Merge branch 'stefano_zampini/feature-fetidp-class'

KSPFETIDP: allow customization of multipliers from KSPSetFromOptions

Merge branch 'master' into tisaac/ts-ex11-amr

* master: (141 commits)
chombo: fix dirname in tarball and update to use snapshot with gcc-6.1 compile fix
petsc4py: fix tarball url [for arbitary c

Merge branch 'master' into tisaac/ts-ex11-amr

* master: (141 commits)
chombo: fix dirname in tarball and update to use snapshot with gcc-6.1 compile fix
petsc4py: fix tarball url [for arbitary commitid] - and dirname in tarball
Plex: Moved ReconstructGradients_Internal() and ApplyLimiter_Internal() to Plex from SNES
CUDA: Added external declaration for cuBLAS handle.
docs: fix reference to KSP_Create in parent commit
Add information on PETSC_EXTERN and PETSC_INTERN to developers manual
Plex: Symbol is shared between DM and SNES, so must be EXTERN
Plex: Remove unused variables
Configure: Fix check for spaces in PETSC_DIR
Plex: Updated examples to new DMPlexCreateBoxMesh()
sick of failure due to incorrect master branch
SNES ex12: Fixed unstructured GMG test
SNES ex12: Added another unstructured GMG test
petsc4py: use the snapshot with the fix for dmplex change
Examples that require Fortran to compile but were listed in tests that did not require Fortran
Plex ex19: Added DMSetFromOptions()
Plex: Store a flag indicating whether the boundary should change during remeshing - Set using -dm_plex_remesh_bd - Changed Remesh_Internal() signature
Always coarsen boundaries.
Plex: Fixed option name
Plex: Protect unused variables
...

Conflicts:
src/dm/impls/plex/makefile
src/snes/utils/dmplexsnes.c

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

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/mat/impls/aij/seq/mkl_pardiso/mkl_pardiso.c

Merge branch 'pr476/psanan/psanan/pc-telescope-subcomm-type/master'

Merge branch 'stefano_zampini/fix-bddcnullspace'

PCTELESCOPE: add option to change subcommunicator type (interlaced or contiguous)

Add a new data field to PCTELESCOPE which allows, before setup only, the user to specify
which type of subcommunicat

PCTELESCOPE: add option to change subcommunicator type (interlaced or contiguous)

Add a new data field to PCTELESCOPE which allows, before setup only, the user to specify
which type of subcommunicator to create. Under the assumption of sequential ordering on
equally-sized compute nodes, this allows the user to specify whether their subcommunicator
lives on a subset of nodes (with the same number of ranks/node), or whether it is striped across nodes (the default).

This commit also adds some missing __FUNCT__ definitions

An example is added which calls KSPView. This isn't ideal, so a better idea of how to test this functionality would be welcome.

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PCBDDC: remove PCBDDCSetNullSpace. Nullspace info is now local and should be attached to the local Neumann matrix

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

Merge branch 'tisaac/sf-fix-multi-sf-leaves' into tisaac/dmp4est-feature-injection

* tisaac/sf-fix-multi-sf-leaves: (174 commits)
PetscSF: fix PetscSFGetMultiSF() for sparse leaves
PetscSF: make

Merge branch 'tisaac/sf-fix-multi-sf-leaves' into tisaac/dmp4est-feature-injection

* tisaac/sf-fix-multi-sf-leaves: (174 commits)
PetscSF: fix PetscSFGetMultiSF() for sparse leaves
PetscSF: make regression test that fails
few more clang static analyzer fixes
many issues detected by clang static analyzer
Update hypre to its release version
Updates for xSDKTrilinos builds
Added --download-xsdktrilinos
Communicator passed to VecCreateSeq should be PETSC_COMM_SELF
PCMG man page: fix typo in options name
Bib: Added refs
DMLabel: Removed unused variable
Metis tries to use backtrace which requires -lexecinfo on some systems such as freebsd Remove -lexecinfo from freebsd configure files since it is only needed by metis
add alternative output that occurs on some systems due to use of random number generator in partitioner
Plex: When creating cohesive submeshes, fix memory leak
Plex ex11: Updated output for new distribution algorithm
Plex: When explicitly distributing the depth label, we must recreate empty strata
Plex: When partitioning, the cell numbering should include hybrid points
Plex: Allow cell and vertex numberings to include hybrid points
need to show diffs of ex22 if it fails
Support two different output for test example, since due to roundoff this example can produce slightly different convergence history
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Merge branch 'pr426/dmay/dmay/pctelescope-mods/master'

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

Merge branch 'barry/remove-pc-nonzero-guess'

Removed PCSetInitialGuessNonzero() and PCGetInitialGuessNonzero();
they make no sense since PCApply() is a operator and cannot depend on the initial guess.
The routines were not used anyway. Also upd

Removed PCSetInitialGuessNonzero() and PCGetInitialGuessNonzero();
they make no sense since PCApply() is a operator and cannot depend on the initial guess.
The routines were not used anyway. Also updated the manual page for PCKSP developers not
to clarify why there is not support for "passing the initial guess" into the inner KSP

Thanks-to: Dave May <dave.mayhem23@gmail.com>

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PCTelescope - New API
* Added API for Get/Set flags indicating whether KSPSetComputeOperators should be used or ignored.

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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PCBDDC: Finally, I was able to get rid of changing the iteration matrix during the KSP, which I've never liked from the very beginning

The code is way simpler now. The change of basis (if any) is pe

PCBDDC: Finally, I was able to get rid of changing the iteration matrix during the KSP, which I've never liked from the very beginning

The code is way simpler now. The change of basis (if any) is performed during PCApply and PCApplyTranspose.
Added interior flag to PCBDDCSetChangeOfBasisMat in order to save some work, if possible

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

Merge branch 'master' into tisaac/dmforest

* master: (87 commits)
fixed --download-xxx=/directory to not mistake other options such as --download-mpich-pm=hydra etc
Correct spelling for Autotool

Merge branch 'master' into tisaac/dmforest

* master: (87 commits)
fixed --download-xxx=/directory to not mistake other options such as --download-mpich-pm=hydra etc
Correct spelling for Autotools libtoolize in commit a0848688a08a6eb150afdc95a2f6ce49cd4cd079
Fix for commit c8b462efbd8e8a5f06df500cf417f3a48f2b88d9 Put back the gitpreReq() check that was needed for MOAB
website: fix Fluidity link
bib/cite: add UMFPACK
nightlybuilds: update test tu use newer intel compiler [detect and use compiler path]
nightlybuilds: fix vec/ex7,ex7f link issue by using the correct LIBS option
Added support for users to provide their own download package installers --download-xxx=/directory where the directory contains the file xxx.py that is a standard PETSc package definition like in config/BuildSystem/config/packages/xxx.py
nightlybuilds: switch default intel compiler [& MKL] from 13.1.3 to 16.0.0.
mkl_pardiso: fix runex125_mkl_pardiso
mkl_pardiso: fix runex2_mkl_pardiso_cholesky
nightlybuilds: switch OSX to use boost from brew [as --download-boost is broken]
trilinos: gitcommit - always specify branch as origin/branch
Add error check to boost.py when running on Mac OS because the shared libraries created do not work since they do not have the proper rpath set
Update output files for mpi matrices that use to be seq
Move PostProcess() runs until after PETSc configure has saved all data to the filesystem so that make install will work correctly.
Switch to Trilinos release candidate for --download-trilinos Tested, failed with unresolved Kokos methods, Issue report to Trilinos team
Some configure packages UnitTest-CPP requires libtoolize to be called before autoreconf on some systems
--download-ideas now downloads unittest-cpp
simplied ./configure packages that need autoreconf to be run first (like moab and unittest-cpp) added unittest-ccp download changed downloadfilename to downloaddirname since that is what it is
...

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

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Merge branch 'pr401/tferma/virs-pcfieldsplit-fix/master'

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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A fix for fieldsplit pcs when using snes virs.

When reset pc fieldsplit saves a copy of the original IS. SNES VIRS then calls a new function, PCFieldSplitRestrictIS, and supplies
the inactive set t

A fix for fieldsplit pcs when using snes virs.

When reset pc fieldsplit saves a copy of the original IS. SNES VIRS then calls a new function, PCFieldSplitRestrictIS, and supplies
the inactive set to create new ISs for the fieldsplit. This is then reindexed and passed down to any nested fieldsplits.

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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

Merge branch 'barry/Sylvain-gmres-symmetric'