Merge branch 'denera/tao-convergence-check-fix' [PR #886]

* denera/tao-convergence-check-fix:
TaoMonitor no longer has double-duty for both monitoring and updating the converged reason.
The converge

Merge branch 'denera/tao-convergence-check-fix' [PR #886]

* denera/tao-convergence-check-fix:
TaoMonitor no longer has double-duty for both monitoring and updating the converged reason.
The convergence function is now called explicitly in the algorithms following the monitor call, mimicking the current implementation of SNES.

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fix propagated throughout, convergence tolerance bug discovered and fixed in toy problem

Merge branch 'denera/fix-tablevels-for-views' [PR #869]

* denera/fix-tablevels-for-views:
Instead of manual push-pop tab operations, views now inherit tablevels automatically.
This makes views consi

Merge branch 'denera/fix-tablevels-for-views' [PR #869]

* denera/fix-tablevels-for-views:
Instead of manual push-pop tab operations, views now inherit tablevels automatically.
This makes views consistent with default convergence monitors.

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Wrapping up for a pull request

Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
ini

Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
initialize ap as complained by the nightly tests
Plex ex3: Update to new point function API
initialize some variables as complained by nightly tests
SNES ex12: Mix misnaming Nf --> Nc
update tests
add tests
add MatView_SeqXAIJ_ASCII_structonly(); enable A->structure_only in MatSetValuesBlocked_SeqBAIJ
typo
fill-in some references
Bib: Fixed ref
Plex: Added PLY to file support
Plex: Adding PLY support
PetscDS: Turn off Fortran bindings for Constants
Plex tests: Updated to new point function API
SNES ex56: Moved tests to new format
DM: Allow field projection functions to take an array of scalars - This will allow us to pass in user data to kernels without void *, more efficiency than aux fields
...

Conflicts:
config/builder.py
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex1.c
src/dm/impls/plex/plexcreate.c
src/dm/impls/plex/plexgmsh.c
src/snes/examples/tutorials/ex63.c

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Merge branch 'master' into knepley/feature-plex-pragmatic-parallel

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes

Merge branch 'master' into knepley/feature-plex-pragmatic-parallel

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes
add help menu for MatCreateSubMatricesMPI()
rename struct Mat_SubMat -> Mat_SubSppt
add a little information to the manual about using tchem
rename MatCreateSubMatrixComposite -> MatCreateSubMatrixVirtual; Mat_SubMatrix -> Mat_SubVirtual
need to protect the \ passed on the makefile on my Mac
Bib: Updated ref
update src/mat/examples/tests/output/ex23_#.out
rename MatGetSubMat -> MatCreateSubMat
Mark MatCreateMPIAIJWithSplitArrays() and MatMPIAIJSetPreallocationCSR() with MAT_NO_OFF_PROC_ENTRIES
superlu: libray is installed in PREFIX/lib64 - fix this to use PREFIX/lib
backport fixes cc105cc3 2b35c90a - required for 3bf428d - that was backported from master - 80c96bb
'echo -n' fails on opensolaris/osx - so avoid using it.
fix diffs in nightlybuilds due to options in ~/.petscrc
add Kelley03 to src/docs/tex/petsc.bib
build: determine moudles, mpi.h used during buildtime and print in 'info'
fix analyzer warnings
fix build failure on opensolaris - where -lm from flibs is removed due to -lm in cxxlibs. But then - only flib gets used for some configure tests [blaslapack, parms]
config: prefer __restrict over C99 restrict keyword
...

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Merge branch 'barry/remove-funct'

Remove the use and definition of __FUNCT__ throughout the code

Since all modern C/C++ compilers provide this functionality we no longer need to provide it manually in PETSc
Time: 1.5 hours
Thanks-t

Remove the use and definition of __FUNCT__ throughout the code

Since all modern C/C++ compilers provide this functionality we no longer need to provide it manually in PETSc
Time: 1.5 hours
Thanks-to: Andreas Mang <andreas@ices.utexas.edu>

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Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Merge branch 'master' into knepley/feature-plex-handle-func-failure

* master: (378 commits)
SNES ex5: Fix coordinate determination for empty subdomains
fixed petsc.bib entry
p4est: fix syntax

Merge branch 'master' into knepley/feature-plex-handle-func-failure

* master: (378 commits)
SNES ex5: Fix coordinate determination for empty subdomains
fixed petsc.bib entry
p4est: fix syntax error with error message
SNES ex5: Correct Jacobian handling on patches
SNES ex5: Stupid complex fixes
DMP4est: fix transfer of labels to parents
petsc4py: update to latest snapshot. Fixes da example breakage in petsc4py test suite
Plex: Correct setting of options on refined or coarsened meshes
Plex: Add info for grid hashing
Plex: Add logging in interpolator creation
Plex: Correct use of tabs in ASCII viewer
DM: Shorten long event name
Plex ex12: Create boundary label automatically at all levels of mesh hierarchy
Plex ex12: Change PetscViewerSetFormat --> PetscViewerPushFormat - Fix order of SetMode and SetFilename
Plex ex12: Change all functions to static
Since DMDA with periodic boundary conditions does support P0 interpolation remove checks that error out under those conditions
ascem-io.py and amanzi.py need to handle self.hdf5.include being None correctly
fix MPI Uni to recycle communicators so it won't run out like with the petsc4py tests also fix check for location of python shared library on mac to check all cases each time
Switch back to Sherry's version since she accepted by pull request
PetscDraw: Update help messages for -draw_save* options
...

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

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Merged petsc/petsc into master

Merge branch 'barry/fix-private-functions'

Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

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

Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcgraph.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcscalingbasic.c
src/ksp/pc/impls/bddc/bddcschurs.c
src/mat/impls/is/matis.c

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labeled a variety of additional internal functions as static
to prevent them from being publically available in the library

Merge branch 'master' into barry/add-pcfieldsplit-logevent

Merge branch 'tisaac/dmforest' of bitbucket.org:petsc/petsc into tisaac/dmforest

Merge branch 'master' into tisaac/dmforest

* master: (136 commits)
Make error message specific to exactly what matrix is supported
Prevent fblaslapack or f2cblaslapack from being compiled with t

Merge branch 'master' into tisaac/dmforest

* master: (136 commits)
Make error message specific to exactly what matrix is supported
Prevent fblaslapack or f2cblaslapack from being compiled with the -no-prec-dev Intel compiler option since it can produce incorrect results
Fix for PCReset_HYPRE to make it reentrant.
replace default superlu_dist '-mat_superlu_dist_colperm METIS_AT_PLUS_A' with MMD_ATA to avoid different random numbers for nightly tests
fixes for merge from maint patch
Added PCReset_HYPRE() so it may be used with SNESVI solvers
remove Microsoft compiler message for paste macros used for handling Blas/Lapack macro name mangling for example
Increase the number of PetscViewerPushFormat() possible to 25 and use a macro PETSCVIEWERFORMATPUSHESMAX for the value
Configure: Remove redundant logging
Bib: Added ref
nightlybuids: fix permissions of script
MatRegisterDestroy() does not exist but it is listed in manual pages
externalpackages-git: save local changes if any - in git stash - before 'git checkout -f' Useful incase --with-package-commit=HEAD option was msissing [perhaps due to a typo]
nightlybuilds: add xsdk builds
Add architectures for testing xsdk package downloads (Trilinos, Hypre, SuperLU)
create another version of TurnForward() for adaptive time stepping specifically
Configure: Give proper default if HOME is missing from the environment
fix abbreviation
allow zeropivot for MatSOR_SeqAIJ_Inode, node size=1
add test case using adpative time stepping for checkpointing type 'NONE'
...

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Merge branch 'master' into barry/add-pcreset-hypre-for-master

Needed to move PCDestroy_HYPRE() added to master to PCReset_HYPRE() since that was introduced
as a bug fix for maint

fixed up formatting of references in manualpages to consistent style

References:
+ 1. - ref1
. 2. - ref2
- 3. - ref3

previously the formatting was varied and ugly

Merge branch 'master' into hongzh/checkpointing

Manual merges for a couple of PetscOptions changes in master

Merge branch 'master' into pr391/zianekhodja/lilia/tsirm/master

Merge branch 'tisaac/dm-label-promote' into tisaac/dmforest

* tisaac/dm-label-promote: (319 commits)
snes tutorial ex69: give mesh a name for regression purposes
DM: make DMLabel labels a part o

Merge branch 'tisaac/dm-label-promote' into tisaac/dmforest

* tisaac/dm-label-promote: (319 commits)
snes tutorial ex69: give mesh a name for regression purposes
DM: make DMLabel labels a part of all DMs
builder: update regression tests
builder: update some missing package requirements
DM: set coordinate vector name
ts tutorials ex11_sa: make it compile
mark variable as unused so compiler doesn't warn about unused value
configure: use 'git cat-file -e' to check for existance of a commit in localrepo. ['git rev-parse' does not give error for a hash thats not in repo]
petsc4py: revert to manually syncing petsc4py with petsc master changes
configure: revert gitcommit default value to Null. If a pacakge using giturl does not change this value - raise an error
fix: revert change in a44bcdf that breaks with pgf90
update test output for fixed to hypre interface that now actually pass the interp vectors to BoomerAMG
Error message should say use negative threshold value to prevent filtering out zeros
Calls to HYPRE_BoomerAMGSetInterpVectors() did not actually copy the vector data pointer from the PETSc vector to the hypre vector thus resulting in the hypre interp vectors being identically zero and hence not affecting the quality of the AMG hierarchy produced/
DMPlex: Silence overzealous compiler warnings
add row/col orientation to MatConvert_Elemental_Dense
fix formatting error in previous commit [broke nightlybuilds]
fix formating of TSTHETA manual page and add missing command line option
run hwloc with MPIEXEC and binding so it runs on the correct machine
fix: memory leaks [in valgrind test]
...

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Merge branch 'barry/petscoptions-object' into stefano_zampini/feature-pardiso-schur

Merge branch 'master' into barry/petscoptions-object

Merge remote-tracking branch 'petsc/master' into moved-partitioning-to-pcgasmsetup