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

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddc.c

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

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcfetidp.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcschurs.c
src/mat/impls/is/matis.c
src/mat/impls/is/matis.h

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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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CUDA: Added external declaration for cuBLAS handle.

Since the variable is not declared in the source file, this resulted
in compilation failures in certain configurations (e.g. ViennaCL with CUDA en

CUDA: Added external declaration for cuBLAS handle.

Since the variable is not declared in the source file, this resulted
in compilation failures in certain configurations (e.g. ViennaCL with CUDA enabled).

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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 'maint'

Merge branch 'pr473/alexfikl/alexfikl/fortran-visibility/maint' into maint

Merge branch 'master' into barral/feature-dmplex-adapt

add missing PETSC_EXTERN to custom Fortran wrappers

Merge branch 'master' into knepley/fix-plex-mf-prec

* master:
GAMG: Fix nearnullspace check
Plex: Must check block size in parallel from DMGetLocalToGlobalMapping() - Small format cleanup
Mov

Merge branch 'master' into knepley/fix-plex-mf-prec

* master:
GAMG: Fix nearnullspace check
Plex: Must check block size in parallel from DMGetLocalToGlobalMapping() - Small format cleanup
Move spinlocks definitions to pinit.c, where they don't depend on PETSC_HAVE_FORTRAN
Allow empty data
Update output files after change in PetscObjectPrintClassNamePrefixType
Deactivate tabs when printing several things in the same line

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Merge branch 'tisaac/dmplex-localize-targeted' into tisaac/dmp4est-set-periodic-domain

* tisaac/dmplex-localize-targeted:
DMLocalizeCoordinates(): make more flexible and targeted
GAMG: Fix nearn

Merge branch 'tisaac/dmplex-localize-targeted' into tisaac/dmp4est-set-periodic-domain

* tisaac/dmplex-localize-targeted:
DMLocalizeCoordinates(): make more flexible and targeted
GAMG: Fix nearnullspace check
Move spinlocks definitions to pinit.c, where they don't depend on PETSC_HAVE_FORTRAN
Allow empty data
Update output files after change in PetscObjectPrintClassNamePrefixType
Deactivate tabs when printing several things in the same line

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Merge branch 'maint'

Merge branch 'jose/maint/tabs-print-class' into maint

Merged in esss/petsc/fix-spinlock-location (pull request #471)

Move spinlocks definitions to pinit.c, where they don't depend on PETSC_HAVE_FORTRAN

Move spinlocks definitions to pinit.c, where they don't depend on PETSC_HAVE_FORTRAN

Merge branch 'master' into knepley/feature-parallel-mesh-load

* master: (59 commits)
Increase patchlevel to 3.7.1
Fix manual page for MatGetTransposeNullSpace()
remove unneeded use of PetscCon

Merge branch 'master' into knepley/feature-parallel-mesh-load

* master: (59 commits)
Increase patchlevel to 3.7.1
Fix manual page for MatGetTransposeNullSpace()
remove unneeded use of PetscContainer to hold iscoloring in SNESComputeNGSDefaultSecant()
added SNESView for ngs, added options database to ngs manual page, removed dead routine
gcov: enable in mpiuni test
incorrect capitalization of an even name
force same number of iterations for output of ml example
changed output for ml example to not be machine dependent
DMP4est: access data after setup
SNESLineSearch_Apply was labeled with PETSC_EXTERN in one place but when declared this was not visible hence library build failed under Microsoft.
Example had print statements of complex numbers
Fix more errors in agmres for 64 bit integers
builds: fix nampespase conflict with 'analyzer-buid' and checkBuilds.py
gcov: add more packages to test
add a couple of KSP that were not represented in testing
gcov: enable more externalpackages for this test
fixes for agmres for 64 bit indices, fix for findvisibleprivatefunctions to be portable for Mac and Linux
get GAMG to get null space (more)
fix c++ compile errors
Add test example for kacmarz preconditioner since gcov indicated there was NONE
...

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

Merge branch 'barry/make-functions-static'

Updated script for detecting visible symbols

Removed unneeded visibility of some symbols
Fixed some namespacing
Removed the use of unneeded implementation includes in the TAO code

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 'master' into sanderarens/fix-plex-neumann-bc

* master: (28 commits)
few more clang static analyzer fixes
many issues detected by clang static analyzer
Update hypre to its release

Merge branch 'master' into sanderarens/fix-plex-neumann-bc

* master: (28 commits)
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
DMLabel: Removed unused variable
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
Plex ex1: Fixed output for empty strata
DMLabel: Added DMLabelHasStratum()
Minor changes and fix to bugs introduced in 82f73ecaa
Modified makefile to fix aijcusparse tests
Add missing code for the case PETSC_HAVE_VECCUDA
Fix bugs introduced in 82f73ecaa
Use VECCUDA with MATAIJCUSPARSE
CUDA: Fixed visibility and disabled Fortran bindings for VecScatters on GPU.
Replace kernels with thrust
...

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Merge branch 'pr421/alex/feature-veccuda'

* pr421/alex/feature-veccuda
The rationale of this pull request is to have GPU-enabled vectors purely based on CUDA,
and with the possibility of placing a u

Merge branch 'pr421/alex/feature-veccuda'

* pr421/alex/feature-veccuda
The rationale of this pull request is to have GPU-enabled vectors purely based on CUDA,
and with the possibility of placing a user-provided array on the GPU side.

Conflicts:
src/vec/vec/impls/seq/seqcusp/cuspvecimpl.h
src/vec/vec/impls/seq/seqviennacl/viennaclvecimpl.h

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Vec: added new type VECCUDA based on VECCUSP

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