Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

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

Merge branch 'master' into tisaac/dmforest

Get 3.6.2 patches

* master: (1360 commits)
remove nasty memory leak with CUDA code when using block Jacobi with multiple blocks per process
print abs

Merge branch 'master' into tisaac/dmforest

Get 3.6.2 patches

* master: (1360 commits)
remove nasty memory leak with CUDA code when using block Jacobi with multiple blocks per process
print abs in Fortran test example in order to have same result with real and complex builds
changed outdate mpirun and -np to mpiexec and -n
force sqrt to be taken in the precision of PetscReal in fortran examples
continuation line too soon for some compilers
stop configure if user selected C++ clanguage, single precision, complex combination since we do not support it
fixes for Fortran examples to compile cleanly in single precision that do not involve complex numbers
fixes to Fortran examples to compile cleanly in single precision complex
fix previous mistake
must cast 1. to PetscScalar before dividing by a PetscScalar (C++ complex class is terrible)
must cast 0.0 to PetscScalar before comparison with a PetscScalar
changed order of suggested locations of downloadable PETSc to Barry's preference
Increase patchlevel to 3.6.2
remove debug print statement from two commits before
remove debug print statements I accidently left in the last commit
PetscDraw: Fix dummy definition of PetscDrawCollective{Begin|End}()
remove cleanupMumps flag from MatDestroy_Mumps() it should always free the memory it allocated Bug detected while adding features to libMesh
improved viewing of fractional counts in xml nested log viewing fixed bug in output of doubles to xml nested log files
chombo: build only libs - not examples
fix typo. 'gcc-4.8 --with-cxx-dialect=C++11' gives a warning with this line - even though its in a #ifdef thats never enabled.
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To add a space to all comments I have made before. Barry pointed out
that a comment without a space right after '/*' may cause bfort to crash

Merge remote-tracking branch 'petsc/master' into fixed-c

To add a space to all comments I have made before. Barry pointed out
that a comment without a space right after '/*' may cause bfort to crash

Merge remote-tracking branch 'petsc/master' into fixed-comment-space

Conflicts:
include/petsc/finclude/petscmat.h
include/petscmat.h
src/mat/examples/tests/makefile
src/mat/impls/aij/mpi/mpiaij.h

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Merge branch 'pr329/master/Fande-Kong/matpartitioning-hierarch' into pr361/master/Fande-Kong/pcgasm-increaseoverlap: need hierarch to build GASM subdomains.

Conflicts:
src/mat/examples/tests/makefi

Merge branch 'pr329/master/Fande-Kong/matpartitioning-hierarch' into pr361/master/Fande-Kong/pcgasm-increaseoverlap: need hierarch to build GASM subdomains.

Conflicts:
src/mat/examples/tests/makefile
src/mat/impls/aij/mpi/mpiaij.h

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Merge branch 'master' into pr352/dmay/pctelescope/master

Merge branch 'master' into pr358/buptphyphy/addmatcreatenormalhermitian/master

Merge branch 'tisaac/dt-fix-geom-punning' into tisaac/plex-feature-tree-fv

Pull in a fix to FE geometry that affects the complex,64bit case

* tisaac/dt-fix-geom-punning: (240 commits)
Plex: fix t

Merge branch 'tisaac/dt-fix-geom-punning' into tisaac/plex-feature-tree-fv

Pull in a fix to FE geometry that affects the complex,64bit case

* tisaac/dt-fix-geom-punning: (240 commits)
Plex: fix type punning problem stuffing (PetscFECellGeom *) in a Vec
PGI compiler cannot handle [restrict] usage therefor disable restrict for PGI compiler Fix ex48.c to use PETSc standard way of marking restrict
PETSC_UNUSED must occur before the typename. With PGI compilers they error if it is after the type name
on solaris in TSAdaptChoose_Basic() negative root for zero could produce -infinity thus causing time step to be decreased even though the error estimate was zero
MatGetSchurComplement: revert test from LUMP back to DIAG and update output
there are no tests for opencl or viennacl so prevent warning message: make[2]: *** No rule to make target `testexamples_OPENCL', needed by `tree'. Stop. make[2]: *** No rule to make target `testexamples_VIENNACL', needed by `tree'. Stop.
incorrect initial conditions function that could produce floating point exception value (and does on windows) due to squareroot of non-negative number
forgot to fix rule for building ex194
move ex193.c to ex194 because someone else created a 193
remove outdate manual page comment
add missing VecRestoreArray()
add missing VecRestoreArray()
missing restore array in example
formating for print statements of test example with __float128 precision
fix example for __float128 precision by using PETSc math macros and casting PetscReal in print statements
remove Tao example custom monitor that produced different results for __float128 precision
all PETSc built in monitors require a valid PetscViewer, NULL is not acceptable
PETSc built in monitors always require viewers to be passed in, no longer support a NULL viewer
use tigher haptol for minres for quad precision because otherwise false positive of indefinite matrix appeared in example
check for PetscMPIInt overflow in ISAllGather()
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Merge branch 'master' into jed/process-options-handler

on solaris in TSAdaptChoose_Basic() negative root for zero could produce -infinity thus
causing time step to be decreased even though the error estimate was zero

Merge branch 'tisaac/dmplex-stable-tet-refinement' into tisaac/plex-feature-tree-fv

This feature branch also changed the topology of nonconforming examples:
I am merging so that I can make the regre

Merge branch 'tisaac/dmplex-stable-tet-refinement' into tisaac/plex-feature-tree-fv

This feature branch also changed the topology of nonconforming examples:
I am merging so that I can make the regression output that should be
correct in master and next

* tisaac/dmplex-stable-tet-refinement: (594 commits)
plex: added tet shape regression test
plexrefine: remove replaced code
plex: update test output for new tet refinement order
plex: fix tet refinement for stable element shape
DMPlex: added test of shape quality to ex1
Better to use the proper error handling version of PetscViewerASCIIGetStdout() instead of PETSC_VIEWER_STDOUT_()
Generate a very useful error message if PetscLogView(), PetscLogEventGetPerfInfo() or PetscLogEventGetFlops() is called with a preceeding call to PetscLogBegin() and friends (also -log_summary which triggers a PetscLogBegin())
fix compile warnings
Plex: Fix bug with bcComps initialization
Turn off elemental shared libraries if --with-shared-libraries=0 is used
Bib: Added refs
Bib: Fixed a bunch of errors
add warning/error flag for '-mat_superlu_dist_parsymbfact' when MatInputMode=GLOBAL
makefile: fix format
tests: add back ex6f, runex6f targets - that got removed in 2f1d3d565a6a43067e6df75b043e6343b05fcd1d
accessing option that may never have been set
typo in DMNetworkSetNumVariables() reported by Sean Shahkarami
superlu_dist: update to using latest 4.1 version
fix compile warnings
Generate an error message when trying to overwrite default options of CN and BEULER
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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 'mat-increaseoverlap' of ssh://bitbucket.org/Fande-Kong/petsc into pr332/master/Fande-Kong/mat-increaseoverlap-scalable

Merge remote-tracking branch 'petsc/master' into pcgasm-increaseoverlap

Merge remote-tracking branch 'petsc/master' into matpartitioning-hierach

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

Merge branch 'master' into knepley/feature-snes-deflation

* master: (239 commits)
Bib: Moved entry
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html - enable cuda in c

Merge branch 'master' into knepley/feature-snes-deflation

* master: (239 commits)
Bib: Moved entry
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html - enable cuda in configure
release: set v3.6 strings
doc: add PCGAMGSetReuseInterpolation() to changes file
fix: workarround static initialization issue (perhaps compiler bug) on opensolaris c/complex build
fix: ex40,ex41 errors in src/ts/examples/tutorials/ on bsd with c++/complex Perhaps this code nees a separate section when 'enorm == 0) - as pow(0,-0.33) = inf.
manual: fix format
more changes..
PCGASM/MatGetSubMatricesMPI() changes in dev.html.
changes: more updates
Add size checks for static arrays of assumed max size [-Warray-bounds]
Doc: Update to Changes
configure: default to useThreads= 0as the useThreads=1 code currently prints output in jumbled order [producing hard to read configure.log]
Delete PETSc viewer attribute if none are left on the linked list instead of putting an empty attribute
MatGetSubMatricesMPI_MPIAIJ(): guard for an empty B-matrix when delogging memory in MatSetSeqMats().
PCBDDC: fix typos in the specification of MPI operation
MPIU_SUM was used with MPIU_INT when it should only be used with MPIU_REAL or MPIU_SCALAR
fixed bad PetscPrintf() formatting in two examples
Plex: In pointwise callbacks, use embedding dimension
updates for generating Apple installations due to changes in locations of include files
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Merge branch 'master' of bitbucket.org:petsc/petsc

Merge branch 'master' into mesgarnejad/feature-plex-globaltonatural

* master: (219 commits)
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html - enable cuda in configure

Merge branch 'master' into mesgarnejad/feature-plex-globaltonatural

* master: (219 commits)
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html - enable cuda in configure
release: set v3.6 strings
doc: add PCGAMGSetReuseInterpolation() to changes file
fix: workarround static initialization issue (perhaps compiler bug) on opensolaris c/complex build
fix: ex40,ex41 errors in src/ts/examples/tutorials/ on bsd with c++/complex Perhaps this code nees a separate section when 'enorm == 0) - as pow(0,-0.33) = inf.
manual: fix format
more changes..
PCGASM/MatGetSubMatricesMPI() changes in dev.html.
changes: more updates
Add size checks for static arrays of assumed max size [-Warray-bounds]
Doc: Update to Changes
configure: default to useThreads= 0as the useThreads=1 code currently prints output in jumbled order [producing hard to read configure.log]
Delete PETSc viewer attribute if none are left on the linked list instead of putting an empty attribute
MatGetSubMatricesMPI_MPIAIJ(): guard for an empty B-matrix when delogging memory in MatSetSeqMats().
PCBDDC: fix typos in the specification of MPI operation
MPIU_SUM was used with MPIU_INT when it should only be used with MPIU_REAL or MPIU_SCALAR
fixed bad PetscPrintf() formatting in two examples
Plex: In pointwise callbacks, use embedding dimension
updates for generating Apple installations due to changes in locations of include files
configure: do not fail when checking MPICH version [similar to 2cadc8fc42fbad3c229d43b955581b8d29e02ad6 ]
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Merge branch 'master' into knepley/fix-configure-logging

* master:
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html - enable cuda in configure
release: set v3.6 strin

Merge branch 'master' into knepley/fix-configure-logging

* master:
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html - enable cuda in configure
release: set v3.6 strings
doc: add PCGAMGSetReuseInterpolation() to changes file
fix: workarround static initialization issue (perhaps compiler bug) on opensolaris c/complex build
fix: ex40,ex41 errors in src/ts/examples/tutorials/ on bsd with c++/complex Perhaps this code nees a separate section when 'enorm == 0) - as pow(0,-0.33) = inf.
manual: fix format
more changes..
PCGASM/MatGetSubMatricesMPI() changes in dev.html.
changes: more updates

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Merge branch 'master' into knepley/fix-pc-composite-dm

* master:
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html - enable cuda in configure
release: set v3.6 strings

Merge branch 'master' into knepley/fix-pc-composite-dm

* master:
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html - enable cuda in configure
release: set v3.6 strings
doc: add PCGAMGSetReuseInterpolation() to changes file
fix: workarround static initialization issue (perhaps compiler bug) on opensolaris c/complex build
fix: ex40,ex41 errors in src/ts/examples/tutorials/ on bsd with c++/complex Perhaps this code nees a separate section when 'enorm == 0) - as pow(0,-0.33) = inf.
manual: fix format
more changes..
PCGASM/MatGetSubMatricesMPI() changes in dev.html.
changes: more updates
Add size checks for static arrays of assumed max size [-Warray-bounds]
Doc: Update to Changes
configure: default to useThreads= 0as the useThreads=1 code currently prints output in jumbled order [producing hard to read configure.log]
Delete PETSc viewer attribute if none are left on the linked list instead of putting an empty attribute
KSPComputeExplicitOperator: use KSP_PCApplyBAorAB

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Merge branch 'master' into knepley/plex-filter

* master:
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html - enable cuda in configure
release: set v3.6 strings
doc:

Merge branch 'master' into knepley/plex-filter

* master:
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html - enable cuda in configure
release: set v3.6 strings
doc: add PCGAMGSetReuseInterpolation() to changes file
fix: workarround static initialization issue (perhaps compiler bug) on opensolaris c/complex build
fix: ex40,ex41 errors in src/ts/examples/tutorials/ on bsd with c++/complex Perhaps this code nees a separate section when 'enorm == 0) - as pow(0,-0.33) = inf.
manual: fix format
more changes..
PCGASM/MatGetSubMatricesMPI() changes in dev.html.
changes: more updates
Add size checks for static arrays of assumed max size [-Warray-bounds]
Doc: Update to Changes
configure: default to useThreads= 0as the useThreads=1 code currently prints output in jumbled order [producing hard to read configure.log]
Delete PETSc viewer attribute if none are left on the linked list instead of putting an empty attribute
KSPComputeExplicitOperator: use KSP_PCApplyBAorAB

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fix: ex40,ex41 errors in src/ts/examples/tutorials/ on bsd with c++/complex
Perhaps this code nees a separate section when 'enorm == 0) - as pow(0,-0.33) = inf.

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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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 '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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