/*
PetscDLLibraryRegister - This function is called when the dynamic library it is in is opened.
This one registers all the mesh generators and partitioners that are in
the basic DM library.
*/
PETSC_EXTERN PetscErrorCode PetscDLLibraryRegister_petscdm(void)
{
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = AOInitializePackage();CHKERRQ(ierr);
ierr = DMInitializePackage();CHKERRQ(ierr);
ierr = PetscFEInitializePackage();CHKERRQ(ierr);
ierr = PetscFVInitializePackage();CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
PetscDLLibraryRegister - This function is called when the dynamic library it is in is opened.
This one registers all the methods that are in the basic PETSc Vec library.
*/
PETSC_EXTERN PetscErrorCode PetscDLLibraryRegister_petscvec(void)
{
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscSFInitializePackage();CHKERRQ(ierr);
ierr = ISInitializePackage();CHKERRQ(ierr);
ierr = AOInitializePackage();CHKERRQ(ierr);
ierr = VecInitializePackage();CHKERRQ(ierr);
ierr = PFInitializePackage();CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
AOCreate - Creates an application ordering.
Collective on MPI_Comm
Input Parameters:
. comm - MPI communicator that is to share AO
Output Parameter:
. ao - the new application ordering
Options Database Key:
+ -ao_type <aotype> - create ao with particular format
- -ao_view - call AOView() at the conclusion of AOCreate()
Level: beginner
.keywords: AO, create
.seealso: AOSetIS(), AODestroy(), AOPetscToApplication(), AOApplicationToPetsc()
@*/
PetscErrorCode AOCreate(MPI_Comm comm,AO *ao)
{
PetscErrorCode ierr;
AO aonew;
PetscFunctionBegin;
PetscValidPointer(ao,2);
*ao = NULL;
ierr = AOInitializePackage();CHKERRQ(ierr);
ierr = PetscHeaderCreate(aonew,_p_AO,struct _AOOps,AO_CLASSID,"AO","Application Ordering","AO",comm,AODestroy,AOView);CHKERRQ(ierr);
ierr = PetscMemzero(aonew->ops, sizeof(struct _AOOps));CHKERRQ(ierr);
*ao = aonew;
PetscFunctionReturn(0);
}
EXTERN_C_BEGIN
#undef __FUNCT__
#define __FUNCT__ "PetscDLLibraryRegister_petscdm"
/*
PetscDLLibraryRegister - This function is called when the dynamic library it is in is opened.
This one registers all the mesh generators and partitioners that are in
the basic DM library.
Input Parameter:
path - library path
*/
PetscErrorCode PetscDLLibraryRegister_petscdm(const char path[])
{
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = AOInitializePackage(path);CHKERRQ(ierr);
ierr = DMInitializePackage(path);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
AOCreate - Creates an application ordering.
Collective on MPI_Comm
Input Parameters:
. comm - MPI communicator that is to share AO
Output Parameter:
. ao - the new application ordering
Options Database Key:
+ -ao_type <aotype> - create ao with particular format
- -ao_view - call AOView() at the conclusion of AOCreate()
Level: beginner
.keywords: AO, create
.seealso: AOSetIS(), AODestroy(), AOPetscToApplication(), AOApplicationToPetsc()
@*/
PetscErrorCode AOCreate(MPI_Comm comm,AO *ao)
{
PetscErrorCode ierr;
AO aonew;
PetscBool opt;
PetscFunctionBegin;
PetscValidPointer(ao,2);
*ao = PETSC_NULL;
#ifndef PETSC_USE_DYNAMIC_LIBRARIES
ierr = AOInitializePackage(PETSC_NULL);CHKERRQ(ierr);
#endif
ierr = PetscHeaderCreate(aonew,_p_AO,struct _AOOps,AO_CLASSID,-1,"AO","Application Ordering","AO",comm,AODestroy,AOView);CHKERRQ(ierr);
ierr = PetscMemzero(aonew->ops, sizeof(struct _AOOps));CHKERRQ(ierr);
*ao = aonew;
opt = PETSC_FALSE;
ierr = PetscOptionsGetBool(PETSC_NULL, "-ao_view", &opt,PETSC_NULL);CHKERRQ(ierr);
if (opt) {
ierr = AOView(aonew, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
/*
PetscInitialize_DynamicLibraries - Adds the default dynamic link libraries to the
search path.
*/
PETSC_INTERN PetscErrorCode PetscInitialize_DynamicLibraries(void)
{
char *libname[32];
PetscErrorCode ierr;
PetscInt nmax,i;
#if defined(PETSC_USE_DYNAMIC_LIBRARIES) && defined(PETSC_USE_SHARED_LIBRARIES)
PetscBool preload;
#endif
PetscFunctionBegin;
nmax = 32;
ierr = PetscOptionsGetStringArray(NULL,NULL,"-dll_prepend",libname,&nmax,NULL);CHKERRQ(ierr);
for (i=0; i<nmax; i++) {
ierr = PetscDLLibraryPrepend(PETSC_COMM_WORLD,&PetscDLLibrariesLoaded,libname[i]);CHKERRQ(ierr);
ierr = PetscFree(libname[i]);CHKERRQ(ierr);
}
#if !defined(PETSC_USE_DYNAMIC_LIBRARIES) || !defined(PETSC_USE_SHARED_LIBRARIES)
/*
This just initializes the most basic PETSc stuff.
The classes, from PetscDraw to PetscTS, are initialized the first
time an XXCreate() is called.
*/
ierr = PetscSysInitializePackage();CHKERRQ(ierr);
#else
preload = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,NULL,"-dynamic_library_preload",&preload,NULL);CHKERRQ(ierr);
if (preload) {
PetscBool found;
#if defined(PETSC_USE_SINGLE_LIBRARY)
ierr = PetscLoadDynamicLibrary("",&found);CHKERRQ(ierr);
if (!found) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_OPEN,"Unable to locate PETSc dynamic library \n You cannot move the dynamic libraries!");
#else
ierr = PetscLoadDynamicLibrary("sys",&found);CHKERRQ(ierr);
if (!found) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_OPEN,"Unable to locate PETSc dynamic library \n You cannot move the dynamic libraries!");
ierr = PetscLoadDynamicLibrary("vec",&found);CHKERRQ(ierr);
if (!found) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_OPEN,"Unable to locate PETSc Vec dynamic library \n You cannot move the dynamic libraries!");
ierr = PetscLoadDynamicLibrary("mat",&found);CHKERRQ(ierr);
if (!found) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_OPEN,"Unable to locate PETSc Mat dynamic library \n You cannot move the dynamic libraries!");
ierr = PetscLoadDynamicLibrary("dm",&found);CHKERRQ(ierr);
if (!found) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_OPEN,"Unable to locate PETSc DM dynamic library \n You cannot move the dynamic libraries!");
ierr = PetscLoadDynamicLibrary("ksp",&found);CHKERRQ(ierr);
if (!found) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_OPEN,"Unable to locate PETSc KSP dynamic library \n You cannot move the dynamic libraries!");
ierr = PetscLoadDynamicLibrary("snes",&found);CHKERRQ(ierr);
if (!found) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_OPEN,"Unable to locate PETSc SNES dynamic library \n You cannot move the dynamic libraries!");
ierr = PetscLoadDynamicLibrary("ts",&found);CHKERRQ(ierr);
if (!found) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_OPEN,"Unable to locate PETSc TS dynamic library \n You cannot move the dynamic libraries!");
#endif
}
#endif
nmax = 32;
ierr = PetscOptionsGetStringArray(NULL,NULL,"-dll_append",libname,&nmax,NULL);CHKERRQ(ierr);
for (i=0; i<nmax; i++) {
ierr = PetscDLLibraryAppend(PETSC_COMM_WORLD,&PetscDLLibrariesLoaded,libname[i]);CHKERRQ(ierr);
ierr = PetscFree(libname[i]);CHKERRQ(ierr);
}
#if defined(PETSC_HAVE_THREADSAFETY)
/* These must be done here because it is not safe for individual threads to call these initialize routines */
ierr = AOInitializePackage();CHKERRQ(ierr);
ierr = PetscSFInitializePackage();CHKERRQ(ierr);
#if !defined(PETSC_USE_COMPLEX)
ierr = CharacteristicInitializePackage();CHKERRQ(ierr);
#endif
ierr = ISInitializePackage();CHKERRQ(ierr);
ierr = VecInitializePackage();CHKERRQ(ierr);
ierr = MatInitializePackage();CHKERRQ(ierr);
ierr = DMInitializePackage();CHKERRQ(ierr);
ierr = PCInitializePackage();CHKERRQ(ierr);
ierr = KSPInitializePackage();CHKERRQ(ierr);
ierr = SNESInitializePackage();CHKERRQ(ierr);
ierr = TSInitializePackage();CHKERRQ(ierr);
ierr = PetscCommDuplicate(PETSC_COMM_SELF,&PETSC_COMM_SELF_INNER,NULL);CHKERRQ(ierr);
ierr = PetscCommDuplicate(PETSC_COMM_WORLD,&PETSC_COMM_WORLD_INNER,NULL);CHKERRQ(ierr);
#endif
PetscFunctionReturn(0);
}
/*@C
AOCreateMapping - Creates a basic application mapping using two integer arrays.
Input Parameters:
+ comm - MPI communicator that is to share AO
. napp - size of integer arrays
. myapp - integer array that defines an ordering
- mypetsc - integer array that defines another ordering (may be NULL to indicate the identity ordering)
Output Parameter:
. aoout - the new application mapping
Options Database Key:
. -ao_view : call AOView() at the conclusion of AOCreateMapping()
Level: beginner
Notes: the arrays myapp and mypetsc need NOT contain the all the integers 0 to napp-1, that is there CAN be "holes" in the indices.
Use AOCreateBasic() or AOCreateBasicIS() if they do not have holes for better performance.
.keywords: AO, create
.seealso: AOCreateBasic(), AOCreateBasic(), AOCreateMappingIS(), AODestroy()
@*/
PetscErrorCode AOCreateMapping(MPI_Comm comm,PetscInt napp,const PetscInt myapp[],const PetscInt mypetsc[],AO *aoout)
{
AO ao;
AO_Mapping *aomap;
PetscInt *allpetsc, *allapp;
PetscInt *petscPerm, *appPerm;
PetscInt *petsc;
PetscMPIInt size, rank,*lens, *disp,nnapp;
PetscInt N, start;
PetscInt i;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidPointer(aoout,5);
*aoout = 0;
ierr = AOInitializePackage();CHKERRQ(ierr);
ierr = PetscHeaderCreate(ao, AO_CLASSID, "AO", "Application Ordering", "AO", comm, AODestroy, AOView);CHKERRQ(ierr);
ierr = PetscNewLog(ao,&aomap);CHKERRQ(ierr);
ierr = PetscMemcpy(ao->ops, &AOps, sizeof(AOps));CHKERRQ(ierr);
ao->data = (void*) aomap;
/* transmit all lengths to all processors */
ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = PetscMalloc2(size, &lens,size,&disp);CHKERRQ(ierr);
nnapp = napp;
ierr = MPI_Allgather(&nnapp, 1, MPI_INT, lens, 1, MPI_INT, comm);CHKERRQ(ierr);
N = 0;
for (i = 0; i < size; i++) {
disp[i] = N;
N += lens[i];
}
aomap->N = N;
ao->N = N;
ao->n = N;
/* If mypetsc is 0 then use "natural" numbering */
if (!mypetsc) {
start = disp[rank];
ierr = PetscMalloc1(napp+1, &petsc);CHKERRQ(ierr);
for (i = 0; i < napp; i++) petsc[i] = start + i;
} else {
petsc = (PetscInt*)mypetsc;
}
/* get all indices on all processors */
ierr = PetscMalloc4(N, &allapp,N,&appPerm,N,&allpetsc,N,&petscPerm);CHKERRQ(ierr);
ierr = MPI_Allgatherv((void*)myapp, napp, MPIU_INT, allapp, lens, disp, MPIU_INT, comm);CHKERRQ(ierr);
ierr = MPI_Allgatherv((void*)petsc, napp, MPIU_INT, allpetsc, lens, disp, MPIU_INT, comm);CHKERRQ(ierr);
ierr = PetscFree2(lens,disp);CHKERRQ(ierr);
/* generate a list of application and PETSc node numbers */
ierr = PetscMalloc4(N, &aomap->app,N,&aomap->appPerm,N,&aomap->petsc,N,&aomap->petscPerm);CHKERRQ(ierr);
ierr = PetscLogObjectMemory((PetscObject)ao, 4*N * sizeof(PetscInt));CHKERRQ(ierr);
for (i = 0; i < N; i++) {
appPerm[i] = i;
petscPerm[i] = i;
}
ierr = PetscSortIntWithPermutation(N, allpetsc, petscPerm);CHKERRQ(ierr);
ierr = PetscSortIntWithPermutation(N, allapp, appPerm);CHKERRQ(ierr);
/* Form sorted arrays of indices */
for (i = 0; i < N; i++) {
aomap->app[i] = allapp[appPerm[i]];
aomap->petsc[i] = allpetsc[petscPerm[i]];
}
/* Invert petscPerm[] into aomap->petscPerm[] */
for (i = 0; i < N; i++) aomap->petscPerm[petscPerm[i]] = i;
/* Form map between aomap->app[] and aomap->petsc[] */
for (i = 0; i < N; i++) aomap->appPerm[i] = aomap->petscPerm[appPerm[i]];
/* Invert appPerm[] into allapp[] */
for (i = 0; i < N; i++) allapp[appPerm[i]] = i;
/* Form map between aomap->petsc[] and aomap->app[] */
for (i = 0; i < N; i++) aomap->petscPerm[i] = allapp[petscPerm[i]];
#if defined(PETSC_USE_DEBUG)
/* Check that the permutations are complementary */
for (i = 0; i < N; i++) {
if (i != aomap->appPerm[aomap->petscPerm[i]]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB, "Invalid ordering");
}
#endif
/* Cleanup */
if (!mypetsc) {
ierr = PetscFree(petsc);CHKERRQ(ierr);
}
ierr = PetscFree4(allapp,appPerm,allpetsc,petscPerm);CHKERRQ(ierr);
ierr = AOViewFromOptions(ao,NULL,"-ao_view");CHKERRQ(ierr);
*aoout = ao;
PetscFunctionReturn(0);
}