/*@
MatColoringApply - Apply the coloring to the matrix, producing index
sets corresponding to a number of independent sets in the induced
graph.
Collective on MatColoring
Input Parameters:
. mc - the MatColoring context
Output Parameter:
. coloring - the ISColoring instance containing the coloring
Level: beginner
.keywords: Coloring, Apply
.seealso: MatColoring, MatColoringCreate()
@*/
PetscErrorCode MatColoringApply(MatColoring mc,ISColoring *coloring)
{
PetscErrorCode ierr;
PetscBool flg;
PetscViewerFormat format;
PetscViewer viewer;
PetscInt nc,ncolors;
PetscFunctionBegin;
PetscValidHeaderSpecific(mc,MAT_COLORING_CLASSID,1);
ierr = PetscLogEventBegin(Mat_Coloring_Apply,mc,0,0,0);CHKERRQ(ierr);
ierr = (*mc->ops->apply)(mc,coloring);CHKERRQ(ierr);
ierr = PetscLogEventEnd(Mat_Coloring_Apply,mc,0,0,0);CHKERRQ(ierr);
/* valid */
if (mc->valid) {
ierr = MatColoringTestValid(mc,*coloring);CHKERRQ(ierr);
}
/* view */
ierr = PetscOptionsGetViewer(PetscObjectComm((PetscObject)mc),((PetscObject)mc)->prefix,"-mat_coloring_view",&viewer,&format,&flg);CHKERRQ(ierr);
if (flg && !PetscPreLoadingOn) {
ierr = PetscViewerPushFormat(viewer,format);CHKERRQ(ierr);
ierr = MatColoringView(mc,viewer);CHKERRQ(ierr);
ierr = MatGetSize(mc->mat,NULL,&nc);CHKERRQ(ierr);
ierr = ISColoringGetIS(*coloring,&ncolors,NULL);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer," Number of colors %d\n",ncolors);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer," Number of total columns %d\n",nc);CHKERRQ(ierr);
if (nc <= 1000) {ierr = ISColoringView(*coloring,viewer);CHKERRQ(ierr);}
ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
int main(int argc, char **argv)
{
DM dm;
char typeString[256] = {'\0'};
PetscViewer viewer = NULL;
PetscBool flg;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr;
ierr = DMCreate(PETSC_COMM_WORLD, &dm);CHKERRQ(ierr);
ierr = PetscStrncpy(typeString,DMFOREST,256);CHKERRQ(ierr);
ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"DM Forest example options",NULL);CHKERRQ(ierr);
ierr = PetscOptionsString("-dm_type","The type of the dm",NULL,DMFOREST,typeString,sizeof(typeString),NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();CHKERRQ(ierr);
ierr = DMSetType(dm,(DMType) typeString);CHKERRQ(ierr);
ierr = DMSetFromOptions(dm);CHKERRQ(ierr);
ierr = DMSetUp(dm);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(PETSC_COMM_WORLD,NULL,"-dm_view",&viewer,NULL,&flg);CHKERRQ(ierr);
if (flg) {
ierr = DMView(dm,viewer);CHKERRQ(ierr);
}
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscViewer viewer,subviewer,subsubviewer;
PetscViewerFormat format;
PetscBool flg;
PetscSubcomm psubcomm,psubsubcomm;
MPI_Comm comm,subcomm,subsubcomm;
PetscMPIInt size;
/*
Every PETSc routine should begin with the PetscInitialize() routine.
argc, argv - These command line arguments are taken to extract the options
supplied to PETSc and options supplied to MPI.
help - When PETSc executable is invoked with the option -help,
it prints the various options that can be applied at
runtime. The user can use the "help" variable place
additional help messages in this printout.
*/
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
comm = PETSC_COMM_WORLD;
ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
if (size < 4) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Must run with at least 4 MPI processes");
ierr = PetscOptionsGetViewer(comm,NULL,"-viewer",&viewer,&format,&flg);CHKERRQ(ierr);
if (!viewer) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Must use -viewer option");
ierr = PetscViewerASCIIPrintf(viewer,"Print called on original full viewer %d\n",PetscGlobalRank);CHKERRQ(ierr);
ierr = PetscSubcommCreate(comm,&psubcomm);CHKERRQ(ierr);
ierr = PetscSubcommSetNumber(psubcomm,2);CHKERRQ(ierr);
ierr = PetscSubcommSetType(psubcomm,PETSC_SUBCOMM_CONTIGUOUS);CHKERRQ(ierr);
/* enable runtime switch of psubcomm type, e.g., '-psubcomm_type interlaced */
ierr = PetscSubcommSetFromOptions(psubcomm);CHKERRQ(ierr);
subcomm = PetscSubcommChild(psubcomm);
ierr = PetscViewerGetSubViewer(viewer,subcomm,&subviewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(subviewer," Print called on sub viewers %d\n",PetscGlobalRank);CHKERRQ(ierr);
ierr = PetscSubcommCreate(subcomm,&psubsubcomm);CHKERRQ(ierr);
ierr = PetscSubcommSetNumber(psubsubcomm,2);CHKERRQ(ierr);
ierr = PetscSubcommSetType(psubsubcomm,PETSC_SUBCOMM_CONTIGUOUS);CHKERRQ(ierr);
/* enable runtime switch of psubcomm type, e.g., '-psubcomm_type interlaced */
ierr = PetscSubcommSetFromOptions(psubsubcomm);CHKERRQ(ierr);
subsubcomm = PetscSubcommChild(psubsubcomm);
ierr = PetscViewerGetSubViewer(subviewer,subsubcomm,&subsubviewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(subsubviewer," Print called on sub sub viewers %d\n",PetscGlobalRank);CHKERRQ(ierr);
ierr = PetscViewerRestoreSubViewer(subviewer,subsubcomm,&subsubviewer);CHKERRQ(ierr);
ierr = PetscViewerRestoreSubViewer(viewer,subcomm,&subviewer);CHKERRQ(ierr);
ierr = PetscSubcommDestroy(&psubsubcomm);CHKERRQ(ierr);
ierr = PetscSubcommDestroy(&psubcomm);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
/*@
SVDSolve - Solves the singular value problem.
Collective on SVD
Input Parameter:
. svd - singular value solver context obtained from SVDCreate()
Options Database Keys:
+ -svd_view - print information about the solver used
- -svd_view_mat binary - save the matrix to the default binary viewer
Level: beginner
.seealso: SVDCreate(), SVDSetUp(), SVDDestroy()
@*/
PetscErrorCode SVDSolve(SVD svd)
{
PetscErrorCode ierr;
PetscBool flg;
PetscInt i,*workperm;
PetscViewer viewer;
PetscViewerFormat format;
PetscFunctionBegin;
PetscValidHeaderSpecific(svd,SVD_CLASSID,1);
ierr = PetscLogEventBegin(SVD_Solve,svd,0,0,0);CHKERRQ(ierr);
/* call setup */
ierr = SVDSetUp(svd);CHKERRQ(ierr);
svd->its = 0;
svd->nconv = 0;
for (i=0;i<svd->ncv;i++) {
svd->sigma[i] = 0.0;
svd->errest[i] = 0.0;
}
ierr = SVDMonitor(svd,svd->its,svd->nconv,svd->sigma,svd->errest,svd->ncv);CHKERRQ(ierr);
ierr = (*svd->ops->solve)(svd);CHKERRQ(ierr);
/* sort singular triplets */
if (svd->which == SVD_SMALLEST) {
for (i=0;i<svd->nconv;i++) svd->perm[i] = i;
ierr = PetscSortRealWithPermutation(svd->nconv,svd->sigma,svd->perm);CHKERRQ(ierr);
} else {
ierr = PetscMalloc(sizeof(PetscInt)*svd->nconv,&workperm);CHKERRQ(ierr);
for (i=0;i<svd->nconv;i++) workperm[i] = i;
ierr = PetscSortRealWithPermutation(svd->nconv,svd->sigma,workperm);CHKERRQ(ierr);
for (i=0;i<svd->nconv;i++) svd->perm[i] = workperm[svd->nconv-i-1];
ierr = PetscFree(workperm);CHKERRQ(ierr);
}
svd->lvecsavail = (svd->leftbasis)? PETSC_TRUE: PETSC_FALSE;
ierr = PetscLogEventEnd(SVD_Solve,svd,0,0,0);CHKERRQ(ierr);
/* various viewers */
ierr = MatViewFromOptions(svd->OP,((PetscObject)svd)->prefix,"-svd_view_mat");CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(PetscObjectComm((PetscObject)svd),((PetscObject)svd)->prefix,"-svd_view",&viewer,&format,&flg);CHKERRQ(ierr);
if (flg && !PetscPreLoadingOn) {
ierr = PetscViewerPushFormat(viewer,format);CHKERRQ(ierr);
ierr = SVDView(svd,viewer);CHKERRQ(ierr);
ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
/* Remove the initial subspaces */
svd->nini = 0;
svd->ninil = 0;
PetscFunctionReturn(0);
}
/*@C
KSPMonitorSetFromOptions - Sets a monitor function and viewer appropriate for the type indicated by the user
Collective on KSP
Input Parameters:
+ ksp - KSP object you wish to monitor
. name - the monitor type one is seeking
. help - message indicating what monitoring is done
. manual - manual page for the monitor
- monitor - the monitor function, the context for this object is a PetscViewerAndFormat
Level: developer
.seealso: PetscOptionsGetViewer(), PetscOptionsGetReal(), PetscOptionsHasName(), PetscOptionsGetString(),
PetscOptionsGetIntArray(), PetscOptionsGetRealArray(), PetscOptionsBool()
PetscOptionsInt(), PetscOptionsString(), PetscOptionsReal(), PetscOptionsBool(),
PetscOptionsName(), PetscOptionsBegin(), PetscOptionsEnd(), PetscOptionsHead(),
PetscOptionsStringArray(),PetscOptionsRealArray(), PetscOptionsScalar(),
PetscOptionsBoolGroupBegin(), PetscOptionsBoolGroup(), PetscOptionsBoolGroupEnd(),
PetscOptionsFList(), PetscOptionsEList()
@*/
PetscErrorCode KSPMonitorSetFromOptions(KSP ksp,const char name[],const char help[], const char manual[],PetscErrorCode (*monitor)(KSP,PetscInt,PetscReal,PetscViewerAndFormat*))
{
PetscErrorCode ierr;
PetscBool flg;
PetscViewer viewer;
PetscViewerFormat format;
PetscFunctionBegin;
ierr = PetscOptionsGetViewer(PetscObjectComm((PetscObject)ksp),((PetscObject)ksp)->options,((PetscObject)ksp)->prefix,name,&viewer,&format,&flg);CHKERRQ(ierr);
ierr = KSPSetupMonitor_Private(ksp, viewer, format, (PetscErrorCode (*)(KSP,PetscInt,PetscReal,void*)) monitor, flg);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode MatFDColoringViewFromOptions(MatFDColoring fd,const char prefix[],const char optionname[])
{
PetscErrorCode ierr;
PetscBool flg;
PetscViewer viewer;
PetscViewerFormat format;
PetscFunctionBegin;
if (prefix) {
ierr = PetscOptionsGetViewer(PetscObjectComm((PetscObject)fd),prefix,optionname,&viewer,&format,&flg);CHKERRQ(ierr);
} else {
ierr = PetscOptionsGetViewer(PetscObjectComm((PetscObject)fd),((PetscObject)fd)->prefix,optionname,&viewer,&format,&flg);CHKERRQ(ierr);
}
if (flg) {
ierr = PetscViewerPushFormat(viewer,format);CHKERRQ(ierr);
ierr = MatFDColoringView(fd,viewer);CHKERRQ(ierr);
ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
PetscViewer viewer;
PetscErrorCode ierr;
PetscViewerFormat format;
PetscBool iascii;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
ierr = PetscOptionsGetViewer(PETSC_COMM_WORLD,NULL,NULL,"-myviewer",&viewer,&format,NULL);CHKERRQ(ierr);
ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr);
if (iascii) {
ierr = PetscViewerPushFormat(viewer,format);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Testing PetscViewerASCIIPrintf %d\n", 0);CHKERRQ(ierr);
ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(PETSC_COMM_WORLD,NULL,NULL,"-myviewer",&viewer,&format,NULL);CHKERRQ(ierr);
ierr = PetscViewerPushFormat(viewer,format);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Testing PetscViewerASCIIPrintf %d\n", 1);CHKERRQ(ierr);
ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);
}
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc,char **args)
{
PetscViewer viewer;
PetscErrorCode ierr;
PetscViewerFormat format;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
ierr = PetscOptionsGetViewer(PETSC_COMM_WORLD,NULL,NULL,"-myviewer",&viewer,&format,NULL);CHKERRQ(ierr);
ierr = PetscViewerPushFormat(viewer,format);CHKERRQ(ierr);
ierr = PetscViewerView(viewer,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
/*@
MFNSolve - Solves the matrix function problem. Given a vector b, the
vector x = f(alpha*A)*b is returned.
Collective on MFN
Input Parameters:
+ mfn - matrix function context obtained from MFNCreate()
- b - the right hand side vector
Output Parameter:
. x - the solution (this may be the same vector as b, then b will be
overwritten with the answer)
Options Database Keys:
+ -mfn_view - print information about the solver used
. -mfn_view_mat binary - save the matrix to the default binary viewer
. -mfn_view_rhs binary - save right hand side vector to the default binary viewer
- -mfn_view_solution binary - save computed solution vector to the default binary viewer
Notes:
The matrix A is specified with MFNSetOperator().
The function f is specified with MFNSetFunction().
The scalar alpha is specified with MFNSetScaleFactor().
Level: beginner
.seealso: MFNCreate(), MFNSetUp(), MFNDestroy(), MFNSetTolerances(),
MFNSetOperator(), MFNSetFunction(), MFNSetScaleFactor()
@*/
PetscErrorCode MFNSolve(MFN mfn,Vec b,Vec x)
{
PetscErrorCode ierr;
PetscBool flg;
PetscViewer viewer;
PetscViewerFormat format;
PetscFunctionBegin;
PetscValidHeaderSpecific(mfn,MFN_CLASSID,1);
PetscValidHeaderSpecific(b,VEC_CLASSID,2);
PetscCheckSameComm(mfn,1,b,2);
if (b!=x) PetscValidHeaderSpecific(x,VEC_CLASSID,3);
if (b!=x) PetscCheckSameComm(mfn,1,x,3);
/* call setup */
ierr = MFNSetUp(mfn);CHKERRQ(ierr);
mfn->its = 0;
ierr = MFNMonitor(mfn,mfn->its,0);CHKERRQ(ierr);
/* call solver */
ierr = PetscLogEventBegin(MFN_Solve,mfn,b,x,0);CHKERRQ(ierr);
ierr = (*mfn->ops->solve)(mfn,b,x);CHKERRQ(ierr);
ierr = PetscLogEventEnd(MFN_Solve,mfn,b,x,0);CHKERRQ(ierr);
if (!mfn->reason) SETERRQ(PetscObjectComm((PetscObject)mfn),PETSC_ERR_PLIB,"Internal error, solver returned without setting converged reason");
if (mfn->errorifnotconverged && mfn->reason < 0) SETERRQ(PetscObjectComm((PetscObject)mfn),PETSC_ERR_NOT_CONVERGED,"MFNSolve has not converged");
/* various viewers */
ierr = MatViewFromOptions(mfn->A,((PetscObject)mfn)->prefix,"-mfn_view_mat");CHKERRQ(ierr);
ierr = VecViewFromOptions(b,((PetscObject)mfn)->prefix,"-mfn_view_rhs");CHKERRQ(ierr);
ierr = VecViewFromOptions(x,((PetscObject)mfn)->prefix,"-mfn_view_solution");CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(PetscObjectComm((PetscObject)mfn),((PetscObject)mfn)->prefix,"-mfn_view",&viewer,&format,&flg);CHKERRQ(ierr);
if (flg && !PetscPreLoadingOn) {
ierr = PetscViewerPushFormat(viewer,format);CHKERRQ(ierr);
ierr = MFNView(mfn,viewer);CHKERRQ(ierr);
ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
/*
ISColoringViewFromOptions - Processes command line options to determine if/how an ISColoring object is to be viewed.
Collective on ISColoring
Input Parameters:
+ obj - the ISColoring object
. prefix - prefix to use for viewing, or NULL to use prefix of 'mat'
- optionname - option to activate viewing
Level: intermediate
Developer Note: This cannot use PetscObjectViewFromOptions() because ISColoring is not a PetscObject
*/
PetscErrorCode ISColoringViewFromOptions(ISColoring obj,PetscObject bobj,const char optionname[])
{
PetscErrorCode ierr;
PetscViewer viewer;
PetscBool flg;
PetscViewerFormat format;
char *prefix;
PetscFunctionBegin;
prefix = bobj ? bobj->prefix : NULL;
ierr = PetscOptionsGetViewer(obj->comm,prefix,optionname,&viewer,&format,&flg);CHKERRQ(ierr);
if (flg) {
ierr = PetscViewerPushFormat(viewer,format);CHKERRQ(ierr);
ierr = ISColoringView(obj,viewer);CHKERRQ(ierr);
ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
/*
ISColoringViewFromOptions - Processes command line options to determine if/how an ISColoring object is to be viewed.
Collective on ISColoring
Input Parameters:
+ obj - the ISColoring object
. prefix - prefix to use for viewing, or NULL to use prefix of 'mat'
- optionname - option to activate viewing
Level: intermediate
Developer Note: This cannot use PetscObjectViewFromOptions() because ISColoring is not a PetscObject
*/
PetscErrorCode ISColoringViewFromOptions(ISColoring obj,const char prefix[],const char optionname[])
{
PetscErrorCode ierr;
PetscViewer viewer;
PetscBool flg;
static PetscBool incall = PETSC_FALSE;
PetscViewerFormat format;
PetscFunctionBegin;
if (incall) PetscFunctionReturn(0);
incall = PETSC_TRUE;
ierr = PetscOptionsGetViewer(obj->comm,prefix,optionname,&viewer,&format,&flg);CHKERRQ(ierr);
if (flg) {
ierr = PetscViewerPushFormat(viewer,format);CHKERRQ(ierr);
ierr = ISColoringView(obj,viewer);CHKERRQ(ierr);
ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
incall = PETSC_FALSE;
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
Mat Amat;
PetscErrorCode ierr;
SNES snes;
KSP ksp;
MPI_Comm comm;
PetscMPIInt npe,rank;
PetscLogStage stage[7];
PetscBool test_nonzero_cols=PETSC_FALSE,use_nearnullspace=PETSC_TRUE;
Vec xx,bb;
PetscInt iter,i,N,dim=3,cells[3]={1,1,1},max_conv_its,local_sizes[7],run_type=1;
DM dm,distdm,basedm;
PetscBool flg;
char convType[256];
PetscReal Lx,mdisp[10],err[10];
const char * const options[10] = {"-ex56_dm_refine 0",
"-ex56_dm_refine 1",
"-ex56_dm_refine 2",
"-ex56_dm_refine 3",
"-ex56_dm_refine 4",
"-ex56_dm_refine 5",
"-ex56_dm_refine 6",
"-ex56_dm_refine 7",
"-ex56_dm_refine 8",
"-ex56_dm_refine 9"};
PetscFunctionBeginUser;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
comm = PETSC_COMM_WORLD;
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &npe);CHKERRQ(ierr);
/* options */
ierr = PetscOptionsBegin(comm,NULL,"3D bilinear Q1 elasticity options","");CHKERRQ(ierr);
{
i = 3;
ierr = PetscOptionsIntArray("-cells", "Number of (flux tube) processor in each dimension", "ex56.c", cells, &i, NULL);CHKERRQ(ierr);
Lx = 1.; /* or ne for rod */
max_conv_its = 3;
ierr = PetscOptionsInt("-max_conv_its","Number of iterations in convergence study","",max_conv_its,&max_conv_its,NULL);CHKERRQ(ierr);
if (max_conv_its<=0 || max_conv_its>7) SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_USER, "Bad number of iterations for convergence test (%D)",max_conv_its);
ierr = PetscOptionsReal("-lx","Length of domain","",Lx,&Lx,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-alpha","material coefficient inside circle","",s_soft_alpha,&s_soft_alpha,NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-test_nonzero_cols","nonzero test","",test_nonzero_cols,&test_nonzero_cols,NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-use_mat_nearnullspace","MatNearNullSpace API test","",use_nearnullspace,&use_nearnullspace,NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-run_type","0: twisting load on cantalever, 1: 3rd order accurate convergence test","",run_type,&run_type,NULL);CHKERRQ(ierr);
i = 3;
ierr = PetscOptionsInt("-mat_block_size","","",i,&i,&flg);CHKERRQ(ierr);
if (!flg || i!=3) SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_USER, "'-mat_block_size 3' must be set (%D) and = 3 (%D)",flg,flg? i : 3);
}
ierr = PetscOptionsEnd();CHKERRQ(ierr);
ierr = PetscLogStageRegister("Mesh Setup", &stage[6]);CHKERRQ(ierr);
ierr = PetscLogStageRegister("1st Setup", &stage[0]);CHKERRQ(ierr);
ierr = PetscLogStageRegister("1st Solve", &stage[1]);CHKERRQ(ierr);
/* create DM, Plex calls DMSetup */
ierr = PetscLogStagePush(stage[6]);CHKERRQ(ierr);
ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, &dm);CHKERRQ(ierr);
{
DMLabel label;
IS is;
ierr = DMCreateLabel(dm, "boundary");CHKERRQ(ierr);
ierr = DMGetLabel(dm, "boundary", &label);CHKERRQ(ierr);
ierr = DMPlexMarkBoundaryFaces(dm, label);CHKERRQ(ierr);
if (run_type==0) {
ierr = DMGetStratumIS(dm, "boundary", 1, &is);CHKERRQ(ierr);
ierr = DMCreateLabel(dm,"Faces");CHKERRQ(ierr);
if (is) {
PetscInt d, f, Nf;
const PetscInt *faces;
PetscInt csize;
PetscSection cs;
Vec coordinates ;
DM cdm;
ierr = ISGetLocalSize(is, &Nf);CHKERRQ(ierr);
ierr = ISGetIndices(is, &faces);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr);
ierr = DMGetDefaultSection(cdm, &cs);CHKERRQ(ierr);
/* Check for each boundary face if any component of its centroid is either 0.0 or 1.0 */
for (f = 0; f < Nf; ++f) {
PetscReal faceCoord;
PetscInt b,v;
PetscScalar *coords = NULL;
PetscInt Nv;
ierr = DMPlexVecGetClosure(cdm, cs, coordinates, faces[f], &csize, &coords);CHKERRQ(ierr);
Nv = csize/dim; /* Calculate mean coordinate vector */
for (d = 0; d < dim; ++d) {
faceCoord = 0.0;
for (v = 0; v < Nv; ++v) faceCoord += PetscRealPart(coords[v*dim+d]);
faceCoord /= Nv;
for (b = 0; b < 2; ++b) {
if (PetscAbs(faceCoord - b) < PETSC_SMALL) { /* domain have not been set yet, still [0,1]^3 */
ierr = DMSetLabelValue(dm, "Faces", faces[f], d*2+b+1);CHKERRQ(ierr);
}
}
}
ierr = DMPlexVecRestoreClosure(cdm, cs, coordinates, faces[f], &csize, &coords);CHKERRQ(ierr);
}
ierr = ISRestoreIndices(is, &faces);CHKERRQ(ierr);
}
ierr = ISDestroy(&is);CHKERRQ(ierr);
ierr = DMGetLabel(dm, "Faces", &label);CHKERRQ(ierr);
ierr = DMPlexLabelComplete(dm, label);CHKERRQ(ierr);
}
}
{
PetscInt dimEmbed, i;
PetscInt nCoords;
PetscScalar *coords,bounds[] = {0,Lx,-.5,.5,-.5,.5,}; /* x_min,x_max,y_min,y_max */
Vec coordinates;
if (run_type==1) {
for (i = 0; i < 2*dim; i++) bounds[i] = (i%2) ? 1 : 0;
}
ierr = DMGetCoordinatesLocal(dm,&coordinates);CHKERRQ(ierr);
ierr = DMGetCoordinateDim(dm,&dimEmbed);CHKERRQ(ierr);
if (dimEmbed != dim) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"dimEmbed != dim %D",dimEmbed);CHKERRQ(ierr);
ierr = VecGetLocalSize(coordinates,&nCoords);CHKERRQ(ierr);
if (nCoords % dimEmbed) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Coordinate vector the wrong size");CHKERRQ(ierr);
ierr = VecGetArray(coordinates,&coords);CHKERRQ(ierr);
for (i = 0; i < nCoords; i += dimEmbed) {
PetscInt j;
PetscScalar *coord = &coords[i];
for (j = 0; j < dimEmbed; j++) {
coord[j] = bounds[2 * j] + coord[j] * (bounds[2 * j + 1] - bounds[2 * j]);
}
}
ierr = VecRestoreArray(coordinates,&coords);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(dm,coordinates);CHKERRQ(ierr);
}
/* convert to p4est, and distribute */
ierr = PetscOptionsBegin(comm, "", "Mesh conversion options", "DMPLEX");CHKERRQ(ierr);
ierr = PetscOptionsFList("-dm_type","Convert DMPlex to another format (should not be Plex!)","ex56.c",DMList,DMPLEX,convType,256,&flg);CHKERRQ(ierr);
ierr = PetscOptionsEnd();
if (flg) {
DM newdm;
ierr = DMConvert(dm,convType,&newdm);CHKERRQ(ierr);
if (newdm) {
const char *prefix;
PetscBool isForest;
ierr = PetscObjectGetOptionsPrefix((PetscObject)dm,&prefix);CHKERRQ(ierr);
ierr = PetscObjectSetOptionsPrefix((PetscObject)newdm,prefix);CHKERRQ(ierr);
ierr = DMIsForest(newdm,&isForest);CHKERRQ(ierr);
if (isForest) {
} else SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_USER, "Converted to non Forest?");
ierr = DMDestroy(&dm);CHKERRQ(ierr);
dm = newdm;
} else SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_USER, "Convert failed?");
} else {
/* Plex Distribute mesh over processes */
ierr = DMPlexDistribute(dm, 0, NULL, &distdm);CHKERRQ(ierr);
if (distdm) {
const char *prefix;
ierr = PetscObjectGetOptionsPrefix((PetscObject)dm,&prefix);CHKERRQ(ierr);
ierr = PetscObjectSetOptionsPrefix((PetscObject)distdm,prefix);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
dm = distdm;
}
}
ierr = PetscLogStagePop();CHKERRQ(ierr);
basedm = dm; dm = NULL;
for (iter=0 ; iter<max_conv_its ; iter++) {
ierr = PetscLogStagePush(stage[6]);CHKERRQ(ierr);
/* make new DM */
ierr = DMClone(basedm, &dm);CHKERRQ(ierr);
ierr = PetscObjectSetOptionsPrefix((PetscObject) dm, "ex56_");CHKERRQ(ierr);
ierr = PetscObjectSetName( (PetscObject)dm,"Mesh");CHKERRQ(ierr);
ierr = PetscOptionsClearValue(NULL,"-ex56_dm_refine");CHKERRQ(ierr);
ierr = PetscOptionsInsertString(NULL,options[iter]);CHKERRQ(ierr);
ierr = DMSetFromOptions(dm);CHKERRQ(ierr); /* refinement done here in Plex, p4est */
/* snes */
ierr = SNESCreate(comm, &snes);CHKERRQ(ierr);
ierr = SNESSetDM(snes, dm);CHKERRQ(ierr);
/* fem */
{
const PetscInt Ncomp = dim;
const PetscInt components[] = {0,1,2};
const PetscInt Nfid = 1, Npid = 1;
const PetscInt fid[] = {1}; /* The fixed faces (x=0) */
const PetscInt pid[] = {2}; /* The faces with loading (x=L_x) */
PetscFE fe;
PetscDS prob;
DM cdm = dm;
ierr = PetscFECreateDefault(dm, dim, dim, PETSC_FALSE, NULL, PETSC_DECIDE, &fe);CHKERRQ(ierr); /* elasticity */
ierr = PetscObjectSetName((PetscObject) fe, "deformation");CHKERRQ(ierr);
/* FEM prob */
ierr = DMGetDS(dm, &prob);CHKERRQ(ierr);
ierr = PetscDSSetDiscretization(prob, 0, (PetscObject) fe);CHKERRQ(ierr);
/* setup problem */
if (run_type==1) {
ierr = PetscDSSetJacobian(prob, 0, 0, NULL, NULL, NULL, g3_uu_3d);CHKERRQ(ierr);
ierr = PetscDSSetResidual(prob, 0, f0_u_x4, f1_u_3d);CHKERRQ(ierr);
} else {
ierr = PetscDSSetJacobian(prob, 0, 0, NULL, NULL, NULL, g3_uu_3d_alpha);CHKERRQ(ierr);
ierr = PetscDSSetResidual(prob, 0, f0_u, f1_u_3d_alpha);CHKERRQ(ierr);
ierr = PetscDSSetBdResidual(prob, 0, f0_bd_u_3d, f1_bd_u);CHKERRQ(ierr);
}
/* bcs */
if (run_type==1) {
PetscInt id = 1;
ierr = DMAddBoundary(dm, DM_BC_ESSENTIAL, "wall", "boundary", 0, 0, NULL, (void (*)()) zero, 1, &id, NULL);CHKERRQ(ierr);
} else {
ierr = PetscDSAddBoundary(prob, DM_BC_ESSENTIAL, "fixed", "Faces", 0, Ncomp, components, (void (*)()) zero, Nfid, fid, NULL);CHKERRQ(ierr);
ierr = PetscDSAddBoundary(prob, DM_BC_NATURAL, "traction", "Faces", 0, Ncomp, components, NULL, Npid, pid, NULL);CHKERRQ(ierr);
}
while (cdm) {
ierr = DMSetDS(cdm,prob);CHKERRQ(ierr);
ierr = DMGetCoarseDM(cdm, &cdm);CHKERRQ(ierr);
}
ierr = PetscFEDestroy(&fe);CHKERRQ(ierr);
}
/* vecs & mat */
ierr = DMCreateGlobalVector(dm,&xx);CHKERRQ(ierr);
ierr = VecDuplicate(xx, &bb);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) bb, "b");CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) xx, "u");CHKERRQ(ierr);
ierr = DMCreateMatrix(dm, &Amat);CHKERRQ(ierr);
ierr = VecGetSize(bb,&N);CHKERRQ(ierr);
local_sizes[iter] = N;
ierr = PetscPrintf(PETSC_COMM_WORLD,"[%d]%s %d global equations, %d vertices\n",rank,PETSC_FUNCTION_NAME,N,N/dim);CHKERRQ(ierr);
if (use_nearnullspace && N/dim > 1) {
/* Set up the near null space (a.k.a. rigid body modes) that will be used by the multigrid preconditioner */
DM subdm;
MatNullSpace nearNullSpace;
PetscInt fields = 0;
PetscObject deformation;
ierr = DMCreateSubDM(dm, 1, &fields, NULL, &subdm);CHKERRQ(ierr);
ierr = DMPlexCreateRigidBody(subdm, &nearNullSpace);CHKERRQ(ierr);
ierr = DMGetField(dm, 0, &deformation);CHKERRQ(ierr);
ierr = PetscObjectCompose(deformation, "nearnullspace", (PetscObject) nearNullSpace);CHKERRQ(ierr);
ierr = DMDestroy(&subdm);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&nearNullSpace);CHKERRQ(ierr); /* created by DM and destroyed by Mat */
}
ierr = DMPlexSetSNESLocalFEM(dm,NULL,NULL,NULL);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes, Amat, Amat, NULL, NULL);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
ierr = DMSetUp(dm);CHKERRQ(ierr);
ierr = PetscLogStagePop();CHKERRQ(ierr);
ierr = PetscLogStagePush(stage[0]);CHKERRQ(ierr);
/* ksp */
ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr);
ierr = KSPSetComputeSingularValues(ksp,PETSC_TRUE);CHKERRQ(ierr);
/* test BCs */
ierr = VecZeroEntries(xx);CHKERRQ(ierr);
if (test_nonzero_cols) {
if (rank==0) ierr = VecSetValue(xx,0,1.0,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecAssemblyBegin(xx);CHKERRQ(ierr);
ierr = VecAssemblyEnd(xx);CHKERRQ(ierr);
}
ierr = VecZeroEntries(bb);CHKERRQ(ierr);
ierr = VecGetSize(bb,&i);CHKERRQ(ierr);
local_sizes[iter] = i;
ierr = PetscPrintf(PETSC_COMM_WORLD,"[%d]%s %d equations in vector, %d vertices\n",rank,PETSC_FUNCTION_NAME,i,i/dim);CHKERRQ(ierr);
/* setup solver, dummy solve to really setup */
if (0) {
ierr = KSPSetTolerances(ksp,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,1);CHKERRQ(ierr);
ierr = SNESSolve(snes, bb, xx);CHKERRQ(ierr);
ierr = KSPSetTolerances(ksp,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,50);CHKERRQ(ierr);
ierr = VecZeroEntries(xx);CHKERRQ(ierr);
}
ierr = PetscLogStagePop();CHKERRQ(ierr);
/* solve */
ierr = PetscLogStagePush(stage[1]);CHKERRQ(ierr);
ierr = SNESSolve(snes, bb, xx);CHKERRQ(ierr);
ierr = PetscLogStagePop();CHKERRQ(ierr);
ierr = VecNorm(xx,NORM_INFINITY,&mdisp[iter]);CHKERRQ(ierr);
ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr);
{
PetscViewer viewer = NULL;
PetscViewerFormat fmt;
ierr = PetscOptionsGetViewer(comm,"ex56_","-vec_view",&viewer,&fmt,&flg);CHKERRQ(ierr);
if (flg) {
ierr = PetscViewerPushFormat(viewer,fmt);CHKERRQ(ierr);
ierr = VecView(xx,viewer);CHKERRQ(ierr);
ierr = VecView(bb,viewer);CHKERRQ(ierr);
ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);
}
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
/* Free work space */
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = SNESDestroy(&snes);CHKERRQ(ierr);
ierr = VecDestroy(&xx);CHKERRQ(ierr);
ierr = VecDestroy(&bb);CHKERRQ(ierr);
ierr = MatDestroy(&Amat);CHKERRQ(ierr);
}
ierr = DMDestroy(&basedm);CHKERRQ(ierr);
if (run_type==1) {
err[0] = 59.975208 - mdisp[0]; /* error with what I think is the exact solution */
} else {
err[0] = 171.038 - mdisp[0];
}
for (iter=1 ; iter<max_conv_its ; iter++) {
if (run_type==1) {
err[iter] = 59.975208 - mdisp[iter];
} else {
err[iter] = 171.038 - mdisp[iter];
}
PetscPrintf(PETSC_COMM_WORLD,"[%d]%s %D) N=%12D, max displ=%9.7e, disp diff=%9.2e, error=%4.3e, rate=%3.2g\n",
rank,PETSC_FUNCTION_NAME,iter,local_sizes[iter],mdisp[iter],
mdisp[iter]-mdisp[iter-1],err[iter],log(err[iter-1]/err[iter])/log(2.));
}
ierr = PetscFinalize();
return ierr;
}
/*@
PEPSolve - Solves the polynomial eigensystem.
Collective on PEP
Input Parameter:
. pep - eigensolver context obtained from PEPCreate()
Options Database Keys:
+ -pep_view - print information about the solver used
- -pep_plot_eigs - plot computed eigenvalues
Level: beginner
.seealso: PEPCreate(), PEPSetUp(), PEPDestroy(), PEPSetTolerances()
@*/
PetscErrorCode PEPSolve(PEP pep)
{
PetscErrorCode ierr;
PetscInt i;
PetscReal re,im;
PetscBool flg,islinear;
PetscViewer viewer;
PetscViewerFormat format;
PetscDraw draw;
PetscDrawSP drawsp;
PetscFunctionBegin;
PetscValidHeaderSpecific(pep,PEP_CLASSID,1);
ierr = PetscLogEventBegin(PEP_Solve,pep,0,0,0);CHKERRQ(ierr);
/* call setup */
ierr = PEPSetUp(pep);CHKERRQ(ierr);
pep->nconv = 0;
pep->its = 0;
for (i=0;i<pep->ncv;i++) {
pep->eigr[i] = 0.0;
pep->eigi[i] = 0.0;
pep->errest[i] = 0.0;
}
ierr = PEPMonitor(pep,pep->its,pep->nconv,pep->eigr,pep->eigi,pep->errest,pep->ncv);CHKERRQ(ierr);
ierr = (*pep->ops->solve)(pep);CHKERRQ(ierr);
ierr = PetscObjectTypeCompare((PetscObject)pep,PEPLINEAR,&islinear);CHKERRQ(ierr);
if (!islinear) {
ierr = STPostSolve(pep->st);CHKERRQ(ierr);
}
if (!pep->reason) SETERRQ(PetscObjectComm((PetscObject)pep),PETSC_ERR_PLIB,"Internal error, solver returned without setting converged reason");
if (!islinear) {
/* Map eigenvalues back to the original problem */
ierr = STGetTransform(pep->st,&flg);CHKERRQ(ierr);
if (flg) {
ierr = STBackTransform(pep->st,pep->nconv,pep->eigr,pep->eigi);CHKERRQ(ierr);
}
}
pep->state = PEP_STATE_SOLVED;
if (pep->refine==PEP_REFINE_SIMPLE && pep->rits>0) {
ierr = PEPComputeVectors(pep);CHKERRQ(ierr);
ierr = PEPNewtonRefinementSimple(pep,&pep->rits,&pep->rtol,pep->nconv);CHKERRQ(ierr);
pep->state = PEP_STATE_EIGENVECTORS;
}
#if !defined(PETSC_USE_COMPLEX)
/* reorder conjugate eigenvalues (positive imaginary first) */
for (i=0;i<pep->nconv-1;i++) {
if (pep->eigi[i] != 0) {
if (pep->eigi[i] < 0) {
pep->eigi[i] = -pep->eigi[i];
pep->eigi[i+1] = -pep->eigi[i+1];
/* the next correction only works with eigenvectors */
ierr = PEPComputeVectors(pep);CHKERRQ(ierr);
ierr = BVScaleColumn(pep->V,i+1,-1.0);CHKERRQ(ierr);
}
i++;
}
}
#endif
/* sort eigenvalues according to pep->which parameter */
ierr = SlepcSortEigenvalues(pep->sc,pep->nconv,pep->eigr,pep->eigi,pep->perm);CHKERRQ(ierr);
ierr = PetscLogEventEnd(PEP_Solve,pep,0,0,0);CHKERRQ(ierr);
/* various viewers */
ierr = PetscOptionsGetViewer(PetscObjectComm((PetscObject)pep),((PetscObject)pep)->prefix,"-pep_view",&viewer,&format,&flg);CHKERRQ(ierr);
if (flg && !PetscPreLoadingOn) {
ierr = PetscViewerPushFormat(viewer,format);CHKERRQ(ierr);
ierr = PEPView(pep,viewer);CHKERRQ(ierr);
ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
flg = PETSC_FALSE;
ierr = PetscOptionsGetBool(((PetscObject)pep)->prefix,"-pep_plot_eigs",&flg,NULL);CHKERRQ(ierr);
if (flg) {
ierr = PetscViewerDrawOpen(PETSC_COMM_SELF,0,"Computed Eigenvalues",PETSC_DECIDE,PETSC_DECIDE,300,300,&viewer);CHKERRQ(ierr);
ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr);
ierr = PetscDrawSPCreate(draw,1,&drawsp);CHKERRQ(ierr);
for (i=0;i<pep->nconv;i++) {
#if defined(PETSC_USE_COMPLEX)
re = PetscRealPart(pep->eigr[i]);
im = PetscImaginaryPart(pep->eigi[i]);
#else
re = pep->eigr[i];
im = pep->eigi[i];
#endif
ierr = PetscDrawSPAddPoint(drawsp,&re,&im);CHKERRQ(ierr);
}
ierr = PetscDrawSPDraw(drawsp,PETSC_TRUE);CHKERRQ(ierr);
ierr = PetscDrawSPDestroy(&drawsp);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
/* Remove the initial subspace */
pep->nini = 0;
PetscFunctionReturn(0);
}
/*@
EPSSolve - Solves the eigensystem.
Collective on EPS
Input Parameter:
. eps - eigensolver context obtained from EPSCreate()
Options Database Keys:
+ -eps_view - print information about the solver used
. -eps_view_mat0 binary - save the first matrix (A) to the default binary viewer
. -eps_view_mat1 binary - save the second matrix (B) to the default binary viewer
- -eps_plot_eigs - plot computed eigenvalues
Level: beginner
.seealso: EPSCreate(), EPSSetUp(), EPSDestroy(), EPSSetTolerances()
@*/
PetscErrorCode EPSSolve(EPS eps)
{
PetscErrorCode ierr;
PetscInt i,nmat;
PetscReal re,im;
PetscScalar dot;
PetscBool flg,iscayley;
PetscViewer viewer;
PetscViewerFormat format;
PetscDraw draw;
PetscDrawSP drawsp;
STMatMode matmode;
Mat A,B;
Vec w,x;
PetscFunctionBegin;
PetscValidHeaderSpecific(eps,EPS_CLASSID,1);
ierr = PetscLogEventBegin(EPS_Solve,eps,0,0,0);CHKERRQ(ierr);
/* call setup */
ierr = EPSSetUp(eps);CHKERRQ(ierr);
eps->nconv = 0;
eps->its = 0;
for (i=0;i<eps->ncv;i++) {
eps->eigr[i] = 0.0;
eps->eigi[i] = 0.0;
eps->errest[i] = 0.0;
}
ierr = EPSMonitor(eps,eps->its,eps->nconv,eps->eigr,eps->eigi,eps->errest,eps->ncv);CHKERRQ(ierr);
/* call solver */
ierr = (*eps->ops->solve)(eps);CHKERRQ(ierr);
eps->state = EPS_STATE_SOLVED;
ierr = STGetMatMode(eps->st,&matmode);CHKERRQ(ierr);
if (matmode == ST_MATMODE_INPLACE && eps->ispositive) {
/* Purify eigenvectors before reverting operator */
ierr = EPSComputeVectors(eps);CHKERRQ(ierr);
}
ierr = STPostSolve(eps->st);CHKERRQ(ierr);
if (!eps->reason) SETERRQ(PetscObjectComm((PetscObject)eps),PETSC_ERR_PLIB,"Internal error, solver returned without setting converged reason");
/* Map eigenvalues back to the original problem, necessary in some
* spectral transformations */
if (eps->ops->backtransform) {
ierr = (*eps->ops->backtransform)(eps);CHKERRQ(ierr);
}
#if !defined(PETSC_USE_COMPLEX)
/* reorder conjugate eigenvalues (positive imaginary first) */
for (i=0; i<eps->nconv-1; i++) {
if (eps->eigi[i] != 0) {
if (eps->eigi[i] < 0) {
eps->eigi[i] = -eps->eigi[i];
eps->eigi[i+1] = -eps->eigi[i+1];
/* the next correction only works with eigenvectors */
ierr = EPSComputeVectors(eps);CHKERRQ(ierr);
ierr = BVScaleColumn(eps->V,i+1,-1.0);CHKERRQ(ierr);
}
i++;
}
}
#endif
ierr = STGetNumMatrices(eps->st,&nmat);CHKERRQ(ierr);
ierr = STGetOperators(eps->st,0,&A);CHKERRQ(ierr);
if (nmat>1) { ierr = STGetOperators(eps->st,1,&B);CHKERRQ(ierr); }
/* In the case of Cayley transform, eigenvectors need to be B-normalized */
ierr = PetscObjectTypeCompare((PetscObject)eps->st,STCAYLEY,&iscayley);CHKERRQ(ierr);
if (iscayley && eps->isgeneralized && eps->ishermitian) {
ierr = MatGetVecs(B,NULL,&w);CHKERRQ(ierr);
ierr = EPSComputeVectors(eps);CHKERRQ(ierr);
for (i=0;i<eps->nconv;i++) {
ierr = BVGetColumn(eps->V,i,&x);CHKERRQ(ierr);
ierr = MatMult(B,x,w);CHKERRQ(ierr);
ierr = VecDot(w,x,&dot);CHKERRQ(ierr);
ierr = VecScale(x,1.0/PetscSqrtScalar(dot));CHKERRQ(ierr);
ierr = BVRestoreColumn(eps->V,i,&x);CHKERRQ(ierr);
}
ierr = VecDestroy(&w);CHKERRQ(ierr);
}
/* sort eigenvalues according to eps->which parameter */
ierr = SlepcSortEigenvalues(eps->sc,eps->nconv,eps->eigr,eps->eigi,eps->perm);CHKERRQ(ierr);
ierr = PetscLogEventEnd(EPS_Solve,eps,0,0,0);CHKERRQ(ierr);
/* various viewers */
ierr = MatViewFromOptions(A,((PetscObject)eps)->prefix,"-eps_view_mat0");CHKERRQ(ierr);
if (nmat>1) { ierr = MatViewFromOptions(B,((PetscObject)eps)->prefix,"-eps_view_mat1");CHKERRQ(ierr); }
ierr = PetscOptionsGetViewer(PetscObjectComm((PetscObject)eps),((PetscObject)eps)->prefix,"-eps_view",&viewer,&format,&flg);CHKERRQ(ierr);
if (flg && !PetscPreLoadingOn) {
ierr = PetscViewerPushFormat(viewer,format);CHKERRQ(ierr);
ierr = EPSView(eps,viewer);CHKERRQ(ierr);
ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
flg = PETSC_FALSE;
ierr = PetscOptionsGetBool(((PetscObject)eps)->prefix,"-eps_plot_eigs",&flg,NULL);CHKERRQ(ierr);
if (flg) {
ierr = PetscViewerDrawOpen(PETSC_COMM_SELF,0,"Computed Eigenvalues",PETSC_DECIDE,PETSC_DECIDE,300,300,&viewer);CHKERRQ(ierr);
ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr);
ierr = PetscDrawSPCreate(draw,1,&drawsp);CHKERRQ(ierr);
for (i=0;i<eps->nconv;i++) {
#if defined(PETSC_USE_COMPLEX)
re = PetscRealPart(eps->eigr[i]);
im = PetscImaginaryPart(eps->eigi[i]);
#else
re = eps->eigr[i];
im = eps->eigi[i];
#endif
ierr = PetscDrawSPAddPoint(drawsp,&re,&im);CHKERRQ(ierr);
}
ierr = PetscDrawSPDraw(drawsp,PETSC_TRUE);CHKERRQ(ierr);
ierr = PetscDrawSPDestroy(&drawsp);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
/* Remove deflation and initial subspaces */
eps->nds = 0;
eps->nini = 0;
PetscFunctionReturn(0);
}
PetscErrorCode PetscOptionsCheckInitial_Private(void)
{
char string[64],mname[PETSC_MAX_PATH_LEN],*f;
MPI_Comm comm = PETSC_COMM_WORLD;
PetscBool flg1 = PETSC_FALSE,flg2 = PETSC_FALSE,flg3 = PETSC_FALSE,flag;
PetscErrorCode ierr;
PetscReal si;
PetscInt intensity;
int i;
PetscMPIInt rank;
char version[256];
#if !defined(PETSC_HAVE_THREADSAFETY)
PetscReal logthreshold;
#endif
#if defined(PETSC_USE_LOG)
PetscViewerFormat format;
PetscBool flg4 = PETSC_FALSE;
#endif
PetscFunctionBegin;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
#if !defined(PETSC_HAVE_THREADSAFETY)
/*
Setup the memory management; support for tracing malloc() usage
*/
ierr = PetscOptionsHasName(NULL,"-malloc_log",&flg3);CHKERRQ(ierr);
logthreshold = 0.0;
ierr = PetscOptionsGetReal(NULL,"-malloc_log_threshold",&logthreshold,&flg1);CHKERRQ(ierr);
if (flg1) flg3 = PETSC_TRUE;
#if defined(PETSC_USE_DEBUG)
ierr = PetscOptionsGetBool(NULL,"-malloc",&flg1,&flg2);CHKERRQ(ierr);
if ((!flg2 || flg1) && !petscsetmallocvisited) {
if (flg2 || !(PETSC_RUNNING_ON_VALGRIND)) {
/* turn off default -malloc if valgrind is being used */
ierr = PetscSetUseTrMalloc_Private();CHKERRQ(ierr);
}
}
#else
ierr = PetscOptionsGetBool(NULL,"-malloc_dump",&flg1,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,"-malloc",&flg2,NULL);CHKERRQ(ierr);
if (flg1 || flg2 || flg3) {ierr = PetscSetUseTrMalloc_Private();CHKERRQ(ierr);}
#endif
if (flg3) {
ierr = PetscMallocSetDumpLogThreshold((PetscLogDouble)logthreshold);CHKERRQ(ierr);
}
flg1 = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,"-malloc_debug",&flg1,NULL);CHKERRQ(ierr);
if (flg1) {
ierr = PetscSetUseTrMalloc_Private();CHKERRQ(ierr);
ierr = PetscMallocDebug(PETSC_TRUE);CHKERRQ(ierr);
}
flg1 = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,"-malloc_test",&flg1,NULL);CHKERRQ(ierr);
#if defined(PETSC_USE_DEBUG)
if (flg1 && !PETSC_RUNNING_ON_VALGRIND) {
ierr = PetscSetUseTrMalloc_Private();CHKERRQ(ierr);
ierr = PetscMallocSetDumpLog();CHKERRQ(ierr);
ierr = PetscMallocDebug(PETSC_TRUE);CHKERRQ(ierr);
}
#endif
flg1 = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,"-malloc_info",&flg1,NULL);CHKERRQ(ierr);
if (!flg1) {
flg1 = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,"-memory_view",&flg1,NULL);CHKERRQ(ierr);
}
if (flg1) {
ierr = PetscMemorySetGetMaximumUsage();CHKERRQ(ierr);
}
#endif
#if defined(PETSC_USE_LOG)
ierr = PetscOptionsHasName(NULL,"-objects_dump",&PetscObjectsLog);CHKERRQ(ierr);
#endif
/*
Set the display variable for graphics
*/
ierr = PetscSetDisplay();CHKERRQ(ierr);
/*
Print the PETSc version information
*/
ierr = PetscOptionsHasName(NULL,"-v",&flg1);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,"-version",&flg2);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,"-help",&flg3);CHKERRQ(ierr);
if (flg1 || flg2 || flg3) {
/*
Print "higher-level" package version message
*/
if (PetscExternalVersionFunction) {
ierr = (*PetscExternalVersionFunction)(comm);CHKERRQ(ierr);
}
ierr = PetscGetVersion(version,256);CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm,"--------------------------------------------\
------------------------------\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm,"%s\n",version);CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm,"%s",PETSC_AUTHOR_INFO);CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm,"See docs/changes/index.html for recent updates.\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm,"See docs/faq.html for problems.\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm,"See docs/manualpages/index.html for help. \n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm,"Libraries linked from %s\n",PETSC_LIB_DIR);CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm,"--------------------------------------------\
------------------------------\n");CHKERRQ(ierr);
}
/*
Print "higher-level" package help message
*/
if (flg3) {
if (PetscExternalHelpFunction) {
ierr = (*PetscExternalHelpFunction)(comm);CHKERRQ(ierr);
}
}
/*
Setup the error handling
*/
flg1 = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,"-on_error_abort",&flg1,NULL);CHKERRQ(ierr);
if (flg1) {
ierr = MPI_Comm_set_errhandler(PETSC_COMM_WORLD,MPI_ERRORS_ARE_FATAL);CHKERRQ(ierr);
ierr = PetscPushErrorHandler(PetscAbortErrorHandler,0);CHKERRQ(ierr);
}
flg1 = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,"-on_error_mpiabort",&flg1,NULL);CHKERRQ(ierr);
if (flg1) { ierr = PetscPushErrorHandler(PetscMPIAbortErrorHandler,0);CHKERRQ(ierr);}
flg1 = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,"-mpi_return_on_error",&flg1,NULL);CHKERRQ(ierr);
if (flg1) {
ierr = MPI_Comm_set_errhandler(comm,MPI_ERRORS_RETURN);CHKERRQ(ierr);
}
flg1 = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,"-no_signal_handler",&flg1,NULL);CHKERRQ(ierr);
if (!flg1) {ierr = PetscPushSignalHandler(PetscSignalHandlerDefault,(void*)0);CHKERRQ(ierr);}
flg1 = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,"-fp_trap",&flg1,NULL);CHKERRQ(ierr);
if (flg1) {ierr = PetscSetFPTrap(PETSC_FP_TRAP_ON);CHKERRQ(ierr);}
ierr = PetscOptionsGetInt(NULL,"-check_pointer_intensity",&intensity,&flag);CHKERRQ(ierr);
if (flag) {ierr = PetscCheckPointerSetIntensity(intensity);CHKERRQ(ierr);}
/*
Setup debugger information
*/
ierr = PetscSetDefaultDebugger();CHKERRQ(ierr);
ierr = PetscOptionsGetString(NULL,"-on_error_attach_debugger",string,64,&flg1);CHKERRQ(ierr);
if (flg1) {
MPI_Errhandler err_handler;
ierr = PetscSetDebuggerFromString(string);CHKERRQ(ierr);
ierr = MPI_Comm_create_errhandler((MPI_Handler_function*)Petsc_MPI_DebuggerOnError,&err_handler);CHKERRQ(ierr);
ierr = MPI_Comm_set_errhandler(comm,err_handler);CHKERRQ(ierr);
ierr = PetscPushErrorHandler(PetscAttachDebuggerErrorHandler,0);CHKERRQ(ierr);
}
ierr = PetscOptionsGetString(NULL,"-debug_terminal",string,64,&flg1);CHKERRQ(ierr);
if (flg1) { ierr = PetscSetDebugTerminal(string);CHKERRQ(ierr); }
ierr = PetscOptionsGetString(NULL,"-start_in_debugger",string,64,&flg1);CHKERRQ(ierr);
ierr = PetscOptionsGetString(NULL,"-stop_for_debugger",string,64,&flg2);CHKERRQ(ierr);
if (flg1 || flg2) {
PetscMPIInt size;
PetscInt lsize,*nodes;
MPI_Errhandler err_handler;
/*
we have to make sure that all processors have opened
connections to all other processors, otherwise once the
debugger has stated it is likely to receive a SIGUSR1
and kill the program.
*/
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size > 2) {
PetscMPIInt dummy = 0;
MPI_Status status;
for (i=0; i<size; i++) {
if (rank != i) {
ierr = MPI_Send(&dummy,1,MPI_INT,i,109,PETSC_COMM_WORLD);CHKERRQ(ierr);
}
}
for (i=0; i<size; i++) {
if (rank != i) {
ierr = MPI_Recv(&dummy,1,MPI_INT,i,109,PETSC_COMM_WORLD,&status);CHKERRQ(ierr);
}
}
}
/* check if this processor node should be in debugger */
ierr = PetscMalloc1(size,&nodes);CHKERRQ(ierr);
lsize = size;
ierr = PetscOptionsGetIntArray(NULL,"-debugger_nodes",nodes,&lsize,&flag);CHKERRQ(ierr);
if (flag) {
for (i=0; i<lsize; i++) {
if (nodes[i] == rank) { flag = PETSC_FALSE; break; }
}
}
if (!flag) {
ierr = PetscSetDebuggerFromString(string);CHKERRQ(ierr);
ierr = PetscPushErrorHandler(PetscAbortErrorHandler,0);CHKERRQ(ierr);
if (flg1) {
ierr = PetscAttachDebugger();CHKERRQ(ierr);
} else {
ierr = PetscStopForDebugger();CHKERRQ(ierr);
}
ierr = MPI_Comm_create_errhandler((MPI_Handler_function*)Petsc_MPI_AbortOnError,&err_handler);CHKERRQ(ierr);
ierr = MPI_Comm_set_errhandler(comm,err_handler);CHKERRQ(ierr);
}
ierr = PetscFree(nodes);CHKERRQ(ierr);
}
ierr = PetscOptionsGetString(NULL,"-on_error_emacs",emacsmachinename,128,&flg1);CHKERRQ(ierr);
if (flg1 && !rank) {ierr = PetscPushErrorHandler(PetscEmacsClientErrorHandler,emacsmachinename);CHKERRQ(ierr);}
/*
Setup profiling and logging
*/
#if defined(PETSC_USE_INFO)
{
char logname[PETSC_MAX_PATH_LEN]; logname[0] = 0;
ierr = PetscOptionsGetString(NULL,"-info",logname,250,&flg1);CHKERRQ(ierr);
if (flg1 && logname[0]) {
ierr = PetscInfoAllow(PETSC_TRUE,logname);CHKERRQ(ierr);
} else if (flg1) {
ierr = PetscInfoAllow(PETSC_TRUE,NULL);CHKERRQ(ierr);
}
}
#endif
#if defined(PETSC_USE_LOG)
mname[0] = 0;
ierr = PetscOptionsGetString(NULL,"-history",mname,PETSC_MAX_PATH_LEN,&flg1);CHKERRQ(ierr);
if (flg1) {
if (mname[0]) {
ierr = PetscOpenHistoryFile(mname,&petsc_history);CHKERRQ(ierr);
} else {
ierr = PetscOpenHistoryFile(NULL,&petsc_history);CHKERRQ(ierr);
}
}
#if defined(PETSC_HAVE_MPE)
flg1 = PETSC_FALSE;
ierr = PetscOptionsHasName(NULL,"-log_mpe",&flg1);CHKERRQ(ierr);
if (flg1) {ierr = PetscLogMPEBegin();CHKERRQ(ierr);}
#endif
flg1 = PETSC_FALSE;
flg3 = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,"-log_all",&flg1,NULL);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,"-log_summary",&flg3);CHKERRQ(ierr);
if (flg1) { ierr = PetscLogAllBegin();CHKERRQ(ierr); }
else if (flg3) { ierr = PetscLogDefaultBegin();CHKERRQ(ierr);}
ierr = PetscOptionsGetString(NULL,"-log_trace",mname,250,&flg1);CHKERRQ(ierr);
if (flg1) {
char name[PETSC_MAX_PATH_LEN],fname[PETSC_MAX_PATH_LEN];
FILE *file;
if (mname[0]) {
sprintf(name,"%s.%d",mname,rank);
ierr = PetscFixFilename(name,fname);CHKERRQ(ierr);
file = fopen(fname,"w");
if (!file) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_FILE_OPEN,"Unable to open trace file: %s",fname);
} else file = PETSC_STDOUT;
ierr = PetscLogTraceBegin(file);CHKERRQ(ierr);
}
ierr = PetscOptionsGetViewer(PETSC_COMM_WORLD,NULL,"-log_view",NULL,&format,&flg4);CHKERRQ(ierr);
if (flg4) {
if (format == PETSC_VIEWER_ASCII_XML){
ierr = PetscLogNestedBegin();CHKERRQ(ierr);
} else {
ierr = PetscLogDefaultBegin();CHKERRQ(ierr);
}
}
#endif
ierr = PetscOptionsGetBool(NULL,"-saws_options",&PetscOptionsPublish,NULL);CHKERRQ(ierr);
#if defined(PETSC_HAVE_CUDA)
ierr = PetscOptionsHasName(NULL,"-cuda_show_devices",&flg1);CHKERRQ(ierr);
if (flg1) {
struct cudaDeviceProp prop;
int devCount;
int device;
cudaError_t err = cudaSuccess;
err = cudaGetDeviceCount(&devCount);
if (err != cudaSuccess) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SYS,"error in cudaGetDeviceCount %s",cudaGetErrorString(err));
for (device = 0; device < devCount; ++device) {
err = cudaGetDeviceProperties(&prop, device);
if (err != cudaSuccess) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SYS,"error in cudaGetDeviceProperties %s",cudaGetErrorString(err));
ierr = PetscPrintf(PETSC_COMM_WORLD, "CUDA device %d: %s\n", device, prop.name);CHKERRQ(ierr);
}
}
{
int size;
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size>1) {
int devCount, device, rank;
cudaError_t err = cudaSuccess;
/* check to see if we force multiple ranks to hit the same GPU */
ierr = PetscOptionsGetInt(NULL,"-cuda_set_device", &device, &flg1);CHKERRQ(ierr);
if (flg1) {
err = cudaSetDevice(device);
if (err != cudaSuccess) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SYS,"error in cudaSetDevice %s",cudaGetErrorString(err));
} else {
/* we're not using the same GPU on multiple MPI threads. So try to allocated different GPUs to different processes */
/* First get the device count */
err = cudaGetDeviceCount(&devCount);
if (err != cudaSuccess) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SYS,"error in cudaGetDeviceCount %s",cudaGetErrorString(err));
/* next determine the rank and then set the device via a mod */
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
device = rank % devCount;
err = cudaSetDevice(device);
if (err != cudaSuccess) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SYS,"error in cudaSetDevice %s",cudaGetErrorString(err));
}
/* set the device flags so that it can map host memory ... do NOT throw exception on err!=cudaSuccess
multiple devices may try to set the flags on the same device. So long as one of them succeeds, things
are ok. */
err = cudaSetDeviceFlags(cudaDeviceMapHost);
if (err != cudaSuccess) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SYS,"error in cudaSetDeviceFlags %s",cudaGetErrorString(err));
} else {
int device;
cudaError_t err = cudaSuccess;
/* the code below works for serial GPU simulations */
ierr = PetscOptionsGetInt(NULL,"-cuda_set_device", &device, &flg1);CHKERRQ(ierr);
if (flg1) {
err = cudaSetDevice(device);
if (err != cudaSuccess) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SYS,"error in cudaSetDevice %s",cudaGetErrorString(err));
}
/* set the device flags so that it can map host memory ... here, we error check. */
err = cudaSetDeviceFlags(cudaDeviceMapHost);
if (err != cudaSuccess) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SYS,"error in cudaSetDeviceFlags %s",cudaGetErrorString(err));
}
}
#endif
/*
Print basic help message
*/
ierr = PetscOptionsHasName(NULL,"-help",&flg1);CHKERRQ(ierr);
if (flg1) {
ierr = (*PetscHelpPrintf)(comm,"Options for all PETSc programs:\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -help: prints help method for each option\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -on_error_abort: cause an abort when an error is detected. Useful \n ");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," only when run in the debugger\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -on_error_attach_debugger [gdb,dbx,xxgdb,ups,noxterm]\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," start the debugger in new xterm\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," unless noxterm is given\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -start_in_debugger [gdb,dbx,xxgdb,ups,noxterm]\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," start all processes in the debugger\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -on_error_emacs <machinename>\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," emacs jumps to error file\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -debugger_nodes [n1,n2,..] Nodes to start in debugger\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -debugger_pause [m] : delay (in seconds) to attach debugger\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -stop_for_debugger : prints message on how to attach debugger manually\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," waits the delay for you to attach\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -display display: Location where X window graphics and debuggers are displayed\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -no_signal_handler: do not trap error signals\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -mpi_return_on_error: MPI returns error code, rather than abort on internal error\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -fp_trap: stop on floating point exceptions\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," note on IBM RS6000 this slows run greatly\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -malloc_dump <optional filename>: dump list of unfreed memory at conclusion\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -malloc: use our error checking malloc\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -malloc no: don't use error checking malloc\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -malloc_info: prints total memory usage\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -malloc_log: keeps log of all memory allocations\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -malloc_debug: enables extended checking for memory corruption\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -options_table: dump list of options inputted\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -options_left: dump list of unused options\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -options_left no: don't dump list of unused options\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -tmp tmpdir: alternative /tmp directory\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -shared_tmp: tmp directory is shared by all processors\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -not_shared_tmp: each processor has separate tmp directory\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -memory_view: print memory usage at end of run\n");CHKERRQ(ierr);
#if defined(PETSC_USE_LOG)
ierr = (*PetscHelpPrintf)(comm," -get_total_flops: total flops over all processors\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -log[_summary _summary_python]: logging objects and events\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -log_trace [filename]: prints trace of all PETSc calls\n");CHKERRQ(ierr);
#if defined(PETSC_HAVE_MPE)
ierr = (*PetscHelpPrintf)(comm," -log_mpe: Also create logfile viewable through Jumpshot\n");CHKERRQ(ierr);
#endif
ierr = (*PetscHelpPrintf)(comm," -info <optional filename>: print informative messages about the calculations\n");CHKERRQ(ierr);
#endif
ierr = (*PetscHelpPrintf)(comm," -v: prints PETSc version number and release date\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -options_file <file>: reads options from file\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -petsc_sleep n: sleeps n seconds before running program\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm,"-----------------------------------------------\n");CHKERRQ(ierr);
}
#if defined(PETSC_HAVE_POPEN)
{
char machine[128];
ierr = PetscOptionsGetString(NULL,"-popen_machine",machine,128,&flg1);CHKERRQ(ierr);
if (flg1) {
ierr = PetscPOpenSetMachine(machine);CHKERRQ(ierr);
}
}
#endif
ierr = PetscOptionsGetReal(NULL,"-petsc_sleep",&si,&flg1);CHKERRQ(ierr);
if (flg1) {
ierr = PetscSleep(si);CHKERRQ(ierr);
}
ierr = PetscOptionsGetString(NULL,"-info_exclude",mname,PETSC_MAX_PATH_LEN,&flg1);CHKERRQ(ierr);
if (flg1) {
ierr = PetscStrstr(mname,"null",&f);CHKERRQ(ierr);
if (f) {
ierr = PetscInfoDeactivateClass(0);CHKERRQ(ierr);
}
}
#if defined(PETSC_HAVE_CUSP) || defined(PETSC_HAVE_VIENNACL)
ierr = PetscOptionsHasName(NULL,"-log_summary",&flg3);CHKERRQ(ierr);
if (!flg3) {
ierr = PetscOptionsHasName(NULL,"-log_view",&flg3);CHKERRQ(ierr);
}
#endif
#if defined(PETSC_HAVE_CUSP)
ierr = PetscOptionsGetBool(NULL,"-cusp_synchronize",&flg3,NULL);CHKERRQ(ierr);
PetscCUSPSynchronize = flg3;
#elif defined(PETSC_HAVE_VIENNACL)
ierr = PetscOptionsGetBool(NULL,"-viennacl_synchronize",&flg3,NULL);CHKERRQ(ierr);
PetscViennaCLSynchronize = flg3;
#endif
PetscFunctionReturn(0);
}
/*@
KSPSetFromOptions - Sets KSP options from the options database.
This routine must be called before KSPSetUp() if the user is to be
allowed to set the Krylov type.
Collective on KSP
Input Parameters:
. ksp - the Krylov space context
Options Database Keys:
+ -ksp_max_it - maximum number of linear iterations
. -ksp_rtol rtol - relative tolerance used in default determination of convergence, i.e.
if residual norm decreases by this factor than convergence is declared
. -ksp_atol abstol - absolute tolerance used in default convergence test, i.e. if residual
norm is less than this then convergence is declared
. -ksp_divtol tol - if residual norm increases by this factor than divergence is declared
. -ksp_converged_use_initial_residual_norm - see KSPConvergedDefaultSetUIRNorm()
. -ksp_converged_use_min_initial_residual_norm - see KSPConvergedDefaultSetUMIRNorm()
. -ksp_norm_type - none - skip norms used in convergence tests (useful only when not using
convergence test (say you always want to run with 5 iterations) to
save on communication overhead
preconditioned - default for left preconditioning
unpreconditioned - see KSPSetNormType()
natural - see KSPSetNormType()
. -ksp_check_norm_iteration it - do not compute residual norm until iteration number it (does compute at 0th iteration)
works only for PCBCGS, PCIBCGS and and PCCG
. -ksp_lag_norm - compute the norm of the residual for the ith iteration on the i+1 iteration; this means that one can use
the norm of the residual for convergence test WITHOUT an extra MPI_Allreduce() limiting global synchronizations.
This will require 1 more iteration of the solver than usual.
. -ksp_guess_type - Type of initial guess generator for repeated linear solves
. -ksp_fischer_guess <model,size> - uses the Fischer initial guess generator for repeated linear solves
. -ksp_constant_null_space - assume the operator (matrix) has the constant vector in its null space
. -ksp_test_null_space - tests the null space set with MatSetNullSpace() to see if it truly is a null space
. -ksp_knoll - compute initial guess by applying the preconditioner to the right hand side
. -ksp_monitor_cancel - cancel all previous convergene monitor routines set
. -ksp_monitor <optional filename> - print residual norm at each iteration
. -ksp_monitor_lg_residualnorm - plot residual norm at each iteration
. -ksp_monitor_solution [ascii binary or draw][:filename][:format option] - plot solution at each iteration
- -ksp_monitor_singular_value - monitor extreme singular values at each iteration
Notes:
To see all options, run your program with the -help option
or consult Users-Manual: ch_ksp
Level: beginner
.keywords: KSP, set, from, options, database
.seealso: KSPSetOptionsPrefix(), KSPResetFromOptions(), KSPSetUseFischerGuess()
@*/
PetscErrorCode KSPSetFromOptions(KSP ksp)
{
PetscInt indx;
const char *convtests[] = {"default","skip","lsqr"};
char type[256], guesstype[256], monfilename[PETSC_MAX_PATH_LEN];
PetscBool flg,flag,reuse,set;
PetscInt model[2]={0,0},nmax;
KSPNormType normtype;
PCSide pcside;
void *ctx;
MPI_Comm comm;
const char *prefix;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(ksp,KSP_CLASSID,1);
ierr = PetscObjectGetComm((PetscObject) ksp, &comm);CHKERRQ(ierr);
ierr = PetscObjectGetOptionsPrefix((PetscObject) ksp, &prefix);CHKERRQ(ierr);
if (!ksp->skippcsetfromoptions) {
if (!ksp->pc) {ierr = KSPGetPC(ksp,&ksp->pc);CHKERRQ(ierr);}
ierr = PCSetFromOptions(ksp->pc);CHKERRQ(ierr);
}
ierr = KSPRegisterAll();CHKERRQ(ierr);
ierr = PetscObjectOptionsBegin((PetscObject)ksp);CHKERRQ(ierr);
ierr = PetscOptionsFList("-ksp_type","Krylov method","KSPSetType",KSPList,(char*)(((PetscObject)ksp)->type_name ? ((PetscObject)ksp)->type_name : KSPGMRES),type,256,&flg);CHKERRQ(ierr);
if (flg) {
ierr = KSPSetType(ksp,type);CHKERRQ(ierr);
}
/*
Set the type if it was never set.
*/
if (!((PetscObject)ksp)->type_name) {
ierr = KSPSetType(ksp,KSPGMRES);CHKERRQ(ierr);
}
ierr = KSPResetViewers(ksp);CHKERRQ(ierr);
ierr = PetscObjectTypeCompare((PetscObject)ksp,KSPPREONLY,&flg);CHKERRQ(ierr);
if (flg) {
ierr = PCGetReusePreconditioner(ksp->pc,&reuse);CHKERRQ(ierr);
ierr = PetscOptionsBool("-ksp_error_if_not_converged","Generate error if solver does not converge","KSPSetErrorIfNotConverged",ksp->errorifnotconverged,&ksp->errorifnotconverged,NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-ksp_reuse_preconditioner","Use initial preconditioner and don't ever compute a new one ","KSPReusePreconditioner",reuse,&reuse,NULL);CHKERRQ(ierr);
ierr = KSPSetReusePreconditioner(ksp,reuse);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view", &ksp->viewer, &ksp->format, &ksp->view);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_converged_reason", &ksp->viewerReason, &ksp->formatReason, &ksp->viewReason);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_mat", &ksp->viewerMat, &ksp->formatMat, &ksp->viewMat);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_pmat", &ksp->viewerPMat, &ksp->formatPMat, &ksp->viewPMat);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_rhs", &ksp->viewerRhs, &ksp->formatRhs, &ksp->viewRhs);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_solution", &ksp->viewerSol, &ksp->formatSol, &ksp->viewSol);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_mat_explicit", &ksp->viewerMatExp, &ksp->formatMatExp, &ksp->viewMatExp);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_final_residual", &ksp->viewerFinalRes,&ksp->formatFinalRes,&ksp->viewFinalRes);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_preconditioned_operator_explicit",&ksp->viewerPOpExp, &ksp->formatPOpExp, &ksp->viewPOpExp);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_diagonal_scale", &ksp->viewerDScale, &ksp->formatDScale, &ksp->viewDScale);CHKERRQ(ierr);
ierr = KSPGetDiagonalScale(ksp,&flag);CHKERRQ(ierr);
ierr = PetscOptionsBool("-ksp_diagonal_scale","Diagonal scale matrix before building preconditioner","KSPSetDiagonalScale",flag,&flag,&flg);CHKERRQ(ierr);
if (flg) {
ierr = KSPSetDiagonalScale(ksp,flag);CHKERRQ(ierr);
}
ierr = KSPGetDiagonalScaleFix(ksp,&flag);CHKERRQ(ierr);
ierr = PetscOptionsBool("-ksp_diagonal_scale_fix","Fix diagonally scaled matrix after solve","KSPSetDiagonalScaleFix",flag,&flag,&flg);CHKERRQ(ierr);
if (flg) {
ierr = KSPSetDiagonalScaleFix(ksp,flag);CHKERRQ(ierr);
}
goto skipoptions;
}
ierr = PetscOptionsInt("-ksp_max_it","Maximum number of iterations","KSPSetTolerances",ksp->max_it,&ksp->max_it,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-ksp_rtol","Relative decrease in residual norm","KSPSetTolerances",ksp->rtol,&ksp->rtol,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-ksp_atol","Absolute value of residual norm","KSPSetTolerances",ksp->abstol,&ksp->abstol,NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-ksp_divtol","Residual norm increase cause divergence","KSPSetTolerances",ksp->divtol,&ksp->divtol,NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-ksp_converged_use_initial_residual_norm","Use initial residual norm for computing relative convergence","KSPConvergedDefaultSetUIRNorm",PETSC_FALSE,&flag,&set);CHKERRQ(ierr);
if (set && flag) {ierr = KSPConvergedDefaultSetUIRNorm(ksp);CHKERRQ(ierr);}
ierr = PetscOptionsBool("-ksp_converged_use_min_initial_residual_norm","Use minimum of initial residual norm and b for computing relative convergence","KSPConvergedDefaultSetUMIRNorm",PETSC_FALSE,&flag,&set);CHKERRQ(ierr);
if (set && flag) {ierr = KSPConvergedDefaultSetUMIRNorm(ksp);CHKERRQ(ierr);}
ierr = PetscOptionsBool("-ksp_initial_guess_nonzero","Use the contents of the solution vector for initial guess","KSPSetInitialNonzero",ksp->guess_zero ? PETSC_FALSE : PETSC_TRUE,&flag,&flg);CHKERRQ(ierr);
if (flg) {
ierr = KSPSetInitialGuessNonzero(ksp,flag);CHKERRQ(ierr);
}
ierr = PCGetReusePreconditioner(ksp->pc,&reuse);CHKERRQ(ierr);
ierr = PetscOptionsBool("-ksp_reuse_preconditioner","Use initial preconditioner and don't ever compute a new one ","KSPReusePreconditioner",reuse,&reuse,NULL);CHKERRQ(ierr);
ierr = KSPSetReusePreconditioner(ksp,reuse);CHKERRQ(ierr);
ierr = PetscOptionsBool("-ksp_knoll","Use preconditioner applied to b for initial guess","KSPSetInitialGuessKnoll",ksp->guess_knoll,&ksp->guess_knoll,NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-ksp_error_if_not_converged","Generate error if solver does not converge","KSPSetErrorIfNotConverged",ksp->errorifnotconverged,&ksp->errorifnotconverged,NULL);CHKERRQ(ierr);
ierr = PetscOptionsFList("-ksp_guess_type","Initial guess in Krylov method",NULL,KSPGuessList,NULL,guesstype,256,&flg);CHKERRQ(ierr);
if (flg) {
ierr = KSPGetGuess(ksp,&ksp->guess);CHKERRQ(ierr);
ierr = KSPGuessSetType(ksp->guess,guesstype);CHKERRQ(ierr);
ierr = KSPGuessSetFromOptions(ksp->guess);CHKERRQ(ierr);
} else { /* old option for KSP */
nmax = 2;
ierr = PetscOptionsIntArray("-ksp_fischer_guess","Use Paul Fischer's algorithm for initial guess","KSPSetUseFischerGuess",model,&nmax,&flag);CHKERRQ(ierr);
if (flag) {
if (nmax != 2) SETERRQ(comm,PETSC_ERR_ARG_OUTOFRANGE,"Must pass in model,size as arguments");
ierr = KSPSetUseFischerGuess(ksp,model[0],model[1]);CHKERRQ(ierr);
}
}
ierr = PetscOptionsEList("-ksp_convergence_test","Convergence test","KSPSetConvergenceTest",convtests,3,"default",&indx,&flg);CHKERRQ(ierr);
if (flg) {
switch (indx) {
case 0:
ierr = KSPConvergedDefaultCreate(&ctx);CHKERRQ(ierr);
ierr = KSPSetConvergenceTest(ksp,KSPConvergedDefault,ctx,KSPConvergedDefaultDestroy);CHKERRQ(ierr);
break;
case 1: ierr = KSPSetConvergenceTest(ksp,KSPConvergedSkip,NULL,NULL);CHKERRQ(ierr); break;
case 2:
ierr = KSPConvergedDefaultCreate(&ctx);CHKERRQ(ierr);
ierr = KSPSetConvergenceTest(ksp,KSPLSQRConvergedDefault,ctx,KSPConvergedDefaultDestroy);CHKERRQ(ierr);
break;
}
}
ierr = KSPSetUpNorms_Private(ksp,PETSC_FALSE,&normtype,NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnum("-ksp_norm_type","KSP Norm type","KSPSetNormType",KSPNormTypes,(PetscEnum)normtype,(PetscEnum*)&normtype,&flg);CHKERRQ(ierr);
if (flg) { ierr = KSPSetNormType(ksp,normtype);CHKERRQ(ierr); }
ierr = PetscOptionsInt("-ksp_check_norm_iteration","First iteration to compute residual norm","KSPSetCheckNormIteration",ksp->chknorm,&ksp->chknorm,NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-ksp_lag_norm","Lag the calculation of the residual norm","KSPSetLagNorm",ksp->lagnorm,&flag,&flg);CHKERRQ(ierr);
if (flg) {
ierr = KSPSetLagNorm(ksp,flag);CHKERRQ(ierr);
}
ierr = KSPGetDiagonalScale(ksp,&flag);CHKERRQ(ierr);
ierr = PetscOptionsBool("-ksp_diagonal_scale","Diagonal scale matrix before building preconditioner","KSPSetDiagonalScale",flag,&flag,&flg);CHKERRQ(ierr);
if (flg) {
ierr = KSPSetDiagonalScale(ksp,flag);CHKERRQ(ierr);
}
ierr = KSPGetDiagonalScaleFix(ksp,&flag);CHKERRQ(ierr);
ierr = PetscOptionsBool("-ksp_diagonal_scale_fix","Fix diagonally scaled matrix after solve","KSPSetDiagonalScaleFix",flag,&flag,&flg);CHKERRQ(ierr);
if (flg) {
ierr = KSPSetDiagonalScaleFix(ksp,flag);CHKERRQ(ierr);
}
ierr = PetscOptionsBool("-ksp_constant_null_space","Add constant null space to Krylov solver matrix","MatSetNullSpace",PETSC_FALSE,&flg,&set);CHKERRQ(ierr);
if (set && flg) {
MatNullSpace nsp;
Mat Amat;
ierr = MatNullSpaceCreate(comm,PETSC_TRUE,0,NULL,&nsp);CHKERRQ(ierr);
ierr = PCGetOperators(ksp->pc,&Amat,NULL);CHKERRQ(ierr);
if (Amat) {
ierr = MatSetNullSpace(Amat,nsp);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&nsp);CHKERRQ(ierr);
} else SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"Cannot set nullspace, matrix has not yet been provided");
}
ierr = PetscOptionsBool("-ksp_monitor_cancel","Remove any hardwired monitor routines","KSPMonitorCancel",PETSC_FALSE,&flg,&set);CHKERRQ(ierr);
/* -----------------------------------------------------------------------*/
/*
Cancels all monitors hardwired into code before call to KSPSetFromOptions()
*/
if (set && flg) {
ierr = KSPMonitorCancel(ksp);CHKERRQ(ierr);
}
ierr = KSPMonitorSetFromOptions(ksp,"-ksp_monitor","Monitor the (preconditioned) residual norm","KSPMonitorDefault",KSPMonitorDefault);CHKERRQ(ierr);
ierr = KSPMonitorSetFromOptions(ksp,"-ksp_monitor_range","Monitor the percentage of large entries in the residual","KSPMonitorRange",KSPMonitorRange);CHKERRQ(ierr);
ierr = KSPMonitorSetFromOptions(ksp,"-ksp_monitor_true_residual","Monitor the unprecondiitoned residual norm","KSPMOnitorTrueResidual",KSPMonitorTrueResidualNorm);CHKERRQ(ierr);
ierr = KSPMonitorSetFromOptions(ksp,"-ksp_monitor_max","Monitor the maximum norm of the residual","KSPMonitorTrueResidualMaxNorm",KSPMonitorTrueResidualMaxNorm);CHKERRQ(ierr);
ierr = KSPMonitorSetFromOptions(ksp,"-ksp_monitor_short","Monitor preconditioned residual norm with fewer digits","KSPMonitorDefaultShort",KSPMonitorDefaultShort);CHKERRQ(ierr);
ierr = KSPMonitorSetFromOptions(ksp,"-ksp_monitor_solution","Monitor the solution","KSPMonitorSolution",KSPMonitorSolution);CHKERRQ(ierr);
ierr = KSPMonitorSetFromOptions(ksp,"-ksp_monitor_singular_value","Monitor singular values","KSPMonitorSingularValue",KSPMonitorSingularValue);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,((PetscObject)ksp)->prefix,"-ksp_monitor_singular_value",&flg);CHKERRQ(ierr);
if (flg) {
ierr = KSPSetComputeSingularValues(ksp,PETSC_TRUE);CHKERRQ(ierr);
}
ierr = PetscObjectTypeCompare((PetscObject)ksp->pc,PCKSP,&flg);CHKERRQ(ierr);
ierr = PetscObjectTypeCompare((PetscObject)ksp->pc,PCBJACOBI,&flag);CHKERRQ(ierr);
if (flg || flag) {
/* A hack for using dynamic tolerance in preconditioner */
ierr = PetscOptionsString("-sub_ksp_dynamic_tolerance","Use dynamic tolerance for PC if PC is a KSP","KSPMonitorDynamicTolerance","stdout",monfilename,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (flg) {
KSPDynTolCtx *scale;
ierr = PetscMalloc1(1,&scale);CHKERRQ(ierr);
scale->bnrm = -1.0;
scale->coef = 1.0;
ierr = PetscOptionsReal("-sub_ksp_dynamic_tolerance_param","Parameter of dynamic tolerance for inner PCKSP","KSPMonitorDynamicToleranceParam",scale->coef,&scale->coef,&flg);CHKERRQ(ierr);
ierr = KSPMonitorSet(ksp,KSPMonitorDynamicTolerance,scale,KSPMonitorDynamicToleranceDestroy);CHKERRQ(ierr);
}
}
/*
Calls Python function
*/
ierr = PetscOptionsString("-ksp_monitor_python","Use Python function","KSPMonitorSet",0,monfilename,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (flg) {ierr = PetscPythonMonitorSet((PetscObject)ksp,monfilename);CHKERRQ(ierr);}
/*
Graphically plots preconditioned residual norm
*/
ierr = PetscOptionsBool("-ksp_monitor_lg_residualnorm","Monitor graphically preconditioned residual norm","KSPMonitorSet",PETSC_FALSE,&flg,&set);CHKERRQ(ierr);
if (set && flg) {
PetscDrawLG ctx;
ierr = KSPMonitorLGResidualNormCreate(comm,NULL,NULL,PETSC_DECIDE,PETSC_DECIDE,400,300,&ctx);CHKERRQ(ierr);
ierr = KSPMonitorSet(ksp,KSPMonitorLGResidualNorm,ctx,(PetscErrorCode (*)(void**))PetscDrawLGDestroy);CHKERRQ(ierr);
}
/*
Graphically plots preconditioned and true residual norm
*/
ierr = PetscOptionsBool("-ksp_monitor_lg_true_residualnorm","Monitor graphically true residual norm","KSPMonitorSet",PETSC_FALSE,&flg,&set);CHKERRQ(ierr);
if (set && flg) {
PetscDrawLG ctx;
ierr = KSPMonitorLGTrueResidualNormCreate(comm,NULL,NULL,PETSC_DECIDE,PETSC_DECIDE,400,300,&ctx);CHKERRQ(ierr);
ierr = KSPMonitorSet(ksp,KSPMonitorLGTrueResidualNorm,ctx,(PetscErrorCode (*)(void**))PetscDrawLGDestroy);CHKERRQ(ierr);
}
/*
Graphically plots preconditioned residual norm and range of residual element values
*/
ierr = PetscOptionsBool("-ksp_monitor_lg_range","Monitor graphically range of preconditioned residual norm","KSPMonitorSet",PETSC_FALSE,&flg,&set);CHKERRQ(ierr);
if (set && flg) {
PetscViewer ctx;
ierr = PetscViewerDrawOpen(comm,NULL,NULL,PETSC_DECIDE,PETSC_DECIDE,400,300,&ctx);CHKERRQ(ierr);
ierr = KSPMonitorSet(ksp,KSPMonitorLGRange,ctx,(PetscErrorCode (*)(void**))PetscViewerDestroy);CHKERRQ(ierr);
}
/* TODO Do these show up in help? */
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view", &ksp->viewer, &ksp->format, &ksp->view);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_pre", &ksp->viewerPre, &ksp->formatPre, &ksp->viewPre);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_converged_reason", &ksp->viewerReason, &ksp->formatReason, &ksp->viewReason);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_mat", &ksp->viewerMat, &ksp->formatMat, &ksp->viewMat);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_pmat", &ksp->viewerPMat, &ksp->formatPMat, &ksp->viewPMat);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_rhs", &ksp->viewerRhs, &ksp->formatRhs, &ksp->viewRhs);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_solution", &ksp->viewerSol, &ksp->formatSol, &ksp->viewSol);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_mat_explicit", &ksp->viewerMatExp, &ksp->formatMatExp, &ksp->viewMatExp);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_eigenvalues", &ksp->viewerEV, &ksp->formatEV, &ksp->viewEV);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_singularvalues", &ksp->viewerSV, &ksp->formatSV, &ksp->viewSV);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_eigenvalues_explicit", &ksp->viewerEVExp, &ksp->formatEVExp, &ksp->viewEVExp);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_final_residual", &ksp->viewerFinalRes,&ksp->formatFinalRes,&ksp->viewFinalRes);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_preconditioned_operator_explicit",&ksp->viewerPOpExp, &ksp->formatPOpExp, &ksp->viewPOpExp);CHKERRQ(ierr);
ierr = PetscOptionsGetViewer(comm,((PetscObject) ksp)->options,prefix,"-ksp_view_diagonal_scale", &ksp->viewerDScale, &ksp->formatDScale, &ksp->viewDScale);CHKERRQ(ierr);
/* Deprecated options */
if (!ksp->viewEV) {ierr = PetscOptionsGetViewer(comm, ((PetscObject) ksp)->options,prefix, "-ksp_compute_eigenvalues", &ksp->viewerEV, &ksp->formatEV, &ksp->viewEV);CHKERRQ(ierr);}
if (!ksp->viewEV) {
ierr = PetscOptionsName("-ksp_plot_eigenvalues", "[deprecated since PETSc 3.9; use -ksp_view_eigenvalues draw]", "KSPView", &ksp->viewEV);CHKERRQ(ierr);
if (ksp->viewEV) {
ksp->formatEV = PETSC_VIEWER_DEFAULT;
ksp->viewerEV = PETSC_VIEWER_DRAW_(comm);
ierr = PetscObjectReference((PetscObject) ksp->viewerEV);CHKERRQ(ierr);
}
}
if (!ksp->viewEV) {
ierr = PetscOptionsName("-ksp_plot_eigencontours", "[deprecated since PETSc 3.9; use -ksp_view_eigenvalues draw::draw_contour]", "KSPView", &ksp->viewEV);CHKERRQ(ierr);
if (ksp->viewEV) {
ksp->formatEV = PETSC_VIEWER_DRAW_CONTOUR;
ksp->viewerEV = PETSC_VIEWER_DRAW_(comm);
ierr = PetscObjectReference((PetscObject) ksp->viewerEV);CHKERRQ(ierr);
}
}
if (!ksp->viewEVExp) {ierr = PetscOptionsGetViewer(comm, ((PetscObject) ksp)->options,prefix, "-ksp_compute_eigenvalues_explicitly", &ksp->viewerEVExp, &ksp->formatEVExp, &ksp->viewEVExp);CHKERRQ(ierr);}
if (!ksp->viewEVExp) {
ierr = PetscOptionsName("-ksp_plot_eigenvalues_explicitly", "[deprecated since PETSc 3.9; use -ksp_view_eigenvalues_explicit draw]", "KSPView", &ksp->viewEVExp);CHKERRQ(ierr);
if (ksp->viewEVExp) {
ksp->formatEVExp = PETSC_VIEWER_DEFAULT;
ksp->viewerEVExp = PETSC_VIEWER_DRAW_(comm);
ierr = PetscObjectReference((PetscObject) ksp->viewerEVExp);CHKERRQ(ierr);
}
}
if (!ksp->viewSV) {ierr = PetscOptionsGetViewer(comm, ((PetscObject) ksp)->options,prefix, "-ksp_compute_singularvalues", &ksp->viewerSV, &ksp->formatSV, &ksp->viewSV);CHKERRQ(ierr);}
if (!ksp->viewFinalRes) {ierr = PetscOptionsGetViewer(comm, ((PetscObject) ksp)->options,prefix, "-ksp_final_residual", &ksp->viewerFinalRes, &ksp->formatFinalRes, &ksp->viewFinalRes);CHKERRQ(ierr);}
#if defined(PETSC_HAVE_SAWS)
/*
Publish convergence information using AMS
*/
ierr = PetscOptionsBool("-ksp_monitor_saws","Publish KSP progress using SAWs","KSPMonitorSet",PETSC_FALSE,&flg,&set);CHKERRQ(ierr);
if (set && flg) {
void *ctx;
ierr = KSPMonitorSAWsCreate(ksp,&ctx);CHKERRQ(ierr);
ierr = KSPMonitorSet(ksp,KSPMonitorSAWs,ctx,KSPMonitorSAWsDestroy);CHKERRQ(ierr);
ierr = KSPSetComputeSingularValues(ksp,PETSC_TRUE);CHKERRQ(ierr);
}
#endif
/* -----------------------------------------------------------------------*/
ierr = KSPSetUpNorms_Private(ksp,PETSC_FALSE,NULL,&pcside);CHKERRQ(ierr);
ierr = PetscOptionsEnum("-ksp_pc_side","KSP preconditioner side","KSPSetPCSide",PCSides,(PetscEnum)pcside,(PetscEnum*)&pcside,&flg);CHKERRQ(ierr);
if (flg) {ierr = KSPSetPCSide(ksp,pcside);CHKERRQ(ierr);}
ierr = PetscOptionsBool("-ksp_compute_singularvalues","Compute singular values of preconditioned operator","KSPSetComputeSingularValues",ksp->calc_sings,&flg,&set);CHKERRQ(ierr);
if (set) { ierr = KSPSetComputeSingularValues(ksp,flg);CHKERRQ(ierr); }
ierr = PetscOptionsBool("-ksp_compute_eigenvalues","Compute eigenvalues of preconditioned operator","KSPSetComputeSingularValues",ksp->calc_sings,&flg,&set);CHKERRQ(ierr);
if (set) { ierr = KSPSetComputeSingularValues(ksp,flg);CHKERRQ(ierr); }
ierr = PetscOptionsBool("-ksp_plot_eigenvalues","Scatter plot extreme eigenvalues","KSPSetComputeSingularValues",PETSC_FALSE,&flg,&set);CHKERRQ(ierr);
if (set) { ierr = KSPSetComputeSingularValues(ksp,flg);CHKERRQ(ierr); }
#if defined(PETSC_HAVE_SAWS)
{
PetscBool set;
flg = PETSC_FALSE;
ierr = PetscOptionsBool("-ksp_saws_block","Block for SAWs at end of KSPSolve","PetscObjectSAWsBlock",((PetscObject)ksp)->amspublishblock,&flg,&set);CHKERRQ(ierr);
if (set) {
ierr = PetscObjectSAWsSetBlock((PetscObject)ksp,flg);CHKERRQ(ierr);
}
}
#endif
if (ksp->ops->setfromoptions) {
ierr = (*ksp->ops->setfromoptions)(PetscOptionsObject,ksp);CHKERRQ(ierr);
}
skipoptions:
/* process any options handlers added with PetscObjectAddOptionsHandler() */
ierr = PetscObjectProcessOptionsHandlers(PetscOptionsObject,(PetscObject)ksp);CHKERRQ(ierr);
ierr = PetscOptionsEnd();CHKERRQ(ierr);
ksp->setfromoptionscalled++;
PetscFunctionReturn(0);
}
PetscErrorCode SNESSetFromOptions_FAS(PetscOptionItems *PetscOptionsObject,SNES snes)
{
SNES_FAS *fas = (SNES_FAS*) snes->data;
PetscInt levels = 1;
PetscBool flg = PETSC_FALSE, upflg = PETSC_FALSE, downflg = PETSC_FALSE, monflg = PETSC_FALSE, galerkinflg = PETSC_FALSE,continuationflg = PETSC_FALSE;
PetscErrorCode ierr;
SNESFASType fastype;
const char *optionsprefix;
SNESLineSearch linesearch;
PetscInt m, n_up, n_down;
SNES next;
PetscBool isFine;
PetscFunctionBegin;
ierr = SNESFASCycleIsFine(snes, &isFine);CHKERRQ(ierr);
ierr = PetscOptionsHead(PetscOptionsObject,"SNESFAS Options-----------------------------------");CHKERRQ(ierr);
/* number of levels -- only process most options on the finest level */
if (isFine) {
ierr = PetscOptionsInt("-snes_fas_levels", "Number of Levels", "SNESFASSetLevels", levels, &levels, &flg);CHKERRQ(ierr);
if (!flg && snes->dm) {
ierr = DMGetRefineLevel(snes->dm,&levels);CHKERRQ(ierr);
levels++;
fas->usedmfornumberoflevels = PETSC_TRUE;
}
ierr = SNESFASSetLevels(snes, levels, NULL);CHKERRQ(ierr);
fastype = fas->fastype;
ierr = PetscOptionsEnum("-snes_fas_type","FAS correction type","SNESFASSetType",SNESFASTypes,(PetscEnum)fastype,(PetscEnum*)&fastype,&flg);CHKERRQ(ierr);
if (flg) {
ierr = SNESFASSetType(snes, fastype);CHKERRQ(ierr);
}
ierr = SNESGetOptionsPrefix(snes, &optionsprefix);CHKERRQ(ierr);
ierr = PetscOptionsInt("-snes_fas_cycles","Number of cycles","SNESFASSetCycles",fas->n_cycles,&m,&flg);CHKERRQ(ierr);
if (flg) {
ierr = SNESFASSetCycles(snes, m);CHKERRQ(ierr);
}
ierr = PetscOptionsBool("-snes_fas_continuation","Corrected grid-sequence continuation","SNESFASSetContinuation",fas->continuation,&continuationflg,&flg);CHKERRQ(ierr);
if (flg) {
ierr = SNESFASSetContinuation(snes,continuationflg);CHKERRQ(ierr);
}
ierr = PetscOptionsBool("-snes_fas_galerkin", "Form coarse problems with Galerkin","SNESFASSetGalerkin",fas->galerkin,&galerkinflg,&flg);CHKERRQ(ierr);
if (flg) {
ierr = SNESFASSetGalerkin(snes, galerkinflg);CHKERRQ(ierr);
}
if (fas->fastype == SNES_FAS_FULL) {
ierr = PetscOptionsBool("-snes_fas_full_downsweep","Smooth on the initial upsweep for full FAS cycles","SNESFASFullSetDownSweep",fas->full_downsweep,&fas->full_downsweep,&flg);CHKERRQ(ierr);
if (flg) {SNESFASFullSetDownSweep(snes,fas->full_downsweep);CHKERRQ(ierr);}
}
ierr = PetscOptionsInt("-snes_fas_smoothup","Number of post-smoothing steps","SNESFASSetNumberSmoothUp",fas->max_up_it,&n_up,&upflg);CHKERRQ(ierr);
ierr = PetscOptionsInt("-snes_fas_smoothdown","Number of pre-smoothing steps","SNESFASSetNumberSmoothDown",fas->max_down_it,&n_down,&downflg);CHKERRQ(ierr);
{
PetscViewer viewer;
PetscViewerFormat format;
ierr = PetscOptionsGetViewer(PetscObjectComm((PetscObject)snes),((PetscObject)snes)->prefix,
"-snes_fas_monitor",&viewer,&format,&monflg);CHKERRQ(ierr);
if (monflg) {
PetscViewerAndFormat *vf;
ierr = PetscViewerAndFormatCreate(viewer,format,&vf);CHKERRQ(ierr);
ierr = PetscObjectDereference((PetscObject)viewer);CHKERRQ(ierr);
ierr = SNESFASSetMonitor(snes,vf,PETSC_TRUE);CHKERRQ(ierr);
}
}
flg = PETSC_FALSE;
monflg = PETSC_TRUE;
ierr = PetscOptionsBool("-snes_fas_log","Log times for each FAS level","SNESFASSetLog",monflg,&monflg,&flg);CHKERRQ(ierr);
if (flg) {ierr = SNESFASSetLog(snes,monflg);CHKERRQ(ierr);}
}
ierr = PetscOptionsTail();CHKERRQ(ierr);
/* setup from the determined types if there is no pointwise procedure or smoother defined */
if (upflg) {
ierr = SNESFASSetNumberSmoothUp(snes,n_up);CHKERRQ(ierr);
}
if (downflg) {
ierr = SNESFASSetNumberSmoothDown(snes,n_down);CHKERRQ(ierr);
}
/* set up the default line search for coarse grid corrections */
if (fas->fastype == SNES_FAS_ADDITIVE) {
if (!snes->linesearch) {
ierr = SNESGetLineSearch(snes, &linesearch);CHKERRQ(ierr);
ierr = SNESLineSearchSetType(linesearch, SNESLINESEARCHL2);CHKERRQ(ierr);
}
}
ierr = SNESFASCycleGetCorrection(snes, &next);CHKERRQ(ierr);
/* recursive option setting for the smoothers */
if (next) {ierr = SNESSetFromOptions(next);CHKERRQ(ierr);}
PetscFunctionReturn(0);
}
int main(int argc, char **argv)
{
Vec vec, tagged, untagged;
VecScatter taggedScatter, untaggedScatter;
PetscInt bs;
PetscInt n, nloc, nint, i, j, k, localStart, localEnd, ntagged, nuntagged;
MPI_Comm comm;
VecTagger tagger;
PetscScalar *array;
PetscRandom rand;
VecTaggerBox *defaultBox;
VecTaggerBox *boxes;
IS is, isBlockGlobal, isComp;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc,&argv,NULL,help);if (ierr) return ierr;
n = 10.;
bs = 1;
comm = PETSC_COMM_WORLD;
ierr = PetscOptionsBegin(comm, "" , "VecTagger Test Options", "Vec");CHKERRQ(ierr);
ierr = PetscOptionsInt("-bs","The block size of the vector","ex1.c",bs,&bs,NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-n","The size of the vector (in blocks)","ex1.c",n,&n,NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();CHKERRQ(ierr);
ierr = PetscRandomCreate(comm,&rand);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rand);CHKERRQ(ierr);
ierr = VecCreate(comm,&vec);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)vec,"Vec to Tag");CHKERRQ(ierr);
ierr = VecSetBlockSize(vec,bs);CHKERRQ(ierr);
ierr = VecSetSizes(vec,PETSC_DECIDE,n);CHKERRQ(ierr);
ierr = VecSetUp(vec);CHKERRQ(ierr);
ierr = VecGetLocalSize(vec,&nloc);CHKERRQ(ierr);
ierr = VecGetArray(vec,&array);CHKERRQ(ierr);
for (i = 0; i < nloc; i++) {
PetscScalar val;
ierr = PetscRandomGetValue(rand,&val);CHKERRQ(ierr);
array[i] = val;
}
ierr = VecRestoreArray(vec,&array);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr);
ierr = VecViewFromOptions(vec,NULL,"-vec_view");CHKERRQ(ierr);
ierr = VecTaggerCreate(comm,&tagger);CHKERRQ(ierr);
ierr = VecTaggerSetBlockSize(tagger,bs);CHKERRQ(ierr);
ierr = VecTaggerSetType(tagger,VECTAGGERABSOLUTE);CHKERRQ(ierr);
ierr = PetscMalloc1(bs,&defaultBox);CHKERRQ(ierr);
for (i = 0; i < bs; i++) {
#if !defined(PETSC_USE_COMPLEX)
defaultBox[i].min = 0.1;
defaultBox[i].max = 1.5;
#else
defaultBox[i].min = PetscCMPLX(0.1,0.1);
defaultBox[i].max = PetscCMPLX(1.5,1.5);
#endif
}
ierr = VecTaggerAbsoluteSetBox(tagger,defaultBox);CHKERRQ(ierr);
ierr = PetscFree(defaultBox);CHKERRQ(ierr);
ierr = VecTaggerSetFromOptions(tagger);CHKERRQ(ierr);
ierr = VecTaggerSetUp(tagger);CHKERRQ(ierr);
ierr = PetscObjectViewFromOptions((PetscObject)tagger,NULL,"-vec_tagger_view");CHKERRQ(ierr);
ierr = VecTaggerGetBlockSize(tagger,&bs);CHKERRQ(ierr);
ierr = VecTaggerComputeBoxes(tagger,vec,&nint,&boxes);
if (ierr && ierr != PETSC_ERR_SUP) CHKERRQ(ierr);
else {
PetscViewer viewer = NULL;
ierr = PetscOptionsGetViewer(comm,NULL,NULL,"-vec_tagger_boxes_view",&viewer,NULL,NULL);CHKERRQ(ierr);
if (viewer) {
PetscBool iascii;
ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr);
if (iascii) {
ierr = PetscViewerASCIIPrintf(viewer,"Num boxes: %D\n",nint);CHKERRQ(ierr);
ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
for (i = 0, k = 0; i < nint; i++) {
ierr = PetscViewerASCIIPrintf(viewer,"%D: ",i);CHKERRQ(ierr);
for (j = 0; j < bs; j++, k++) {
if (j) {ierr = PetscViewerASCIIPrintf(viewer," x ");CHKERRQ(ierr);}
#if !defined(PETSC_USE_COMPLEX)
ierr = PetscViewerASCIIPrintf(viewer,"[%g,%g]",(double)boxes[k].min,(double)boxes[k].max);CHKERRQ(ierr);
#else
ierr = PetscViewerASCIIPrintf(viewer,"[%g+%gi,%g+%gi]",(double)PetscRealPart(boxes[k].min),(double)PetscImaginaryPart(boxes[k].min),(double)PetscRealPart(boxes[k].max),(double)PetscImaginaryPart(boxes[k].max));CHKERRQ(ierr);
#endif
}
ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr);
}
ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
}
}
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = PetscFree(boxes);CHKERRQ(ierr);
}
ierr = VecTaggerComputeIS(tagger,vec,&is);CHKERRQ(ierr);
ierr = ISGetBlockGlobalIS(is,vec,bs,&isBlockGlobal);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)isBlockGlobal,"Tagged IS (block global)");CHKERRQ(ierr);
ierr = ISViewFromOptions(isBlockGlobal,NULL,"-tagged_is_view");CHKERRQ(ierr);
ierr = VecGetOwnershipRange(vec,&localStart,&localEnd);CHKERRQ(ierr);
ierr = ISComplement(isBlockGlobal,localStart,localEnd,&isComp);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)isComp,"Untagged IS (global)");CHKERRQ(ierr);
ierr = ISViewFromOptions(isComp,NULL,"-untagged_is_view");CHKERRQ(ierr);
ierr = ISGetLocalSize(isBlockGlobal,&ntagged);CHKERRQ(ierr);
ierr = ISGetLocalSize(isComp,&nuntagged);CHKERRQ(ierr);
ierr = VecCreate(comm,&tagged);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)tagged,"Tagged selection");CHKERRQ(ierr);
ierr = VecSetSizes(tagged,ntagged,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetUp(tagged);CHKERRQ(ierr);
ierr = VecCreate(comm,&untagged);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)untagged,"Untagged selection");CHKERRQ(ierr);
ierr = VecSetSizes(untagged,nuntagged,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = VecSetUp(untagged);CHKERRQ(ierr);
ierr = VecScatterCreate(vec,isBlockGlobal,tagged,NULL,&taggedScatter);CHKERRQ(ierr);
ierr = VecScatterCreate(vec,isComp,untagged,NULL,&untaggedScatter);CHKERRQ(ierr);
ierr = VecScatterBegin(taggedScatter,vec,tagged,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterEnd(taggedScatter,vec,tagged,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterBegin(untaggedScatter,vec,untagged,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterEnd(untaggedScatter,vec,untagged,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecViewFromOptions(tagged,NULL,"-tagged_vec_view");CHKERRQ(ierr);
ierr = VecViewFromOptions(untagged,NULL,"-untagged_vec_view");CHKERRQ(ierr);
ierr = VecScatterDestroy(&untaggedScatter);CHKERRQ(ierr);
ierr = VecScatterDestroy(&taggedScatter);CHKERRQ(ierr);
ierr = VecDestroy(&untagged);CHKERRQ(ierr);
ierr = VecDestroy(&tagged);CHKERRQ(ierr);
ierr = ISDestroy(&isComp);CHKERRQ(ierr);
ierr = ISDestroy(&isBlockGlobal);CHKERRQ(ierr);
ierr = ISDestroy(&is);CHKERRQ(ierr);
ierr = VecTaggerDestroy(&tagger);CHKERRQ(ierr);
ierr = VecDestroy(&vec);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}