PetscSubComm:
* Added method to return parent comm

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
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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
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Conflicts:
config/builder.py

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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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Merge branch 'mat-increaseoverlap' of ssh://bitbucket.org/Fande-Kong/petsc into pr332/master/Fande-Kong/mat-increaseoverlap-scalable

Merge remote-tracking branch 'petsc/jed/mat-assembly-perf' into matpartitioning-hierach

To make the interface PetscCommBuildTwoSided(MPI_Comm comm,PetscMPIInt count,MPI_Datatype dtype,PetscInt nto,c

Merge remote-tracking branch 'petsc/jed/mat-assembly-perf' into matpartitioning-hierach

To make the interface PetscCommBuildTwoSided(MPI_Comm comm,PetscMPIInt count,MPI_Datatype dtype,PetscInt nto,const PetscMPIInt *toranks,const void *todata,PetscInt *nfrom,PetscMPIInt **fromranks,void *fromdata) compatible with Jed's new changes.
DataType of 'nto' and 'nfrom' is changed to PetscMPIInt.

Conflicts:
include/petscsys.h
src/sys/utils/sorti.c
src/vec/vec/examples/tests/makefile

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Merge remote-tracking branch 'petsc/jed/mat-assembly-perf' into mat-increaseoverlap

To make the interface PetscCommBuildTwoSided(MPI_Comm comm,PetscMPIInt count,MPI_Datatype dtype,PetscInt nto,const

Merge remote-tracking branch 'petsc/jed/mat-assembly-perf' into mat-increaseoverlap

To make the interface PetscCommBuildTwoSided(MPI_Comm comm,PetscMPIInt count,MPI_Datatype dtype,PetscInt nto,const PetscMPIInt *toranks,const void *todata,PetscInt *nfrom,PetscMPIInt **fromranks,void *fromdata) compatible with Jed's new changes.
DataType of 'nto' and 'nfrom' changed to PetscMPIInt.

Conflicts:
include/petscsys.h
src/sys/utils/sorti.c
src/vec/vec/examples/tests/makefile

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

Merged in barry/error-on-extern-c-of-petscincludes (pull request #335)

add a tester in the basic include file that checks if the PETSc include files

add a tester in the basic include file that checks if the PETSc include files
are enclosed within a extern "C" which they never should be and presents that
error to the user in a somewhat useful way

add a tester in the basic include file that checks if the PETSc include files
are enclosed within a extern "C" which they never should be and presents that
error to the user in a somewhat useful way so they know that PETSc includes
should never be within an extern "C"

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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' of bitbucket.org:petsc/petsc

Merge branch 'mat-increaseoverlap' into pcgasm-increaseoverlap

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

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

Merged in PR312: karpeev/ksp-pcgasm-overhaul.

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

* master: (32 commits)
MatGetSubmatrix() could hang when some processes thought the entire matrix as being selected and others did not.

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

* master: (32 commits)
MatGetSubmatrix() could hang when some processes thought the entire matrix as being selected and others did not.
PetscOptionsStringToScalar() and hence PetscOptionsScalarArray() did not work correctly for complex numbers with negative imaginary part
Have SNESCOMPOSITE honour -snes_max_fail for the number of inner solver failures it will tolerate.
fiat: add fallback url
added Stefano and Lisandro to PETSc authors list updated PETSc version number to 3.6 and year of publication to 2015 in the users manuals
deeper cleanup of matrix when the type is reset
need to call KSPSetFromOptions() after KSPSetOperators() so that command line null space is attached to correct matrix updated example output for null space not attached to KSP
Doc: Acknowledge Patrick
bugs in example that should never have gotten into next bug in code calling VecGetArray() on read only vector
doc: seperate -> separate
configure: help - prevent from printing duplcate sections - all PACAKGENAMEs should be CAPS
remove C99 code from example update output from example
updated list of PETSc enum objects that bfort will treat as native for generating Fortran stubs
-help would print the various -xxx_type values on multiple lines making a | grep -ksp_type (for example) not list all the possible options
fix memory leak as reported by the nightly tests
print help message for PetscOptionsGetViewer() the message is rather long
removed dead code about PETSc web server
removed unneeded custom XXXViewFromOptions() functions and updated to use PetscObject as second argument calling sequence
changed second argument of PetscObjectViewFromOptions() to PetscObject and all routines that use this routine
bugfix as reported by PETSc blame digest (next) 2015-05-25
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Merge branch 'master' of bitbucket.org:petsc/petsc

Merge branch 'barry/fix-petscobjectviewfromoptions'

removed dead code about PETSc web server

changed second argument of PetscObjectViewFromOptions() to PetscObject and all routines that use this routine

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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Merged petsc/petsc into master