completed initial implementation of PetscCitationsRegister() and added proper cites for hypre, ml, mumps

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

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

Merge branch 'jed/segbuffer-size_t'

* jed/segbuffer-size_t:
SegBuffer: use size_t instead of PetscInt

Merge branch 'jed/segbuffer-size_t' of bitbucket.org:petsc/petsc into barry/citations

-citations option causes the print out of approriate bibtex citation indices for all packages USED in the run
Most of the appropriate citations still need to be added

SegBuffer: use size_t instead of PetscInt

This is more natural as a "buffer" interface.

fixed bug where XXXViewFromOptions() used prefix of object rather than appropriate prefix of KSP or SNES

Merge branch 'jed/stack-call-blas'

Fix performance bug that calling BLAS takes an amount of time dependent
on the number of memory allocations that the program has made.

* jed/stack-call-blas:
Pe

Merge branch 'jed/stack-call-blas'

Fix performance bug that calling BLAS takes an amount of time dependent
on the number of memory allocations that the program has made.

* jed/stack-call-blas:
PetscStackCallBLAS: new macro instead of PetscStackCall (skip CHKMEMQ)
Stack: consolidate handling of PetscStack

show more ...

Merge branch 'jed/petscdlopen-extern'

* jed/petscdlopen-extern:
PetscDL: use PETSC_EXTERN and remove obsolete header

Merge branch 'jed/matmatmult-sort'

New version provides in the neighborhood of 20% speedup for MatMatMult
as used in PCGAMG.

* jed/matmatmult-sort:
MatMatMultSymbolic_SeqAIJ_SeqAIJ: switch to "so

Merge branch 'jed/matmatmult-sort'

New version provides in the neighborhood of 20% speedup for MatMatMult
as used in PCGAMG.

* jed/matmatmult-sort:
MatMatMultSymbolic_SeqAIJ_SeqAIJ: switch to "sort" version as default
segbuffer: g++ does not like casting int*restrict* to void*, void** okay
MatMatMult_SeqAIJ_SeqAIJ_Sort: new implementation using char flags and sorting
segbuffer: add PetscSegBufferGetInts() to encourage use of PETSC_RESTRICT
segbuffer: create wrapper structure
segbuffer: add PetscSegBufferGetSize() and PetscSegBufferUnuse()
segbuffer: fix bug in which seg->used was not reset

show more ...

PetscStackCallBLAS: new macro instead of PetscStackCall (skip CHKMEMQ)

When CHKMEMQ occurs on every call to BLAS or Lapack, we sometimes see
unacceptable performance degradation (orders of magnitude

PetscStackCallBLAS: new macro instead of PetscStackCall (skip CHKMEMQ)

When CHKMEMQ occurs on every call to BLAS or Lapack, we sometimes see
unacceptable performance degradation (orders of magnitude).
PetscStackCallBLAS is currently identical to PetscStackCall except for
skipping CHKMEMQ, but such checking could be made optional in the
future.

show more ...

PetscDL: use PETSC_EXTERN and remove obsolete header

Merge branch 'jed/matmatmult-sort' into jed/fix-optionsinsertfile-large

Branch contains segbuffer enhancements in addition to
MatMatMult_SeqAIJ_SeqAIJ_Sort. I need the segbuffer enhancements, one of

Merge branch 'jed/matmatmult-sort' into jed/fix-optionsinsertfile-large

Branch contains segbuffer enhancements in addition to
MatMatMult_SeqAIJ_SeqAIJ_Sort. I need the segbuffer enhancements, one of
which is a portability fix that was applied after the
MatMatMult_SeqAIJ_SeqAIJ_Sort commit.

* jed/matmatmult-sort:
segbuffer: g++ does not like casting int*restrict* to void*, void** okay
MatMatMult_SeqAIJ_SeqAIJ_Sort: new implementation using char flags and sorting
segbuffer: add PetscSegBufferGetInts() to encourage use of PETSC_RESTRICT
segbuffer: create wrapper structure
segbuffer: add PetscSegBufferGetSize() and PetscSegBufferUnuse()
segbuffer: fix bug in which seg->used was not reset

show more ...

Merge bug fix/patch releases up to 3.2-p7 into maint-3.2

* commit 'a9157d915ed96804280c3dc077186a2a633fd603': (157 commits)
Fix PyPI download URL to help pip figure out the release version
#1109

Merge bug fix/patch releases up to 3.2-p7 into maint-3.2

* commit 'a9157d915ed96804280c3dc077186a2a633fd603': (157 commits)
Fix PyPI download URL to help pip figure out the release version
#110990 fix timestamp order for .so vs .a during 'make install'
Update FFTW download
Increase patchlevel to 3.2-p7
...

show more ...

Merge branch 'maint'

* maint:
petscsys: conditional define of {MPICH,OMPI}_SKIP_MPICXX

Conflicts:
include/petscsys.h ("mpi.h" to <mpi.h>)

petscsys: conditional define of {MPICH,OMPI}_SKIP_MPICXX

Merge branch 'barry/rm-xxxregisteralldestroy'

* barry/rm-xxxregisteralldestroy:
TSSSP: Fix to use proper TSSSPInitializePackage() system
flag should have been false
removed unnneeded and unuse

Merge branch 'barry/rm-xxxregisteralldestroy'

* barry/rm-xxxregisteralldestroy:
TSSSP: Fix to use proper TSSSPInitializePackage() system
flag should have been false
removed unnneeded and unused XXXRegisterDestroy() routines
removed PetscFunctionListDestroyAll() and put PetscFunctionListDestroy(&XXXList) into the package finalize

show more ...

Merged petsc/petsc into rmills/petsc master

removed unnneeded and unused XXXRegisterDestroy() routines

Merge branch 'jed/options-viewer-enum'

* jed/options-viewer-enum:
PetscEnumFind: fix bad PetscBool cast when I meant PetscEnum
PetscOptionsGetViewer: test ex4: removed redundant
PetscOptionsGe

Merge branch 'jed/options-viewer-enum'

* jed/options-viewer-enum:
PetscEnumFind: fix bad PetscBool cast when I meant PetscEnum
PetscOptionsGetViewer: test ex4: removed redundant
PetscOptionsGetViewer: support ":append" for arbitrary viewer type
PetscOptionsGetViewer: fix error handling with PETSC_VIEWER_XX_()
PetscOptionsGetViewer: new test: write to named ASCII output file with format
PetscOptionsGetViewer: simplify logic and use PetscEnumFind()
PetscOptionsGetEList: use PetscEListFind()
PetscEListFind() and PetscEnumFind()
PetscFileModes: add string enumeration for PetscFileMode
PetscViewer: added tests/ex4 to testexamples
PetscViewer: added files for :append test
PetscOptionsGetViewer: last commit broke PetscOptionsGetViewer, fixed it
PetscOptionsGetViewer: added [:append] to ascii

show more ...

Merge branch 'jed/functionlist-nocast'

* jed/functionlist-nocast:
docs: simplify explanation of function lists/composition
PetscObjectQueryFunction: use macro to hide PetscVoidFunction* cast
P

Merge branch 'jed/functionlist-nocast'

* jed/functionlist-nocast:
docs: simplify explanation of function lists/composition
PetscObjectQueryFunction: use macro to hide PetscVoidFunction* cast
PetscFunctionListAdd: use macro to hide (PetscVoidFunction) cast
PetscFunctionListFind: use macro to hide (PetscVoidFunction*) cast

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 ...

PetscObjectQueryFunction: use macro to hide PetscVoidFunction* cast

Rationale is the same as the parent. This makes all of
PetscFunctionListAdd(), PetscFunctionListFind(),
PetscObjectComposeFunction

PetscObjectQueryFunction: use macro to hide PetscVoidFunction* cast

Rationale is the same as the parent. This makes all of
PetscFunctionListAdd(), PetscFunctionListFind(),
PetscObjectComposeFunction(), and PetscObjectQueryFunction() consistent
regarding function pointer return types.

show more ...

PetscFunctionListAdd: use macro to hide (PetscVoidFunction) cast

Same rationale as the last commit:

Casting using PetscVoidFunction instead of (void(*)(void)) is needed
with C++ compilers that will

PetscFunctionListAdd: use macro to hide (PetscVoidFunction) cast

Same rationale as the last commit:

Casting using PetscVoidFunction instead of (void(*)(void)) is needed
with C++ compilers that will not implicitly convert C++ language linkage
to C language linkage. Since PetscFunctionListAdd() is meant to operate
on generic function pointers, we hide this language linkage detail
(which is inconsistently implemented) in a cast.

show more ...

PetscFunctionListFind: use macro to hide (PetscVoidFunction*) cast

Casting using PetscVoidFunction* instead of (void(**)(void)) is needed
with C++ compilers that will not implicitly convert C++ lang

PetscFunctionListFind: use macro to hide (PetscVoidFunction*) cast

Casting using PetscVoidFunction* instead of (void(**)(void)) is needed
with C++ compilers that will not implicitly convert C++ language linkage
to C language linkage. Since PetscFunctionListFind() is meant to operate
on generic function pointers, we hide this language linkage detail
(which is inconsistently implemented) in a cast.

show more ...