History log of /petsc/src/vec/is/sf/interface/sf.c (Results 451 – 475 of 486)
Revision Date Author Comments
# 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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# 244aa513 28-Nov-2013 Barry Smith <bsmith@mcs.anl.gov>

Merge branch 'barry/minor-draw-improvements' into jed/chem


# b3331239 21-Nov-2013 Matthew G. Knepley <knepley@gmail.com>

Merge branch 'knepley/fix-hash-scaling'

* knepley/fix-hash-scaling: (25 commits)
PetscSF: Register logging events
PetscSF: Added logging
DMPlex: Bug fix for interpolated adjacency formation

Merge branch 'knepley/fix-hash-scaling'

* knepley/fix-hash-scaling: (25 commits)
PetscSF: Register logging events
PetscSF: Added logging
DMPlex: Bug fix for interpolated adjacency formation
DMPlex: Fast adjacency graph construction for interpolated meshes
DMPlex: Fixed error in new events
DMPlex: More events for distribution
DMPlex: Fixed allocation bug in reordering
DMPlex: Fixed mismatched Malloc2 in reordering
DMLabel: Split Malloc3 into Malloc2 and Malloc
Hash+DMPlex: Changed PetscHashIPut() to eliminate pass-by-ref - Jed can sleep soundly tonight
DMPlex: Use PetscHashIHasKey() to check for membership
Hash; Added PetscHashIHasKey() - PetscHashIMap does not match the documentation
DMPlex: Added simple DMLabel test
DMPlex: Fix missing restore Reported-by: Jed Brown <jedbrown@mcs.anl.gov>
DMPlex: Use DMLabelDistribute() in DMPlexDistribute()
DMPlex: Use DMLabelGetStrautmBounds() in DMPlexGetDepth/HeightStratum()
DMPlex: Added DMLabelDistribute()
DMPlex: Added DMLabelGetStratumBounds()
DMPlex: Fixed quadratic behavior of DMLabel insert - Added hash table for each label value for insertion - Added arrayValid flag which says whether array data or hash table data is valid - Convert between representations using DMLabelMakeValid_Private() and DMLabelMakeInvalid_Private() - Split up allocation of stratumValues and stratumSize/Offsets - Most functions only use the array representation, but some can use both (should probably expand this with GetStratum) - Moved the DMLabelFIlter() function
Hash: Added PetscHashIPut() and PetscHashIDel() - Removed unused variable
...

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# 563ffbab 18-Nov-2013 Matthew G. Knepley <knepley@gmail.com>

PetscSF: Added logging


# 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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# eeb04156 08-Nov-2013 Barry Smith <bsmith@mcs.anl.gov>

Merge branch 'barry/saws'


# 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


# 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


# ffc3e64b 09-Oct-2013 Peter Brune <brune@mcs.anl.gov>

Merge branch 'master' into prbrune/removeunwrappedmathfunctions


# d090c6a4 07-Oct-2013 Matthew G. Knepley <knepley@gmail.com>

Merge branch 'knepley/fix-plex-preallocation'

* knepley/fix-plex-preallocation:
PetscSF: Fixed PetscSFCreateEmbeddedSF() - We were using sf->nleaves for the leaf buffer, which is completely wrong.

Merge branch 'knepley/fix-plex-preallocation'

* knepley/fix-plex-preallocation:
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[]
DMPlex: Fix completely broken code in PetscSFCreateRemoteOffsets() - Non-broken example was in PetscSFDistributeSection()
DMPlex: Fix leaks in preallocation debugging
DMPlex: Put in guard for preallocation sections which are smaller than the SF

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# 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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# 0511a646 02-Oct-2013 Matthew G. Knepley <knepley@gmail.com>

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[]


# 25a75388 01-Oct-2013 Jed Brown <jedbrown@mcs.anl.gov>

Merge branch 'jed/remove-dynamic-loading-option'

Option --with-dynamic-loading has been removed. Similar functionality
is available via the run-time option -dynamic_library_preload.

* jed/remove-d

Merge branch 'jed/remove-dynamic-loading-option'

Option --with-dynamic-loading has been removed. Similar functionality
is available via the run-time option -dynamic_library_preload.

* jed/remove-dynamic-loading-option:
Sys: PetscContainerCreate must call PetscSysInitializePackage
Remove --with-dynamic-loading / PETSC_USE_DYNAMIC_LIBRARIES

Conflicts:
src/dm/impls/mesh/mesh.c
src/dm/interface/dlregisdmdm.c
src/docs/website/documentation/changes/dev.html

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# 256ff83f 11-Sep-2013 Barry Smith <bsmith@mcs.anl.gov>

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

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


# a264d7a6 10-Sep-2013 Barry Smith <bsmith@mcs.anl.gov>

fix name for PetscOptionsFList() and get FList() and EList() working properly with SAWs legal values


# aa2d57e9 30-Aug-2013 Jed Brown <jedbrown@mcs.anl.gov>

Remove --with-dynamic-loading / PETSC_USE_DYNAMIC_LIBRARIES

This option was mostly redundant because normal shared libraries satisfy
all the same needs. This commit adds the run-time option
-dynami

Remove --with-dynamic-loading / PETSC_USE_DYNAMIC_LIBRARIES

This option was mostly redundant because normal shared libraries satisfy
all the same needs. This commit adds the run-time option
-dynamic_library_preload that can be used to load/initialize all the
packages in advance, as used to be done when --with-dynamic-loading.

The PetscDLLibraryRegister_petscxxx functions have been kept, but are
not called unless -dynamic_library_preload is used. The petsc-dev
discussion, "Why --with-dynamic-loading?" did not reach consensus about
whether this was ever useful, so it may also be removable.

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# 9a6158bf 19-Jun-2013 Jed Brown <jedbrown@mcs.anl.gov>

Merge branch 'barry/fix-PetscObjectPrintClassNamePrefixType'

* barry/fix-PetscObjectPrintClassNamePrefixType:
update tests of src/mat/examples/tests/ex136.c
Use classname in object for object na

Merge branch 'barry/fix-PetscObjectPrintClassNamePrefixType'

* barry/fix-PetscObjectPrintClassNamePrefixType:
update tests of src/mat/examples/tests/ex136.c
Use classname in object for object name when calling PetscObjectPrintClassNamePrefixType() instead of some string with less precise name passed in

Conflicts:
src/snes/interface/snes.c

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# e33c197d 11-Jun-2013 Richard Mills <rtm@eecs.utk.edu>

Merged petsc/petsc into rmills/petsc master.


# dae58748 22-May-2013 Barry Smith <bsmith@mcs.anl.gov>

Use classname in object for object name when calling PetscObjectPrintClassNamePrefixType() instead of some string with less precise name passed in


# 7d71e715 26-Apr-2013 Jed Brown <jedbrown@mcs.anl.gov>

Merge branch 'jed/sf-mpich1'

The last release of MPICH1 had some MPI-2 functions without essential
parts. They strictly adhere to MPIX_* naming now so that this problem
does not occur.

* jed/sf-mp

Merge branch 'jed/sf-mpich1'

The last release of MPICH1 had some MPI-2 functions without essential
parts. They strictly adhere to MPIX_* naming now so that this problem
does not occur.

* jed/sf-mpich1:
SF: define MPIU_REPLACE to work around missing MPI_REPLACE
SF: define and work around missing MPI_COMBINER_DUP [reconfigure-needed]

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# 8bfbc91c 19-Apr-2013 Jed Brown <jed@59A2.org>

SF: define MPIU_REPLACE to work around missing MPI_REPLACE


# 7e7d4f0d 10-Apr-2013 Richard Mills <rtm@eecs.utk.edu>

Merged petsc/petsc into rmills/petsc master


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