PetscErrorCode MatSolve_Matlab(Mat A,Vec b,Vec x)
{
PetscErrorCode ierr;
const char *_A,*_b,*_x;
PetscFunctionBegin;
/* make sure objects have names; use default if not */
ierr = PetscObjectName((PetscObject)b);
CHKERRQ(ierr);
ierr = PetscObjectName((PetscObject)x);
CHKERRQ(ierr);
ierr = PetscObjectGetName((PetscObject)A,&_A);
CHKERRQ(ierr);
ierr = PetscObjectGetName((PetscObject)b,&_b);
CHKERRQ(ierr);
ierr = PetscObjectGetName((PetscObject)x,&_x);
CHKERRQ(ierr);
ierr = PetscMatlabEnginePut(PETSC_MATLAB_ENGINE_(PetscObjectComm((PetscObject)A)),(PetscObject)b);
CHKERRQ(ierr);
ierr = PetscMatlabEngineEvaluate(PETSC_MATLAB_ENGINE_(PetscObjectComm((PetscObject)A)),"%s = u%s\\(l%s\\(p%s*%s));",_x,_A,_A,_A,_b);
CHKERRQ(ierr);
ierr = PetscMatlabEngineEvaluate(PETSC_MATLAB_ENGINE_(PetscObjectComm((PetscObject)A)),"%s = 0;",_b);
CHKERRQ(ierr);
/* ierr = PetscMatlabEnginePrintOutput(PETSC_MATLAB_ENGINE_(PetscObjectComm((PetscObject)A)),stdout);CHKERRQ(ierr); */
ierr = PetscMatlabEngineGet(PETSC_MATLAB_ENGINE_(PetscObjectComm((PetscObject)A)),(PetscObject)x);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *newdm)
{
PetscInt dim = user->dim;
PetscBool cellSimplex = user->cellSimplex;
PetscErrorCode ierr;
PetscFunctionBegin;
switch (dim) {
case 2:
if (cellSimplex) {
ierr = CreateSimplex_2D(comm, newdm);CHKERRQ(ierr);
} else {
ierr = CreateQuad_2D(comm, newdm);CHKERRQ(ierr);
}
break;
case 3:
if (cellSimplex) {
ierr = CreateSimplex_3D(comm, newdm);CHKERRQ(ierr);
} else {
ierr = CreateHex_3D(comm, newdm);CHKERRQ(ierr);
}
break;
default:
SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim);
}
if (user->refinementLimit > 0.0) {
DM rdm;
const char *name;
ierr = DMPlexSetRefinementUniform(*newdm, PETSC_FALSE);CHKERRQ(ierr);
ierr = DMPlexSetRefinementLimit(*newdm, user->refinementLimit);CHKERRQ(ierr);
ierr = DMRefine(*newdm, PETSC_COMM_SELF, &rdm);CHKERRQ(ierr);
ierr = PetscObjectGetName((PetscObject) *newdm, &name);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) rdm, name);CHKERRQ(ierr);
ierr = DMDestroy(newdm);CHKERRQ(ierr);
*newdm = rdm;
}
if (user->interpolate) {
DM idm = NULL;
const char *name;
ierr = DMPlexInterpolate(*newdm, &idm);CHKERRQ(ierr);
ierr = PetscObjectGetName((PetscObject) *newdm, &name);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) idm, name);CHKERRQ(ierr);
ierr = DMPlexCopyCoordinates(*newdm, idm);CHKERRQ(ierr);
ierr = DMDestroy(newdm);CHKERRQ(ierr);
*newdm = idm;
}
ierr = DMSetFromOptions(*newdm);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PETSC_EXTERN PetscErrorCode PetscDrawCreate_TikZ(PetscDraw draw)
{
PetscDraw_TikZ *win;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscMemcpy(draw->ops,&DvOps,sizeof(DvOps));CHKERRQ(ierr);
ierr = PetscNew(PetscDraw_TikZ,&win);CHKERRQ(ierr);
ierr = PetscLogObjectMemory(draw,sizeof(PetscDraw_TikZ));CHKERRQ(ierr);
draw->data = (void*) win;
if (draw->title) {
ierr = PetscStrallocpy(draw->title,&win->filename);CHKERRQ(ierr);
} else {
const char *fname;
ierr = PetscObjectGetName((PetscObject)draw,&fname);CHKERRQ(ierr);
ierr = PetscStrallocpy(fname,&win->filename);CHKERRQ(ierr);
}
ierr = PetscFOpen(PetscObjectComm((PetscObject)draw),win->filename,"w",&win->fd);CHKERRQ(ierr);
ierr = PetscFPrintf(PetscObjectComm((PetscObject)draw),win->fd,TikZ_BEGIN_DOCUMENT);CHKERRQ(ierr);
ierr = PetscFPrintf(PetscObjectComm((PetscObject)draw),win->fd,TikZ_BEGIN_FRAME);CHKERRQ(ierr);
win->written = PETSC_FALSE;
PetscFunctionReturn(0);
}
PetscErrorCode PetscViewerGetSubcomm_ASCII(PetscViewer viewer,MPI_Comm subcomm,PetscViewer *outviewer)
{
PetscErrorCode ierr;
PetscViewer_ASCII *vascii = (PetscViewer_ASCII *)viewer->data,*ovascii;
const char *name;
PetscFunctionBegin;
if (vascii->sviewer) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Subcomm viewer already obtained from PetscViewer and not restored");
/* Note that we need to open vascii->filename for the subcomm:
we can't count on reusing viewer's fd since the root in comm and subcomm may differ.
Further, if the subcomm happens to be the same as comm, PetscViewerASCIIOpen() will
will return the current viewer, having increfed it.
*/
ierr = PetscViewerASCIIOpen(subcomm,vascii->filename, outviewer);CHKERRQ(ierr);
if(*outviewer == viewer) PetscFunctionReturn(0);
ovascii = (PetscViewer_ASCII*)(*outviewer)->data;
ovascii->tab = vascii->tab;
vascii->sviewer = *outviewer;
(*outviewer)->format = viewer->format;
(*outviewer)->iformat = viewer->iformat;
ierr = PetscObjectGetName((PetscObject)viewer,&name);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)(*outviewer),name);CHKERRQ(ierr);
((PetscViewer_ASCII*)((*outviewer)->data))->bviewer = viewer;
(*outviewer)->ops->destroy = PetscViewerDestroy_ASCII_Subcomm;
PetscFunctionReturn(0);
}
/*@C
PetscDrawSetSave - Saves images produced in a PetscDraw into a file as a Gif file using AfterImage
Collective on PetscDraw
Input Parameter:
+ draw - the graphics context
. filename - name of the file, if NULL uses name of draw object
- movie - produce a movie of all the images
Options Database Command:
+ -draw_save <filename>
- -draw_save_movie
Level: intermediate
Concepts: X windows^graphics
Notes: You should call this BEFORE calling PetscDrawClear() and creating your image.
Requires that PETSc be configured with the option --with-afterimage to save the images and ffmpeg must be in your path to make the movie
If X windows generates an error message about X_CreateWindow() failing then Afterimage was installed without X windows. Reinstall Afterimage using the
./configure flags --x-includes=/pathtoXincludes --x-libraries=/pathtoXlibraries For example under Mac OS X Mountain Lion --x-includes=/opt/X11/include -x-libraries=/opt/X11/lib
.seealso: PetscDrawSetFromOptions(), PetscDrawCreate(), PetscDrawDestroy()
@*/
PetscErrorCode PetscDrawSetSave(PetscDraw draw,const char *filename,PetscBool movie)
{
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(draw,PETSC_DRAW_CLASSID,1);
ierr = PetscFree(draw->savefilename);
CHKERRQ(ierr);
draw->savefilemovie = movie;
if (filename && filename[0]) {
ierr = PetscStrallocpy(filename,&draw->savefilename);
CHKERRQ(ierr);
} else {
const char *name;
ierr = PetscObjectGetName((PetscObject)draw,&name);
CHKERRQ(ierr);
ierr = PetscStrallocpy(name,&draw->savefilename);
CHKERRQ(ierr);
}
if (draw->ops->setsave) {
ierr = (*draw->ops->setsave)(draw,filename);
CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode PetscViewerGetSingleton_ASCII(PetscViewer viewer,PetscViewer *outviewer)
{
PetscMPIInt rank;
PetscErrorCode ierr;
PetscViewer_ASCII *vascii = (PetscViewer_ASCII*)viewer->data,*ovascii;
const char *name;
PetscFunctionBegin;
if (vascii->sviewer) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Singleton already obtained from PetscViewer and not restored");
ierr = PetscViewerCreate(PETSC_COMM_SELF,outviewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(*outviewer,PETSCVIEWERASCII);CHKERRQ(ierr);
ovascii = (PetscViewer_ASCII*)(*outviewer)->data;
ovascii->fd = vascii->fd;
ovascii->tab = vascii->tab;
vascii->sviewer = *outviewer;
(*outviewer)->format = viewer->format;
ierr = PetscObjectGetName((PetscObject)viewer,&name);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)(*outviewer),name);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)viewer),&rank);CHKERRQ(ierr);
((PetscViewer_ASCII*)((*outviewer)->data))->bviewer = viewer;
(*outviewer)->ops->destroy = PetscViewerDestroy_ASCII_Singleton;
if (rank) (*outviewer)->ops->flush = 0;
else (*outviewer)->ops->flush = PetscViewerFlush_ASCII_Singleton_0;
PetscFunctionReturn(0);
}
PetscErrorCode MatView_MPIAdj_ASCII(Mat A,PetscViewer viewer)
{
Mat_MPIAdj *a = (Mat_MPIAdj*)A->data;
PetscErrorCode ierr;
PetscInt i,j,m = A->rmap->n;
const char *name;
PetscViewerFormat format;
PetscFunctionBegin;
ierr = PetscObjectGetName((PetscObject)A,&name);CHKERRQ(ierr);
ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr);
if (format == PETSC_VIEWER_ASCII_INFO) {
PetscFunctionReturn(0);
} else if (format == PETSC_VIEWER_ASCII_MATLAB) {
SETERRQ(PETSC_ERR_SUP,"Matlab format not supported");
} else {
ierr = PetscViewerASCIIUseTabs(viewer,PETSC_NO);CHKERRQ(ierr);
for (i=0; i<m; i++) {
ierr = PetscViewerASCIISynchronizedPrintf(viewer,"row %D:",i+A->rmap->rstart);CHKERRQ(ierr);
for (j=a->i[i]; j<a->i[i+1]; j++) {
ierr = PetscViewerASCIISynchronizedPrintf(viewer," %D ",a->j[j]);CHKERRQ(ierr);
}
ierr = PetscViewerASCIISynchronizedPrintf(viewer,"\n");CHKERRQ(ierr);
}
ierr = PetscViewerASCIIUseTabs(viewer,PETSC_YES);CHKERRQ(ierr);
}
ierr = PetscViewerFlush(viewer);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode PetscSectionVecView(PetscSection s, Vec v, PetscViewer viewer)
{
PetscBool isascii;
PetscInt f;
PetscErrorCode ierr;
PetscFunctionBegin;
if (!viewer) {ierr = PetscViewerASCIIGetStdout(PetscObjectComm((PetscObject)v), &viewer);CHKERRQ(ierr);}
PetscValidHeaderSpecific(v, VEC_CLASSID, 2);
PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 3);
ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERASCII, &isascii);CHKERRQ(ierr);
if (isascii) {
const char *name;
ierr = PetscObjectGetName((PetscObject) v, &name);CHKERRQ(ierr);
if (s->numFields) {
ierr = PetscViewerASCIIPrintf(viewer, "%s with %d fields\n", name, s->numFields);CHKERRQ(ierr);
for (f = 0; f < s->numFields; ++f) {
ierr = PetscViewerASCIIPrintf(viewer, " field %d with %d components\n", f, s->numFieldComponents[f]);CHKERRQ(ierr);
ierr = PetscSectionVecView_ASCII(s->field[f], v, viewer);CHKERRQ(ierr);
}
} else {
ierr = PetscViewerASCIIPrintf(viewer, "%s\n", name);CHKERRQ(ierr);
ierr = PetscSectionVecView_ASCII(s, v, viewer);CHKERRQ(ierr);
}
}
PetscFunctionReturn(0);
}
/*@C
PetscRandomView - Views a random number generator object.
Collective on PetscRandom
Input Parameters:
+ rnd - The random number generator context
- viewer - an optional visualization context
Notes:
The available visualization contexts include
+ PETSC_VIEWER_STDOUT_SELF - standard output (default)
- PETSC_VIEWER_STDOUT_WORLD - synchronized standard
output where only the first processor opens
the file. All other processors send their
data to the first processor to print.
You can change the format the vector is printed using the
option PetscViewerSetFormat().
Level: beginner
.seealso: PetscRealView(), PetscScalarView(), PetscIntView()
@*/
PetscErrorCode PetscRandomView(PetscRandom rnd,PetscViewer viewer)
{
PetscErrorCode ierr;
PetscBool iascii;
#if defined(PETSC_HAVE_SAWS)
PetscBool issaws;
#endif
PetscFunctionBegin;
PetscValidHeaderSpecific(rnd,PETSC_RANDOM_CLASSID,1);
PetscValidType(rnd,1);
if (!viewer) {
ierr = PetscViewerASCIIGetStdout(PetscObjectComm((PetscObject)rnd),&viewer);
CHKERRQ(ierr);
}
PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,2);
PetscCheckSameComm(rnd,1,viewer,2);
ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);
CHKERRQ(ierr);
#if defined(PETSC_HAVE_SAWS)
ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERSAWS,&issaws);
CHKERRQ(ierr);
#endif
if (iascii) {
PetscMPIInt rank;
ierr = PetscObjectPrintClassNamePrefixType((PetscObject)rnd,viewer);
CHKERRQ(ierr);
ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)rnd),&rank);
CHKERRQ(ierr);
ierr = PetscViewerASCIIPushSynchronized(viewer);
CHKERRQ(ierr);
ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Random type %s, seed %D\n",rank,((PetscObject)rnd)->type_name,rnd->seed);
CHKERRQ(ierr);
ierr = PetscViewerFlush(viewer);
CHKERRQ(ierr);
ierr = PetscViewerASCIIPopSynchronized(viewer);
CHKERRQ(ierr);
#if defined(PETSC_HAVE_SAWS)
} else if (issaws) {
PetscMPIInt rank;
const char *name;
ierr = PetscObjectGetName((PetscObject)rnd,&name);
CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);
CHKERRQ(ierr);
if (!((PetscObject)rnd)->amsmem && !rank) {
char dir[1024];
ierr = PetscObjectViewSAWs((PetscObject)rnd,viewer);
CHKERRQ(ierr);
ierr = PetscSNPrintf(dir,1024,"/PETSc/Objects/%s/Low",name);
CHKERRQ(ierr);
PetscStackCallSAWs(SAWs_Register,(dir,&rnd->low,1,SAWs_READ,SAWs_DOUBLE));
}
#endif
}
PetscFunctionReturn(0);
}
PetscErrorCode MatDestroy_matlab(Mat A)
{
PetscErrorCode ierr;
const char *_A;
PetscFunctionBegin;
ierr = PetscObjectGetName((PetscObject)A,&_A);CHKERRQ(ierr);
ierr = PetscMatlabEngineEvaluate(PETSC_MATLAB_ENGINE_(PetscObjectComm((PetscObject)A)),"delete %s l_%s u_%s;",_A,_A,_A);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
PetscDrawSetSave - Saves images produced in a PetscDraw into a file
Collective on PetscDraw
Input Parameter:
+ draw - the graphics context
. filename - name of the file, if .ext then uses name of draw object plus .ext using .ext to determine the image type
- movieext - if not NULL, produces a movie of all the images
Options Database Command:
+ -draw_save <filename> - filename could be name.ext or .ext (where .ext determines the type of graphics file to save, for example .png)
. -draw_save_movie <.ext> - saves a movie to filename.ext
. -draw_save_final_image [optional filename] - saves the final image displayed in a window
- -draw_save_single_file - saves each new image in the same file, normally each new image is saved in a new file with filename/filename_%d.ext
Level: intermediate
Concepts: X windows^graphics
Notes: You should call this BEFORE creating your image and calling PetscDrawSave().
The supported image types are .png, .gif, .jpg, and .ppm (PETSc chooses the default in that order).
Support for .png images requires configure --with-libpng.
Support for .gif images requires configure --with-giflib.
Support for .jpg images requires configure --with-libjpeg.
Support for .ppm images is built-in. The PPM format has no compression (640x480 pixels ~ 900 KiB).
The ffmpeg utility must be in your path to make the movie.
.seealso: PetscDrawSetFromOptions(), PetscDrawCreate(), PetscDrawDestroy(), PetscDrawSetSaveFinalImage()
@*/
PetscErrorCode PetscDrawSetSave(PetscDraw draw,const char filename[],const char movieext[])
{
const char *savename = NULL;
const char *imageext = NULL;
char buf[PETSC_MAX_PATH_LEN];
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(draw,PETSC_DRAW_CLASSID,1);
if (filename) PetscValidCharPointer(filename,2);
if (movieext) PetscValidCharPointer(movieext,2);
/* determine save filename and image extension */
if (filename && filename[0]) {
ierr = PetscStrchr(filename,'.',(char **)&imageext);CHKERRQ(ierr);
if (!imageext) savename = filename;
else if (imageext != filename) {
size_t l1 = 0,l2 = 0;
ierr = PetscStrlen(filename,&l1);CHKERRQ(ierr);
ierr = PetscStrlen(imageext,&l2);CHKERRQ(ierr);
ierr = PetscStrncpy(buf,filename,l1-l2+1);CHKERRQ(ierr);
savename = buf;
}
}
if (!savename) {ierr = PetscObjectGetName((PetscObject)draw,&savename);CHKERRQ(ierr);}
ierr = PetscDrawImageCheckFormat(&imageext);CHKERRQ(ierr);
if (movieext) {ierr = PetscDrawMovieCheckFormat(&movieext);CHKERRQ(ierr);}
if (movieext) draw->savesinglefile = PETSC_FALSE; /* otherwise we cannot generage movies */
if (draw->savesinglefile) {
ierr = PetscInfo2(NULL,"Will save image to file %s%s\n",savename,imageext);CHKERRQ(ierr);
} else {
ierr = PetscInfo3(NULL,"Will save images to file %s/%s_%%d%s\n",savename,savename,imageext);CHKERRQ(ierr);
}
if (movieext) {
ierr = PetscInfo2(NULL,"Will save movie to file %s%s\n",savename,movieext);CHKERRQ(ierr);
}
draw->savefilecount = 0;
ierr = PetscFree(draw->savefilename);CHKERRQ(ierr);
ierr = PetscFree(draw->saveimageext);CHKERRQ(ierr);
ierr = PetscFree(draw->savemovieext);CHKERRQ(ierr);
ierr = PetscStrallocpy(savename,&draw->savefilename);CHKERRQ(ierr);
ierr = PetscStrallocpy(imageext,&draw->saveimageext);CHKERRQ(ierr);
ierr = PetscStrallocpy(movieext,&draw->savemovieext);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode ISView_Block(IS is, PetscViewer viewer)
{
IS_Block *sub = (IS_Block*)is->data;
PetscErrorCode ierr;
PetscInt i,bs,n,*idx = sub->idx;
PetscBool iascii;
PetscFunctionBegin;
ierr = PetscLayoutGetBlockSize(is->map, &bs);CHKERRQ(ierr);
ierr = PetscLayoutGetLocalSize(is->map, &n);CHKERRQ(ierr);
n /= bs;
ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr);
if (iascii) {
PetscViewerFormat fmt;
ierr = PetscViewerGetFormat(viewer,&fmt);CHKERRQ(ierr);
if (fmt == PETSC_VIEWER_ASCII_MATLAB) {
IS ist;
const char *name;
const PetscInt *idx;
PetscInt n;
ierr = PetscObjectGetName((PetscObject)is,&name);CHKERRQ(ierr);
ierr = ISGetLocalSize(is,&n);CHKERRQ(ierr);
ierr = ISGetIndices(is,&idx);CHKERRQ(ierr);
ierr = ISCreateGeneral(PetscObjectComm((PetscObject)is),n,idx,PETSC_USE_POINTER,&ist);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)ist,name);CHKERRQ(ierr);
ierr = ISView(ist,viewer);CHKERRQ(ierr);
ierr = ISDestroy(&ist);CHKERRQ(ierr);
ierr = ISRestoreIndices(is,&idx);CHKERRQ(ierr);
} else {
ierr = PetscViewerASCIIPushSynchronized(viewer);CHKERRQ(ierr);
if (is->isperm) {
ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Block Index set is permutation\n");CHKERRQ(ierr);
}
ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Block size %D\n",bs);CHKERRQ(ierr);
ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Number of block indices in set %D\n",n);CHKERRQ(ierr);
ierr = PetscViewerASCIISynchronizedPrintf(viewer,"The first indices of each block are\n");CHKERRQ(ierr);
for (i=0; i<n; i++) {
ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Block %D Index %D\n",i,idx[i]);CHKERRQ(ierr);
}
ierr = PetscViewerFlush(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPopSynchronized(viewer);CHKERRQ(ierr);
}
}
PetscFunctionReturn(0);
}
PetscErrorCode DMPatchView_Ascii(DM dm, PetscViewer viewer)
{
DM_Patch *mesh = (DM_Patch*) dm->data;
PetscViewerFormat format;
const char *name;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscViewerGetFormat(viewer, &format);CHKERRQ(ierr);
/* if (format == PETSC_VIEWER_ASCII_INFO_DETAIL) */
ierr = PetscObjectGetName((PetscObject) dm, &name);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer, "Patch DM %s\n", name);CHKERRQ(ierr);
ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer, "Coarse DM\n");CHKERRQ(ierr);
ierr = DMView(mesh->dmCoarse, viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode MatView_BlockMat(Mat A,PetscViewer viewer)
{
Mat_BlockMat *a = (Mat_BlockMat*)A->data;
PetscErrorCode ierr;
const char *name;
PetscViewerFormat format;
PetscFunctionBegin;
ierr = PetscObjectGetName((PetscObject)A,&name);CHKERRQ(ierr);
ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr);
if (format == PETSC_VIEWER_ASCII_FACTOR_INFO || format == PETSC_VIEWER_ASCII_INFO) {
ierr = PetscViewerASCIIPrintf(viewer,"Nonzero block matrices = %D \n",a->nz);CHKERRQ(ierr);
if (A->symmetric) {
ierr = PetscViewerASCIIPrintf(viewer,"Only upper triangular part of symmetric matrix is stored\n");CHKERRQ(ierr);
}
}
PetscFunctionReturn(0);
}
PetscErrorCode TSTrajectorySet_Singlefile(TSTrajectory jac,TS ts,PetscInt stepnum,PetscReal time,Vec X)
{
TSTrajectory_Singlefile *sf = (TSTrajectory_Singlefile*)jac->data;
PetscErrorCode ierr;
const char *filename;
PetscFunctionBeginUser;
if (stepnum == 0) {
ierr = PetscViewerCreate(PETSC_COMM_WORLD, &sf->viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(sf->viewer, PETSCVIEWERBINARY);CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(sf->viewer,FILE_MODE_WRITE);CHKERRQ(ierr);
ierr = PetscObjectGetName((PetscObject)jac,&filename);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(sf->viewer, filename);CHKERRQ(ierr);
}
ierr = VecView(X,sf->viewer);CHKERRQ(ierr);
ierr = PetscViewerBinaryWrite(sf->viewer,&time,1,PETSC_REAL,PETSC_FALSE);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
dErr dFSSubElementMeshView(dFS fs,dViewer view)
{
dErr err;
dInt nelem,nverts,nconn,*suboff,*subind,n,bs;
dEntTopology *subtopo;
Vec X,Xc;
const dReal *x;
const char *name;
dFunctionBegin;
err = dFSGetSubElementMeshSize(fs,&nelem,&nverts,&nconn);
dCHK(err);
dASSERT(nconn == 8*nelem); /* Assume Hex */
err = dMallocA3(nelem,&subtopo,nelem+1,&suboff,nconn,&subind);
dCHK(err);
err = dFSGetSubElementMesh(fs,nelem,nconn,subtopo,suboff,subind);
dCHK(err);
err = PetscObjectGetName((dObject)fs,&name);
dCHK(err);
err = PetscViewerASCIIPrintf(view,"SubElementMesh name=%s nelem=%D nverts=%D\n",name,nelem,nverts);
dCHK(err);
err = dIntTableView(nelem,8,subind,view,"subconn");
dCHK(err);
err = dFree3(subtopo,suboff,subind);
dCHK(err);
err = dFSGetNodalCoordinatesGlobal(fs,&X);
dCHK(err);
err = VecDohpGetClosure(X,&Xc);
dCHK(err);
err = VecGetLocalSize(Xc,&n);
dCHK(err);
err = VecGetBlockSize(Xc,&bs);
dCHK(err);
err = VecGetArrayRead(Xc,&x);
dCHK(err);
err = dRealTableView(n/bs,bs,x,view,"coords");
dCHK(err);
err = VecRestoreArrayRead(Xc,&x);
dCHK(err);
err = VecDohpRestoreClosure(X,&Xc);
dCHK(err);
dFunctionReturn(0);
}
/*@C
PetscDrawSetSaveFinalImage - Saves the final image produced in a PetscDraw into a file
Collective on PetscDraw
Input Parameter:
+ draw - the graphics context
- filename - name of the file, if NULL or empty uses name set with PetscDrawSetSave() or name of draw object
Options Database Command:
. -draw_save_final_image <filename> - filename could be name.ext or .ext (where .ext determines the type of graphics file to save, for example .png)
Level: intermediate
Concepts: X windows^graphics
Notes: You should call this BEFORE creating your image and calling PetscDrawSave().
The supported image types are .png, .gif, and .ppm (PETSc chooses the default in that order).
Support for .png images requires configure --with-libpng.
Support for .gif images requires configure --with-giflib.
Support for .jpg images requires configure --with-libjpeg.
Support for .ppm images is built-in. The PPM format has no compression (640x480 pixels ~ 900 KiB).
.seealso: PetscDrawSetFromOptions(), PetscDrawCreate(), PetscDrawDestroy(), PetscDrawSetSave()
@*/
PetscErrorCode PetscDrawSetSaveFinalImage(PetscDraw draw,const char filename[])
{
char buf[PETSC_MAX_PATH_LEN];
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(draw,PETSC_DRAW_CLASSID,1);
if (!filename || !filename[0]) {
if (!draw->savefilename) {
ierr = PetscObjectGetName((PetscObject)draw,&filename);CHKERRQ(ierr);
} else {
ierr = PetscSNPrintf(buf,sizeof(buf),"%s%s",draw->savefilename,draw->saveimageext);CHKERRQ(ierr);
filename = buf;
}
}
ierr = PetscFree(draw->savefinalfilename);CHKERRQ(ierr);
ierr = PetscStrallocpy(filename,&draw->savefinalfilename);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode DMView_GLVis(DM dm, PetscViewer viewer, PetscErrorCode (*DMView_GLVis_ASCII)(DM,PetscViewer))
{
PetscErrorCode ierr;
PetscBool isglvis,isascii;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm,DM_CLASSID,1);
PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERGLVIS,&isglvis);CHKERRQ(ierr);
ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&isascii);CHKERRQ(ierr);
if (!isglvis && !isascii) SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"Viewer must be of type VIEWERGLVIS or VIEWERASCII");
if (isglvis) {
PetscViewerGLVisType type;
PetscViewer view;
ierr = PetscViewerGLVisGetType_Private(viewer,&type);CHKERRQ(ierr);
ierr = PetscViewerGLVisGetDMWindow_Private(viewer,&view);CHKERRQ(ierr);
if (!view) PetscFunctionReturn(0); /* socket window has been closed */
if (type == PETSC_VIEWER_GLVIS_SOCKET) {
PetscMPIInt size,rank;
PetscInt sdim;
const char* name;
ierr = MPI_Comm_size(PetscObjectComm((PetscObject)dm),&size);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm),&rank);CHKERRQ(ierr);
ierr = DMGetCoordinateDim(dm,&sdim);CHKERRQ(ierr);
ierr = PetscObjectGetName((PetscObject)dm,&name);CHKERRQ(ierr);
ierr = PetscGLVisCollectiveBegin(PetscObjectComm((PetscObject)dm),&view);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(view,"parallel %d %d\nmesh\n",size,rank);CHKERRQ(ierr);
ierr = DMView_GLVis_ASCII(dm,view);CHKERRQ(ierr);
ierr = PetscViewerGLVisInitWindow_Private(view,PETSC_TRUE,sdim,name);CHKERRQ(ierr);
ierr = PetscGLVisCollectiveEnd(PetscObjectComm((PetscObject)dm),&view);CHKERRQ(ierr);
} else {
ierr = DMView_GLVis_ASCII(dm,view);CHKERRQ(ierr);
}
ierr = PetscViewerGLVisRestoreDMWindow_Private(viewer,&view);CHKERRQ(ierr);
} else {
ierr = DMView_GLVis_ASCII(dm,viewer);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
static PetscErrorCode DMDAVTKWriteAll_VTS(DM da,PetscViewer viewer)
{
#if defined(PETSC_USE_REAL_SINGLE)
const char precision[] = "Float32";
#elif defined(PETSC_USE_REAL_DOUBLE)
const char precision[] = "Float64";
#else
const char precision[] = "UnknownPrecision";
#endif
MPI_Comm comm = ((PetscObject)da)->comm;
PetscViewer_VTK *vtk = (PetscViewer_VTK*)viewer->data;
PetscViewerVTKObjectLink link;
FILE *fp;
PetscMPIInt rank,size,tag;
DMDALocalInfo info;
PetscInt dim,mx,my,mz,bs,boffset,maxnnodes,i,j,k,f,r;
PetscInt rloc[6],(*grloc)[6] = PETSC_NULL;
PetscScalar *array,*array2;
PetscReal gmin[3],gmax[3];
PetscErrorCode ierr;
PetscFunctionBegin;
#if defined(PETSC_USE_COMPLEX)
SETERRQ(comm,PETSC_ERR_SUP,"Complex values not supported");
#endif
ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);
ierr = DMDAGetInfo(da,&dim, &mx,&my,&mz, 0,0,0, &bs,0,0,0,0,0);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr);
ierr = DMDAGetBoundingBox(da,gmin,gmax);CHKERRQ(ierr);
ierr = PetscFOpen(comm,vtk->filename,"wb",&fp);CHKERRQ(ierr);
ierr = PetscFPrintf(comm,fp,"<?xml version=\"1.0\"?>\n");CHKERRQ(ierr);
#ifdef PETSC_WORDS_BIGENDIAN
ierr = PetscFPrintf(comm,fp,"<VTKFile type=\"StructuredGrid\" version=\"0.1\" byte_order=\"BigEndian\">\n");CHKERRQ(ierr);
#else
ierr = PetscFPrintf(comm,fp,"<VTKFile type=\"StructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\">\n");CHKERRQ(ierr);
#endif
ierr = PetscFPrintf(comm,fp," <StructuredGrid WholeExtent=\"%D %D %D %D %D %D\">\n",0,mx-1,0,my-1,0,mz-1);CHKERRQ(ierr);
if (!rank) {ierr = PetscMalloc(size*6*sizeof(PetscInt),&grloc);CHKERRQ(ierr);}
rloc[0] = info.xs;
rloc[1] = info.xm;
rloc[2] = info.ys;
rloc[3] = info.ym;
rloc[4] = info.zs;
rloc[5] = info.zm;
ierr = MPI_Gather(rloc,6,MPIU_INT,&grloc[0][0],6,MPIU_INT,0,comm);CHKERRQ(ierr);
/* Write XML header */
maxnnodes = 0; /* Used for the temporary array size on rank 0 */
boffset = 0; /* Offset into binary file */
for (r=0; r<size; r++) {
PetscInt xs=-1,xm=-1,ys=-1,ym=-1,zs=-1,zm=-1,nnodes = 0;
if (!rank) {
xs = grloc[r][0];
xm = grloc[r][1];
ys = grloc[r][2];
ym = grloc[r][3];
zs = grloc[r][4];
zm = grloc[r][5];
nnodes = xm*ym*zm;
}
maxnnodes = PetscMax(maxnnodes,nnodes);
#if 0
switch (dim) {
case 1:
ierr = PetscFPrintf(comm,fp," <Piece Extent=\"%D %D %D %D %D %D\">\n",xs,xs+xm-1,0,0,0,0);CHKERRQ(ierr);
break;
case 2:
ierr = PetscFPrintf(comm,fp," <Piece Extent=\"%D %D %D %D %D %D\">\n",xs,xs+xm,ys+ym-1,xs,xs+xm-1,0,0);CHKERRQ(ierr);
break;
case 3:
ierr = PetscFPrintf(comm,fp," <Piece Extent=\"%D %D %D %D %D %D\">\n",xs,xs+xm-1,ys,ys+ym-1,zs,zs+zm-1);CHKERRQ(ierr);
break;
default: SETERRQ1(((PetscObject)da)->comm,PETSC_ERR_SUP,"No support for dimension %D",dim);
}
#endif
ierr = PetscFPrintf(comm,fp," <Piece Extent=\"%D %D %D %D %D %D\">\n",xs,xs+xm-1,ys,ys+ym-1,zs,zs+zm-1);CHKERRQ(ierr);
ierr = PetscFPrintf(comm,fp," <Points>\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm,fp," <DataArray type=\"%s\" Name=\"Position\" NumberOfComponents=\"3\" format=\"appended\" offset=\"%D\" />\n",precision,boffset);CHKERRQ(ierr);
boffset += 3*nnodes*sizeof(PetscScalar) + sizeof(int);
ierr = PetscFPrintf(comm,fp," </Points>\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm,fp," <PointData Scalars=\"ScalarPointData\">\n");CHKERRQ(ierr);
for (link=vtk->link; link; link=link->next) {
Vec X = (Vec)link->vec;
const char *vecname = "";
if (((PetscObject)X)->name || link != vtk->link) { /* If the object is already named, use it. If it is past the first link, name it to disambiguate. */
ierr = PetscObjectGetName((PetscObject)X,&vecname);CHKERRQ(ierr);
}
for (i=0; i<bs; i++) {
char buf[256];
const char *fieldname;
ierr = DMDAGetFieldName(da,i,&fieldname);CHKERRQ(ierr);
if (!fieldname) {
ierr = PetscSNPrintf(buf,sizeof(buf),"Unnamed%D",i);CHKERRQ(ierr);
fieldname = buf;
}
ierr = PetscFPrintf(comm,fp," <DataArray type=\"%s\" Name=\"%s%s\" NumberOfComponents=\"1\" format=\"appended\" offset=\"%D\" />\n",precision,vecname,fieldname,boffset);CHKERRQ(ierr);
boffset += nnodes*sizeof(PetscScalar) + sizeof(int);
}
}
ierr = PetscFPrintf(comm,fp," </PointData>\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm,fp," </Piece>\n");CHKERRQ(ierr);
}
ierr = PetscFPrintf(comm,fp," </StructuredGrid>\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm,fp," <AppendedData encoding=\"raw\">\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm,fp,"_");CHKERRQ(ierr);
/* Now write the arrays. */
tag = ((PetscObject)viewer)->tag;
ierr = PetscMalloc2(maxnnodes*PetscMax(3,bs),PetscScalar,&array,maxnnodes*3,PetscScalar,&array2);CHKERRQ(ierr);
for (r=0; r<size; r++) {
MPI_Status status;
PetscInt xs=-1,xm=-1,ys=-1,ym=-1,zs=-1,zm=-1,nnodes = 0;
if (!rank) {
xs = grloc[r][0];
xm = grloc[r][1];
ys = grloc[r][2];
ym = grloc[r][3];
zs = grloc[r][4];
zm = grloc[r][5];
nnodes = xm*ym*zm;
} else if (r == rank) {
nnodes = info.xm*info.ym*info.zm;
}
{ /* Write the coordinates */
Vec Coords;
ierr = DMGetCoordinates(da,&Coords);CHKERRQ(ierr);
if (Coords) {
const PetscScalar *coords;
ierr = VecGetArrayRead(Coords,&coords);CHKERRQ(ierr);
if (!rank) {
if (r) {
PetscMPIInt nn;
ierr = MPI_Recv(array,nnodes*dim,MPIU_SCALAR,r,tag,comm,&status);CHKERRQ(ierr);
ierr = MPI_Get_count(&status,MPIU_SCALAR,&nn);CHKERRQ(ierr);
if (nn != nnodes*dim) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Array size mismatch");
} else {
ierr = PetscMemcpy(array,coords,nnodes*dim*sizeof(PetscScalar));CHKERRQ(ierr);
}
/* Transpose coordinates to VTK (C-style) ordering */
for (k=0; k<zm; k++) {
for (j=0; j<ym; j++) {
for (i=0; i<xm; i++) {
PetscInt Iloc = i+xm*(j+ym*k);
array2[Iloc*3+0] = array[Iloc*dim + 0];
array2[Iloc*3+1] = dim > 1 ? array[Iloc*dim + 1] : 0;
array2[Iloc*3+2] = dim > 2 ? array[Iloc*dim + 2] : 0;
}
}
}
} else if (r == rank) {
ierr = MPI_Send((void*)coords,nnodes*dim,MPIU_SCALAR,0,tag,comm);CHKERRQ(ierr);
}
ierr = VecRestoreArrayRead(Coords,&coords);CHKERRQ(ierr);
} else { /* Fabricate some coordinates using grid index */
for (k=0; k<zm; k++) {
for (j=0; j<ym; j++) {
for (i=0; i<xm; i++) {
PetscInt Iloc = i+xm*(j+ym*k);
array2[Iloc*3+0] = xs+i;
array2[Iloc*3+1] = ys+j;
array2[Iloc*3+2] = zs+k;
}
}
}
}
ierr = PetscViewerVTKFWrite(viewer,fp,array2,nnodes*3,PETSC_SCALAR);CHKERRQ(ierr);
}
/* Write each of the objects queued up for this file */
for (link=vtk->link; link; link=link->next) {
Vec X = (Vec)link->vec;
const PetscScalar *x;
ierr = VecGetArrayRead(X,&x);CHKERRQ(ierr);
if (!rank) {
if (r) {
PetscMPIInt nn;
ierr = MPI_Recv(array,nnodes*bs,MPIU_SCALAR,r,tag,comm,&status);CHKERRQ(ierr);
ierr = MPI_Get_count(&status,MPIU_SCALAR,&nn);CHKERRQ(ierr);
if (nn != nnodes*bs) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Array size mismatch receiving from rank %D",r);
} else {
ierr = PetscMemcpy(array,x,nnodes*bs*sizeof(PetscScalar));CHKERRQ(ierr);
}
for (f=0; f<bs; f++) {
/* Extract and transpose the f'th field */
for (k=0; k<zm; k++) {
for (j=0; j<ym; j++) {
for (i=0; i<xm; i++) {
PetscInt Iloc = i+xm*(j+ym*k);
array2[Iloc] = array[Iloc*bs + f];
}
}
}
ierr = PetscViewerVTKFWrite(viewer,fp,array2,nnodes,PETSC_SCALAR);CHKERRQ(ierr);
}
} else if (r == rank) {
ierr = MPI_Send((void*)x,nnodes*bs,MPIU_SCALAR,0,tag,comm);CHKERRQ(ierr);
}
ierr = VecRestoreArrayRead(X,&x);CHKERRQ(ierr);
}
}
ierr = PetscFree2(array,array2);CHKERRQ(ierr);
ierr = PetscFree(grloc);CHKERRQ(ierr);
ierr = PetscFPrintf(comm,fp,"\n </AppendedData>\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm,fp,"</VTKFile>\n");CHKERRQ(ierr);
ierr = PetscFClose(comm,fp);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
KSPView - Prints the KSP data structure.
Collective on KSP
Input Parameters:
+ ksp - the Krylov space context
- viewer - visualization context
Options Database Keys:
. -ksp_view - print the ksp data structure at the end of a KSPSolve call
Note:
The available visualization contexts include
+ PETSC_VIEWER_STDOUT_SELF - standard output (default)
- PETSC_VIEWER_STDOUT_WORLD - synchronized standard
output where only the first processor opens
the file. All other processors send their
data to the first processor to print.
The user can open an alternative visualization context with
PetscViewerASCIIOpen() - output to a specified file.
Level: beginner
.keywords: KSP, view
.seealso: PCView(), PetscViewerASCIIOpen()
@*/
PetscErrorCode KSPView(KSP ksp,PetscViewer viewer)
{
PetscErrorCode ierr;
PetscBool iascii,isbinary,isdraw;
#if defined(PETSC_HAVE_SAWS)
PetscBool issaws;
#endif
PetscFunctionBegin;
PetscValidHeaderSpecific(ksp,KSP_CLASSID,1);
if (!viewer) {
ierr = PetscViewerASCIIGetStdout(PetscObjectComm((PetscObject)ksp),&viewer);CHKERRQ(ierr);
}
PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,2);
PetscCheckSameComm(ksp,1,viewer,2);
ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr);
ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr);
ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr);
#if defined(PETSC_HAVE_SAWS)
ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERSAWS,&issaws);CHKERRQ(ierr);
#endif
if (iascii) {
ierr = PetscObjectPrintClassNamePrefixType((PetscObject)ksp,viewer);CHKERRQ(ierr);
if (ksp->ops->view) {
ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
ierr = (*ksp->ops->view)(ksp,viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
}
if (ksp->guess_zero) {
ierr = PetscViewerASCIIPrintf(viewer," maximum iterations=%D, initial guess is zero\n",ksp->max_it);CHKERRQ(ierr);
} else {
ierr = PetscViewerASCIIPrintf(viewer," maximum iterations=%D\n", ksp->max_it);CHKERRQ(ierr);
}
if (ksp->guess_knoll) {ierr = PetscViewerASCIIPrintf(viewer," using preconditioner applied to right hand side for initial guess\n");CHKERRQ(ierr);}
ierr = PetscViewerASCIIPrintf(viewer," tolerances: relative=%g, absolute=%g, divergence=%g\n",(double)ksp->rtol,(double)ksp->abstol,(double)ksp->divtol);CHKERRQ(ierr);
if (ksp->pc_side == PC_RIGHT) {
ierr = PetscViewerASCIIPrintf(viewer," right preconditioning\n");CHKERRQ(ierr);
} else if (ksp->pc_side == PC_SYMMETRIC) {
ierr = PetscViewerASCIIPrintf(viewer," symmetric preconditioning\n");CHKERRQ(ierr);
} else {
ierr = PetscViewerASCIIPrintf(viewer," left preconditioning\n");CHKERRQ(ierr);
}
if (ksp->guess) {ierr = PetscViewerASCIIPrintf(viewer," using Fischers initial guess method %D with size %D\n",ksp->guess->method,ksp->guess->maxl);CHKERRQ(ierr);}
if (ksp->dscale) {ierr = PetscViewerASCIIPrintf(viewer," diagonally scaled system\n");CHKERRQ(ierr);}
if (!ksp->guess_zero) {ierr = PetscViewerASCIIPrintf(viewer," using nonzero initial guess\n");CHKERRQ(ierr);}
ierr = PetscViewerASCIIPrintf(viewer," using %s norm type for convergence test\n",KSPNormTypes[ksp->normtype]);CHKERRQ(ierr);
} else if (isbinary) {
PetscInt classid = KSP_FILE_CLASSID;
MPI_Comm comm;
PetscMPIInt rank;
char type[256];
ierr = PetscObjectGetComm((PetscObject)ksp,&comm);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);
if (!rank) {
ierr = PetscViewerBinaryWrite(viewer,&classid,1,PETSC_INT,PETSC_FALSE);CHKERRQ(ierr);
ierr = PetscStrncpy(type,((PetscObject)ksp)->type_name,256);CHKERRQ(ierr);
ierr = PetscViewerBinaryWrite(viewer,type,256,PETSC_CHAR,PETSC_FALSE);CHKERRQ(ierr);
}
if (ksp->ops->view) {
ierr = (*ksp->ops->view)(ksp,viewer);CHKERRQ(ierr);
}
} else if (isdraw) {
PetscDraw draw;
char str[36];
PetscReal x,y,bottom,h;
PetscBool flg;
ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr);
ierr = PetscDrawGetCurrentPoint(draw,&x,&y);CHKERRQ(ierr);
ierr = PetscObjectTypeCompare((PetscObject)ksp,KSPPREONLY,&flg);CHKERRQ(ierr);
if (!flg) {
ierr = PetscStrcpy(str,"KSP: ");CHKERRQ(ierr);
ierr = PetscStrcat(str,((PetscObject)ksp)->type_name);CHKERRQ(ierr);
ierr = PetscDrawStringBoxed(draw,x,y,PETSC_DRAW_RED,PETSC_DRAW_BLACK,str,NULL,&h);CHKERRQ(ierr);
bottom = y - h;
} else {
bottom = y;
}
ierr = PetscDrawPushCurrentPoint(draw,x,bottom);CHKERRQ(ierr);
#if defined(PETSC_HAVE_SAWS)
} else if (issaws) {
PetscMPIInt rank;
const char *name;
ierr = PetscObjectGetName((PetscObject)ksp,&name);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
if (!((PetscObject)ksp)->amsmem && !rank) {
char dir[1024];
ierr = PetscObjectViewSAWs((PetscObject)ksp,viewer);CHKERRQ(ierr);
ierr = PetscSNPrintf(dir,1024,"/PETSc/Objects/%s/its",name);CHKERRQ(ierr);
PetscStackCallSAWs(SAWs_Register,(dir,&ksp->its,1,SAWs_READ,SAWs_INT));
if (!ksp->res_hist) {
ierr = KSPSetResidualHistory(ksp,NULL,PETSC_DECIDE,PETSC_TRUE);CHKERRQ(ierr);
}
ierr = PetscSNPrintf(dir,1024,"/PETSc/Objects/%s/res_hist",name);CHKERRQ(ierr);
PetscStackCallSAWs(SAWs_Register,(dir,ksp->res_hist,10,SAWs_READ,SAWs_DOUBLE));
}
#endif
} else if (ksp->ops->view) {
ierr = (*ksp->ops->view)(ksp,viewer);CHKERRQ(ierr);
}
if (!ksp->skippcsetfromoptions) {
if (!ksp->pc) {ierr = KSPGetPC(ksp,&ksp->pc);CHKERRQ(ierr);}
ierr = PCView(ksp->pc,viewer);CHKERRQ(ierr);
}
if (isdraw) {
PetscDraw draw;
ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr);
ierr = PetscDrawPopCurrentPoint(draw);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode ISView_General_HDF5(IS is, PetscViewer viewer)
{
hid_t filespace; /* file dataspace identifier */
hid_t chunkspace; /* chunk dataset property identifier */
hid_t plist_id; /* property list identifier */
hid_t dset_id; /* dataset identifier */
hid_t memspace; /* memory dataspace identifier */
hid_t inttype; /* int type (H5T_NATIVE_INT or H5T_NATIVE_LLONG) */
hid_t file_id, group;
herr_t status;
hsize_t dim, maxDims[3], dims[3], chunkDims[3], count[3],offset[3];
PetscInt bs, N, n, timestep, low;
const PetscInt *ind;
const char *isname;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = ISGetBlockSize(is,&bs);CHKERRQ(ierr);
ierr = PetscViewerHDF5OpenGroup(viewer, &file_id, &group);CHKERRQ(ierr);
ierr = PetscViewerHDF5GetTimestep(viewer, ×tep);CHKERRQ(ierr);
/* Create the dataspace for the dataset.
*
* dims - holds the current dimensions of the dataset
*
* maxDims - holds the maximum dimensions of the dataset (unlimited
* for the number of time steps with the current dimensions for the
* other dimensions; so only additional time steps can be added).
*
* chunkDims - holds the size of a single time step (required to
* permit extending dataset).
*/
dim = 0;
if (timestep >= 0) {
dims[dim] = timestep+1;
maxDims[dim] = H5S_UNLIMITED;
chunkDims[dim] = 1;
++dim;
}
ierr = ISGetSize(is, &N);CHKERRQ(ierr);
ierr = ISGetLocalSize(is, &n);CHKERRQ(ierr);
ierr = PetscHDF5IntCast(N/bs,dims + dim);CHKERRQ(ierr);
maxDims[dim] = dims[dim];
chunkDims[dim] = dims[dim];
++dim;
if (bs >= 1) {
dims[dim] = bs;
maxDims[dim] = dims[dim];
chunkDims[dim] = dims[dim];
++dim;
}
filespace = H5Screate_simple(dim, dims, maxDims);
if (filespace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Cannot H5Screate_simple()");
#if defined(PETSC_USE_64BIT_INDICES)
inttype = H5T_NATIVE_LLONG;
#else
inttype = H5T_NATIVE_INT;
#endif
/* Create the dataset with default properties and close filespace */
ierr = PetscObjectGetName((PetscObject) is, &isname);CHKERRQ(ierr);
if (!H5Lexists(group, isname, H5P_DEFAULT)) {
/* Create chunk */
chunkspace = H5Pcreate(H5P_DATASET_CREATE);
if (chunkspace == -1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_LIB, "Cannot H5Pcreate()");
status = H5Pset_chunk(chunkspace, dim, chunkDims);CHKERRQ(status);
#if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
dset_id = H5Dcreate2(group, isname, inttype, filespace, H5P_DEFAULT, chunkspace, H5P_DEFAULT);
#else
dset_id = H5Dcreate(group, isname, inttype, filespace, H5P_DEFAULT);
#endif
if (dset_id == -1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_LIB, "Cannot H5Dcreate2()");
status = H5Pclose(chunkspace);CHKERRQ(status);
} else {
dset_id = H5Dopen2(group, isname, H5P_DEFAULT);
status = H5Dset_extent(dset_id, dims);CHKERRQ(status);
}
status = H5Sclose(filespace);CHKERRQ(status);
/* Each process defines a dataset and writes it to the hyperslab in the file */
dim = 0;
if (timestep >= 0) {
count[dim] = 1;
++dim;
}
ierr = PetscHDF5IntCast(n/bs,count + dim);CHKERRQ(ierr);
++dim;
if (bs >= 1) {
count[dim] = bs;
++dim;
}
if (n > 0) {
memspace = H5Screate_simple(dim, count, NULL);
if (memspace == -1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_LIB, "Cannot H5Screate_simple()");
} else {
/* Can't create dataspace with zero for any dimension, so create null dataspace. */
memspace = H5Screate(H5S_NULL);
if (memspace == -1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_LIB, "Cannot H5Screate()");
}
/* Select hyperslab in the file */
ierr = PetscLayoutGetRange(is->map, &low, NULL);CHKERRQ(ierr);
dim = 0;
if (timestep >= 0) {
offset[dim] = timestep;
++dim;
}
ierr = PetscHDF5IntCast(low/bs,offset + dim);CHKERRQ(ierr);
++dim;
if (bs >= 1) {
offset[dim] = 0;
++dim;
}
if (n > 0) {
filespace = H5Dget_space(dset_id);
if (filespace == -1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_LIB, "Cannot H5Dget_space()");
status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, count, NULL);CHKERRQ(status);
} else {
/* Create null filespace to match null memspace. */
filespace = H5Screate(H5S_NULL);
if (filespace == -1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_LIB, "Cannot H5Screate(H5S_NULL)");
}
/* Create property list for collective dataset write */
plist_id = H5Pcreate(H5P_DATASET_XFER);
if (plist_id == -1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_LIB, "Cannot H5Pcreate()");
#if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
status = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);CHKERRQ(status);
#endif
/* To write dataset independently use H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT) */
ierr = ISGetIndices(is, &ind);CHKERRQ(ierr);
status = H5Dwrite(dset_id, inttype, memspace, filespace, plist_id, ind);CHKERRQ(status);
status = H5Fflush(file_id, H5F_SCOPE_GLOBAL);CHKERRQ(status);
ierr = ISGetIndices(is, &ind);CHKERRQ(ierr);
/* Close/release resources */
if (group != file_id) {status = H5Gclose(group);CHKERRQ(status);}
status = H5Pclose(plist_id);CHKERRQ(status);
status = H5Sclose(filespace);CHKERRQ(status);
status = H5Sclose(memspace);CHKERRQ(status);
status = H5Dclose(dset_id);CHKERRQ(status);
ierr = PetscInfo1(is, "Wrote IS object with name %s\n", isname);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
DMPlexPermute - Reorder the mesh according to the input permutation
Collective on DM
Input Parameter:
+ dm - The DMPlex object
- perm - The point permutation, perm[old point number] = new point number
Output Parameter:
. pdm - The permuted DM
Level: intermediate
.keywords: mesh
.seealso: MatPermute()
@*/
PetscErrorCode DMPlexPermute(DM dm, IS perm, DM *pdm)
{
DM_Plex *plex = (DM_Plex *) dm->data, *plexNew;
PetscSection section, sectionNew;
PetscInt dim;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
PetscValidHeaderSpecific(perm, IS_CLASSID, 2);
PetscValidPointer(pdm, 3);
ierr = DMCreate(PetscObjectComm((PetscObject) dm), pdm);CHKERRQ(ierr);
ierr = DMSetType(*pdm, DMPLEX);CHKERRQ(ierr);
ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = DMSetDimension(*pdm, dim);CHKERRQ(ierr);
ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr);
if (section) {
ierr = PetscSectionPermute(section, perm, §ionNew);CHKERRQ(ierr);
ierr = DMSetDefaultSection(*pdm, sectionNew);CHKERRQ(ierr);
ierr = PetscSectionDestroy(§ionNew);CHKERRQ(ierr);
}
plexNew = (DM_Plex *) (*pdm)->data;
/* Ignore ltogmap, ltogmapb */
/* Ignore sf, defaultSF */
/* Ignore globalVertexNumbers, globalCellNumbers */
/* Remap coordinates */
{
DM cdm, cdmNew;
PetscSection csection, csectionNew;
Vec coordinates, coordinatesNew;
PetscScalar *coords, *coordsNew;
const PetscInt *pperm;
PetscInt pStart, pEnd, p;
const char *name;
ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr);
ierr = DMGetDefaultSection(cdm, &csection);CHKERRQ(ierr);
ierr = PetscSectionPermute(csection, perm, &csectionNew);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
ierr = VecDuplicate(coordinates, &coordinatesNew);CHKERRQ(ierr);
ierr = PetscObjectGetName((PetscObject)coordinates,&name);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)coordinatesNew,name);CHKERRQ(ierr);
ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
ierr = VecGetArray(coordinatesNew, &coordsNew);CHKERRQ(ierr);
ierr = PetscSectionGetChart(csectionNew, &pStart, &pEnd);CHKERRQ(ierr);
ierr = ISGetIndices(perm, &pperm);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
PetscInt dof, off, offNew, d;
ierr = PetscSectionGetDof(csectionNew, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(csection, p, &off);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(csectionNew, pperm[p], &offNew);CHKERRQ(ierr);
for (d = 0; d < dof; ++d) coordsNew[offNew+d] = coords[off+d];
}
ierr = ISRestoreIndices(perm, &pperm);CHKERRQ(ierr);
ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
ierr = VecRestoreArray(coordinatesNew, &coordsNew);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(*pdm, &cdmNew);CHKERRQ(ierr);
ierr = DMSetDefaultSection(cdmNew, csectionNew);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(*pdm, coordinatesNew);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&csectionNew);CHKERRQ(ierr);
ierr = VecDestroy(&coordinatesNew);CHKERRQ(ierr);
}
/* Reorder labels */
{
PetscInt numLabels, l;
DMLabel label, labelNew;
ierr = DMGetNumLabels(dm, &numLabels);CHKERRQ(ierr);
for (l = numLabels-1; l >= 0; --l) {
ierr = DMGetLabelByNum(dm, l, &label);CHKERRQ(ierr);
ierr = DMLabelPermute(label, perm, &labelNew);CHKERRQ(ierr);
ierr = DMAddLabel(*pdm, labelNew);CHKERRQ(ierr);
}
if (plex->subpointMap) {ierr = DMLabelPermute(plex->subpointMap, perm, &plexNew->subpointMap);CHKERRQ(ierr);}
}
/* Reorder topology */
{
const PetscInt *pperm;
PetscInt maxConeSize, maxSupportSize, n, pStart, pEnd, p;
ierr = DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);CHKERRQ(ierr);
plexNew->maxConeSize = maxConeSize;
plexNew->maxSupportSize = maxSupportSize;
ierr = PetscSectionDestroy(&plexNew->coneSection);CHKERRQ(ierr);
ierr = PetscSectionPermute(plex->coneSection, perm, &plexNew->coneSection);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(plexNew->coneSection, &n);CHKERRQ(ierr);
ierr = PetscMalloc1(n, &plexNew->cones);CHKERRQ(ierr);
ierr = PetscMalloc1(n, &plexNew->coneOrientations);CHKERRQ(ierr);
ierr = ISGetIndices(perm, &pperm);CHKERRQ(ierr);
ierr = PetscSectionGetChart(plex->coneSection, &pStart, &pEnd);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
PetscInt dof, off, offNew, d;
ierr = PetscSectionGetDof(plexNew->coneSection, pperm[p], &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(plex->coneSection, p, &off);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(plexNew->coneSection, pperm[p], &offNew);CHKERRQ(ierr);
for (d = 0; d < dof; ++d) {
plexNew->cones[offNew+d] = pperm[plex->cones[off+d]];
plexNew->coneOrientations[offNew+d] = plex->coneOrientations[off+d];
}
}
ierr = PetscSectionDestroy(&plexNew->supportSection);CHKERRQ(ierr);
ierr = PetscSectionPermute(plex->supportSection, perm, &plexNew->supportSection);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(plexNew->supportSection, &n);CHKERRQ(ierr);
ierr = PetscMalloc1(n, &plexNew->supports);CHKERRQ(ierr);
ierr = PetscSectionGetChart(plex->supportSection, &pStart, &pEnd);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
PetscInt dof, off, offNew, d;
ierr = PetscSectionGetDof(plexNew->supportSection, pperm[p], &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(plex->supportSection, p, &off);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(plexNew->supportSection, pperm[p], &offNew);CHKERRQ(ierr);
for (d = 0; d < dof; ++d) {
plexNew->supports[offNew+d] = pperm[plex->supports[off+d]];
}
}
ierr = ISRestoreIndices(perm, &pperm);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
static PetscErrorCode DMPlexVTKWriteAll_ASCII(DM dm, PetscViewer viewer)
{
MPI_Comm comm;
PetscViewer_VTK *vtk = (PetscViewer_VTK*) viewer->data;
FILE *fp;
PetscViewerVTKObjectLink link;
PetscSection coordSection, globalCoordSection;
PetscLayout vLayout;
Vec coordinates;
PetscReal lengthScale;
PetscInt vMax, totVertices, totCells;
PetscBool hasPoint = PETSC_FALSE, hasCell = PETSC_FALSE, writePartition = PETSC_FALSE;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
ierr = PetscFOpen(comm, vtk->filename, "wb", &fp);CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "# vtk DataFile Version 2.0\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "Simplicial Mesh Example\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "ASCII\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "DATASET UNSTRUCTURED_GRID\n");CHKERRQ(ierr);
/* Vertices */
ierr = DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale);CHKERRQ(ierr);
ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
ierr = PetscSectionCreateGlobalSection(coordSection, dm->sf, PETSC_FALSE, PETSC_FALSE, &globalCoordSection);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, NULL, NULL, NULL, &vMax);CHKERRQ(ierr);
if (vMax >= 0) {
PetscInt pStart, pEnd, p, localSize = 0;
ierr = PetscSectionGetChart(globalCoordSection, &pStart, &pEnd);CHKERRQ(ierr);
pEnd = PetscMin(pEnd, vMax);
for (p = pStart; p < pEnd; ++p) {
PetscInt dof;
ierr = PetscSectionGetDof(globalCoordSection, p, &dof);CHKERRQ(ierr);
if (dof > 0) ++localSize;
}
ierr = PetscLayoutCreate(PetscObjectComm((PetscObject)dm), &vLayout);CHKERRQ(ierr);
ierr = PetscLayoutSetLocalSize(vLayout, localSize);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize(vLayout, 1);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(vLayout);CHKERRQ(ierr);
} else {
ierr = PetscSectionGetPointLayout(PetscObjectComm((PetscObject)dm), globalCoordSection, &vLayout);CHKERRQ(ierr);
}
ierr = PetscLayoutGetSize(vLayout, &totVertices);CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "POINTS %d double\n", totVertices);CHKERRQ(ierr);
ierr = DMPlexVTKWriteSection_ASCII(dm, coordSection, globalCoordSection, coordinates, fp, 3, PETSC_DETERMINE, lengthScale);CHKERRQ(ierr);
/* Cells */
ierr = DMPlexVTKWriteCells_ASCII(dm, fp, &totCells);CHKERRQ(ierr);
/* Vertex fields */
for (link = vtk->link; link; link = link->next) {
if ((link->ft == PETSC_VTK_POINT_FIELD) || (link->ft == PETSC_VTK_POINT_VECTOR_FIELD)) hasPoint = PETSC_TRUE;
if ((link->ft == PETSC_VTK_CELL_FIELD) || (link->ft == PETSC_VTK_CELL_VECTOR_FIELD)) hasCell = PETSC_TRUE;
}
if (hasPoint) {
ierr = PetscFPrintf(comm, fp, "POINT_DATA %d\n", totVertices);CHKERRQ(ierr);
for (link = vtk->link; link; link = link->next) {
Vec X = (Vec) link->vec;
DM dmX;
PetscSection section, globalSection, newSection = NULL;
const char *name;
PetscInt enforceDof = PETSC_DETERMINE;
if ((link->ft != PETSC_VTK_POINT_FIELD) && (link->ft != PETSC_VTK_POINT_VECTOR_FIELD)) continue;
if (link->ft == PETSC_VTK_POINT_VECTOR_FIELD) enforceDof = 3;
ierr = PetscObjectGetName(link->vec, &name);CHKERRQ(ierr);
ierr = VecGetDM(X, &dmX);CHKERRQ(ierr);
if (dmX) {
DMLabel subpointMap, subpointMapX;
PetscInt dim, dimX, pStart, pEnd, qStart, qEnd;
ierr = DMGetDefaultSection(dmX, §ion);CHKERRQ(ierr);
/* Here is where we check whether dmX is a submesh of dm */
ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = DMGetDimension(dmX, &dimX);CHKERRQ(ierr);
ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr);
ierr = DMPlexGetChart(dmX, &qStart, &qEnd);CHKERRQ(ierr);
ierr = DMPlexGetSubpointMap(dm, &subpointMap);CHKERRQ(ierr);
ierr = DMPlexGetSubpointMap(dmX, &subpointMapX);CHKERRQ(ierr);
if (((dim != dimX) || ((pEnd-pStart) < (qEnd-qStart))) && subpointMap && !subpointMapX) {
const PetscInt *ind = NULL;
IS subpointIS;
PetscInt n = 0, q;
ierr = PetscSectionGetChart(section, &qStart, &qEnd);CHKERRQ(ierr);
ierr = DMPlexCreateSubpointIS(dm, &subpointIS);CHKERRQ(ierr);
if (subpointIS) {
ierr = ISGetLocalSize(subpointIS, &n);CHKERRQ(ierr);
ierr = ISGetIndices(subpointIS, &ind);CHKERRQ(ierr);
}
ierr = PetscSectionCreate(comm, &newSection);CHKERRQ(ierr);
ierr = PetscSectionSetChart(newSection, pStart, pEnd);CHKERRQ(ierr);
for (q = qStart; q < qEnd; ++q) {
PetscInt dof, off, p;
ierr = PetscSectionGetDof(section, q, &dof);CHKERRQ(ierr);
if (dof) {
ierr = PetscFindInt(q, n, ind, &p);CHKERRQ(ierr);
if (p >= pStart) {
ierr = PetscSectionSetDof(newSection, p, dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(section, q, &off);CHKERRQ(ierr);
ierr = PetscSectionSetOffset(newSection, p, off);CHKERRQ(ierr);
}
}
}
if (subpointIS) {
ierr = ISRestoreIndices(subpointIS, &ind);CHKERRQ(ierr);
ierr = ISDestroy(&subpointIS);CHKERRQ(ierr);
}
/* No need to setup section */
section = newSection;
}
} else {
ierr = PetscObjectQuery(link->vec, "section", (PetscObject*) §ion);CHKERRQ(ierr);
if (!section) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Vector %s had no PetscSection composed with it", name);
}
if (!section) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Vector %s had no PetscSection composed with it", name);
ierr = PetscSectionCreateGlobalSection(section, dm->sf, PETSC_FALSE, PETSC_FALSE, &globalSection);CHKERRQ(ierr);
ierr = DMPlexVTKWriteField_ASCII(dm, section, globalSection, X, name, fp, enforceDof, PETSC_DETERMINE, 1.0);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&globalSection);CHKERRQ(ierr);
if (newSection) {ierr = PetscSectionDestroy(&newSection);CHKERRQ(ierr);}
}
}
/* Cell Fields */
ierr = PetscOptionsGetBool(((PetscObject) dm)->prefix, "-dm_view_partition", &writePartition, NULL);CHKERRQ(ierr);
if (hasCell || writePartition) {
ierr = PetscFPrintf(comm, fp, "CELL_DATA %d\n", totCells);CHKERRQ(ierr);
for (link = vtk->link; link; link = link->next) {
Vec X = (Vec) link->vec;
DM dmX;
PetscSection section, globalSection;
const char *name;
PetscInt enforceDof = PETSC_DETERMINE;
if ((link->ft != PETSC_VTK_CELL_FIELD) && (link->ft != PETSC_VTK_CELL_VECTOR_FIELD)) continue;
if (link->ft == PETSC_VTK_CELL_VECTOR_FIELD) enforceDof = 3;
ierr = PetscObjectGetName(link->vec, &name);CHKERRQ(ierr);
ierr = VecGetDM(X, &dmX);CHKERRQ(ierr);
if (dmX) {
ierr = DMGetDefaultSection(dmX, §ion);CHKERRQ(ierr);
} else {
PetscContainer c;
ierr = PetscObjectQuery(link->vec, "section", (PetscObject*) &c);CHKERRQ(ierr);
if (!c) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Vector %s had no PetscSection composed with it", name);
ierr = PetscContainerGetPointer(c, (void**) §ion);CHKERRQ(ierr);
}
if (!section) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Vector %s had no PetscSection composed with it", name);
ierr = PetscSectionCreateGlobalSection(section, dm->sf, PETSC_FALSE, PETSC_FALSE, &globalSection);CHKERRQ(ierr);
ierr = DMPlexVTKWriteField_ASCII(dm, section, globalSection, X, name, fp, enforceDof, PETSC_DETERMINE, 1.0);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&globalSection);CHKERRQ(ierr);
}
if (writePartition) {
ierr = PetscFPrintf(comm, fp, "SCALARS partition int 1\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "LOOKUP_TABLE default\n");CHKERRQ(ierr);
ierr = DMPlexVTKWritePartition_ASCII(dm, fp);CHKERRQ(ierr);
}
}
/* Cleanup */
ierr = PetscSectionDestroy(&globalCoordSection);CHKERRQ(ierr);
ierr = PetscLayoutDestroy(&vLayout);CHKERRQ(ierr);
ierr = PetscFClose(comm, fp);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode private_DMSwarmView_XDMF(DM dm,PetscViewer viewer)
{
PetscBool isswarm = PETSC_FALSE;
const char *viewername;
char datafile[PETSC_MAX_PATH_LEN];
PetscViewer fviewer;
PetscInt k,ng,dim;
Vec dvec;
long int *bytes = NULL;
PetscContainer container = NULL;
const char *dmname;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscObjectQuery((PetscObject)viewer,"XDMFViewerContext",(PetscObject*)&container);CHKERRQ(ierr);
if (container) {
ierr = PetscContainerGetPointer(container,(void**)&bytes);CHKERRQ(ierr);
} else SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"Valid to find attached data XDMFViewerContext");
ierr = PetscObjectTypeCompare((PetscObject)dm,DMSWARM,&isswarm);CHKERRQ(ierr);
if (!isswarm) SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"Only valid for DMSwarm");
ierr = PetscObjectCompose((PetscObject)viewer,"DMSwarm",(PetscObject)dm);CHKERRQ(ierr);
ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
ierr = PetscObjectGetName((PetscObject)dm,&dmname);CHKERRQ(ierr);
if (!dmname) {
ierr = DMGetOptionsPrefix(dm,&dmname);CHKERRQ(ierr);
}
if (!dmname) {
ierr = PetscViewerASCIIPrintf(viewer,"<Grid Name=\"DMSwarm\" GridType=\"Uniform\">\n");CHKERRQ(ierr);
} else {
ierr = PetscViewerASCIIPrintf(viewer,"<Grid Name=\"DMSwarm[%s]\" GridType=\"Uniform\">\n",dmname);CHKERRQ(ierr);
}
/* create a sub-viewer for topology, geometry and all data fields */
/* name is viewer.name + "_swarm_fields.pbin" */
ierr = PetscViewerCreate(PetscObjectComm((PetscObject)viewer),&fviewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(fviewer,PETSCVIEWERBINARY);CHKERRQ(ierr);
ierr = PetscViewerBinarySetSkipHeader(fviewer,PETSC_TRUE);CHKERRQ(ierr);
ierr = PetscViewerBinarySetSkipInfo(fviewer,PETSC_TRUE);CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(fviewer,FILE_MODE_WRITE);CHKERRQ(ierr);
ierr = PetscViewerFileGetName(viewer,&viewername);CHKERRQ(ierr);
ierr = private_CreateDataFileNameXDMF(viewername,datafile);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(fviewer,datafile);CHKERRQ(ierr);
ierr = DMSwarmGetSize(dm,&ng);CHKERRQ(ierr);
/* write topology header */
ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"<Topology Dimensions=\"%D\" TopologyType=\"Mixed\">\n",ng);CHKERRQ(ierr);
ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Int\" Dimensions=\"%D\" Seek=\"%D\">\n",ng*3,bytes[0]);CHKERRQ(ierr);
ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"%s\n",datafile);CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"</DataItem>\n");CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"</Topology>\n");CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
/* write topology data */
for (k=0; k<ng; k++) {
PetscInt pvertex[3];
pvertex[0] = 1;
pvertex[1] = 1;
pvertex[2] = k;
ierr = PetscViewerBinaryWrite(fviewer,pvertex,3,PETSC_INT,PETSC_FALSE);CHKERRQ(ierr);
}
bytes[0] += sizeof(PetscInt) * ng * 3;
/* write geometry header */
ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr);
switch (dim) {
case 1:
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for 1D");
break;
case 2:
ierr = PetscViewerASCIIPrintf(viewer,"<Geometry Type=\"XY\">\n");CHKERRQ(ierr);
break;
case 3:
ierr = PetscViewerASCIIPrintf(viewer,"<Geometry Type=\"XYZ\">\n");CHKERRQ(ierr);
break;
}
ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Float\" Precision=\"8\" Dimensions=\"%D %D\" Seek=\"%D\">\n",ng,dim,bytes[0]);CHKERRQ(ierr);
ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"%s\n",datafile);CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"</DataItem>\n");CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"</Geometry>\n");CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
/* write geometry data */
ierr = DMSwarmCreateGlobalVectorFromField(dm,DMSwarmPICField_coor,&dvec);CHKERRQ(ierr);
ierr = VecView(dvec,fviewer);CHKERRQ(ierr);
ierr = DMSwarmDestroyGlobalVectorFromField(dm,DMSwarmPICField_coor,&dvec);CHKERRQ(ierr);
bytes[0] += sizeof(PetscReal) * ng * dim;
ierr = PetscViewerDestroy(&fviewer);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode private_ISView_Swarm_XDMF(IS is,PetscViewer viewer)
{
long int *bytes = NULL;
PetscContainer container = NULL;
const char *viewername;
char datafile[PETSC_MAX_PATH_LEN];
PetscViewer fviewer;
PetscInt N,bs;
const char *vecname;
char fieldname[PETSC_MAX_PATH_LEN];
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscObjectQuery((PetscObject)viewer,"XDMFViewerContext",(PetscObject*)&container);CHKERRQ(ierr);
if (container) {
ierr = PetscContainerGetPointer(container,(void**)&bytes);CHKERRQ(ierr);
} else SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"Valid to find attached data XDMFViewerContext");
ierr = PetscViewerFileGetName(viewer,&viewername);CHKERRQ(ierr);
ierr = private_CreateDataFileNameXDMF(viewername,datafile);CHKERRQ(ierr);
/* re-open a sub-viewer for all data fields */
/* name is viewer.name + "_swarm_fields.pbin" */
ierr = PetscViewerCreate(PetscObjectComm((PetscObject)viewer),&fviewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(fviewer,PETSCVIEWERBINARY);CHKERRQ(ierr);
ierr = PetscViewerBinarySetSkipHeader(fviewer,PETSC_TRUE);CHKERRQ(ierr);
ierr = PetscViewerBinarySetSkipInfo(fviewer,PETSC_TRUE);CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(fviewer,FILE_MODE_APPEND);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(fviewer,datafile);CHKERRQ(ierr);
ierr = ISGetSize(is,&N);CHKERRQ(ierr);
ierr = ISGetBlockSize(is,&bs);CHKERRQ(ierr);
N = N/bs;
ierr = PetscObjectGetName((PetscObject)is,&vecname);CHKERRQ(ierr);
if (!vecname) {
ierr = PetscSNPrintf(fieldname,PETSC_MAX_PATH_LEN-1,"swarmfield_%D",((PetscObject)is)->tag);CHKERRQ(ierr);
} else {
ierr = PetscSNPrintf(fieldname,PETSC_MAX_PATH_LEN-1,"%s",vecname);CHKERRQ(ierr);
}
/* write data header */
ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"<Attribute Center=\"Node\" Name=\"%s\" Type=\"None\">\n",fieldname);CHKERRQ(ierr);
ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
if (bs == 1) {
ierr = PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Int\" Precision=\"4\" Dimensions=\"%D\" Seek=\"%D\">\n",N,bytes[0]);CHKERRQ(ierr);
} else {
ierr = PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Int\" Precision=\"4\" Dimensions=\"%D %D\" Seek=\"%D\">\n",N,bs,bytes[0]);CHKERRQ(ierr);
}
ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"%s\n",datafile);CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"</DataItem>\n");CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"</Attribute>\n");CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
/* write data */
ierr = ISView(is,fviewer);CHKERRQ(ierr);
bytes[0] += sizeof(PetscInt) * N * bs;
ierr = PetscViewerDestroy(&fviewer);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
This should handle properly the cases where PetscInt is 32 or 64 and hsize_t is 32 or 64. These means properly casting with
checks back and forth between the two types of variables.
*/
PetscErrorCode VecLoad_HDF5(Vec xin, PetscViewer viewer)
{
hid_t file_id, group, dset_id, filespace, memspace, plist_id;
hsize_t rdim, dim;
hsize_t dims[4], count[4], offset[4];
herr_t status;
PetscInt n, N, bs = 1, bsInd, lenInd, low, timestep;
PetscScalar *x;
const char *vecname;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscViewerHDF5OpenGroup(viewer, &file_id, &group);CHKERRQ(ierr);
ierr = PetscViewerHDF5GetTimestep(viewer, ×tep);CHKERRQ(ierr);
ierr = VecGetBlockSize(xin,&bs);CHKERRQ(ierr);
/* Create the dataset with default properties and close filespace */
ierr = PetscObjectGetName((PetscObject)xin,&vecname);CHKERRQ(ierr);
#if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800)
dset_id = H5Dopen2(group, vecname, H5P_DEFAULT);
#else
dset_id = H5Dopen(group, vecname);
#endif
if (dset_id == -1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Could not H5Dopen() with Vec named %s",vecname);
/* Retrieve the dataspace for the dataset */
filespace = H5Dget_space(dset_id);
if (filespace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Could not H5Dget_space()");
dim = 0;
if (timestep >= 0) ++dim;
++dim;
if (bs >= 1) ++dim;
#if defined(PETSC_USE_COMPLEX)
++dim;
#endif
rdim = H5Sget_simple_extent_dims(filespace, dims, NULL);
#if defined(PETSC_USE_COMPLEX)
bsInd = rdim-2;
#else
bsInd = rdim-1;
#endif
lenInd = timestep >= 0 ? 1 : 0;
if (rdim != dim) {
if (rdim == dim+1 && bs == -1) bs = dims[bsInd];
else SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Dimension of array in file %d not %d as expected",rdim,dim);
} else if (bs >= 1 && bs != (PetscInt) dims[bsInd]) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Block size %d specified for vector does not match blocksize in file %d",bs,dims[bsInd]);
/* Set Vec sizes,blocksize,and type if not already set */
if ((xin)->map->n < 0 && (xin)->map->N < 0) {
ierr = VecSetSizes(xin, PETSC_DECIDE, dims[lenInd]*bs);CHKERRQ(ierr);
}
/* If sizes and type already set,check if the vector global size is correct */
ierr = VecGetSize(xin, &N);CHKERRQ(ierr);
if (N/bs != (PetscInt) dims[lenInd]) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Vector in file different length (%d) then input vector (%d)", (PetscInt) dims[lenInd], N/bs);
/* Each process defines a dataset and reads it from the hyperslab in the file */
ierr = VecGetLocalSize(xin, &n);CHKERRQ(ierr);
dim = 0;
if (timestep >= 0) {
count[dim] = 1;
++dim;
}
ierr = PetscHDF5IntCast(n/bs,count + dim);CHKERRQ(ierr);
++dim;
if (bs >= 1) {
count[dim] = bs;
++dim;
}
#if defined(PETSC_USE_COMPLEX)
count[dim] = 2;
++dim;
#endif
memspace = H5Screate_simple(dim, count, NULL);
if (memspace == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Could not H5Screate_simple()");
/* Select hyperslab in the file */
ierr = VecGetOwnershipRange(xin, &low, NULL);CHKERRQ(ierr);
dim = 0;
if (timestep >= 0) {
offset[dim] = timestep;
++dim;
}
ierr = PetscHDF5IntCast(low/bs,offset + dim);CHKERRQ(ierr);
++dim;
if (bs >= 1) {
offset[dim] = 0;
++dim;
}
#if defined(PETSC_USE_COMPLEX)
offset[dim] = 0;
++dim;
#endif
status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, count, NULL);CHKERRQ(status);
/* Create property list for collective dataset read */
plist_id = H5Pcreate(H5P_DATASET_XFER);
if (plist_id == -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Could not H5Pcreate()");
#if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
status = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);CHKERRQ(status);
#endif
/* To write dataset independently use H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT) */
ierr = VecGetArray(xin, &x);CHKERRQ(ierr);
status = H5Dread(dset_id, H5T_NATIVE_DOUBLE, memspace, filespace, plist_id, x);CHKERRQ(status);
ierr = VecRestoreArray(xin, &x);CHKERRQ(ierr);
/* Close/release resources */
if (group != file_id) {
status = H5Gclose(group);CHKERRQ(status);
}
status = H5Pclose(plist_id);CHKERRQ(status);
status = H5Sclose(filespace);CHKERRQ(status);
status = H5Sclose(memspace);CHKERRQ(status);
status = H5Dclose(dset_id);CHKERRQ(status);
ierr = VecAssemblyBegin(xin);CHKERRQ(ierr);
ierr = VecAssemblyEnd(xin);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc, char **argv)
{
SNES snes; /* nonlinear solver */
DM dm; /* problem definition */
Vec u,r; /* solution, residual vectors */
Mat A,J; /* Jacobian matrix */
MatNullSpace nullSpace; /* May be necessary for pressure */
AppCtx user; /* user-defined work context */
JacActionCtx userJ; /* context for Jacobian MF action */
PetscInt its; /* iterations for convergence */
PetscReal error = 0.0; /* L_2 error in the solution */
PetscInt numComponents = 0, f;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, NULL, help);CHKERRQ(ierr);
ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr);
ierr = SNESCreate(PETSC_COMM_WORLD, &snes);CHKERRQ(ierr);
ierr = CreateMesh(PETSC_COMM_WORLD, &user, &dm);CHKERRQ(ierr);
ierr = SNESSetDM(snes, dm);CHKERRQ(ierr);
ierr = SetupElement(dm, &user);CHKERRQ(ierr);
for (f = 0; f < NUM_FIELDS; ++f) {
PetscInt numComp;
ierr = PetscFEGetNumComponents(user.fe[f], &numComp);CHKERRQ(ierr);
numComponents += numComp;
}
ierr = PetscMalloc(NUM_FIELDS * sizeof(void (*)(const PetscReal[], PetscScalar *)), &user.exactFuncs);CHKERRQ(ierr);
user.fem.bcFuncs = (void (**)(const PetscReal[], PetscScalar *)) user.exactFuncs;
ierr = SetupExactSolution(dm, &user);CHKERRQ(ierr);
ierr = SetupSection(dm, &user);CHKERRQ(ierr);
ierr = DMPlexCreateClosureIndex(dm, NULL);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(dm, &u);CHKERRQ(ierr);
ierr = VecDuplicate(u, &r);CHKERRQ(ierr);
ierr = DMSetMatType(dm,MATAIJ);CHKERRQ(ierr);
ierr = DMCreateMatrix(dm, &J);CHKERRQ(ierr);
if (user.jacobianMF) {
PetscInt M, m, N, n;
ierr = MatGetSize(J, &M, &N);CHKERRQ(ierr);
ierr = MatGetLocalSize(J, &m, &n);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD, &A);CHKERRQ(ierr);
ierr = MatSetSizes(A, m, n, M, N);CHKERRQ(ierr);
ierr = MatSetType(A, MATSHELL);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = MatShellSetOperation(A, MATOP_MULT, (void (*)(void))FormJacobianAction);CHKERRQ(ierr);
userJ.dm = dm;
userJ.J = J;
userJ.user = &user;
ierr = DMCreateLocalVector(dm, &userJ.u);CHKERRQ(ierr);
ierr = DMPlexProjectFunctionLocal(dm, user.fe, user.exactFuncs, INSERT_BC_VALUES, userJ.u);CHKERRQ(ierr);
ierr = MatShellSetContext(A, &userJ);CHKERRQ(ierr);
} else {
A = J;
}
ierr = CreatePressureNullSpace(dm, &user, &nullSpace);CHKERRQ(ierr);
ierr = MatSetNullSpace(J, nullSpace);CHKERRQ(ierr);
if (A != J) {
ierr = MatSetNullSpace(A, nullSpace);CHKERRQ(ierr);
}
ierr = DMSNESSetFunctionLocal(dm, (PetscErrorCode (*)(DM,Vec,Vec,void*))DMPlexComputeResidualFEM,&user);CHKERRQ(ierr);
ierr = DMSNESSetJacobianLocal(dm, (PetscErrorCode (*)(DM,Vec,Mat,Mat,MatStructure*,void*))DMPlexComputeJacobianFEM,&user);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes, A, J, NULL, NULL);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
ierr = DMPlexProjectFunction(dm, user.fe, user.exactFuncs, INSERT_ALL_VALUES, u);CHKERRQ(ierr);
if (user.showInitial) {ierr = DMVecViewLocal(dm, u, PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);}
if (user.runType == RUN_FULL) {
ierr = DMPlexProjectFunction(dm, user.fe, user.initialGuess, INSERT_VALUES, u);CHKERRQ(ierr);
if (user.showInitial) {ierr = DMVecViewLocal(dm, u, PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);}
if (user.debug) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");CHKERRQ(ierr);
ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = SNESSolve(snes, NULL, u);CHKERRQ(ierr);
ierr = SNESGetIterationNumber(snes, &its);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Number of SNES iterations = %D\n", its);CHKERRQ(ierr);
ierr = DMPlexComputeL2Diff(dm, user.fe, user.exactFuncs, u, &error);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %.3g\n", error);CHKERRQ(ierr);
if (user.showSolution) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "Solution\n");CHKERRQ(ierr);
ierr = VecChop(u, 3.0e-9);CHKERRQ(ierr);
ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
} else {
PetscReal res = 0.0;
/* Check discretization error */
ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");CHKERRQ(ierr);
ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = DMPlexComputeL2Diff(dm, user.fe, user.exactFuncs, u, &error);CHKERRQ(ierr);
if (error >= 1.0e-11) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %g\n", error);CHKERRQ(ierr);
} else {
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: < 1.0e-11\n", error);CHKERRQ(ierr);
}
/* Check residual */
ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial Residual\n");CHKERRQ(ierr);
ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr);
ierr = VecView(r, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Residual: %g\n", res);CHKERRQ(ierr);
/* Check Jacobian */
{
Vec b;
MatStructure flag;
PetscBool isNull;
ierr = SNESComputeJacobian(snes, u, &A, &A, &flag);CHKERRQ(ierr);
ierr = MatNullSpaceTest(nullSpace, J, &isNull);CHKERRQ(ierr);
if (!isNull) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_PLIB, "The null space calculated for the system operator is invalid.");
ierr = VecDuplicate(u, &b);CHKERRQ(ierr);
ierr = VecSet(r, 0.0);CHKERRQ(ierr);
ierr = SNESComputeFunction(snes, r, b);CHKERRQ(ierr);
ierr = MatMult(A, u, r);CHKERRQ(ierr);
ierr = VecAXPY(r, 1.0, b);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Au - b = Au + F(0)\n");CHKERRQ(ierr);
ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr);
ierr = VecView(r, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Linear L_2 Residual: %g\n", res);CHKERRQ(ierr);
}
}
if (user.runType == RUN_FULL) {
PetscViewer viewer;
Vec uLocal;
const char *name;
ierr = PetscViewerCreate(PETSC_COMM_WORLD, &viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSCVIEWERVTK);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(viewer, PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, "ex62_sol.vtk");CHKERRQ(ierr);
ierr = DMGetLocalVector(dm, &uLocal);CHKERRQ(ierr);
ierr = PetscObjectGetName((PetscObject) u, &name);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) uLocal, name);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm, u, INSERT_VALUES, uLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm, u, INSERT_VALUES, uLocal);CHKERRQ(ierr);
ierr = VecView(uLocal, viewer);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &uLocal);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
ierr = PetscFree(user.exactFuncs);CHKERRQ(ierr);
ierr = DestroyElement(&user);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&nullSpace);CHKERRQ(ierr);
if (user.jacobianMF) {
ierr = VecDestroy(&userJ.u);CHKERRQ(ierr);
}
if (A != J) {
ierr = MatDestroy(&A);CHKERRQ(ierr);
}
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = VecDestroy(&r);CHKERRQ(ierr);
ierr = SNESDestroy(&snes);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscErrorCode DMView_AKKT(DM dm, PetscViewer v) {
DM_AKKT* kkt = (DM_AKKT*)(dm->data);
PetscErrorCode ierr;
PetscBool isascii;
PetscInt i, tab, vtab;
const char* name, *prefix;
PetscFunctionBegin;
ierr = PetscObjectTypeCompare((PetscObject)v, PETSCVIEWERASCII, &isascii); CHKERRQ(ierr);
if(!isascii) SETERRQ(((PetscObject)dm)->comm, PETSC_ERR_SUP, "No support for non-ASCII viewers");
ierr = PetscObjectGetTabLevel((PetscObject)dm, &tab); CHKERRQ(ierr);
ierr = PetscObjectGetName((PetscObject)dm, &name); CHKERRQ(ierr);
ierr = PetscObjectGetOptionsPrefix((PetscObject)dm, &prefix); CHKERRQ(ierr);
ierr = PetscViewerASCIIUseTabs(v,PETSC_TRUE); CHKERRQ(ierr);
ierr = PetscViewerASCIIGetTab(v,&vtab); CHKERRQ(ierr);
ierr = PetscViewerASCIISetTab(v,tab); CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(v, "DM Algebraic KKT, name: %s, prefix: %s\n", ((PetscObject)dm)->name, ((PetscObject)dm)->prefix); CHKERRQ(ierr);
if(kkt->dm) {
ierr = PetscViewerASCIIPrintf(v, "DM:\n"); CHKERRQ(ierr);
ierr = PetscViewerASCIIPushTab(v); CHKERRQ(ierr);
ierr = DMView(kkt->dm,v); CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(v); CHKERRQ(ierr);
}
if(kkt->Aff) {
ierr = PetscViewerASCIIPrintf(v, "Aff:\n"); CHKERRQ(ierr);
ierr = PetscViewerASCIIPushTab(v); CHKERRQ(ierr);
ierr = MatView(kkt->Aff,v); CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(v); CHKERRQ(ierr);
}
if(kkt->dname) {
ierr = PetscViewerASCIIPrintf(v, "Decomposition, name %s:\n"); CHKERRQ(ierr);
}
for(i = 0; i < 2; ++i) {
const char* label;
if(i == 0) {
label = "Primal";
}
else {
label = "Dual";
}
if(kkt->names[i]) {
ierr = PetscViewerASCIIPrintf(v, "%s, name %s:\n", label, kkt->names[i]); CHKERRQ(ierr);
}
if(kkt->isf[i]){
ierr = PetscViewerASCIIPrintf(v, "%s, IS:\n",label); CHKERRQ(ierr);
ierr = PetscViewerASCIIPushTab(v); CHKERRQ(ierr);
ierr = ISView(kkt->isf[i],v); CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(v); CHKERRQ(ierr);
}
if(kkt->dmf[i]){
ierr = PetscViewerASCIIPrintf(v, "%s, DM:\n", label); CHKERRQ(ierr);
ierr = PetscViewerASCIIPushTab(v); CHKERRQ(ierr);
ierr = DMView(kkt->dmf[i],v); CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(v); CHKERRQ(ierr);
}
}
if(kkt->Pfc) {
ierr = PetscViewerASCIIPrintf(v, "Prolongation:\n"); CHKERRQ(ierr);
ierr = PetscViewerASCIIPushTab(v); CHKERRQ(ierr);
ierr = MatView(kkt->Pfc,v); CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(v); CHKERRQ(ierr);
}
ierr = PetscViewerASCIISetTab(v,vtab); CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
DM da2D;
PetscInt i,j,ixs, ixm, iys, iym;;
PetscViewer H5viewer;
PetscScalar xm = -1.0, xp=1.0;
PetscScalar ym = -1.0, yp=1.0;
PetscScalar value = 1.0,dx,dy;
PetscInt Nx = 40, Ny=40;
Vec gauss,input;
PetscScalar **gauss_ptr;
PetscReal norm;
const char *vecname;
dx=(xp-xm)/(Nx-1);
dy=(yp-ym)/(Ny-1);
/* Initialize the Petsc context */
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,Nx,Ny,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,&da2D);CHKERRQ(ierr);
ierr = DMSetFromOptions(da2D);CHKERRQ(ierr);
ierr = DMSetUp(da2D);CHKERRQ(ierr);
/* Set the coordinates */
ierr = DMDASetUniformCoordinates(da2D, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0);CHKERRQ(ierr);
/* Declare gauss as a DMDA component */
ierr = DMCreateGlobalVector(da2D,&gauss);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) gauss, "pressure");CHKERRQ(ierr);
/* Initialize vector gauss with a constant value (=1) */
ierr = VecSet(gauss,value);CHKERRQ(ierr);
/* Get the coordinates of the corners for each process */
ierr = DMDAGetCorners(da2D, &ixs, &iys, 0, &ixm, &iym, 0);CHKERRQ(ierr);
/* Build the gaussian profile (exp(-x^2-y^2)) */
ierr = DMDAVecGetArray(da2D,gauss,&gauss_ptr);CHKERRQ(ierr);
for (j=iys; j<iys+iym; j++) {
for (i=ixs; i<ixs+ixm; i++) {
gauss_ptr[j][i]=PetscExpScalar(-(xm+i*dx)*(xm+i*dx)-(ym+j*dy)*(ym+j*dy));
}
}
ierr = DMDAVecRestoreArray(da2D,gauss,&gauss_ptr);CHKERRQ(ierr);
/* Create the HDF5 viewer */
ierr = PetscViewerHDF5Open(PETSC_COMM_WORLD,"gauss.h5",FILE_MODE_WRITE,&H5viewer);CHKERRQ(ierr);
ierr = PetscViewerSetFromOptions(H5viewer);CHKERRQ(ierr);
/* Write the H5 file */
ierr = VecView(gauss,H5viewer);CHKERRQ(ierr);
/* Close the viewer */
ierr = PetscViewerDestroy(&H5viewer);CHKERRQ(ierr);
ierr = VecDuplicate(gauss,&input);CHKERRQ(ierr);
ierr = PetscObjectGetName((PetscObject)gauss,&vecname);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)input,vecname);CHKERRQ(ierr);
/* Create the HDF5 viewer for reading */
ierr = PetscViewerHDF5Open(PETSC_COMM_WORLD,"gauss.h5",FILE_MODE_READ,&H5viewer);CHKERRQ(ierr);
ierr = PetscViewerSetFromOptions(H5viewer);CHKERRQ(ierr);
ierr = VecLoad(input,H5viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&H5viewer);CHKERRQ(ierr);
ierr = VecAXPY(input,-1.0,gauss);CHKERRQ(ierr);
ierr = VecNorm(input,NORM_2,&norm);CHKERRQ(ierr);
if (norm > 1.e-6) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_PLIB,"Vec read in does not match vector written out");
ierr = VecDestroy(&input);CHKERRQ(ierr);
ierr = VecDestroy(&gauss);CHKERRQ(ierr);
ierr = DMDestroy(&da2D);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
/*@C
DMPlexDistribute - Distributes the mesh and any associated sections.
Not Collective
Input Parameter:
+ dm - The original DMPlex object
. partitioner - The partitioning package, or NULL for the default
- overlap - The overlap of partitions, 0 is the default
Output Parameter:
+ sf - The PetscSF used for point distribution
- parallelMesh - The distributed DMPlex object, or NULL
Note: If the mesh was not distributed, the return value is NULL.
The user can control the definition of adjacency for the mesh using DMPlexGetAdjacencyUseCone() and
DMPlexSetAdjacencyUseClosure(). They should choose the combination appropriate for the function
representation on the mesh.
Level: intermediate
.keywords: mesh, elements
.seealso: DMPlexCreate(), DMPlexDistributeByFace(), DMPlexSetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure()
@*/
PetscErrorCode DMPlexDistribute(DM dm, const char partitioner[], PetscInt overlap, PetscSF *sf, DM *dmParallel)
{
DM_Plex *mesh = (DM_Plex*) dm->data, *pmesh;
MPI_Comm comm;
const PetscInt height = 0;
PetscInt dim, numRemoteRanks;
IS origCellPart, origPart, cellPart, part;
PetscSection origCellPartSection, origPartSection, cellPartSection, partSection;
PetscSFNode *remoteRanks;
PetscSF partSF, pointSF, coneSF;
ISLocalToGlobalMapping renumbering;
PetscSection originalConeSection, newConeSection;
PetscInt *remoteOffsets;
PetscInt *cones, *newCones, newConesSize;
PetscBool flg;
PetscMPIInt rank, numProcs, p;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
if (sf) PetscValidPointer(sf,4);
PetscValidPointer(dmParallel,5);
ierr = PetscLogEventBegin(DMPLEX_Distribute,dm,0,0,0);CHKERRQ(ierr);
ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &numProcs);CHKERRQ(ierr);
*dmParallel = NULL;
if (numProcs == 1) PetscFunctionReturn(0);
ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
/* Create cell partition - We need to rewrite to use IS, use the MatPartition stuff */
ierr = PetscLogEventBegin(DMPLEX_Partition,dm,0,0,0);CHKERRQ(ierr);
if (overlap > 1) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Overlap > 1 not yet implemented");
ierr = DMPlexCreatePartition(dm, partitioner, height, overlap > 0 ? PETSC_TRUE : PETSC_FALSE, &cellPartSection, &cellPart, &origCellPartSection, &origCellPart);CHKERRQ(ierr);
/* Create SF assuming a serial partition for all processes: Could check for IS length here */
if (!rank) numRemoteRanks = numProcs;
else numRemoteRanks = 0;
ierr = PetscMalloc1(numRemoteRanks, &remoteRanks);CHKERRQ(ierr);
for (p = 0; p < numRemoteRanks; ++p) {
remoteRanks[p].rank = p;
remoteRanks[p].index = 0;
}
ierr = PetscSFCreate(comm, &partSF);CHKERRQ(ierr);
ierr = PetscSFSetGraph(partSF, 1, numRemoteRanks, NULL, PETSC_OWN_POINTER, remoteRanks, PETSC_OWN_POINTER);CHKERRQ(ierr);
ierr = PetscOptionsHasName(((PetscObject) dm)->prefix, "-partition_view", &flg);CHKERRQ(ierr);
if (flg) {
ierr = PetscPrintf(comm, "Cell Partition:\n");CHKERRQ(ierr);
ierr = PetscSectionView(cellPartSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = ISView(cellPart, NULL);CHKERRQ(ierr);
if (origCellPart) {
ierr = PetscPrintf(comm, "Original Cell Partition:\n");CHKERRQ(ierr);
ierr = PetscSectionView(origCellPartSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = ISView(origCellPart, NULL);CHKERRQ(ierr);
}
ierr = PetscSFView(partSF, NULL);CHKERRQ(ierr);
}
/* Close the partition over the mesh */
ierr = DMPlexCreatePartitionClosure(dm, cellPartSection, cellPart, &partSection, &part);CHKERRQ(ierr);
ierr = ISDestroy(&cellPart);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&cellPartSection);CHKERRQ(ierr);
/* Create new mesh */
ierr = DMPlexCreate(comm, dmParallel);CHKERRQ(ierr);
ierr = DMPlexSetDimension(*dmParallel, dim);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) *dmParallel, "Parallel Mesh");CHKERRQ(ierr);
pmesh = (DM_Plex*) (*dmParallel)->data;
/* Distribute sieve points and the global point numbering (replaces creating remote bases) */
ierr = PetscSFConvertPartition(partSF, partSection, part, &renumbering, &pointSF);CHKERRQ(ierr);
if (flg) {
ierr = PetscPrintf(comm, "Point Partition:\n");CHKERRQ(ierr);
ierr = PetscSectionView(partSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = ISView(part, NULL);CHKERRQ(ierr);
ierr = PetscSFView(pointSF, NULL);CHKERRQ(ierr);
ierr = PetscPrintf(comm, "Point Renumbering after partition:\n");CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingView(renumbering, NULL);CHKERRQ(ierr);
}
ierr = PetscLogEventEnd(DMPLEX_Partition,dm,0,0,0);CHKERRQ(ierr);
ierr = PetscLogEventBegin(DMPLEX_DistributeCones,dm,0,0,0);CHKERRQ(ierr);
/* Distribute cone section */
ierr = DMPlexGetConeSection(dm, &originalConeSection);CHKERRQ(ierr);
ierr = DMPlexGetConeSection(*dmParallel, &newConeSection);CHKERRQ(ierr);
ierr = PetscSFDistributeSection(pointSF, originalConeSection, &remoteOffsets, newConeSection);CHKERRQ(ierr);
ierr = DMSetUp(*dmParallel);CHKERRQ(ierr);
{
PetscInt pStart, pEnd, p;
ierr = PetscSectionGetChart(newConeSection, &pStart, &pEnd);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
PetscInt coneSize;
ierr = PetscSectionGetDof(newConeSection, p, &coneSize);CHKERRQ(ierr);
pmesh->maxConeSize = PetscMax(pmesh->maxConeSize, coneSize);
}
}
/* Communicate and renumber cones */
ierr = PetscSFCreateSectionSF(pointSF, originalConeSection, remoteOffsets, newConeSection, &coneSF);CHKERRQ(ierr);
ierr = DMPlexGetCones(dm, &cones);CHKERRQ(ierr);
ierr = DMPlexGetCones(*dmParallel, &newCones);CHKERRQ(ierr);
ierr = PetscSFBcastBegin(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr);
ierr = PetscSFBcastEnd(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(newConeSection, &newConesSize);CHKERRQ(ierr);
ierr = ISGlobalToLocalMappingApplyBlock(renumbering, IS_GTOLM_MASK, newConesSize, newCones, NULL, newCones);CHKERRQ(ierr);
ierr = PetscOptionsHasName(((PetscObject) dm)->prefix, "-cones_view", &flg);CHKERRQ(ierr);
if (flg) {
ierr = PetscPrintf(comm, "Serial Cone Section:\n");CHKERRQ(ierr);
ierr = PetscSectionView(originalConeSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(comm, "Parallel Cone Section:\n");CHKERRQ(ierr);
ierr = PetscSectionView(newConeSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscSFView(coneSF, NULL);CHKERRQ(ierr);
}
ierr = DMPlexGetConeOrientations(dm, &cones);CHKERRQ(ierr);
ierr = DMPlexGetConeOrientations(*dmParallel, &newCones);CHKERRQ(ierr);
ierr = PetscSFBcastBegin(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr);
ierr = PetscSFBcastEnd(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr);
ierr = PetscSFDestroy(&coneSF);CHKERRQ(ierr);
ierr = PetscLogEventEnd(DMPLEX_DistributeCones,dm,0,0,0);CHKERRQ(ierr);
/* Create supports and stratify sieve */
{
PetscInt pStart, pEnd;
ierr = PetscSectionGetChart(pmesh->coneSection, &pStart, &pEnd);CHKERRQ(ierr);
ierr = PetscSectionSetChart(pmesh->supportSection, pStart, pEnd);CHKERRQ(ierr);
}
ierr = DMPlexSymmetrize(*dmParallel);CHKERRQ(ierr);
ierr = DMPlexStratify(*dmParallel);CHKERRQ(ierr);
/* Distribute Coordinates */
{
PetscSection originalCoordSection, newCoordSection;
Vec originalCoordinates, newCoordinates;
PetscInt bs;
const char *name;
ierr = DMGetCoordinateSection(dm, &originalCoordSection);CHKERRQ(ierr);
ierr = DMGetCoordinateSection(*dmParallel, &newCoordSection);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &originalCoordinates);CHKERRQ(ierr);
ierr = VecCreate(comm, &newCoordinates);CHKERRQ(ierr);
ierr = PetscObjectGetName((PetscObject) originalCoordinates, &name);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) newCoordinates, name);CHKERRQ(ierr);
ierr = DMPlexDistributeField(dm, pointSF, originalCoordSection, originalCoordinates, newCoordSection, newCoordinates);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(*dmParallel, newCoordinates);CHKERRQ(ierr);
ierr = VecGetBlockSize(originalCoordinates, &bs);CHKERRQ(ierr);
ierr = VecSetBlockSize(newCoordinates, bs);CHKERRQ(ierr);
ierr = VecDestroy(&newCoordinates);CHKERRQ(ierr);
}
/* Distribute labels */
ierr = PetscLogEventBegin(DMPLEX_DistributeLabels,dm,0,0,0);CHKERRQ(ierr);
{
DMLabel next = mesh->labels, newNext = pmesh->labels;
PetscInt numLabels = 0, l;
/* Bcast number of labels */
while (next) {++numLabels; next = next->next;}
ierr = MPI_Bcast(&numLabels, 1, MPIU_INT, 0, comm);CHKERRQ(ierr);
next = mesh->labels;
for (l = 0; l < numLabels; ++l) {
DMLabel labelNew;
PetscBool isdepth;
/* Skip "depth" because it is recreated */
if (!rank) {ierr = PetscStrcmp(next->name, "depth", &isdepth);CHKERRQ(ierr);}
ierr = MPI_Bcast(&isdepth, 1, MPIU_BOOL, 0, comm);CHKERRQ(ierr);
if (isdepth) {if (!rank) next = next->next; continue;}
ierr = DMLabelDistribute(next, partSection, part, renumbering, &labelNew);CHKERRQ(ierr);
/* Insert into list */
if (newNext) newNext->next = labelNew;
else pmesh->labels = labelNew;
newNext = labelNew;
if (!rank) next = next->next;
}
}
ierr = PetscLogEventEnd(DMPLEX_DistributeLabels,dm,0,0,0);CHKERRQ(ierr);
/* Setup hybrid structure */
{
const PetscInt *gpoints;
PetscInt depth, n, d;
for (d = 0; d <= dim; ++d) {pmesh->hybridPointMax[d] = mesh->hybridPointMax[d];}
ierr = MPI_Bcast(pmesh->hybridPointMax, dim+1, MPIU_INT, 0, comm);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingGetSize(renumbering, &n);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingGetIndices(renumbering, &gpoints);CHKERRQ(ierr);
ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr);
for (d = 0; d <= dim; ++d) {
PetscInt pmax = pmesh->hybridPointMax[d], newmax = 0, pEnd, stratum[2], p;
if (pmax < 0) continue;
ierr = DMPlexGetDepthStratum(dm, d > depth ? depth : d, &stratum[0], &stratum[1]);CHKERRQ(ierr);
ierr = DMPlexGetDepthStratum(*dmParallel, d, NULL, &pEnd);CHKERRQ(ierr);
ierr = MPI_Bcast(stratum, 2, MPIU_INT, 0, comm);CHKERRQ(ierr);
for (p = 0; p < n; ++p) {
const PetscInt point = gpoints[p];
if ((point >= stratum[0]) && (point < stratum[1]) && (point >= pmax)) ++newmax;
}
if (newmax > 0) pmesh->hybridPointMax[d] = pEnd - newmax;
else pmesh->hybridPointMax[d] = -1;
}
ierr = ISLocalToGlobalMappingRestoreIndices(renumbering, &gpoints);CHKERRQ(ierr);
}
/* Cleanup Partition */
ierr = ISLocalToGlobalMappingDestroy(&renumbering);CHKERRQ(ierr);
ierr = PetscSFDestroy(&partSF);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&partSection);CHKERRQ(ierr);
ierr = ISDestroy(&part);CHKERRQ(ierr);
/* Create point SF for parallel mesh */
ierr = PetscLogEventBegin(DMPLEX_DistributeSF,dm,0,0,0);CHKERRQ(ierr);
{
const PetscInt *leaves;
PetscSFNode *remotePoints, *rowners, *lowners;
PetscInt numRoots, numLeaves, numGhostPoints = 0, p, gp, *ghostPoints;
PetscInt pStart, pEnd;
ierr = DMPlexGetChart(*dmParallel, &pStart, &pEnd);CHKERRQ(ierr);
ierr = PetscSFGetGraph(pointSF, &numRoots, &numLeaves, &leaves, NULL);CHKERRQ(ierr);
ierr = PetscMalloc2(numRoots,&rowners,numLeaves,&lowners);CHKERRQ(ierr);
for (p=0; p<numRoots; p++) {
rowners[p].rank = -1;
rowners[p].index = -1;
}
if (origCellPart) {
/* Make sure points in the original partition are not assigned to other procs */
const PetscInt *origPoints;
ierr = DMPlexCreatePartitionClosure(dm, origCellPartSection, origCellPart, &origPartSection, &origPart);CHKERRQ(ierr);
ierr = ISGetIndices(origPart, &origPoints);CHKERRQ(ierr);
for (p = 0; p < numProcs; ++p) {
PetscInt dof, off, d;
ierr = PetscSectionGetDof(origPartSection, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(origPartSection, p, &off);CHKERRQ(ierr);
for (d = off; d < off+dof; ++d) {
rowners[origPoints[d]].rank = p;
}
}
ierr = ISRestoreIndices(origPart, &origPoints);CHKERRQ(ierr);
ierr = ISDestroy(&origPart);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&origPartSection);CHKERRQ(ierr);
}
ierr = ISDestroy(&origCellPart);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&origCellPartSection);CHKERRQ(ierr);
ierr = PetscSFBcastBegin(pointSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr);
ierr = PetscSFBcastEnd(pointSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr);
for (p = 0; p < numLeaves; ++p) {
if (lowners[p].rank < 0 || lowners[p].rank == rank) { /* Either put in a bid or we know we own it */
lowners[p].rank = rank;
lowners[p].index = leaves ? leaves[p] : p;
} else if (lowners[p].rank >= 0) { /* Point already claimed so flag so that MAXLOC does not listen to us */
lowners[p].rank = -2;
lowners[p].index = -2;
}
}
for (p=0; p<numRoots; p++) { /* Root must not participate in the rediction, flag so that MAXLOC does not use */
rowners[p].rank = -3;
rowners[p].index = -3;
}
ierr = PetscSFReduceBegin(pointSF, MPIU_2INT, lowners, rowners, MPI_MAXLOC);CHKERRQ(ierr);
ierr = PetscSFReduceEnd(pointSF, MPIU_2INT, lowners, rowners, MPI_MAXLOC);CHKERRQ(ierr);
ierr = PetscSFBcastBegin(pointSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr);
ierr = PetscSFBcastEnd(pointSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr);
for (p = 0; p < numLeaves; ++p) {
if (lowners[p].rank < 0 || lowners[p].index < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Cell partition corrupt: point not claimed");
if (lowners[p].rank != rank) ++numGhostPoints;
}
ierr = PetscMalloc1(numGhostPoints, &ghostPoints);CHKERRQ(ierr);
ierr = PetscMalloc1(numGhostPoints, &remotePoints);CHKERRQ(ierr);
for (p = 0, gp = 0; p < numLeaves; ++p) {
if (lowners[p].rank != rank) {
ghostPoints[gp] = leaves ? leaves[p] : p;
remotePoints[gp].rank = lowners[p].rank;
remotePoints[gp].index = lowners[p].index;
++gp;
}
}
ierr = PetscFree2(rowners,lowners);CHKERRQ(ierr);
ierr = PetscSFSetGraph((*dmParallel)->sf, pEnd - pStart, numGhostPoints, ghostPoints, PETSC_OWN_POINTER, remotePoints, PETSC_OWN_POINTER);CHKERRQ(ierr);
ierr = PetscSFSetFromOptions((*dmParallel)->sf);CHKERRQ(ierr);
}
pmesh->useCone = mesh->useCone;
pmesh->useClosure = mesh->useClosure;
ierr = PetscLogEventEnd(DMPLEX_DistributeSF,dm,0,0,0);CHKERRQ(ierr);
/* Copy BC */
ierr = DMPlexCopyBoundary(dm, *dmParallel);CHKERRQ(ierr);
/* Cleanup */
if (sf) {*sf = pointSF;}
else {ierr = PetscSFDestroy(&pointSF);CHKERRQ(ierr);}
ierr = DMSetFromOptions(*dmParallel);CHKERRQ(ierr);
ierr = PetscLogEventEnd(DMPLEX_Distribute,dm,0,0,0);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
