Merge branch 'bermeo/add-mkl-pardiso' (pull request #105 - rebased)

mkl_pardiso: change -pc_factor_mat_solver_package from pardiso to mkl_pardiso [and other names]

Added support for mkl-pardiso
also rebase to latest petsc-master [and fix -ksp_view]

Merge branch 'stefano_zampini/matis_getmpixaij' into stefano_zampini/pcbddc_deluxe

MATIS: MatISGetMPIXAIJ is now well tested and can be public. Moved to MATIS source

minor corrections to matis.c

Merge branch 'prbrune/matcoloring-power'

* prbrune/matcoloring-power:
MatColoringPower: Add MatColoringPower, which one-colors powers of the mat

Merged upstream/master to feature-dmmoab

Merge remote-tracking branch 'upstream/master'

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
...

show more ...

Merge branch 'master' into barry/saws-options

Merge branch 'jed/dmda-memusage'

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

show more ...

fixes for DA1d creation with scaled sizes of X direction logical coordinates

removed blocked versions of ISLocalToGlobalMapping in Vec and Mat
the single ISLocalToGlobalMapping supports ISLocalToGlobalMappingApply and ISLocalToGlobalMappingApplyBlock
still some fixes need for

removed blocked versions of ISLocalToGlobalMapping in Vec and Mat
the single ISLocalToGlobalMapping supports ISLocalToGlobalMappingApply and ISLocalToGlobalMappingApplyBlock
still some fixes need for these extensive changes

show more ...

Merge branch 'hzhang/mumps-options'

Merge branch 'master' of bitbucket.org:petsc/petsc

rename INFO -> Info; INFOG ->Infog

add MatMumpsGetxxx() as requested by Zafer Leylek

doc: fix getpdflabels to count manual chapters correctly.
Also fix URLs from man pages to manual.pdf

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

Merged petsc/petsc into master

MatColoringPower: Add MatColoringPower, which one-colors powers of the mat

Merge branch 'prbrune/matcoloring-reworkjpmis'

* prbrune/matcoloring-reworkjpmis:
MatColoring: Remove MatColoringMIS
MatColoringJP: One more small fix.
MatColoringJP: Fix unused variable warni

Merge branch 'prbrune/matcoloring-reworkjpmis'

* prbrune/matcoloring-reworkjpmis:
MatColoring: Remove MatColoringMIS
MatColoringJP: One more small fix.
MatColoringJP: Fix unused variable warning.
MatColoringJP: Add timings for MatColoringJP
MatColoringJP: Added an option to turn off the initial local coloring.
MatColoringJP: Add local coloring phase to cut down on the number of rounds.
MatColoringJP: Remove redundant allocations
MatColoring: comm-lite version of Jones-Plassmann coloring.

show more ...

Merge branch 'prbrune/matcoloring-weights'

* prbrune/matcoloring-weights:
MatColoring: Cleanup of weight computation.
MatColoring: Add ex19 run to nightlies.
MatColoring: Add a run example w

Merge branch 'prbrune/matcoloring-weights'

* prbrune/matcoloring-weights:
MatColoring: Cleanup of weight computation.
MatColoring: Add ex19 run to nightlies.
MatColoring: Add a run example with greedy coloring and LF weights.
MatColoring: Set random to be the default weighting scheme.
MatColoring: MatColoringSetWeights for custom weighting.
MatColoring: Added an initial implementation of smallest-last weights.
MatColoring: MatColoringCreateWeights() replaces duplicate routines.
MatColoring: Make weight computation directly use AIJ for speed.
MatColoring: Add a generalized collection of weight computations.

show more ...

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

show more ...