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

Merge branch 'barry/feature-vec-lock'

Added VecLockPush() and VecLockPop() to make vector read only
Used VecLockPush() and VecLockPop() in a couple of key locations; PCApply(), KSPSolve(), MatMult()
Fixed many uses of VecGetArray() to Ve

Added VecLockPush() and VecLockPop() to make vector read only
Used VecLockPush() and VecLockPop() in a couple of key locations; PCApply(), KSPSolve(), MatMult()
Fixed many uses of VecGetArray() to VecGetArrayRead()
Added VecGet/RestoreArrayPair() for commonly occuring pattern
Added const to many locations driven by use of VecGetArrayRead()

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

Merge branch 'barry/update-suitesparse-version'

Conflicts:
src/ksp/ksp/examples/tests/makefile

Completed support for SuiteSparse Cholmod using GPUs

configure: --with-cuda --download-suitesparse-gpu --with-64-bit-indices (SuiteSparse limitation)
Runtime: -mat_cholmod_useGPU 1 or 0 default is 1

Updated to support SuiteSparse 4.4.1
added UMFPACK and CHOLMOD examples to test suite
updated documentation to better unify klu,umfpack, and cholmod
In response to bitbucket issue 88

Did not add CHO

Updated to support SuiteSparse 4.4.1
added UMFPACK and CHOLMOD examples to test suite
updated documentation to better unify klu,umfpack, and cholmod
In response to bitbucket issue 88

Did not add CHOLMOD GPU support usage to --download-suitesparse yet

Reported-by: Sean Farley <sean.michael.farley@gmail.com>

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Merge branch 'master' into barry/ksp-converged-reason-viewer

Conflicts:
src/sys/objects/options.c

Merge branch 'barry/fix-damp-not-one-pcapplyrichardson'

CHOLMOD: Fixed return for void function

missing ierr declaration

-ksp_richardson_scale was ignored when PCApplyRichardson() was used
Fix: turn off PCApplyRichardson() when scale is not 1 and print PetscInfo warning

Reported-by: Mark Adams <mfadams@lbl.gov>

Fixed

-ksp_richardson_scale was ignored when PCApplyRichardson() was used
Fix: turn off PCApplyRichardson() when scale is not 1 and print PetscInfo warning

Reported-by: Mark Adams <mfadams@lbl.gov>

Fixed missing carriage return in uses of PetscInfo() and missing ierr CHKERRQ() usage

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Merge branch 'barry/remove-unneeded-paren-petscmalloc'

Conflicts:
src/mat/impls/baij/seq/baij.c

convert some PetscMalloc() to PetscMalloc1()
remove unneeded () in first argument to PetscMalloc/Calloc1()
fixes for MATLAB examples

Merge branch 'barry/fix-options-default'

Conflicts:
src/ksp/ksp/examples/tutorials/ex52.c

update use of PetscOptionsBool() to not rely on default setting automatically

fixed documentation for PetscOptionsXXX that refered to "default value" when they really mean current value
also fixed usage of PetscOptionsEnum() with regards to current value in several calls

Repo

fixed documentation for PetscOptionsXXX that refered to "default value" when they really mean current value
also fixed usage of PetscOptionsEnum() with regards to current value in several calls

Reported-by: Ed Bueler <elbueler@alaska.edu>

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CholmodOrderingMethods is defined but never used, compiler complains

Merge branch 'master' into prbrune/snes-fascontinuation

* master: (855 commits)
fix for moab example had wrong blocksize of mapping
docs:remove src/docs/doxygen/manual [per Barry's instructions]

Merge branch 'master' into prbrune/snes-fascontinuation

* master: (855 commits)
fix for moab example had wrong blocksize of mapping
docs:remove src/docs/doxygen/manual [per Barry's instructions]
gfortran: remove 132 char limit from f90 free-form
SNES: Set up matrix-free *after* copying the user Jacobian to snes->pc
DMPlex-Gmsh: Use trueNumCells when building the coordinate section
Sys: Got guard logic reversed
Sys: The #define guard for PetscMalloc*() must match the one for PetscFree*()
PetscFV: I hate fucking complex
removed ltog scatter from DMDA since functionality can be obtained with gtol scatter and less memory
fix test of DMLocalToGlobalBegin/End and add actual test cases
improve object memory logging for DA, ISLocalToGlobal and ISBLOCK
lower high water mark of constructing parallel scatter by allocating only as much room in svalues as needed
owner in VecScatter construction is the rank, therefor can use PetscMPIInt to hold it do not PetscInt
another reuse of allocated array in 2d/3d DMDA create
improved high water mark of DMDASetups by implementing and using PETSC_USE_POINTER for ISCreateBlock()
PetscFV: Another complex fix
DMPlex+TS: Fixing types
ISIdentity() was wrong for block IS! Indices are NOT scaled by bs
PetscFV: Straighten out complex types
TS ex11: Fix casts and remove unused variable
...

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Merge branch 'master' into barry/saws-options

Merge branch 'master' into stefano_zampini/pcbddc-multilevel-improvement

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

Merge branch 'master' into stefano_zampini/pcbddc-multilevel-improvement

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

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Merge remote-tracking branch 'origin/master' into feature-dmmoab

Merged petsc/petsc into master

Merge branch 'master' into knepley/feature-plex-hdf5-parallel-load

* master: (125 commits)
since PETSc cannot view factored matrices, generate an error rather than display the wrong stuff (this wa

Merge branch 'master' into knepley/feature-plex-hdf5-parallel-load

* master: (125 commits)
since PETSc cannot view factored matrices, generate an error rather than display the wrong stuff (this was really bad)
outdated example that doesn't match coding style removed and buggy
petscversion.h: workaround ifort -cpp lack of referential transparency
configure: ignore AR, MAKEFLAGS [if set in env]
incorrect first entry in array being zeroed in example
sizeof.c: remove dependence on petsc [and fix syntax error]
nightlybuilds: use consistant PETSC_ARCH, machine names
TS: Allow viewing of TS solutions
DMPlex: Fix comparison for complex
change MPIVersion streams to use MPI_Wtime() to be portable to Windows do not use scalar square root on real number; it upsets Microsoft
cannot use I in PETSc code because in complex it sometimes represents imaginary number cannot pass PetscScalar * to VecNorm()
in dashboard don't warn about SSL and BOI deprecated
TS ex11: Fixed output formatting
Doc+DMPlex: Added function documentation for some refinement functions
streams: translate code from 'bash' to 'sh' [fix freebsd]
barry is an idiot who doesn't have a clue as to what he is doing (and git's unfriendlyness doesn't help matters)
don't list examples under C that don't work with complex!
forgotten output file
removed valgrind warning about sending uninitialized data
nightly builds ignore unrecognized pragma and .c file as C++ code
...

Conflicts:
include/petsc-private/dmpleximpl.h

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Merge branch 'shri/update-SuiteSparse'