MatShift_MPI/SeqXAIJ() could hang if some processes had no entries on a process while others had entries
because some processes would attempt a parallel preallocation and the others would not.

Fixed

MatShift_MPI/SeqXAIJ() could hang if some processes had no entries on a process while others had entries
because some processes would attempt a parallel preallocation and the others would not.

Fixed by first checking if no preallocation was done, and if not doing. Otherwise preallocation is only done
if approprate by each process on the diagonal block portion of the matrix, thus not requiring all processes
that share the matrix to call the parallel preallocation routine

Reported-by: Patrick Lacasse <patrick.m.lacasse@gmail.com>

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Mat: Removed PBGL

Replaced PetscViewerASCIISynchronizedAllow() with PetscViewerASCIIPushSynchronized() PetscViewerASCIIPopSynchronized()

Merge branch 'barry/add-concurrencykit' into barry/fix-petscviewer-attempt-2

Merge branch 'matpartitioning-hierach' into pcgasm-increaseoverlap

Got an example ( /src/mat/examples/tests) from matpartitioning-hierach

Conflicts:
src/mat/impls/adj/mpi/mpiadj.c

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

Merge branch 'maint'

* maint:
MatGetGhosts: add missing implementation for MPIAIJ
error in manual page from cut and paste

MatGetGhosts: add missing implementation for MPIAIJ

Only MPIBAIJ was supported before.

Reported-by: Alicia Klinvex <amklinv@sandia.gov>

merged PetscViewerGetSingleton() and PetscViewerGetSubcomm() into PetscViewerGetSubViewer()

Does not currently work, needs fixes to work correctly recursively

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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Formatting for several manual pages need fixing

Reported-by: Dave May <dave.mayhem23@gmail.com>

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' 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/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
...

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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Mat+Doc: More Fortran docs