Merge branch 'master' into barry/xcode

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fix outdated PetscOptionsList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

show more ...

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
...

show more ...

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

Merge branch 'balay/remove-sdir'

__SDIR__ is gone. This is an ABI change (PetscError) so dependent
packages must be recompiled.

* balay/remove-sdir:
__SDIR__: remove remaining traces and documen

Merge branch 'balay/remove-sdir'

__SDIR__ is gone. This is an ABI change (PetscError) so dependent
packages must be recompiled.

* balay/remove-sdir:
__SDIR__: remove remaining traces and document in changes.html
__SDIR__: remove usage of __SDIR__ from PETSc sources.

This merge fixes one instance of __SDIR__ that was added after
'balay/remove-sdir' branched off.

show more ...

__SDIR__: remove usage of __SDIR__ from PETSc sources.

Merge branch 'master' into jed/ts-eimex

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

Conflicts:
src/ts/interface/tsregall.c

removed a bunch of duplicate unneeded includes of std include files

Hg-commit: b6c9f3e2b0eb8b7277fe131cc83beede5d495522

Uncrustified src/sys/*

Hg-commit: 9f71677807bad7b55428a6cc0f5ccc5052e91805

Commit after merge

Hg-commit: 29c41d281e3ece3127c753661dccfd04e452b7f8

removed trailing blanks from source code
added rule rmtrailingblanks accessible via make ACTION=remtrailingblanks tree

Hg-commit: 6e3652165d48aa5f3e94dd66bf607adea6fac27a

backout all chmod stuff in bf971ba58125
[but keep diffs to src/mat/impls/aij/mpi/mpimatmatmult.c ]

Hg-commit: 4a812fc1f35496ce2717c7da9ef12ffabbd13258

removed a spurious call to MatSetBlockSize.

Hg-commit: bf971ba58125bd8cf7ceb2a9d0f5cdf27c27cc6a

commit after merge

Hg-commit: d540875a63b3c979c82b6a7fa7f062571e906d10

Mass revert file modes that were made executable in f6e61ee9c329

Hg-commit: 116d90d0b66125cee0db3e7351047057e756baf5

Merge

Hg-commit: ee8d91ae0580d1d4fa92be38a18d40c838b9a257

changed MatMatMult to MatTranposeMatMult.

Hg-commit: f6e61ee9c329774cd5343eea1ee6b7432be17c3f

Use #include <header.h> instead of #include "header.h" when there is no intent to search the current directory for header.h

Hg-commit: bd7216e80cc035071a5136364ab9d04bf9f41a07

Merged

Hg-commit: d8c12016d3250a8d659fa779bc1698da4d6c5237

removed #define PETSCXXX_DLL from top of all source files

Hg-commit: b784aa18ddcf5337d4011d34f0fa008681695ac1

Merge.

Hg-commit: dbd6603baa0301f54f7391c043f07dcfbf07f03e

moved definition of PETSC_STDCALL to private/fortranimpl.h where it belongs
removed all DLL export/import stuff since it was never used and never will be
removed MatPermuteSparsify() since it sucked.

moved definition of PETSC_STDCALL to private/fortranimpl.h where it belongs
removed all DLL export/import stuff since it was never used and never will be
removed MatPermuteSparsify() since it sucked.

Hg-commit: 72f7a5e60333f6c9780d56fcce45657940d16b13

show more ...

Merge.

Hg-commit: 9701f074fd20019a272d7c76f3b333aafe4932b0

commit after merge

Hg-commit: 6c2d63125265475c8c2a2df4be98d34f2fbbab4c

added -pc_sacuda_cycles option

Hg-commit: a6a7991be63fbbae8e9c4de8f5c0220ab293621a