Merge branch 'barry/get-factor-failure-information-from-mat'

Added MatFactorGetErrorZeroPivot()

Time: 2 hours
Reported-by: Glenn E Hammond <gehammo@sandia.gov>

Merge branch 'barry/add-matshell-matgetdiagonalblock-fortran'

add support for MatShellSetOperation(Mat,MATOP_GET_DIAGONAL_BLOCK, for Fortran

This required changing the handling of MatGetDiagonalBlock() from a query function based
method to a regular method in

add support for MatShellSetOperation(Mat,MATOP_GET_DIAGONAL_BLOCK, for Fortran

This required changing the handling of MatGetDiagonalBlock() from a query function based
method to a regular method in the function table

Time: .75 hours
Reported-by: Steven Dargaville <dargaville.steven@gmail.com>
Thanks-to: Dave May <dave.mayhem23@gmail.com>

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Merge branch 'tisaac/sys-fix-realloc' into tisaac/petscfe-matching-quadrature-order

* tisaac/sys-fix-realloc: (71 commits)
Sys: fix PetscTrReallocDefault() and PetscReallocAlign()
clearify when

Merge branch 'tisaac/sys-fix-realloc' into tisaac/petscfe-matching-quadrature-order

* tisaac/sys-fix-realloc: (71 commits)
Sys: fix PetscTrReallocDefault() and PetscReallocAlign()
clearify when MatMkl_CPardisoSetCntl() can be used in the manual pages
Fixed manual page for -snes_anderson_beta
Update zfftf.c
remove Hermitian information from output since it is only produced in complex case and thus produces different test output
fixes for 64 bit integers in test example, fix uninitialized variable in test example
tests: move runex49 to TESTEXAMPLES_C_NOTSINGLE
add a PCView_SVD to show parameters
-petscpartitioner_type simple was not being picked up by options thus generating test error
missing CHKERRQ(ierr) on PetscPrintf() statements in newly added test example
PetscViewerVTK: Move DM reference increment into the VTK viewer and out of the DM implementation, as suggested by Jed Brown
missing crosslinks between manual pages
Updated 3.7 release notes to clearly indicate how to update usage of KSP/SNES/TS/SetMonitor(xxx,XXXMonitorDefault,NULL,NULL);
Fix for commit b6480e041dd2293a65f96222772d68cdb4ed6306 that broke this example
Example of factorization of a singular matrix may actually work due to round off
removed unused variables
matshell: clean up and add some new MATOPs to Fortran.
Remove unneeded checks for use of the compressed row for diagonal block of matrices in GAMG
ptscotch: update to version 6.0.4
ptscotch: fix buggy pthread detection code on Mac/Linux
...

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Merge branch 'barry/fix-successful-numerical-factorization-after-failure/master'

Update to patch commit 04545d6dccef0bc76f6a1a6548f816a384daa3de to make it work with master

Now the patch respects the data encapsulation of _p_Mat and does not access into it directly.

Time: .1 ho

Update to patch commit 04545d6dccef0bc76f6a1a6548f816a384daa3de to make it work with master

Now the patch respects the data encapsulation of _p_Mat and does not access into it directly.

Time: .1 hours

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Merge branch 'master' into barry/fix-successful-numerical-factorization-after-failure/master

The maint patch for the given problem cannot merge cleanly into next due to changes
in the same code in m

Merge branch 'master' into barry/fix-successful-numerical-factorization-after-failure/master

The maint patch for the given problem cannot merge cleanly into next due to changes
in the same code in master (the introduction of MatFactorGetError()) therefor need
to merge in master and use the new construct before merging to next

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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 'maint'

Merge branch 'barry/add-missing-apis/maint' into maint

Added MatFDColoringSetType() C and Fortran and test case for it

Reported-by: Adrian Croucher <a.croucher@auckland.ac.nz>

Merge branch 'barry/housekeeping-2'

removed a variety of #include <xxximpl.h> from source code that was not needed

moved MatCoarsen infrastructure into its own include file

since it contains too many private data structures not needed by all
code what works with matrices

Merge remote-tracking branch 'origin/pr464/pieter_ghysels/pghysels/strumpack-interface-rebased/master'

Add support for MAT_FACTOR_ILU (using low-rank compression).
Add PETSc functions to set some options.

Remove aij/seq/strumpack.
Rename aij/mpi/strumpack_mpi to aij/mpi/strumpack.
Make aij/mpi/strumpack work for MPISEQAIJ.
Rename CENTRALIZED to REPLICATED.

Add interface to STRUMPACK-sparse.

STRUMPACK-sparse is a sparse direct solver and
preconditioner (using Hierarchically Semi-Separable matrices),
developed at LBNL, released under a BSD license:
http

Add interface to STRUMPACK-sparse.

STRUMPACK-sparse is a sparse direct solver and
preconditioner (using Hierarchically Semi-Separable matrices),
developed at LBNL, released under a BSD license:
http://portal.nersc.gov/project/sparse/strumpack/

This commit adds 2 interfaces to STRUMPACK-sparse: one for
aij/seq and one for aij/mpi matrices. It also adds a script to
the buildsystem to download/compile/install STRUMPACK-sparse.

I can get everything compiled with
./configure --download-strumpack --with-cxx-dialect=C++11 \
--with-openmp --download-scalapack --download-parmetis
--download-metis --download-ptscotch
(There was an issue compiling STRUMPACK-sparse as a shared
library, so it is now always static)

I tested the new code with the src/snes/examples/tutorials/ex5.c
example:
OMP_NUM_THREADS=2 mpirun -n 2 ./ex5 -da_grid_x 100 \
-da_grid_y 100 \
-pc_type lu -pc_factor_mat_solver_package strumpack_mpi \
-ksp_monitor -mat_strumpack_mpi_matinput DISTRIBUTED \
--sp_mc64job 0 --sp_reordering_method scotch --sp_verbose

The aij/mpi solver is called 'strumpack_mpi', the aij/seq solver
is 'strumpack'. All command line options are passed to the
STRUMPACK solver, including -h, which prints out the STRUMPACK
options.

STRUMPACK-sparse has 3 interfaces:
* A sequential/nulti-threaded interface. This one is used with
aij/seq matrices by selecting the 'strumpack' solver.
* A distributed memory solver with replicated interface. This
interface has the same input on every MPI proc (entire matrix
and rhs and solution vectors). Select this for aij/mpi, with
"-pc_type lu -pc_factor_mat_solver_package strumpack_mpi -mat_strumpack_mpi_matinput GLOBAL"
* A fully distributed solver, works with the aij/mpi block-row
distributed input matrix directly. Use with:
"-pc_type lu -pc_factor_mat_solver_package strumpack_mpi -mat_strumpack_mpi_matinput DISTRIBUTED"

Pieter

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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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Merge branch 'hzhang/superlu_dist-getdiaU'

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 'master' into barral/feature-dmplex-adapt

Merge branch 'barry/housekeeping-1'

added test for all the coloring algorithms and checks they produce correct colorings

Reported-by: gcov