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 '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

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 'master' into barry/fix-petscviewer-attempt-2

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

* master: (75 commits)
increase the size of the ex25.c multigrid example so that the eigenestimator does not produce numbers that depend on mac

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

* master: (75 commits)
increase the size of the ex25.c multigrid example so that the eigenestimator does not produce numbers that depend on machine roundoff and thus are different on different OS/hardware and produce different test restults. Previously the GMRES converged to 16 digits in 4 iterations and spent the next 6 churning but that churning produced different eigenvalues which produced different convergence for the multigrid method
Bib: More references
example used int and double !
added long forgotten test output file
removed tao test example run that uses random numbers since not reproducable on different systems
Jason changed a default TAO tolerance but did not update example test output that viewer the tolerance
Plex: Correct complex problem
Plex ex12: Now PCMG monitor creates its own coarse solutions
Plex ex12: Put in working setting for PCMG coarsening test
XDMF: Now take a bunch of files as input
SNES ex12: Use monitors instead of brute force to monitor errors
SNES ex12: Renumber meshes to match MG numbering
PC+SNES: Attach a level id to subsolvers in a multilevel solve - We should have done this years ago
Plex: Added epsilon to point location check
Plex ex12: Added error output on each level
Plex: Added DMPlexComputeL2DiffVec() - This puts cellwise error integrals in a Vec
Plex: Fix complex conversion
Plex: Fix variable init
Add an option to ex12 to dump the coarsened hierarchy to disk.
Plex: Fixed unused variables
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Merge remote-tracking branch 'origin/knepley/feature-snes-deflation'

* origin/knepley/feature-snes-deflation: (55 commits)
Plex: Correct complex problem
Plex ex12: Now PCMG monitor creates its o

Merge remote-tracking branch 'origin/knepley/feature-snes-deflation'

* origin/knepley/feature-snes-deflation: (55 commits)
Plex: Correct complex problem
Plex ex12: Now PCMG monitor creates its own coarse solutions
Plex ex12: Put in working setting for PCMG coarsening test
XDMF: Now take a bunch of files as input
SNES ex12: Use monitors instead of brute force to monitor errors
SNES ex12: Renumber meshes to match MG numbering
PC+SNES: Attach a level id to subsolvers in a multilevel solve - We should have done this years ago
Plex ex12: Added error output on each level
Plex: Added DMPlexComputeL2DiffVec() - This puts cellwise error integrals in a Vec
Plex: Fix variable init
Add an option to ex12 to dump the coarsened hierarchy to disk.
Plex: Fixed unused variables
Plex: Fixed PetscScalar conversion problem
Plex: Fixed function header
Profile DMCreateInterpolation (nontrivial cost for nonnested meshes)
Replace the arguments for coarsening in ex12 with correct ones
Plex: Using a refinement function
Plex: Added DMPlexGet/SetRefinementFunction() - Use to do non-uniform refinement
Events for DMCoarsen and DMLocatePoints
Update the pragmatic build script to use master, not my branch
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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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PC+SNES: Attach a level id to subsolvers in a multilevel solve
- We should have done this years ago

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

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

* master:
added -pc_hypre_boomeramg_nodal_coarsen <n> and -pc_hypre_boomeramg_vec_interp_variant <v> options to allow PCType of PCHYPRE Bo

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

* master:
added -pc_hypre_boomeramg_nodal_coarsen <n> and -pc_hypre_boomeramg_vec_interp_variant <v> options to allow PCType of PCHYPRE BoomerAMG to take advantage of MatSetNearNullSpace()
allow clearing the NullSpace or NearNullSpace of a matrix by passing in a NULL
Fixed some PetscValidLogicalCollective calls that used the wrong typename One of these caused problems for a user with 64 bit integers
when using -start_in_debugger option do not use PetscErrorPrintf() function to display message to user since it prepends the message with PETSC ERROR potentially confusing the user since there is no error
Changed VecNorm( NORM_1) to use traditional 1 norm of the 2 norm of the complex entries instead of the previous 1 norm of the 1 norm of the complex entries
KSPCreateVecs() would under certain uncommon circumstances return incorrectly sized vectors for rectangular vectors
When configure options like --with-cusp-include=xxx are given and no corresponding --with-cusp-lib=yyy is needed configure will no longer print an inaccurate error message that you must also set a --with-cusp-lib=yyy but instead correctly use the provided value
update help menu for DMNetworkDistribute()
IS: Added a bunch of Fortran bindings
Bib: More refs
Formatting for several manual pages need fixing
petsc4py: update to snapshot that syncs with the change to PetscSectionCreateGlobalSection()
update to petscthreads.html to reflect our current thinking
TSAdjointEventMonitor should be called before TSAdjointStep
Plex ex5: Added test output
Plex ex2: Added empty output
Plex ex4: Added missing test output
Plex ex1: Fixed test output - CGNS test was broken - Fluent mesh is missing
SNES ex5: Added MMS

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Merge branch 'maint'

KSPCreateVecs() would under certain uncommon circumstances return incorrectly sized vectors
for rectangular vectors

Reported-by: Lars Kielhorn <lars.kielhorn@tailsit.com>

PCApply() used the wrong m

KSPCreateVecs() would under certain uncommon circumstances return incorrectly sized vectors
for rectangular vectors

Reported-by: Lars Kielhorn <lars.kielhorn@tailsit.com>

PCApply() used the wrong matrix to determine sizes for checking for vector length compatibility

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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' 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' of bitbucket.org:petsc/petsc

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

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

doc fixes

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