Sys: add PetscMalloc1 macro, array allocation without redundant types

The type is inferred from the pointer return type. This patch is
automated via the following script:

git grep -l 'PetscMalloc(

Sys: add PetscMalloc1 macro, array allocation without redundant types

The type is inferred from the pointer return type. This patch is
automated via the following script:

git grep -l 'PetscMalloc(.*sizeof' src | xargs perl -pi -e 's@PetscMalloc\(([^,;]*[^,; ]) *\* *sizeof\([^,;()]+\),@PetscMalloc1($1,@'

This commit contains an additional bug-fix in csrperm.c, fixing pointer
arity. The code was introduced in 2006, but the allocation could not
have been correct at any time. This probably means that
MatDuplicate_SeqAIJPERM has never been tested.

a54129beb540034ba105796c682d589e7e1111f2
Richard Tran Mills <rmills@ornl.gov>

Added MATSEQCSRPERM support for MatDuplicate() and conversion to/from
MATSEQAIJ. Note that these changes are not quite debugged.

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Merge branch 'master' into barry/wirth-fusion-materials

Conflicts:
src/ts/examples/tutorials/advection-diffusion-reaction/ex10.c

Merge branch 'barry/dmvecmattypes' into barry/saws

Needed to work with version of PETSc that did not have constant calls to VecSetFromOptions() etc

Conflicts:
src/ksp/ksp/interface/ams/kspams.c
s

Merge branch 'barry/dmvecmattypes' into barry/saws

Needed to work with version of PETSc that did not have constant calls to VecSetFromOptions() etc

Conflicts:
src/ksp/ksp/interface/ams/kspams.c
src/snes/impls/composite/snescomposite.c
src/snes/impls/gs/snesgs.c
src/snes/impls/nasm/nasm.c
src/snes/impls/ngmres/snesngmres.c

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Merge branch 'master' into knepley/feature-dt-fem

* master: (211 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries

Merge branch 'master' into knepley/feature-dt-fem

* master: (211 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries
Bib: Updates
AO: fix erroneous processing of -ao_view and factor into AOViewFromOptions
doc: fix named argument in {Vec,Mat,DM}ViewFromOptions
Sys: add PetscDataTypeFromString() and test code
Mat: Should say that it has a nullspace in MatView()
parms: update tarball with fix for namespace conflict with metis
fix citation 'Golub_Varga_1961'
parmetis: update tarball to parmetis-4.0.2-p5 which fixes an install issue with cygwin
Sys Logging: revert parent traversal
fixed hdf5.py so that if self.libraries.compression is None the code still runs correctly
DMDA: fix bad cast of DM_DA to PetscObject
MatClique: follow DistMultiVec API changes
MatClique: remove unused variables
config cmakeboot: add C++ flags any time compiler is available
config OpenMP: check for C++ flag any time the compiler is available
replaced all left-over uses of a single PetscMalloc() to allocated multiple arrays: replaced with PetscMallocN() The only ones left are when the second array is set into the first array and one ugly usage in the MUMPS interface that cannot be easily fixed
...

Conflicts:
config/builder.py
src/dm/impls/plex/plexgeometry.c

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Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (273 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib

Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (273 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries
Bib: Updates
AO: fix erroneous processing of -ao_view and factor into AOViewFromOptions
doc: fix named argument in {Vec,Mat,DM}ViewFromOptions
Sys: add PetscDataTypeFromString() and test code
Mat: Should say that it has a nullspace in MatView()
parms: update tarball with fix for namespace conflict with metis
fix citation 'Golub_Varga_1961'
parmetis: update tarball to parmetis-4.0.2-p5 which fixes an install issue with cygwin
Sys Logging: revert parent traversal
fixed hdf5.py so that if self.libraries.compression is None the code still runs correctly
DMDA: fix bad cast of DM_DA to PetscObject
MatClique: follow DistMultiVec API changes
MatClique: remove unused variables
config cmakeboot: add C++ flags any time compiler is available
config OpenMP: check for C++ flag any time the compiler is available
replaced all left-over uses of a single PetscMalloc() to allocated multiple arrays: replaced with PetscMallocN() The only ones left are when the second array is set into the first array and one ugly usage in the MUMPS interface that cannot be easily fixed
...

Conflicts:
include/petscdmplex.h

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Merge branch 'master' into knepley/feature-dmda-section

* master: (287 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib e

Merge branch 'master' into knepley/feature-dmda-section

* master: (287 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries
Bib: Updates
AO: fix erroneous processing of -ao_view and factor into AOViewFromOptions
doc: fix named argument in {Vec,Mat,DM}ViewFromOptions
Sys: add PetscDataTypeFromString() and test code
Mat: Should say that it has a nullspace in MatView()
parms: update tarball with fix for namespace conflict with metis
fix citation 'Golub_Varga_1961'
parmetis: update tarball to parmetis-4.0.2-p5 which fixes an install issue with cygwin
Sys Logging: revert parent traversal
fixed hdf5.py so that if self.libraries.compression is None the code still runs correctly
DMDA: fix bad cast of DM_DA to PetscObject
MatClique: follow DistMultiVec API changes
MatClique: remove unused variables
config cmakeboot: add C++ flags any time compiler is available
config OpenMP: check for C++ flag any time the compiler is available
replaced all left-over uses of a single PetscMalloc() to allocated multiple arrays: replaced with PetscMallocN() The only ones left are when the second array is set into the first array and one ugly usage in the MUMPS interface that cannot be easily fixed
...

show more ...

Merge branch 'master' of bitbucket.org:petsc/petsc

Merge branch 'barry/improve-memory-logging'

Conflicts:
src/ksp/pc/impls/redundant/redundant.c
src/mat/interface/matnull.c

logging memory now credits to all ancestors

Merge branch 'master' into jed/ts-eimex

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

Conflicts:
src/ts/interface/tsregall.c

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

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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

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commit after merge

Hg-commit: 32055445bddb00b7bba909014f94a3e96e6d287d

Merge remote-tracking branch 'petsc-3.3/master'

* MPIAIJ: Remove block size optimization

Conflicts:
src/mat/impls/aij/mpi/mmaij.c

Hg-commit: 4c66be4268a4b6566f5b0b6636183886fc85ef74

repleced comments with #if 0

Hg-commit: 0e1ba702053f94be2fffe929907840e81eedac5a

MPIAIJ: Remove block size optimization

This optimization cannot be determined locally, thus it is not safe
without an additional reduction or different rules. Since this code is
executed on each ass

MPIAIJ: Remove block size optimization

This optimization cannot be determined locally, thus it is not safe
without an additional reduction or different rules. Since this code is
executed on each assembly, the additional reduction is not
attractive. If the optimization is deemed important, there are several
possible resolutions.

1. Guarantee full blocks at the matrix preallocation stage.
This is complicated to implement for AIJ and prevents use of
incomplete blocks. This would affect preallocation and dynamic
allocation, so it is not attractive.

2. Pad the blocks in the data structure.
This has most of the disadvantages of above.

3. Pad the VecScatter.
This is viable since the usual assumption with blocks is that most of
the entries are needed, but is more complicated to implement.

4. Perform the analysis earlier so that reduction can coalesce.
A reduction would still be required when MAT_NO_OFF_PROC_ENTRIES, or
the implementation would have to assume one way or the other.

5. Make VecScatter coalesce blocks internally.
This is attractive because the code could be used in many other
circumstances, but VecScatter is not easy to hack on.


History
~~~~~~~

4442702a5bc776781b96301ae6b1541cf7cf1fc2 Barry Smith
Original implementation, not safe because it assumes the local
conclusion applies everywhere.

a85625d104df12863d7d1735f9fdbe9b281ef7d2 Mark Adams
Modified logic, effectively disabling in all cases

c997baff1558fd165412be034e812bb69f90972a Barry Smith
Added back an ability to choose blocks (again unsafe because it can
choose inconsistently)

fb7e4343253b73d3fb40857991a8c6d5d0c7c56b Mark Adams
Add debugging check and modify actual construction of blocked map

Hg-commit: e419f8ed3683c4afe83f06aa49a4cff60b53a94c

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commit after merge

Hg-commit: 6debfa70dcdfef2cb504d744ca51ab3e2a9c44af

removed blocked IS optimization in MatMPIAIJ, fixed bug in ex56.c

Hg-commit: ce498238a46ac5e928140016fa24d7b163d5daad

commit after merge.

Hg-commit: 3124aef9aa443b8d243a05473b752da7151dece1

removed some isimpl.h dependencies from some Mat impls and documented others
moved CUSP flag from vecimpl.h to petscimpl.h

Hg-commit: 2c48aa9e76aa67a361ac3f6b034d78e9e3c7b825

added PetscObjectComm() and used it to replace (((PetscObject)obj)->comm)

Hg-commit: 3da37c458124ad48ae939f4e9823e4430ee0b8be

Merge branch 'private-impl-headers'

petsc-private/petscimpl.h and vecimpl.h are no longer included by
petscsys.h and petscvec.h. Some inline functions become normal functions
as a consequence of the

Merge branch 'private-impl-headers'

petsc-private/petscimpl.h and vecimpl.h are no longer included by
petscsys.h and petscvec.h. Some inline functions become normal functions
as a consequence of these changes.

Hg-commit: 5c59734726c7c41f493a5f5b9303cfab5c66ae21

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Make petscimpl.h private

Hg-commit: 910e8b03a54a915953944da6f75eb81c807d7428

removed PETSC_NULL from C and Fortran (except declaration in C for backward compatibility). Kept PETSC_NULL_xxx for Fortran
Fixed a few bugs where PETSC_NULL had been used incorrectly.

Hg-commit: 05

removed PETSC_NULL from C and Fortran (except declaration in C for backward compatibility). Kept PETSC_NULL_xxx for Fortran
Fixed a few bugs where PETSC_NULL had been used incorrectly.

Hg-commit: 054705a517d7f4388a8a084415d7478cbe95dff4

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