_IS*)A->data;
IS from,to;
Vec global;
PetscFunctionBegin;
PetscCheckSameComm(A,1,rmapping,2);
if (rmapping != cmapping) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_INCOMP,"MATIS requires the row and column mappings to be identical");
if (is->mapping) { /* Currenly destroys the objects that will be created by this routine. Is there anything else that should be checked? */
ierr = ISLocalToGlobalMappingDestroy(&is->mapping);CHKERRQ(ierr);
ierr = VecDestroy(&is->x);CHKERRQ(ierr);
ierr = VecDestroy(&is->y);CHKERRQ(ierr);
ierr = VecScatterDestroy(&is->ctx);CHKERRQ(ierr);
ierr = MatDestroy(&is->A);CHKERRQ(ierr);
}
ierr = PetscObjectReference((PetscObject)rmapping);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingDestroy(&is->mapping);CHKERRQ(ierr);
is->mapping = rmapping;
/*
ierr = PetscLayoutSetISLocalToGlobalMapping(A->rmap,rmapping);CHKERRQ(ierr);
ierr = PetscLayoutSetISLocalToGlobalMapping(A->cmap,cmapping);CHKERRQ(ierr);
*/
/* Create the local matrix A */
ierr = ISLocalToGlobalMappingGetSize(rmapping,&n);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingGetBlockSize(rmapping,&bs);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_SELF,&is->A);CHKERRQ(ierr);
if (bs > 1) {
ierr = MatSetType(is->A,MATSEQBAIJ);CHKERRQ(ierr);
} else {
ierr = MatSetType(is->A,MATSEQAIJ);CHKERRQ(ierr);
}
ierr = MatSetSizes(is->A,n,n,n,n);CHKERRQ(ierr);
ierr = MatSetBlockSize(is->A,bs);CHKERRQ(ierr);
ierr = MatSetOptionsPrefix(is->A,((PetscObject)A)->prefix);CHKERRQ(ierr);
ierr = MatAppendOptionsPrefix(is->A,"is_");CHKERRQ(ierr);
ierr = MatSetFromOptions(is->A);CHKERRQ(ierr);
/* Create the local work vectors */
ierr = VecCreate(PETSC_COMM_SELF,&is->x);CHKERRQ(ierr);
ierr = VecSetBlockSize(is->x,bs);CHKERRQ(ierr);
ierr = VecSetSizes(is->x,n,n);CHKERRQ(ierr);
ierr = VecSetOptionsPrefix(is->x,((PetscObject)A)->prefix);CHKERRQ(ierr);
ierr = VecAppendOptionsPrefix(is->x,"is_");CHKERRQ(ierr);
ierr = VecSetFromOptions(is->x);CHKERRQ(ierr);
ierr = VecDuplicate(is->x,&is->y);CHKERRQ(ierr);
/* setup the global to local scatter */
ierr = ISCreateStride(PETSC_COMM_SELF,n,0,1,&to);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingApplyIS(rmapping,to,&from);CHKERRQ(ierr);
ierr = MatCreateVecs(A,&global,NULL);CHKERRQ(ierr);
ierr = VecScatterCreate(global,from,is->x,to,&is->ctx);CHKERRQ(ierr);
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = ISDestroy(&to);CHKERRQ(ierr);
ierr = ISDestroy(&from);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
void FETI_Operations::set_jacobi_precond_vector()
{
homemade_assert_msg(m_bC_RR_MatrixSet,"Preconditioner matrix not set yet!");
// Create and set the vector
VecCreate(m_comm.get(),&m_coupling_jacobi_precond_vec);
VecSetSizes(m_coupling_jacobi_precond_vec,m_C_RR_M_local,m_C_RR_M);
VecSetFromOptions(m_coupling_jacobi_precond_vec);
// Get the diagonal
MatGetDiagonal(m_C_RR,m_coupling_jacobi_precond_vec);
// Calculate the reciprocal
VecReciprocal(m_coupling_jacobi_precond_vec);
// Export it
write_PETSC_vector(m_coupling_jacobi_precond_vec,m_scratch_folder_path + "/precond_Jacobi_vector.petscvec",m_comm.rank(),m_comm.get());
// Print MatLab debugging output? Variable defined at "carl_headers.h"
#ifdef PRINT_MATLAB_DEBUG
write_PETSC_vector_MATLAB(m_coupling_jacobi_precond_vec,m_scratch_folder_path + "/precond_Jacobi_vector.m",m_comm.get());
#endif
// Set flag
m_bCreatedPrecondJacobiVec = true;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscInt time_steps = 100,steps;
PetscMPIInt size;
Vec global;
PetscReal dt,ftime;
TS ts;
MatStructure A_structure;
Mat A = 0;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-time",&time_steps,NULL);CHKERRQ(ierr);
/* set initial conditions */
ierr = VecCreate(PETSC_COMM_WORLD,&global);CHKERRQ(ierr);
ierr = VecSetSizes(global,PETSC_DECIDE,3);CHKERRQ(ierr);
ierr = VecSetFromOptions(global);CHKERRQ(ierr);
ierr = Initial(global,NULL);CHKERRQ(ierr);
/* make timestep context */
ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
ierr = TSMonitorSet(ts,Monitor,NULL,NULL);CHKERRQ(ierr);
dt = 0.1;
/*
The user provides the RHS and Jacobian
*/
ierr = TSSetRHSFunction(ts,NULL,RHSFunction,NULL);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,3,3);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = RHSJacobian(ts,0.0,global,&A,&A,&A_structure,NULL);CHKERRQ(ierr);
ierr = TSSetRHSJacobian(ts,A,A,RHSJacobian,NULL);CHKERRQ(ierr);
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,0.0,dt);CHKERRQ(ierr);
ierr = TSSetDuration(ts,time_steps,1);CHKERRQ(ierr);
ierr = TSSetSolution(ts,global);CHKERRQ(ierr);
ierr = TSSolve(ts,global);CHKERRQ(ierr);
ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr);
ierr = TSGetTimeStepNumber(ts,&steps);CHKERRQ(ierr);
/* free the memories */
ierr = TSDestroy(&ts);CHKERRQ(ierr);
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscErrorCode DMCreateGlobalVector_DA(DM da,Vec* g)
{
PetscErrorCode ierr;
DM_DA *dd = (DM_DA*)da->data;
PetscFunctionBegin;
PetscValidHeaderSpecific(da,DM_CLASSID,1);
PetscValidPointer(g,2);
if (da->defaultSection) {
ierr = DMCreateGlobalVector_Section_Private(da,g);CHKERRQ(ierr);
} else {
ierr = VecCreate(((PetscObject)da)->comm,g);CHKERRQ(ierr);
ierr = VecSetSizes(*g,dd->Nlocal,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetBlockSize(*g,dd->w);CHKERRQ(ierr);
ierr = VecSetType(*g,da->vectype);CHKERRQ(ierr);
ierr = VecSetFromOptions(*g);CHKERRQ(ierr);
ierr = VecSetDM(*g, da);CHKERRQ(ierr);
ierr = VecSetLocalToGlobalMapping(*g,da->ltogmap);CHKERRQ(ierr);
ierr = VecSetLocalToGlobalMappingBlock(*g,da->ltogmapb);CHKERRQ(ierr);
}
ierr = VecSetOperation(*g,VECOP_VIEW,(void(*)(void))VecView_MPI_DA);CHKERRQ(ierr);
ierr = VecSetOperation(*g,VECOP_LOAD,(void(*)(void))VecLoad_Default_DA);CHKERRQ(ierr);
ierr = VecSetOperation(*g,VECOP_DUPLICATE,(void(*)(void))VecDuplicate_MPI_DA);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode MatWrapML_SHELL(ML_Operator *mlmat,MatReuse reuse,Mat *newmat)
{
PetscErrorCode ierr;
PetscInt m,n;
ML_Comm *MLcomm;
Mat_MLShell *shellctx;
PetscFunctionBegin;
m = mlmat->outvec_leng;
n = mlmat->invec_leng;
if (reuse){
ierr = MatShellGetContext(*newmat,(void **)&shellctx);CHKERRQ(ierr);
shellctx->mlmat = mlmat;
PetscFunctionReturn(0);
}
MLcomm = mlmat->comm;
ierr = PetscNew(Mat_MLShell,&shellctx);CHKERRQ(ierr);
ierr = MatCreateShell(MLcomm->USR_comm,m,n,PETSC_DETERMINE,PETSC_DETERMINE,shellctx,newmat);CHKERRQ(ierr);
ierr = MatShellSetOperation(*newmat,MATOP_MULT,(void(*)(void))MatMult_ML);CHKERRQ(ierr);
ierr = MatShellSetOperation(*newmat,MATOP_MULT_ADD,(void(*)(void))MatMultAdd_ML);CHKERRQ(ierr);
shellctx->A = *newmat;
shellctx->mlmat = mlmat;
shellctx->work = PETSC_NULL;
ierr = VecCreate(MLcomm->USR_comm,&shellctx->y);CHKERRQ(ierr);
ierr = VecSetSizes(shellctx->y,m,PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetFromOptions(shellctx->y);CHKERRQ(ierr);
(*newmat)->ops->destroy = MatDestroy_ML;
PetscFunctionReturn(0);
}
void linearSystemPETSc<scalar>::allocate(int nbRows)
{
int commSize;
MPI_Comm_size(_comm, &commSize);
int blockSize = _getBlockSizeFromParameters();
clear();
_try(MatCreate(_comm, &_a));
_try(MatSetSizes(_a, blockSize * nbRows, blockSize * nbRows, PETSC_DETERMINE, PETSC_DETERMINE));
if (blockSize > 1) {
if (commSize > 1) {
_try(MatSetType(_a, MATMPIBAIJ));
}
else {
_try(MatSetType(_a, MATSEQBAIJ));
}
}
// override the default options with the ones from the option
// database (if any)
if (this->_parameters.count("petscOptions"))
_try(PetscOptionsInsertString(this->_parameters["petscOptions"].c_str()));
if (this->_parameters.count("petscPrefix"))
_try(MatAppendOptionsPrefix(_a, this->_parameters["petscPrefix"].c_str()));
_try(MatSetFromOptions(_a));
//since PETSc 3.3 GetOwnershipRange and MatGetSize cannot be called before MatXXXSetPreallocation
_localSize = nbRows;
#ifdef HAVE_MPI
if (commSize>1){
_localRowStart = 0;
if (Msg::GetCommRank() != 0) {
MPI_Status status;
MPI_Recv((void*)&_localRowStart, 1, MPI_INT, Msg::GetCommRank() - 1, 1, MPI_COMM_WORLD, &status);
}
_localRowEnd = _localRowStart + nbRows;
if (Msg::GetCommRank() != Msg::GetCommSize() - 1) {
MPI_Send((void*)&_localRowEnd, 1, MPI_INT, Msg::GetCommRank() + 1, 1, MPI_COMM_WORLD);
}
MPI_Allreduce((void*)&_localSize, (void*)&_globalSize, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
}
else{
_localRowStart = 0;
_localRowEnd = nbRows;
_globalSize = _localSize;
}
#else
_localRowStart = 0;
_localRowEnd = nbRows;
_globalSize = _localSize;
#endif
// preallocation option must be set after other options
_try(VecCreate(_comm, &_x));
_try(VecSetSizes(_x, blockSize * nbRows, PETSC_DETERMINE));
// override the default options with the ones from the option
// database (if any)
if (this->_parameters.count("petscPrefix"))
_try(VecAppendOptionsPrefix(_x, this->_parameters["petscPrefix"].c_str()));
_try(VecSetFromOptions(_x));
_try(VecDuplicate(_x, &_b));
_isAllocated = true;
_entriesPreAllocated = false;
}
Real SAMpatchPETSc::normL2(const Vector& x, char dofType) const
{
#ifdef HAVE_MPI
if (adm.isParallel()) {
if (dofIS.find(dofType) == dofIS.end())
setupIS(dofType);
Vec lx;
VecCreateSeqWithArray(PETSC_COMM_SELF, 1, x.size(), x.data(), &lx);
Vec gx;
VecCreate(*adm.getCommunicator(), &gx);
VecSetSizes(gx, dofIS[dofType].nDofs, PETSC_DETERMINE);
VecSetFromOptions(gx);
PetscInt n;
VecGetSize(gx, &n);
if (!dofIS[dofType].scatterCreated) {
VecScatterCreate(lx, dofIS[dofType].local, gx, dofIS[dofType].global, &dofIS[dofType].ctx);
dofIS[dofType].scatterCreated = true;
}
VecScatterBegin(dofIS[dofType].ctx, lx, gx, INSERT_VALUES, SCATTER_FORWARD);
VecScatterEnd(dofIS[dofType].ctx, lx, gx, INSERT_VALUES, SCATTER_FORWARD);
PetscReal d;
VecNorm(gx, NORM_2, &d);
VecDestroy(&lx);
VecDestroy(&gx);
return d / sqrt(double(n));
}
#endif
return this->SAM::normL2(x, dofType);
}
long initialize(long numele)
{
initialized = true;
n = numele;
neg_one = -1.0;
one = 1.0;
argc = 0;
args = 0;
// -------------------
PetscInitialize(&argc,&args,(char *)0,help);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size != 1) SETERRQ(1,"This is a uniprocessor example only!");
ierr = PetscOptionsGetInt(PETSC_NULL,"-n",&n,PETSC_NULL);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Compute the matrix and right-hand-side vector that define
the linear system, Ax = b.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) x, "Solution");CHKERRQ(ierr);
ierr = VecSetSizes(x,PETSC_DECIDE,n);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
ierr = VecDuplicate(x,&b);CHKERRQ(ierr);
// ierr = VecDuplicate(x,&u);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,n,n);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
VecCreate(PETSC_COMM_WORLD,&temp_input);
ierr = PetscObjectSetName((PetscObject) temp_input, "Tempinput");CHKERRQ(ierr);
VecSetSizes(temp_input,PETSC_DECIDE,n);
ierr = VecSetFromOptions(temp_input);CHKERRQ(ierr);
VecCreate(PETSC_COMM_WORLD,&temp_output);
ierr = PetscObjectSetName((PetscObject) temp_output, "Tempoutput");CHKERRQ(ierr);
VecSetSizes(temp_output,PETSC_DECIDE,n);
ierr = VecSetFromOptions(temp_output);CHKERRQ(ierr);
return 0;
}
void Field_solver::alloc_petsc_vector( Vec *x, int size, const char *name )
{
PetscErrorCode ierr;
ierr = VecCreate( PETSC_COMM_WORLD, x ); CHKERRXX( ierr );
ierr = PetscObjectSetName( (PetscObject) *x, name ); CHKERRXX( ierr );
ierr = VecSetSizes( *x, PETSC_DECIDE, size ); CHKERRXX( ierr );
ierr = VecSetFromOptions( *x ); CHKERRXX( ierr );
return;
}
PetscErrorCode loadVec(const char *path, Vec* v, MPI_Comm comm, PetscViewer* fd){
PetscErrorCode err;
err = PetscViewerBinaryOpen(comm, path, FILE_MODE_READ, fd); CHKERRQ(err);
err = VecCreate(comm, v); CHKERRQ(err);
err = VecSetFromOptions(*v); CHKERRQ(err);
err = VecLoad(*v, *fd); CHKERRQ(err);
err = PetscViewerDestroy(fd); CHKERRQ(err);
return err;
}
int main(int argc, char **argv)
{
PetscErrorCode ierr;
Vec *V,t;
PetscInt i,j,reps,n=15,k=6;
PetscRandom rctx;
PetscScalar *val_dot,*val_mdot,*tval_dot,*tval_mdot;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = PetscOptionsGetInt(NULL,NULL,"-n",&n,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-k",&k,NULL);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Test with %D random vectors of length %D",k,n);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"\n",k,n);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rctx);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rctx);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&t);CHKERRQ(ierr);
ierr = VecSetSizes(t,n,PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetFromOptions(t);CHKERRQ(ierr);
ierr = VecDuplicateVecs(t,k,&V);CHKERRQ(ierr);
ierr = VecSetRandom(t,rctx);CHKERRQ(ierr);
ierr = PetscMalloc1(k,&val_dot);CHKERRQ(ierr);
ierr = PetscMalloc1(k,&val_mdot);CHKERRQ(ierr);
ierr = PetscMalloc1(k,&tval_dot);CHKERRQ(ierr);
ierr = PetscMalloc1(k,&tval_mdot);CHKERRQ(ierr);
for (i=0; i<k; i++) { ierr = VecSetRandom(V[i],rctx);CHKERRQ(ierr); }
for (reps=0; reps<20; reps++) {
for (i=1; i<k; i++) {
ierr = VecMDot(t,i,V,val_mdot);CHKERRQ(ierr);
ierr = VecMTDot(t,i,V,tval_mdot);CHKERRQ(ierr);
for (j=0;j<i;j++) {
ierr = VecDot(t,V[j],&val_dot[j]);CHKERRQ(ierr);
ierr = VecTDot(t,V[j],&tval_dot[j]);CHKERRQ(ierr);
}
/* Check result */
for (j=0;j<i;j++) {
if (PetscAbsScalar(val_mdot[j] - val_dot[j])/PetscAbsScalar(val_dot[j]) > 1e-5) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "[TEST FAILED] i=%D, j=%D, val_mdot[j]=%g, val_dot[j]=%g\n",i,j,(double)PetscAbsScalar(val_mdot[j]), (double)PetscAbsScalar(val_dot[j]));CHKERRQ(ierr);
break;
}
if (PetscAbsScalar(tval_mdot[j] - tval_dot[j])/PetscAbsScalar(tval_dot[j]) > 1e-5) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "[TEST FAILED] i=%D, j=%D, tval_mdot[j]=%g, tval_dot[j]=%g\n",i,j,(double)PetscAbsScalar(tval_mdot[j]), (double)PetscAbsScalar(tval_dot[j]));CHKERRQ(ierr);
break;
}
}
}
}
ierr = PetscPrintf(PETSC_COMM_WORLD,"Test completed successfully!\n",k,n);CHKERRQ(ierr);
ierr = PetscFree(val_dot);CHKERRQ(ierr);
ierr = PetscFree(val_mdot);CHKERRQ(ierr);
ierr = PetscFree(tval_dot);CHKERRQ(ierr);
ierr = PetscFree(tval_mdot);CHKERRQ(ierr);
ierr = VecDestroyVecs(k,&V);CHKERRQ(ierr);
ierr = VecDestroy(&t);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&rctx);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscMPIInt rank;
PetscInt i,N;
PetscScalar one = 1.0;
Vec x;
PetscInitialize(&argc,&argv,(char *)0,help);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
/*
Create a parallel vector.
- In this case, we specify the size of each processor's local
portion, and PETSc computes the global size. Alternatively,
if we pass the global size and use PETSC_DECIDE for the
local size PETSc will choose a reasonable partition trying
to put nearly an equal number of elements on each processor.
*/
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,rank+1,PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
ierr = VecGetSize(x,&N);CHKERRQ(ierr);
ierr = VecSet(x,one);CHKERRQ(ierr);
/*
Set the vector elements.
- Always specify global locations of vector entries.
- Each processor can contribute any vector entries,
regardless of which processor "owns" them; any nonlocal
contributions will be transferred to the appropriate processor
during the assembly process.
- In this example, the flag ADD_VALUES indicates that all
contributions will be added together.
*/
for (i=0; i<N-rank; i++) {
ierr = VecSetValues(x,1,&i,&one,ADD_VALUES);CHKERRQ(ierr);
}
/*
Assemble vector, using the 2-step process:
VecAssemblyBegin(), VecAssemblyEnd()
Computations can be done while messages are in transition
by placing code between these two statements.
*/
ierr = VecAssemblyBegin(x);CHKERRQ(ierr);
ierr = VecAssemblyEnd(x);CHKERRQ(ierr);
/*
View the vector; then destroy it.
*/
ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecDestroy(x);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
PetscErrorCode generateVector(int size, Vec * v){
PetscErrorCode ierr;
ierr=VecCreate(PETSC_COMM_WORLD,v);CHKERRQ(ierr);
ierr=VecSetSizes(*v,PETSC_DECIDE,size);CHKERRQ(ierr);
ierr=VecSetFromOptions(*v);CHKERRQ(ierr);
/*initiate the vector to its norm*/
return 0;
}