History log of /petsc/src/mat/impls/baij/seq/baij.c (Results 576 – 600 of 1525)
Revision Date Author Comments
# edbbd480 10-Dec-2013 Barry Smith <bsmith@mcs.anl.gov>

Merge branch 'master' into barry/xcode


# e0133700 05-Dec-2013 Barry Smith <bsmith@mcs.anl.gov>

Merge branch 'barry/saws-push-header-body' into barry/saws-options


# fb3f26da 04-Dec-2013 Jed Brown <jedbrown@mcs.anl.gov>

Merge branch 'jed/malloc-array'

Type arguments dropped from PetscMalloc[2-7], PetscNew, and PetscNewLog,
added PetscMalloc1 for allocating typed arrays, add PetscCalloc[1-7] for
allocating cleared (

Merge branch 'jed/malloc-array'

Type arguments dropped from PetscMalloc[2-7], PetscNew, and PetscNewLog,
added PetscMalloc1 for allocating typed arrays, add PetscCalloc[1-7] for
allocating cleared (zeroed) memory.

* jed/malloc-array:
Sys: Add pointer casts from (void **) in calls to PetscMalloc1()
Sys: drop explicit type arguments from PetscNew() and PetscNewLog()
Sys: add PetscCalloc[1-7]
Sys: add PetscMalloc1 macro, array allocation without redundant types
PetscMalloc[2-7]: remove type arguments, infer from pointer type
SNESComputeJacobianDefaultColor: fix uninitialized variable

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# b00a9115 03-Dec-2013 Jed Brown <jedbrown@mcs.anl.gov>

Sys: drop explicit type arguments from PetscNew() and PetscNewLog()

git grep -l 'PetscNew\(Log\)\?(' -- $1 | xargs perl -pi -e '
s@PetscNew\([^,;()]+ *, *@PetscNew(@;
s@PetscNewLog\(([^,;()]+) *,[^,

Sys: drop explicit type arguments from PetscNew() and PetscNewLog()

git grep -l 'PetscNew\(Log\)\?(' -- $1 | xargs perl -pi -e '
s@PetscNew\([^,;()]+ *, *@PetscNew(@;
s@PetscNewLog\(([^,;()]+) *,[^,;()]+, *@PetscNewLog($1,@'

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# 1795a4d1 03-Dec-2013 Jed Brown <jedbrown@mcs.anl.gov>

Sys: add PetscCalloc[1-7]

Replace lots of places where PetscMemzero is called immediately after
allocation.


# 785e854f 03-Dec-2013 Jed Brown <jedbrown@mcs.anl.gov>

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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# dcca6d9d 03-Dec-2013 Jed Brown <jedbrown@mcs.anl.gov>

PetscMalloc[2-7]: remove type arguments, infer from pointer type

This change can be performed almost entirely by this script:

git grep -l PetscMalloc[2-7] $1 | xargs perl -pi \
-e '
s@PetscMalloc

PetscMalloc[2-7]: remove type arguments, infer from pointer type

This change can be performed almost entirely by this script:

git grep -l PetscMalloc[2-7] $1 | xargs perl -pi \
-e '
s@PetscMalloc2\(([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+)\)@PetscMalloc2($1,$3,$4,$6)@;
s@PetscMalloc3\(([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+)\)@PetscMalloc3($1,$3,$4,$6,$7,$9)@;
s@PetscMalloc4\(([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+)\)@PetscMalloc4($1,$3,$4,$6,$7,$9,$10,$12)@;
s@PetscMalloc5\(([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+)\)@PetscMalloc5($1,$3,$4,$6,$7,$9,$10,$12,$13,$15)@;
s@PetscMalloc6\(([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+)\)@PetscMalloc6($1,$3,$4,$6,$7,$9,$10,$12,$13,$15,$16,$18)@;
s@PetscMalloc7\(([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+)\)@PetscMalloc7($1,$3,$4,$6,$7,$9,$10,$12,$13,$15,$16,$18,$19,$21)@;
'

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# cd4f0679 18-Nov-2013 Matthew G. Knepley <knepley@gmail.com>

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

* master: (528 commits)
Doc: Fixed configure doc
Nightly summary: Added configure section.
TSSetErrorIfStepFails: fix __FUNCT__
TS: fi

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

* master: (528 commits)
Doc: Fixed configure doc
Nightly summary: Added configure section.
TSSetErrorIfStepFails: fix __FUNCT__
TS: fix for TSGetRHSMats_Private() in the creation of the Arhs and Brhs matrices
protect logging of objects (which uses global variables) with PETSC_USE_LOG
error handler API had been previously changed but this example was not updated to new API.
DMPlex: Fixed bug in coordinate permutation
PetscSection: Doc fix for permutation
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bugfix of MatCreateSeqAIJFromTriple() contributed by Nicolas Marsic <nicolas.marsic@montefiore.ulg.ac.be>
bib: rename ref with duplicate key
Webpage: Corrected '-dm_mat_type cusp' to 'dm_mat_type aijcusp'.
completed removing server code that was not removed in previous commit
removed PETSc webserver and configure package files that supported it
Allow calling MatGetBlockSize[s]() before matrix preallocation
SNESLINESEARCHBT: Set the norms when exiting early due to negligible step.
fix outdated PetscOptionsList
SNESQN: only monitor real part of dot product (fails with C++ complex)
Fix for multiple definitions in mat/color/interface/ custom fortran bindings
...

Conflicts:
config/builder.py
include/petscdmplex.h
src/dm/impls/da/dageometry.c
src/dm/impls/plex/examples/tests/ex4.c
src/dm/impls/plex/plex.c
src/dm/impls/plex/plexinterpolate.c

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# c4fbd833 08-Nov-2013 Matthew G. Knepley <knepley@gmail.com>

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

* master: (593 commits)
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bib: rename ref with duplicate key

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

* master: (593 commits)
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bib: rename ref with duplicate key
Webpage: Corrected '-dm_mat_type cusp' to 'dm_mat_type aijcusp'.
Allow calling MatGetBlockSize[s]() before matrix preallocation
SNESLINESEARCHBT: Set the norms when exiting early due to negligible step.
SNESQN: only monitor real part of dot product (fails with C++ complex)
Corrected the #include statement in the man pages for the PetscObjectComposedDataSet/Getwhatever routines.
DMPlex: Added doc for DMPlexGetHybridBounds()
winzip: detect if winzip is used to extract petsc.tar.gz and error out.
configure: remove self.archIndependent as its not being used. [it is used to create externalpackages/package/arch dir which is unused]
configure: fix packages using package-dir/PETSC_ARCH as out-of-source-build location Perhaps this should be changed to package-dir/build?
configure: remove dead code previously used to download BuildSystem
configure: check if compilerDefines [and compilerFixes] exist in framework before using them
configure: save/restore reconfigure.py when --with-clean is used
configure: add --with-clean option to delete buildfiles/externalpackages in PETSC_DIR/PETSC_ARCH and potential externalpackages in --with-external-package-dir/PETSC_ARCH
configure: With --with-externalpackages-dir=dir store/build packages in dir/PETSC_ARCH
Add MatSeqSBAIJSetPreallocationCSR()
configure: switch to using PETSC_DIR/PETSC_ARCH/externalpackages by updating package.py to use externalpackages.py as the externalPackagesDirProvider
configure: move dead code configureExternalPackagesDir() from petscdir.py to externalpackagesdir.py Also set PETSC_DIR/PETSC_ARCH/externalpackages as the externalpackagesdir
...

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# 7737a228 31-Oct-2013 Barry Smith <bsmith@mcs.anl.gov>

Merge branch 'master' into barry/saws

Conflicts:
src/ksp/pc/impls/gamg/gamg.c
src/sys/classes/viewer/impls/ams/ams.c
src/sys/objects/pinit.c


# a76eec0e 25-Oct-2013 Hong Zhang <hzhang@mcs.anl.gov>

Merge branch 'hzhang/snes-jacobiancoloropt'


# 6346027a 21-Oct-2013 Jed Brown <jedbrown@mcs.anl.gov>

MatFD: remove trailing whitespace introduced in branch


# 1919a2e2 21-Oct-2013 Jed Brown <jedbrown@mcs.anl.gov>

Merge branch 'madams/mat-residual' into hzhang/snes-jacobiancoloropt

Fix conflict between new MATOP_RESIDUAL and MATOP_FDCOLORING_SETUP.

* madams/mat-residual:
refactored residuals by adding a 'r

Merge branch 'madams/mat-residual' into hzhang/snes-jacobiancoloropt

Fix conflict between new MATOP_RESIDUAL and MATOP_FDCOLORING_SETUP.

* madams/mat-residual:
refactored residuals by adding a 'residual' method to Mat

Conflicts:
include/finclude/petscmat.h
include/petsc-private/matimpl.h
include/petscmat.h
src/mat/impls/aij/mpi/mpiaij.c
src/mat/impls/aij/seq/aij.c
src/mat/impls/baij/mpi/mpibaij.c
src/mat/impls/baij/seq/baij.c

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# 08eee6ab 19-Oct-2013 Jed Brown <jedbrown@mcs.anl.gov>

Merge branch 'jed/mat-baij-row-oriented'

API change: MatSeqBAIJSetPreallocationCSR and
MatMPIBAIJSetPreallocationCSR now expect values to match documented BAIJ
internal format (list of column-major

Merge branch 'jed/mat-baij-row-oriented'

API change: MatSeqBAIJSetPreallocationCSR and
MatMPIBAIJSetPreallocationCSR now expect values to match documented BAIJ
internal format (list of column-major bs*bs blocks).

* jed/mat-baij-row-oriented:
Mat BAIJ: fix typos (build errors)
Mat BAIJ: respect MAT_ROW_ORIENTED in Mat*BAIJSetPreallocationCSR

Conflicts:
src/docs/website/documentation/changes/dev.html

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# 170be9ae 16-Oct-2013 Matthew G. Knepley <knepley@gmail.com>

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

* master: (397 commits)
PetscSynchronizedFGets: fix deadlock at EOF
Compiler: Fix warnings from MPI impls which do not initialize outputs

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

* master: (397 commits)
PetscSynchronizedFGets: fix deadlock at EOF
Compiler: Fix warnings from MPI impls which do not initialize outputs
Increase patchlevel to 3.4.3
SNES: Now work vectors come from the DM
SNES ex62: Remove code generation
SNES: Move setup involving snes->vec_sol from SNESSetUp() to SNESolve()
Compiler: Fix warnings from MPI impls which do not initialize outputs
DMPlex ex7: Added missing test output
SNES ex52: Removed old Jacobian stuff, and fixed call to DMPlexProjectFunction() - Fixed calls for new element handling
SNES ex12: Added a performance profiling mode
DMPlex ex8: Fixed leak
PetscSection: Must reset the section when changing the number of fields
DMPlex ex7: Fixed test output - Corrected orientations in interpolation
DMPlex ex1: Fixed test output - Uniform refinement for quads changed
DMPlex: Fix overagressive checks
PC: Removed support graph PC
configure: both downloadonWindows and worksonWindows refer to MS compilers. Also fix isWindows() -> isWindows(CC).
MatXAIJSetPreallocation: use array[] notation to help out Fortran
__float128: when blas/lapack is not found instruct using f2cblaslapack
Configure: Package.downloadonWindows is supposed to mean that Windows compilers work. not Cygwin - Also changed doc for Package.worksonWindows, which does refer to Cygwin
...

Conflicts:
src/dm/impls/da/dalocal.c

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# 0a58a46c 10-Oct-2013 Matthew G. Knepley <knepley@gmail.com>

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

* knepley/fix-plex-examples: (36 commits)
DMPlex ex7: Added missing test output
SNES ex52: Removed old Jacobian stuff

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

* knepley/fix-plex-examples: (36 commits)
DMPlex ex7: Added missing test output
SNES ex52: Removed old Jacobian stuff, and fixed call to DMPlexProjectFunction() - Fixed calls for new element handling
SNES ex12: Added a performance profiling mode
DMPlex ex8: Fixed leak
PetscSection: Must reset the section when changing the number of fields
DMPlex ex7: Fixed test output - Corrected orientations in interpolation
DMPlex ex1: Fixed test output - Uniform refinement for quads changed
DMPlex: Fix overagressive checks
configure: both downloadonWindows and worksonWindows refer to MS compilers. Also fix isWindows() -> isWindows(CC).
MatXAIJSetPreallocation: use array[] notation to help out Fortran
__float128: when blas/lapack is not found instruct using f2cblaslapack
Configure: Package.downloadonWindows is supposed to mean that Windows compilers work. not Cygwin - Also changed doc for Package.worksonWindows, which does refer to Cygwin
SNES example: fix bad merge
config: only define DATAFILESPATH for non-null value
config: define lang-specific macros in petscconf.h, choose in petscsys.h
Mat: add MATOP_ values for missing functions
DMPlex: use VECSTANDARD for coordinates
PetscSF: Fixed PetscSFCreateEmbeddedSF() - We were using sf->nleaves for the leaf buffer, which is completely wrong. We have to use the largest thing in sf->mine[]
replaced ISCreateGeneral in CompositeDM with ISCreateStride. MatNest calls ISStrideGetInfo on these vectors, which was causing errors
DMPlex: Fix completely broken code in PetscSFCreateRemoteOffsets() - Non-broken example was in PetscSFDistributeSection()
...

Conflicts:
src/dm/impls/plex/plex.c

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# 16407d4f 09-Oct-2013 Peter Brune <brune@mcs.anl.gov>

Merge branch 'master' into prbrune/mat-matcolor

Conflicts:
src/snes/interface/snesj2.c


# 93dfae19 09-Oct-2013 Hong Zhang <hzhang@mcs.anl.gov>

implement MatFDColoringCreate_SeqXAIJ() s.t. it sets default brows and bcols.


# f86b9fba 09-Oct-2013 Hong Zhang <hzhang@mcs.anl.gov>

add MatFDColoringSetUp(); rename MatFDColoringCreate_xxx -> MatFDColoringSetUp_xxx


# 05852b61 06-Oct-2013 Jed Brown <jedbrown@mcs.anl.gov>

Merge branch 'mlange05/threadcomm-matmult-baij'

* mlange05/threadcomm-matmult-baij:
Threadcomm: Threading MatMult_SeqBAIJ
Threadcomm: Adding "first touch" allocation to Mat_SeqBAIJ


# 32029c4c 06-Oct-2013 Matthew G. Knepley <knepley@gmail.com>

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

* master: (149 commits)
Bib: Added papers referencing PETSc from ResearchGate
Bib: Fixed urls for some refs Suggested-by: Michele De Ste

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

* master: (149 commits)
Bib: Added papers referencing PETSc from ResearchGate
Bib: Fixed urls for some refs Suggested-by: Michele De Stefano
fixed bug that has appeared recently of false positive errors when there are zero local equations on coarse grids in gamg-agg.
MatSchurComplement: Must initialize KSP package
bib: fix inbook citation
Bib: Updated some refs
SNES: fix copy/paste in man page
fortran: fix KSPCONVERGEDDEFAULT and SNESCONVERGEDSKIP in fortran includes
Mat SBAIJ: avoid invalid memory read in MatSOR_SBAIJ
Revert "MatMPIBAIJSetPreallocationCSR() handled the input matrix entries incorrectly, it treated them as if each row of values"
PCGAMG: fix corruption for multiple solves when MatSetNearNullSpace is used
PCGAMG: remove distracting comment
KSP ex49: restrict near-null space for elasticity example with sym BC
MatMPIBAIJSetPreallocationCSR() handled the input matrix entries incorrectly, it treated them as if each row of values was provided ordered by row within the block rows instead of by block as it was originally designed to be. Also added more discussion to the manual pages on the expected order of the values
Fix accidental creation of the matrices in SNESNCG used for linear analogue LS.
PCGAMG: add man page for PCGAMGType
fortran: fix snesconvergedskip_() kspconvergedskip_() kspconvergeddefault*_()
rm //
Sys: new_ir changed from PetscInt to PetscObjectState - so fix mallocs to use the new type
SNES: Fixed package init in SNESLineSearchCreate()
...

Conflicts:
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex5.c
src/dm/impls/plex/plex.c
src/dm/interface/dm.c

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# 59507afe 06-Oct-2013 Hong Zhang <hzhang@mcs.anl.gov>

Merge branch 'hzhang/snes-jacobiancoloropt' of bitbucket.org:petsc/petsc into hzhang/snes-jacobiancoloropt


# 625f6d37 02-Oct-2013 Hong Zhang <hzhang@mcs.anl.gov>

cleanup MatGetColumnIJ_SeqAIJ_Color and MatGetColumnIJ_SeqBAIJ_Color


# d47bf9aa 30-Sep-2013 Jed Brown <jedbrown@mcs.anl.gov>

Mat BAIJ: fix typos (build errors)


# 3adadaf3 29-Sep-2013 Jed Brown <jedbrown@mcs.anl.gov>

Mat BAIJ: respect MAT_ROW_ORIENTED in Mat*BAIJSetPreallocationCSR

MatMPIBAIJSetPreallocationCSR() used to handle the input matrix entries
in a peculiar way, treating them as if each row of values wa

Mat BAIJ: respect MAT_ROW_ORIENTED in Mat*BAIJSetPreallocationCSR

MatMPIBAIJSetPreallocationCSR() used to handle the input matrix entries
in a peculiar way, treating them as if each row of values was provided
ordered by row within the block rows instead of by block as it was
originally intended to be. Now treat as array of contiguous blocks for
which the ordering within blocks is row-major or column-major according
to the MAT_ROW_ORIENTED option.

This also affects MatCreateMPIBAIJWithArrays() which now expects
contiguous blocks with column-major ordering within blocks, just like
the internal storage format. MatCreateSeqBAIJWithArrays is unaffected
since it uses the array as provided.

Reported-by: Matteo Parsani <parsani.matteo@gmail.com>
Reported-by: Lisandro Dalcin <dalcinl@gmail.com>
Helped-by: Barry Smith <bsmith@mcs.anl.gov>

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