Merge branch 'master' into knepley/fix-examples-plex

* master: (112 commits)
correct expression for implict ODE/DAE in table 11 of users manual
remove warning about deprecated MPI call in exampl

Merge branch 'master' into knepley/fix-examples-plex

* master: (112 commits)
correct expression for implict ODE/DAE in table 11 of users manual
remove warning about deprecated MPI call in examples
rm variables declared in middle of subroutine
tolerance for equality in PETSc test should depend on machine epsilon
tolerance for acccuracy in test example should depend on machine epsilon
increase convergence tolerance to get same result in single precision as double for convergence history
update no change output for gasm test which had not been properly updated
remove C++ // comment
example mistakenly used MPI_COMM_WORLD as if it was rank in print statement thus producing output only with MPI Uni
grep out name of DM object since on some systems the address printed has extra zeros thus producing a false difference in output
increase tolerance for test example
build: revert el6-4 build to cg - as el6 compilers give link errors
fix error type
insure similar convergence history for single, double, quad
fix ex104.c based on Barry's suggestion
increase example convergence tolerance to get matching convergence history in single and double precision
increase convergence tolerance so that test example has similar convergence history in single and double precisions
changed from cg to gmres for eigenestimator since in single precision cg produced a possible indefinite matrix report
change test example tolerance to depend on machine epsilon so as to give correct results in various precisions
loosen convergence tolerance to have similar convergence history with single, double, quad precisions
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Merge branch 'master' into shri/add-tsevent-to-powergrid-examples

Merge branch 'master' into stefano_zampini/feature-pardiso-schur

Branch got out of sync with master

We always start with petsc/master. Trying to fix a bug (submatrix reuse) reported by
Dmitry.
Merge remote-tracking branch 'petsc/master' into fix-pcgasm-reuse

Merge branch 'master' into pr263/PierreBdR/ts-domain-error-in-stage/master

Merge branch 'master' into barry/improve-git-download

fix violations of PETSc style guide: Usage of SETERRQ and NULL

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 remote-tracking branch 'petsc/master' into mat-increaseoverlap

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
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Conflicts:
config/builder.py

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Merged petsc/petsc into master

Merge branch 'master' into tisaac/dmforest

directory layout changed again: merging to switching branches back and forth
doesn't cause reconfigure to have a hard time

* master: (357 commits)
remov

Merge branch 'master' into tisaac/dmforest

directory layout changed again: merging to switching branches back and forth
doesn't cause reconfigure to have a hard time

* master: (357 commits)
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
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
add a test for MatPtAP()
small cleanup; add tests
cleanup MatPtAPSymbolic_MPIAIJ_MPIAIJ()
Fix nonzerostate tracking in all MATMPI types.
update location of test matrices in faq.html file
unused variable still declared
Fix for MatLoad_MPIDense() from sparsely stored matrix also fix for MatLoad_MPIDense_DenseInFile() when matrix has not had its local sizes preset by user
Preserve the B nonzerostate during disassembly.
TSEvent: Fix arch-mswin nightly errors due to declaring variables in the middle of a function.
Fix error in parallel loading of dense format matrix
removed KSPSetNullSpace() since mat already carries that information and having two locations for it is confusing, unnecessary and prone to error added MatSetTransposeNullSpace() for providing the null space of the transpose of the matrix and added support in KSPSolve() to remove this null space from the right handside of the linear system thus making the system consistent.
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Merge branch 'barry/propagate-pcsetup-failures'

Infrastructure that allows failures in PCSetUp(), PCApply(), MatMult() etc due to, for example a zero pivot or function evaluation outside its domain, to propagate up and become a KSP_DIVERGED inste

Infrastructure that allows failures in PCSetUp(), PCApply(), MatMult() etc due to, for example a zero pivot or function evaluation outside its domain, to propagate up and become a KSP_DIVERGED instead of generating an error that stops the program. In response to Issue 96. This includes failures in MatCreateSNESMF() applications due to domain errors. The mechanism to propagate some errors is by setting Info or Nan into the output vector and using the norm or inner product reductions in SNES or KSP to propagate the error condition to all processes and then handling them immediately after the norm or inner product.

This allows, for example, ODE integrators to try again with a smaller time-step if the PCSetUp failed instead of requiring a complete restart of the run with other options.

Currently some error conditions, such as function domain error in a line search may not get progated up using the correct SNESConvergedReason

See src/snes/examples/tests/ex69.c for the handling of several conditions

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Merge branch 'master' into knepley/feature-composable-callbacks

* master: (151 commits)
PetscMalloc: Fix handling of zero-sized allocations
add note to DMGetLocal/GlobalVector() about intended s

Merge branch 'master' into knepley/feature-composable-callbacks

* master: (151 commits)
PetscMalloc: Fix handling of zero-sized allocations
add note to DMGetLocal/GlobalVector() about intended short-time usage of the vectors.
sf: use patched openmpi tarball that has a potential fix for sf example hang
SNES problems that set VI bounds must use a VI solver since the other solvers ignore the bounds
pounders viewer did not cast PetscReal to double in printf nor use %D instead of %d
fix ts ex20adj
fix ts theta
fixed another variable declaration in the middle of a code block
example main() had PetscInt return type and argument that should be int
DMDAVTKWriteAll_VTS: Fix handling of higher-dimension coordinates
fixed example that declared variables in the middle of a function
C programs do not return PetscInt nor do they take an argument that is PetscInt, fixed example that did
You cannot declare variables in the middle of functions in PETSc.
add ierr checking to PetscOptionsBegin/End() in example
configure: add error check if user specifies PETSC_ARCH=-dbg [i.e starts with a '-']
scale norm of vector difference by norm of vector to insure it is small enough to consider the two vectors equal
missing PetscViewerDestroy() added
MatNestGetISs: use custom fortranstub to handle PETSC_NULL_OBJECT
update location of open-mx website on FAQ page
If the user sets bounds and calls a solver that does not support them, throw an error.
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Merge remote-tracking branch 'origin/stefano_zampini/mattransposedense-ldafix' into stefano_zampini/pcbddc-adaptive-selection

Merged petsc/petsc into master

Merge branch 'pr306/pefarrell/pefarrell/snes-composite-vi-fixes/master'

If the user sets bounds and calls a solver that does not support them, throw an error.

Merge branch 'pr192/Fande-Kong/scalable-matincreaseoverlap/master' of https://bitbucket.org/petsc/petsc

Merged petsc/petsc into master

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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Merged master into semihozmen/ksp-fcg-eigen-comp-support

Merge branch 'master' into pr192/Fande-Kong/scalable-matincreaseoverlap/master

Needed to merge master to update to new calling sequence PetscCommBuildTwoSided

Merged petsc/petsc into master