Merged master into semihozmen/ksp-fcg-eigen-comp-support

Merge branch 'master' into pr192/Fande-Kong/scalable-matincreaseoverlap/master

Needed to merge master to update to new calling sequence PetscCommBuildTwoSided

Merged petsc/petsc into master

Merge branch 'barry/fix-directory-layout'

updated PETSc directory layout to match standard packaging strategies

include/petsc finclude,private,mpiuni
lib/petsc conf
bin/petsc*

Merge branch 'master' into tisaac/dmforest

If we're going to start developing on this again, the recent changes to the
location of configuration files will make it annoying to switch to and from
thi

Merge branch 'master' into tisaac/dmforest

If we're going to start developing on this again, the recent changes to the
location of configuration files will make it annoying to switch to and from
this branch. Matt's and my fixes in DMPlex will also be relevant.

* master: (1557 commits)
MatLoad_MPIDense() always allocated array space even if it was previously provided
Clarified lumping options for PCFieldSplitSchurPreType SELFP.
fixed up PetscInfo in GAMG
TSErrorWeightedNorm[2|Infinity]: API changes
MatLoad_SeqDense() always allocated new space for the data even if the user already provided it
Fixed DMCompositeGetAccessArray() to support readonly vectors
Fix obviously-wrong aspects of documentation on SNESVINEWTONRSLS and SNESVINEWTONSSLS.
fixed example to compile - demonstrates a bug
var name 'len' was F90 key word
For user provided Jacobian functions they should always assembly into the second matrix, the one from which the preconditioner is built because the first may be used as matrix-free with -snes_mf_operator
Suggest --with-64-bit-indices if users mistakenly use --with-64bit-indices
Fix configure logging of integer size.
missing underscore in #define of vecgetarrayread translation of fortran stub for VECGETARRAYREAD
updated test output files to reflect differences introduced previously in PCView output
-ksp_type preonly does not support -ksp_monitor_short so remove from test line to prevent extranious warning output
missing CHKERRQ; and ugly double declaration of ierr
Plex ex3: For want of a semicolon, the kingdom was lost
MatSetValuesMPISBAIJ will now print correct global indices when error generated due to new nonzero location
completed basic use of MatSetValuesBlocked_SeqBAIJ_Inlined() by MatSetValuesBlocked_MPIBAIJ() to allow proper global indices being printed when error generated by new nonzero locations.
Added inline version of MatSetValuesBlocked_SeqBAIJ() to be used by MatSetValuesBlocked_MPIBAIJ() to print error message for nonzero block with global indices
...

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Merge branch 'master' into shri/ts-is-for-differential-variables

Conflicts:
include/petsc-private/tsimpl.h
src/ts/impls/eimex/eimex.c
src/ts/interface/ts.c

Merge branch 'master' into jed/chem
Note merging a branch with good stuff in it for a year and a half is insane!

Conflicts:
src/ts/examples/tutorials/makefile
src/ts/interface/ts.c

Merge branch 'master' into stefano_zampini/pcbddc-adaptive-selection

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c
src/sys/threadcomm/interface/threadcomm.c

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Merge branch 'master' into pr252/dmay/PetscViewerBinarySkipHeaderVecViewLoad
Manual merge of makefile

Conflicts:
src/sys/classes/viewer/examples/tutorials/makefile

Merge branch 'barry/feature-vec-lock'

Added VecLockPush/Pop() around SNES callbacks etc
Added DADAVecGetArray[DOF]Read()
Added use of GetArrayRead() as needed
Added many more const as needed

Note DMDAVecGetArray[DOF]Read() does not yet

Added VecLockPush/Pop() around SNES callbacks etc
Added DADAVecGetArray[DOF]Read()
Added use of GetArrayRead() as needed
Added many more const as needed

Note DMDAVecGetArray[DOF]Read() does not yet require correctly consted argument

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Merge branch 'master' of bitbucket.org:petsc/petsc into mark/gamg-crs-ksp2

mv include/finclude to include/petsc-finclude for namespacing in installs

mv include/finclude to include/petsc-finclude for namespacing in installs

Merge branch 'master' into mlange/refactor-plex-distribute

Conflicts:
src/dm/impls/plex/examples/tests/output/ex12_1.out
src/dm/impls/plex/examples/tests/output/ex12_2.out

Fixes and formats to some manual pages

Reported-by: Andrew Cramer <a.cramer@uq.edu.au>

Merge branch 'master' into shri/ts-events

Conflicts:
src/ts/interface/ts.c

Merge branch 'master' into shri/feature-dm-circuit

Conflicts:
src/dm/impls/makefile

Merge branch 'master' into barry/wirth-fusion-materials
bad manual merge needs to be fixed
this is what happens when branches hang around too long

Conflicts:
src/ts/examples/tutorials/advection-dif

Merge branch 'master' into barry/wirth-fusion-materials
bad manual merge needs to be fixed
this is what happens when branches hang around too long

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

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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

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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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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