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'

Fixed some PetscValidLogicalCollective calls that used the wrong typename
One of these caused problems for a user with 64 bit integers

Reported-by: Erik Andreassen <erand@mek.dtu.dk>

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

* master: (206 commits)
Bib: Added ref
fix the output file for the ts example ex20adj
Bugfix: setting post-step function in ztsf.c
f

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

* master: (206 commits)
Bib: Added ref
fix the output file for the ts example ex20adj
Bugfix: setting post-step function in ztsf.c
fix makefile format error with 'all-legacy'
doc: handle missing dev.html in a release tarball
doc: add in petscistypes.h to doc sourcefile list
Increase patchlevel to 3.6.1
update some example output files
Doc+Vec: Fixed VecSetValuesBlocked() Reported by: Shao-Ching Huang <huangsc@gmail.com>
clarify that PETSc's "thread safe" code only works with OpenMP
allow adjoint integration over split time intervals
DT: Goddman it. Why are people stepping on my commits
Bib: Added ref
fix the bug in the endpoint version of discrete adjoint theta and correct the affected example outputs
SNES: Added SNESQN types to Fortran Reported-by: Chris Bradley <c.bradley@auckland.ac.nz>
fix: buggy change in 33da457b864643cfcac2768e47197c286471a5a4
updated petscthreads.html with information on thread per object model
fix for ex56
removed the dead links to threads.html
send petsc repository messages to Karl no longer from his mcs address
...

Conflicts:
config/builder.py
src/dm/impls/plex/examples/tests/ex3.c
src/dm/impls/plex/examples/tests/makefile
src/dm/impls/plex/makefile

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Merge branch 'master' into knepley/feature-plex-point-location

* master: (202 commits)
Bib: Added ref
fix makefile format error with 'all-legacy'
Increase patchlevel to 3.6.1
update some exa

Merge branch 'master' into knepley/feature-plex-point-location

* master: (202 commits)
Bib: Added ref
fix makefile format error with 'all-legacy'
Increase patchlevel to 3.6.1
update some example output files
Doc+Vec: Fixed VecSetValuesBlocked() Reported by: Shao-Ching Huang <huangsc@gmail.com>
clarify that PETSc's "thread safe" code only works with OpenMP
allow adjoint integration over split time intervals
DT: Goddman it. Why are people stepping on my commits
Bib: Added ref
fix the bug in the endpoint version of discrete adjoint theta and correct the affected example outputs
SNES: Added SNESQN types to Fortran Reported-by: Chris Bradley <c.bradley@auckland.ac.nz>
fix: buggy change in 33da457b864643cfcac2768e47197c286471a5a4
updated petscthreads.html with information on thread per object model
fix for ex56
removed the dead links to threads.html
send petsc repository messages to Karl no longer from his mcs address
Plex: Fix for all the hidebound morons living with c89. Good luck doing computational science in the 80s!
DT: Fix tanh-sinh - Removed wrong var
SNES: Added SNESQN types to Fortran Reported-by: Chris Bradley <c.bradley@auckland.ac.nz>
Bib: More refs
...

Conflicts:
config/builder.py

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

Merge branch 'barry/remove-pcsetup-mg-changeofpreonly/master'

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

* master: (111 commits)
add filters for website tests that removes warnings about MPI type tag mismatches due to const
remove

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

* master: (111 commits)
add filters for website tests that removes warnings about MPI type tag mismatches due to const
remove Peter from blame-email list.
don't warn about MPI const long * versus long long *
Configure: Added GMP an MPRF - These allow arbitrary precision arithmetic
SNES ex69: SolCx finally works - Fixed order of parameters - Made different versions of pointwise functions
SNES ex69: Fixed bug where SolKx and SolCx have different numbers of parameters
SNES ex69: Small bug fixes - Initialize coordinates for SolCx - Fixed declaration length
I believe this call on line 357: ierr = DMSetFromOptions(dau); should actually set `dak`. The DM `dau` is already set on line 349.
SNESSolve_KSPOnly() did not compute function at new solution unless monitoring is turned on but SNESSolve_FAS() internals assume that each subsnes solve it calls does compute the new function value so broke when -fas_levels_snes_monitor was not turned on but -fas_levels_snes_type kspmonitor was used
Have SNESVIGetInactiveSet return the *actual* current inactive set.
One now passes the nullspace in the matrix for a linear system as the first Amat argument to KSPSetOperators, SNESSetOperators, TSSetIJacobian() not the second pmat argument
Remove change documentation of Removed MatMFFDAddNullSpace() just use MatSetNullSpace() as it is now backported in maint (36.html)
MatMFFD doesn't need to have its own null space management cherry-picked from 39601f4 (barry/remove-matmffdaddnullspace/master)
Removed trailing '\\' in the authors line.
add note to PetscOptionsInsertFile() that it should not be used for PETSc wide options
Add Fortran stub for SNESSetUpdate()
improve manual page slightly for clarity
PCGASM.
Basic PCGASM description added to manual.
add DMDAVecGet/RestoreArrayReadF90()
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previously PCSetUp_MG() would change the KSP type from preonly to gmres unless the PC was LU, Cholesky, redundant, SVD, or bjacobi (with one block per process). I have removed this code; it is now th

previously PCSetUp_MG() would change the KSP type from preonly to gmres unless the PC was LU, Cholesky, redundant, SVD, or bjacobi (with one block per process). I have removed this code; it is now the users responsibility if they change the PC and wish to use an iterative KSP they must change the KSP. The reason for the change was the check for bjacobi required that the matrices had already been provided and setup called on the submatrices which need not be the case; plus the code to change to gmres was ad hoc and doesn't match the style of PETSc which is not to change solvers unless directed by the user.

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

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

fixing EM petsc params

added PREONLY default for coarse grid solver in GAMG

added PREONLY default for coarse grid solver in GAMG

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

Merge branch 'maint'

remove nonexistent -pc_mg_monitor from documentation

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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