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 'knepley/fix-vec-visibility' into knepley/feature-dm-point-location-failure

* knepley/fix-vec-visibility:
Vec: DuplicateVecs_Default and DestroyVecs_Default should be available to the

Merge branch 'knepley/fix-vec-visibility' into knepley/feature-dm-point-location-failure

* knepley/fix-vec-visibility:
Vec: DuplicateVecs_Default and DestroyVecs_Default should be available to the user - This is needed is IBAMR
Fix error in MPI-uni when creating additional MPI communicators did not properly mark them as active
OSX: fix .dmg create script to set PETSC_DIR Also fix paths to work on case sensitive file systems.
Configure: Fix pickling error This is still a problem since it reveals that something is not cleaning up correctly. Configure needs a global rewrite badly
Configure: Silence warning on test compile
Configure: Bump MPFR version
remove multiple the the constructs
cd src/benchmarks/steams should be: cd src/benchmarks/streams
missing seealso for NASM

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Merge branch 'knepley/fix-configure-mpfr'

* knepley/fix-configure-mpfr:
Configure: Fix pickling error This is still a problem since it reveals that something is not cleaning up correctly. Configur

Merge branch 'knepley/fix-configure-mpfr'

* knepley/fix-configure-mpfr:
Configure: Fix pickling error This is still a problem since it reveals that something is not cleaning up correctly. Configure needs a global rewrite badly
Configure: Silence warning on test compile
Configure: Bump MPFR version

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Configure: Fix pickling error
This is still a problem since it reveals that something is not cleaning up correctly. Configure needs a global rewrite badly

Merge branch 'barry/fix-nonew-notcollective/maint' into jed/mat-assembly-perf

Jed this fucking 6+ month running thing in next that is not in master is a royal fucking pain in the ass and
an abuse of

Merge branch 'barry/fix-nonew-notcollective/maint' into jed/mat-assembly-perf

Jed this fucking 6+ month running thing in next that is not in master is a royal fucking pain in the ass and
an abuse of git. I think it is not justified to ever have anything in next for more than a few weeks at most.
Either take it out of next if it is broken or put it in master if it is not broken. Hanging around in next but
not master for ever is not a good policy.

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Merge branch 'master' into knepley/solkx

* master: (6933 commits)
Bib: Added reference
Includegraph: Updated for compatibility with new folder layout.
Add SNESLineSearchReason to fortran inclu

Merge branch 'master' into knepley/solkx

* master: (6933 commits)
Bib: Added reference
Includegraph: Updated for compatibility with new folder layout.
Add SNESLineSearchReason to fortran includes Also truncate names to fit 32 char fortran limit
fix compile warnings /usr/home/balay/petsc.clone-2/src/vec/vec/interface/vector.c:1944: warning: division by zero in '1.0e+0 / 0.' /usr/home/balay/petsc.clone-2/src/ksp/ksp/interface/itfunc.c:508: warning: 'vec_rhs' may be used uninitialized in this function
updated output for new trust region initial size
initial size of the trust region is set as a percent of the norm of the initial guess, it should not be related to the initial norm of the function (which is kind of nuts).
The default bounds for SNESVISetVariableBounds() in the manual page were reversed from correct values
Bib: Added refs
Bib: Update MPICH webpage
Plex: Forgot to close file
removed nonexistent ex46f from makefile test rule
Revert "fixed bad merge into master"
fixed bad merge into master
fix memory leak in mkl_pardiso fix some formatting in mkl_pardiso code
mv runex111 from TESTEXAMPLES_C to TESTEXAMPLES_DATAFILESPATH
Mat+Doc: More Fortran docs
Plex ex3: Run tests with the correct number of field components
Bib: Added TetGen cite
parmetis: make sure 'ldd libparmetis.so' points to the correct libmetis.so that its linked with.
small fix as reported by the nightly test
...

Conflicts:
config/builder.py

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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 '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 shri/adjoints-and-events

Need to update the branch to get the changes made by Hong to the adjoint code.

Merge branch 'knepley/feature-parallel-configure'

* knepley/feature-parallel-configure:
Revert bad ML fix in ba4f728f6c00f645cbd73e74de34ed390600afde
Configure: Fix ML for 64-bit integers
Conf

Merge branch 'knepley/feature-parallel-configure'

* knepley/feature-parallel-configure:
Revert bad ML fix in ba4f728f6c00f645cbd73e74de34ed390600afde
Configure: Fix ML for 64-bit integers
Configure: Trying to clean up use of installer, decoupled mpi4py and petsc4py from PETSc.Configure - One problem is that this changes meaning. In the pkg-config, the install dir is $PETSC_DIR instead of $PETSC_ADIR/$PETSC_ARCH
Configure: Must capture output when rerunning configure on a required object
Configure+MPI: Remove redundant function
Configure: Framework should print out regular errors as well
Configure: Replace self.log.write with self.logWrite
Configure: Check for Queue support - Python 2.4 should fail this
Configure: If --useThreads=0, use serial configuration
Configure: Improve error logging in parallel
Configure: Can set the number of threads using --useThreads=<num>
Configure: functions module should depend on libraries
Configure: Objects should not use log or argDB from framework
Configure: Enable concurrent execution - Should fallback to serial evaluation, but we might want a flag for this
Configure: Removed redundant code
Configure: Removing dependence cycles - Cannot depend on oneself (a depressing realization) - Make cannot depend on MPI - MPI implementations cannot depend on MPI - debugging cannot depend on setCompilers - PETSc cannot depend on mpi4py and petsc4py
Configure: Allow thread local logging

Conflicts:
config/BuildSystem/config/packages/SuperLU_DIST.py
config/BuildSystem/config/packages/sowing.py

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Configure: Allow thread local logging

Merge branch 'master' into jed/ts-eimex

Sync to include Git conversion, PETSC_EXTERN, and minor API changes.

Conflicts:
src/ts/interface/tsregall.c

Merge branch 'master' into tautges/dmmoab

Obtain config/BuildSystem as subtree.

Merge subtree 'buildsystem/master'

Merge branch 'maint' (config/BuildSystem subtree)

Merge branch 'maint' of buildsystem into maint

Merge branch 'maint-3.2' into maint (BuildSystem subtree)

Add 'config/BuildSystem/' from commit '94fb7d1092a023a10eba9cdace78f25709a190fd'

git-subtree-dir: config/BuildSystem
git-subtree-mainline: d24caab14e29d890d97b19b2c7aadd37e4d931ee
git-subtree-split:

Add 'config/BuildSystem/' from commit '94fb7d1092a023a10eba9cdace78f25709a190fd'

git-subtree-dir: config/BuildSystem
git-subtree-mainline: d24caab14e29d890d97b19b2c7aadd37e4d931ee
git-subtree-split: 94fb7d1092a023a10eba9cdace78f25709a190fd

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