Merge branch 'master' into pr263/PierreBdR/ts-domain-error-in-stage/master

Merge branch 'master' into barry/improve-git-download

Introduce MPIU_Allreduce() to detect cases where all processes that share an MPI comm do not call the same sequence of MPI_Allreduce()
This is a bug that can be difficult to track down.

Suggested-by

Introduce MPIU_Allreduce() to detect cases where all processes that share an MPI comm do not call the same sequence of MPI_Allreduce()
This is a bug that can be difficult to track down.

Suggested-by: Eric Chamberland <Eric.Chamberland@giref.ulaval.ca>
Suggested-by: Patrick Lacasse <placasse@giref.ulaval.ca>

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fix violations of PETSc style guide: Usage of SETERRQ and NULL

Merge remote-tracking branch 'origin/stefano_zampini/feature-pardiso-schur' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
include/petscmat.h
src/ksp/pc/impls/bddc/bddcschurs.c
src/ma

Merge remote-tracking branch 'origin/stefano_zampini/feature-pardiso-schur' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
include/petscmat.h
src/ksp/pc/impls/bddc/bddcschurs.c
src/mat/impls/aij/mpi/mumps/mumps.c

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MatFactor: move MatMumps APIs for Schur Complement to MatFactor namespace

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

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

Merge branch 'master' into tisaac/dmforest

Get 3.6.2 patches

* master: (1360 commits)
remove nasty memory leak with CUDA code when using block Jacobi with multiple blocks per process
print abs

Merge branch 'master' into tisaac/dmforest

Get 3.6.2 patches

* master: (1360 commits)
remove nasty memory leak with CUDA code when using block Jacobi with multiple blocks per process
print abs in Fortran test example in order to have same result with real and complex builds
changed outdate mpirun and -np to mpiexec and -n
force sqrt to be taken in the precision of PetscReal in fortran examples
continuation line too soon for some compilers
stop configure if user selected C++ clanguage, single precision, complex combination since we do not support it
fixes for Fortran examples to compile cleanly in single precision that do not involve complex numbers
fixes to Fortran examples to compile cleanly in single precision complex
fix previous mistake
must cast 1. to PetscScalar before dividing by a PetscScalar (C++ complex class is terrible)
must cast 0.0 to PetscScalar before comparison with a PetscScalar
changed order of suggested locations of downloadable PETSc to Barry's preference
Increase patchlevel to 3.6.2
remove debug print statement from two commits before
remove debug print statements I accidently left in the last commit
PetscDraw: Fix dummy definition of PetscDrawCollective{Begin|End}()
remove cleanupMumps flag from MatDestroy_Mumps() it should always free the memory it allocated Bug detected while adding features to libMesh
improved viewing of fractional counts in xml nested log viewing fixed bug in output of doubles to xml nested log files
chombo: build only libs - not examples
fix typo. 'gcc-4.8 --with-cxx-dialect=C++11' gives a warning with this line - even though its in a #ifdef thats never enabled.
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PCBDDC: bugfix

PCBDDC: use benign_original_mat instead of M

PCBDDC: allow adaptive selection of constraints using the exact Schur complement instead of the (possibly) incorrect one

In order to implement this efficiently and to reuse the solvers, some modific

PCBDDC: allow adaptive selection of constraints using the exact Schur complement instead of the (possibly) incorrect one

In order to implement this efficiently and to reuse the solvers, some modifications has been made to the code

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PCBDDC: added support to local primal computations with factored matrix whose size is not equal to n_R

To add a space to all comments I have made before. Barry pointed out
that a comment without a space right after '/*' may cause bfort to crash

Merge remote-tracking branch 'petsc/master' into fixed-c

To add a space to all comments I have made before. Barry pointed out
that a comment without a space right after '/*' may cause bfort to crash

Merge remote-tracking branch 'petsc/master' into fixed-comment-space

Conflicts:
include/petsc/finclude/petscmat.h
include/petscmat.h
src/mat/examples/tests/makefile
src/mat/impls/aij/mpi/mpiaij.h

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PCBDDC: added API for the specification of primal vertices in global ordering

propagate info on primal vertices to coarser levels when using the benign subspace trick (still need to be improved)

Merge branch 'pr329/master/Fande-Kong/matpartitioning-hierarch' into pr361/master/Fande-Kong/pcgasm-increaseoverlap: need hierarch to build GASM subdomains.

Conflicts:
src/mat/examples/tests/makefi

Merge branch 'pr329/master/Fande-Kong/matpartitioning-hierarch' into pr361/master/Fande-Kong/pcgasm-increaseoverlap: need hierarch to build GASM subdomains.

Conflicts:
src/mat/examples/tests/makefile
src/mat/impls/aij/mpi/mpiaij.h

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PCBDDC: fixes for multiple PCSetUp calls using the benign trick

PCBDDC: added MatSeqAIJCompress to remove zero entries from SeqAIJ matrices

this is very very useful when changing the local basis with a PtAP operation, which does not care about possible zero entr

PCBDDC: added MatSeqAIJCompress to remove zero entries from SeqAIJ matrices

this is very very useful when changing the local basis with a PtAP operation, which does not care about possible zero entries in the result
MatDetectSubdomains now implements a threshold check for square dense matrices

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PCBDDC: call restore indices after having used idxs

PCBDDC: major improvement in benign code

Allows for multiple local benign dofs (in case any of the local matrices represents disconnected subdomains)
Extended accordingly BDDC class and BDDCGraph cl

PCBDDC: major improvement in benign code

Allows for multiple local benign dofs (in case any of the local matrices represents disconnected subdomains)
Extended accordingly BDDC class and BDDCGraph class
Added MatDetectDisconnectedComponent to identify them

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Merge branch 'master' into pr358/buptphyphy/addmatcreatenormalhermitian/master

PCBDDC: complex build fixes

Merge branch 'tisaac/dt-fix-geom-punning' into tisaac/plex-feature-tree-fv

Pull in a fix to FE geometry that affects the complex,64bit case

* tisaac/dt-fix-geom-punning: (240 commits)
Plex: fix t

Merge branch 'tisaac/dt-fix-geom-punning' into tisaac/plex-feature-tree-fv

Pull in a fix to FE geometry that affects the complex,64bit case

* tisaac/dt-fix-geom-punning: (240 commits)
Plex: fix type punning problem stuffing (PetscFECellGeom *) in a Vec
PGI compiler cannot handle [restrict] usage therefor disable restrict for PGI compiler Fix ex48.c to use PETSc standard way of marking restrict
PETSC_UNUSED must occur before the typename. With PGI compilers they error if it is after the type name
on solaris in TSAdaptChoose_Basic() negative root for zero could produce -infinity thus causing time step to be decreased even though the error estimate was zero
MatGetSchurComplement: revert test from LUMP back to DIAG and update output
there are no tests for opencl or viennacl so prevent warning message: make[2]: *** No rule to make target `testexamples_OPENCL', needed by `tree'. Stop. make[2]: *** No rule to make target `testexamples_VIENNACL', needed by `tree'. Stop.
incorrect initial conditions function that could produce floating point exception value (and does on windows) due to squareroot of non-negative number
forgot to fix rule for building ex194
move ex193.c to ex194 because someone else created a 193
remove outdate manual page comment
add missing VecRestoreArray()
add missing VecRestoreArray()
missing restore array in example
formating for print statements of test example with __float128 precision
fix example for __float128 precision by using PETSc math macros and casting PetscReal in print statements
remove Tao example custom monitor that produced different results for __float128 precision
all PETSc built in monitors require a valid PetscViewer, NULL is not acceptable
PETSc built in monitors always require viewers to be passed in, no longer support a NULL viewer
use tigher haptol for minres for quad precision because otherwise false positive of indefinite matrix appeared in example
check for PetscMPIInt overflow in ISAllGather()
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Merge branch 'master' into jed/process-options-handler

Merge branch 'tisaac/dmplex-stable-tet-refinement' into tisaac/plex-feature-tree-fv

This feature branch also changed the topology of nonconforming examples:
I am merging so that I can make the regre

Merge branch 'tisaac/dmplex-stable-tet-refinement' into tisaac/plex-feature-tree-fv

This feature branch also changed the topology of nonconforming examples:
I am merging so that I can make the regression output that should be
correct in master and next

* tisaac/dmplex-stable-tet-refinement: (594 commits)
plex: added tet shape regression test
plexrefine: remove replaced code
plex: update test output for new tet refinement order
plex: fix tet refinement for stable element shape
DMPlex: added test of shape quality to ex1
Better to use the proper error handling version of PetscViewerASCIIGetStdout() instead of PETSC_VIEWER_STDOUT_()
Generate a very useful error message if PetscLogView(), PetscLogEventGetPerfInfo() or PetscLogEventGetFlops() is called with a preceeding call to PetscLogBegin() and friends (also -log_summary which triggers a PetscLogBegin())
fix compile warnings
Plex: Fix bug with bcComps initialization
Turn off elemental shared libraries if --with-shared-libraries=0 is used
Bib: Added refs
Bib: Fixed a bunch of errors
add warning/error flag for '-mat_superlu_dist_parsymbfact' when MatInputMode=GLOBAL
makefile: fix format
tests: add back ex6f, runex6f targets - that got removed in 2f1d3d565a6a43067e6df75b043e6343b05fcd1d
accessing option that may never have been set
typo in DMNetworkSetNumVariables() reported by Sean Shahkarami
superlu_dist: update to using latest 4.1 version
fix compile warnings
Generate an error message when trying to overwrite default options of CN and BEULER
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PCBDDC: Workaround for rhs in benign subspace

When the rhs is already in the benign space for Darcy, CG suffers a lot (still need to write down some formulas to understand why); instead GMRES conver

PCBDDC: Workaround for rhs in benign subspace

When the rhs is already in the benign space for Darcy, CG suffers a lot (still need to write down some formulas to understand why); instead GMRES converges in 1 (!) iteration.
With this, CG converges without iterating

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