Merge branch 'knepley/fix-mat-chop' into master

* knepley/fix-mat-chop:
Mat: Changes to MatRestoreRow() broke MatChop()

Merge branch 'jed/fix-nightly-examples'

* jed/fix-nightly-examples:
SuperLU_DIST: upgrade to v3.3 @ 2013-04-10
parmetis: update to parmetis-4.0.2-p4.tar.gz fixes nightly build src/ksp/ksp/exampl

Merge branch 'jed/fix-nightly-examples'

* jed/fix-nightly-examples:
SuperLU_DIST: upgrade to v3.3 @ 2013-04-10
parmetis: update to parmetis-4.0.2-p4.tar.gz fixes nightly build src/ksp/ksp/examples/tests/ex31 in examples_next_arch-freebsd-cxx-pkgs-opt_wii.log
Mat test: compare using MatMultEqual (fuzzy) instead of MatEqual
DM test: move variable declaration due to unused warning
Fortran: define DMLabel for use --with-fortran-interfaces
tests: fix misuse of 64-bit indices
DM test: use "Interp" for variable name instead of imaginary "I"
TS: remove broken phasefield heat example from nightlies
AO ex3.cxx: include petsc header before mpi.h to deal with broken C++
TS ex9: s/static inline/PETSC_STATIC_INLINE/ for MSVC/C89
Mat ex125: initialize info.shifttype
TS ex2f: initialize variables before PetscOptionsGetBool
Mat inode: fix invalid access past end of array
IS test: fix typo in runex2 target
SF: do not use MPI_Type_free when MPI_Type_dup() was not available
SNES ex48: optimized SSE2 code cannot use __float128
SNES ex7: use PetscReal instead of double
MatGetFactor_seqaij_cusparse: set block size before preallocation

show more ...

MatGetFactor_seqaij_cusparse: set block size before preallocation

Preallocation configures the PetscLayout, initializing to bs=1 if not
set yet, so we must call MatSetBlockSize first.

Merge branch 'jed/aijcusparse-icc'

* jed/aijcusparse-icc:
MatSeqAIJCUSPARSE: make private functions static
txpetscgpu: upgrade to version 0.1.0
aijcusparse : fixed MatGetFactor and other small

Merge branch 'jed/aijcusparse-icc'

* jed/aijcusparse-icc:
MatSeqAIJCUSPARSE: make private functions static
txpetscgpu: upgrade to version 0.1.0
aijcusparse : fixed MatGetFactor and other small issues in this class
ksp tests: new tests for ksp algorithms using aijcusparse methods
vscatcusp : fixed compiler warnings
MatSeqAIJCUSPARSE: white space, style issues, static and extern functions
aijcusparse: ICC/Cholesky preconditioners

Conflicts:
src/mat/impls/aij/seq/seqcusparse/aijcusparse.cu (PetscObjectComposeFunction usage)

show more ...

Merged petsc/petsc into rmills/petsc master

MatSeqAIJCUSPARSE: make private functions static

aijcusparse : fixed MatGetFactor and other small issues in this class

Fixed MatGetFactor_seqaij_cusparse to have a more standard set of
of function calls (similar to aij/seq/umfpack or superlu) for

aijcusparse : fixed MatGetFactor and other small issues in this class

Fixed MatGetFactor_seqaij_cusparse to have a more standard set of
of function calls (similar to aij/seq/umfpack or superlu) for
setting up the factorization. In particular, I replaced the scoping
call to MatGetFactor_seqaij_petsc with the sequence MatCreate,
MatSetSizes, MatSetType, and MatXXXSetPreallocation. With these changes,
all tests that use aijcusparse class pass in optimized and debug builds.
Moreover, all memory leaks have been removed.

Additional small fixes to this class include the removal
of unnecessary PETSC_CUDA_EXTERN_C_BEGIN/END and poor use of
PETSC_COMM_WORLD in this file. Lastly, a few missing error checks
around several PETSc API method calls for symmetry/hermitian tests
were added.

show more ...

MatSeqAIJCUSPARSE: white space, style issues, static and extern functions

Conflicts:
src/mat/impls/aij/seq/seqcusparse/aijcusparse.cu

[Jed] Touch-up to conform to style guide

aijcusparse: ICC/Cholesky preconditioners

This is a patch for ICC/Cholesky preconditioners on GPUs for the
aijcusparse(aijcusp) class. One uses ICC by loading an upper triangular
matrix into the cus

aijcusparse: ICC/Cholesky preconditioners

This is a patch for ICC/Cholesky preconditioners on GPUs for the
aijcusparse(aijcusp) class. One uses ICC by loading an upper triangular
matrix into the cusparse class, and then setting the symmetry option,
i.e.

ierr = MatCreateSeqAIJCUSPARSE(comm,n,m,PETSC_NULL,num_entries_per_row,&A);CHKERRQ(ierr);
ierr = MatSetOption(A,MAT_SYMMETRIC,PETSC_TRUE);

This contains contains both the organization and implementation of the
preconditioner. The solves are done under the hood in the txpetscgpu
package. Currently, the factorization is done in the aij/seq/aijfact.c
routines. aijcusparse.cu makes scoping calls to these methods. Then, the
matrix is rebuilt into a form that is palatable for the GPU. This is
done in the method MatSeqAIJCUSPARSEBuildICCTriMatrices.

[Jed] Formatting and 'static' cleanup

show more ...

Merge branch 'barry/rm-xxxregisterdynamic'

* barry/rm-xxxregisterdynamic:
Registration: remove stale 'XXRegisterDynamic)' entries in man pages
TS examples: fix use of PetscFunctionList and add t

Merge branch 'barry/rm-xxxregisterdynamic'

* barry/rm-xxxregisterdynamic:
Registration: remove stale 'XXRegisterDynamic)' entries in man pages
TS examples: fix use of PetscFunctionList and add to nightlies
Changes: Note updates to XRegisterDynamic/PetscObjectComposeFunctionDynamic
PetscObjectComposeFunctionDynamic: remove stale docs and usage
developers.tex: remove complications from function composition with dlls
removed string version of function name for XXXRegister(), PetscFunctionListAdd() and PetscObjectComposeFunction()
changes: document PetscFunctionListAdd() API change
developers.tex: update documentation of PetscObjectComposeFunction
removed path and MPI_Comm arguments from PetscFunctionListFind/Add()
removed path argument to XXXInitializePackage() and XXXRegister()
removed XXXRegisterDynamic() but kept the APIs for everything else underneath the same phase I of the update to handling registering function pointers

show more ...

Merge branch 'barry/rm-xxxregisterdynamic' into jed/ts-eimex

PetscObjectComposeFunctionDynamic() and TSRegisterDynamic() were
replaced by PetscObjectComposeFunction() and TSRegister(), both of which

Merge branch 'barry/rm-xxxregisterdynamic' into jed/ts-eimex

PetscObjectComposeFunctionDynamic() and TSRegisterDynamic() were
replaced by PetscObjectComposeFunction() and TSRegister(), both of which
drop the string name argument.

* barry/rm-xxxregisterdynamic: (82 commits)
...

Conflicts:
src/ts/interface/tsregall.c

show more ...

removed string version of function name for XXXRegister(), PetscFunctionListAdd() and PetscObjectComposeFunction()

Merge branch 'master' into jed/ts-eimex

Sync to include Git conversion, PETSC_EXTERN, and minor API changes.

Conflicts:
src/ts/interface/tsregall.c

cuda nightlybuild: fix PETSC_EXERN

Hg-commit: 68694490132f1e98095aa7043aaa6c4acda98c97

merge

Hg-commit: 7389c209275f9836f3a0d332eaa5c591108892c4

commit after merge

Hg-commit: 80e3b40382438d2055338ca769fd5995f4eb79a9

cuda: compile fix

Hg-commit: 7e6d88e18f60d97cb6540186d6a9d8fb7f042960

Automerge.

Hg-commit: b6659d546870fb013f3da5bcd5066d1dc0dc329c

Merge branch 'master' of gitifyhg::ssh://hg@bitbucket.org/BarryFSmith/petsc-dev-simp

Symbol visibility and namespacing.

C++ builds always set extern "C" and can be called from plain C. Most
users w

Merge branch 'master' of gitifyhg::ssh://hg@bitbucket.org/BarryFSmith/petsc-dev-simp

Symbol visibility and namespacing.

C++ builds always set extern "C" and can be called from plain C. Most
users will only want --with-clanguage=C++ for std::complex.


Hg-commit: f848d02318cae92d7b32037c7ee88f92dbe46347

show more ...

Change all PETSC_EXTERN_C to PETSC_EXTERN

Hg-commit: 8d2ebbb193fb583bccc64015e35640c4e08c3426

Change all PETSC_EXTERN_C to PETSC_EXTERN


Hg-commit: ba0cf153561ff2dc521f42e94b7164fbe7b5d798

completed removing unneeded EXTERN_C_BEGIN/END from Mat directories and converting to PETSC_EXTERN_C for constructors
tested with and without dynamic with and without C++

Hg-commit: 7d27d7f4d9ea3bfe

completed removing unneeded EXTERN_C_BEGIN/END from Mat directories and converting to PETSC_EXTERN_C for constructors
tested with and without dynamic with and without C++

Hg-commit: 7d27d7f4d9ea3bfe6616fafdfb32d046b5db53a1

show more ...

Automerge.

Hg-commit: 2a552fd584bf855b9dc42efec9e8ab778063a84f

changed use of PetscObjectComposeFunctionDynamic() to PetscObjectComposeFunction() to allow use of static for functions for standard use in PETSc
PetscObjectComposeFunctionDynamic() is still availabl

changed use of PetscObjectComposeFunctionDynamic() to PetscObjectComposeFunction() to allow use of static for functions for standard use in PETSc
PetscObjectComposeFunctionDynamic() is still available for use if needed
also fixed calls to PetscObjectComposeFunction() to not wrap lines (per PETSc coding style)

Hg-commit: 822f9ddaac95a8ff6c2a9ad77fbf07d02d2c20d9

show more ...

MATSOLVERCUSPARSE: man page corrections

From Paul Mullowney, with formatting fixes. [petsc-maint #154925]

Hg-commit: 30d11ca8f9e7c6b8feb627446337c6db560a7413