Merge branch 'master' of https://bitbucket.org/Fande-Kong/petsc-matincreaseoverlap

Merged petsc/petsc into master

Merge branch 'master' of bitbucket.org:petsc/petsc into mark/matnestmatconvert

Options: Add PetscOptionsGetEnumArray() and PetscOptionsEnumArray()

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

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcscalingbasic.c
src/mat/impls/aij/mpi/mumps/mumps.c
s

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

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcscalingbasic.c
src/mat/impls/aij/mpi/mumps/mumps.c
src/mat/impls/is/matis.h

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Merge branch 'master' into tisaac/dmforest

If we're going to start developing on this again, the recent changes to the
location of configuration files will make it annoying to switch to and from
thi

Merge branch 'master' into tisaac/dmforest

If we're going to start developing on this again, the recent changes to the
location of configuration files will make it annoying to switch to and from
this branch. Matt's and my fixes in DMPlex will also be relevant.

* master: (1557 commits)
MatLoad_MPIDense() always allocated array space even if it was previously provided
Clarified lumping options for PCFieldSplitSchurPreType SELFP.
fixed up PetscInfo in GAMG
TSErrorWeightedNorm[2|Infinity]: API changes
MatLoad_SeqDense() always allocated new space for the data even if the user already provided it
Fixed DMCompositeGetAccessArray() to support readonly vectors
Fix obviously-wrong aspects of documentation on SNESVINEWTONRSLS and SNESVINEWTONSSLS.
fixed example to compile - demonstrates a bug
var name 'len' was F90 key word
For user provided Jacobian functions they should always assembly into the second matrix, the one from which the preconditioner is built because the first may be used as matrix-free with -snes_mf_operator
Suggest --with-64-bit-indices if users mistakenly use --with-64bit-indices
Fix configure logging of integer size.
missing underscore in #define of vecgetarrayread translation of fortran stub for VECGETARRAYREAD
updated test output files to reflect differences introduced previously in PCView output
-ksp_type preonly does not support -ksp_monitor_short so remove from test line to prevent extranious warning output
missing CHKERRQ; and ugly double declaration of ierr
Plex ex3: For want of a semicolon, the kingdom was lost
MatSetValuesMPISBAIJ will now print correct global indices when error generated due to new nonzero location
completed basic use of MatSetValuesBlocked_SeqBAIJ_Inlined() by MatSetValuesBlocked_MPIBAIJ() to allow proper global indices being printed when error generated by new nonzero locations.
Added inline version of MatSetValuesBlocked_SeqBAIJ() to be used by MatSetValuesBlocked_MPIBAIJ() to print error message for nonzero block with global indices
...

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Merge branch 'hzhang/add-OptionsScalarArray'

add PetscOptionsScalarArray() as requested by Jose E. Roman

Merge branch 'master' into shri/ts-is-for-differential-variables

Conflicts:
include/petsc-private/tsimpl.h
src/ts/impls/eimex/eimex.c
src/ts/interface/ts.c

Merge branch 'master' into jed/chem
Note merging a branch with good stuff in it for a year and a half is insane!

Conflicts:
src/ts/examples/tutorials/makefile
src/ts/interface/ts.c

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

Merge branch 'master' into knepley/feature-harmonic-advection

* master: (205 commits)
Bib: Added bio refs
Don't print SAWs URL since it disturbs all the test output
missing (double) cast in pr

Merge branch 'master' into knepley/feature-harmonic-advection

* master: (205 commits)
Bib: Added bio refs
Don't print SAWs URL since it disturbs all the test output
missing (double) cast in print statement
don't output to test file all 12 digits of values
fixes and additions to SNESQM manual pages
PetscViewerBinaryGetDescriptor() is now a collective and must be treated as such fixed some calls to PetscViewerBinarySetUseMPIIO() removed some test runs that take too long
removed dead routine
ViennaCL: Added MCS download mirror URL for version 1.6.2
shift order of processing options for TS to be compatiable with SAWs Fix options handling for SAWs to duplicate array that previously was deleted too soon for SAWs processing
remove some dead code for AD and old AMS java and Matlab utilities
add missing PetscFunctionBegin; that messed up displaying of stack
Viewer: Fixed PetscViewerBinarySetUseMPIIO() in some examples
removed unused variables, removed dead code from AMS
git is so freaking annoying I accidently made a bunch of updates in next which I pushed lets see if this diff makes the same changes in my branch Why can't git just forbid me to make changes or next or set up some utility to prevent it!
moved saws directory to proper share directory location updated source to point to it.
rm checkboxes at top of pcoptions.html (ugly and not useful) and centered display of solver
PetscOptionsObject->prefix was freed before using in SAWs post processing hence SAWs was unable to change any type which had a prefix
display URL to point to to access SAWs server
missing break in case for handling string arguments better description for Options database option handling
removed extern PC_CLASSID and KSP_CLASSID that don't belong in petscoptions.h
...

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Merge branch 'barry/saws-options-merge-master'

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

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

git is so freaking annoying I accidently made a bunch of updates in next which I pushed
lets see if this diff makes the same changes in my branch
Why can't git just forbid me to make changes or next

git is so freaking annoying I accidently made a bunch of updates in next which I pushed
lets see if this diff makes the same changes in my branch
Why can't git just forbid me to make changes or next or set up some utility to prevent it!

show more ...

removed extern PC_CLASSID and KSP_CLASSID that don't belong in petscoptions.h

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c
src/sys/threadcomm/interface/threadcomm.c

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

Merge branch 'knepley/fix-fieldsplit-mg'

* knepley/fix-fieldsplit-mg:
PetscOptions: Name the struct
PCMG: Disconnect coarsening from DMKSP propagation - If a user called KSPSetComputeOperator()

Merge branch 'knepley/fix-fieldsplit-mg'

* knepley/fix-fieldsplit-mg:
PetscOptions: Name the struct
PCMG: Disconnect coarsening from DMKSP propagation - If a user called KSPSetComputeOperator() on the level solves before PCMG creates the level DMs, then when DMCoarsen() is called the first time, the DM will get the DMKSP from the top level. However, for each subsequent coarsening, it will keep the top-level DMKSP and wipe out those on the coarser levels. - To fix this, I just decouple coarsening from KSPSetDM()
FieldSplit: Was assuming the Options functions set the default value

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Merge branch 'master' into pr252/dmay/PetscViewerBinarySkipHeaderVecViewLoad
Manual merge of makefile

Conflicts:
src/sys/classes/viewer/examples/tutorials/makefile

PetscOptions: Name the struct

Merge branch 'barry/experiment'

simplify option object names

fixes for merge with HAVE_LOG protection for PETSc object logging

moved PetscOptionsObject from global variable to local variable in functions