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

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

Plex: Added viewing in native format using the global to natural mapping

SF: Added PetscSFCreateFromZero()

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'

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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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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Merge branch 'barry/propagate-pcsetup-failures'

Infrastructure that allows failures in PCSetUp(), PCApply(), MatMult() etc due to, for example a zero pivot or function evaluation outside its domain, to propagate up and become a KSP_DIVERGED inste

Infrastructure that allows failures in PCSetUp(), PCApply(), MatMult() etc due to, for example a zero pivot or function evaluation outside its domain, to propagate up and become a KSP_DIVERGED instead of generating an error that stops the program. In response to Issue 96. This includes failures in MatCreateSNESMF() applications due to domain errors. The mechanism to propagate some errors is by setting Info or Nan into the output vector and using the norm or inner product reductions in SNES or KSP to propagate the error condition to all processes and then handling them immediately after the norm or inner product.

This allows, for example, ODE integrators to try again with a smaller time-step if the PCSetUp failed instead of requiring a complete restart of the run with other options.

Currently some error conditions, such as function domain error in a line search may not get progated up using the correct SNESConvergedReason

See src/snes/examples/tests/ex69.c for the handling of several conditions

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Merge branch 'master' into stefano_zampini/pcbddc-adaptive-selection

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcscalingbasic.c
src/mat/impls/aij/mpi/mumps/mumps.c
s

Merge branch 'master' into stefano_zampini/pcbddc-adaptive-selection

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcscalingbasic.c
src/mat/impls/aij/mpi/mumps/mumps.c
src/mat/impls/is/matis.h

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Merge branch 'master' into tisaac/dmforest

If we're going to start developing on this again, the recent changes to the
location of configuration files will make it annoying to switch to and from
thi

Merge branch 'master' into tisaac/dmforest

If we're going to start developing on this again, the recent changes to the
location of configuration files will make it annoying to switch to and from
this branch. Matt's and my fixes in DMPlex will also be relevant.

* master: (1557 commits)
MatLoad_MPIDense() always allocated array space even if it was previously provided
Clarified lumping options for PCFieldSplitSchurPreType SELFP.
fixed up PetscInfo in GAMG
TSErrorWeightedNorm[2|Infinity]: API changes
MatLoad_SeqDense() always allocated new space for the data even if the user already provided it
Fixed DMCompositeGetAccessArray() to support readonly vectors
Fix obviously-wrong aspects of documentation on SNESVINEWTONRSLS and SNESVINEWTONSSLS.
fixed example to compile - demonstrates a bug
var name 'len' was F90 key word
For user provided Jacobian functions they should always assembly into the second matrix, the one from which the preconditioner is built because the first may be used as matrix-free with -snes_mf_operator
Suggest --with-64-bit-indices if users mistakenly use --with-64bit-indices
Fix configure logging of integer size.
missing underscore in #define of vecgetarrayread translation of fortran stub for VECGETARRAYREAD
updated test output files to reflect differences introduced previously in PCView output
-ksp_type preonly does not support -ksp_monitor_short so remove from test line to prevent extranious warning output
missing CHKERRQ; and ugly double declaration of ierr
Plex ex3: For want of a semicolon, the kingdom was lost
MatSetValuesMPISBAIJ will now print correct global indices when error generated due to new nonzero location
completed basic use of MatSetValuesBlocked_SeqBAIJ_Inlined() by MatSetValuesBlocked_MPIBAIJ() to allow proper global indices being printed when error generated by new nonzero locations.
Added inline version of MatSetValuesBlocked_SeqBAIJ() to be used by MatSetValuesBlocked_MPIBAIJ() to print error message for nonzero block with global indices
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Merge branch 'knepley/feature-harmonic-advection'

* knepley/feature-harmonic-advection: (86 commits)
SNES: Some docs for NASM
TS: Added view for MIMEX
Plex: Silence compiler warnings
Builder

Merge branch 'knepley/feature-harmonic-advection'

* knepley/feature-harmonic-advection: (86 commits)
SNES: Some docs for NASM
TS: Added view for MIMEX
Plex: Silence compiler warnings
Builder: Check for missing numProcs was wrong
PetscFE: Turn off Fortran binding for PetscFECompositeGetMapping()
Plex: Fix big bug in DMPlexGetGlobalFieldOffset_Internal() - If offset is negative (dof is on another proc), then we must have end < start
Builder: Allow override of numProcs
Plex: Fix Fortran wrappers for DMLabelView() and DMPlexDistribute()
Plex+Label: Added Fortran wrapper for DMPlexCreateLabel()
Plex: Dammit, how did this not get checked in?
Plex: Refiner check for hybrid cells must use hybrid faces as well - Ghost cells in FV method are hybrid
TS: MIMEX now uses work vectors for correct grid
Plex: Adding support for FV in automatic interpolator construction - Notice that the injector cannot do the right thing until we scrap VecScatter
Plex+FEM: Using PetscFVGetDualSpace()
SNES+Doc: Added Options Database keys
PetscFV: Added PetscFVRefine() - This allows interpolation to finer grids needed for FAS
PetscFV: Added a dual space for calculating projections
DM: Better error checking in DMCoarsen()
DMDT+PetscFE: Added PetscQuadratureExpandComposite() - Replaces PetscFECompositeExpandQuadrature() - Added PetscFECompositeGetMapping()
Plex: Fixed complex type error
...

Conflicts:
src/dm/impls/plex/ftn-custom/makefile
src/ts/interface/ts.c

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Merge branch 'master' into shri/ts-is-for-differential-variables

Conflicts:
include/petsc-private/tsimpl.h
src/ts/impls/eimex/eimex.c
src/ts/interface/ts.c

Section+Vec: Added PetscSectionGet/RestoreField_Internal() and PetscSectionVecNorm()
- This allows a user to get the hypernorm for a vector with several fields in it

Merge branch 'master' into jed/chem
Note merging a branch with good stuff in it for a year and a half is insane!

Conflicts:
src/ts/examples/tutorials/makefile
src/ts/interface/ts.c

Merge branch 'master' into stefano_zampini/pcbddc-adaptive-selection

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

Merge branch 'jed/assembly-perf' into jed/mat-assembly-perf

Improve VecAssembly performance using BuildTwoSided

* jed/assembly-perf: (27 commits)
Vec: document when InsertMode cannot change betwe

Merge branch 'jed/assembly-perf' into jed/mat-assembly-perf

Improve VecAssembly performance using BuildTwoSided

* jed/assembly-perf: (27 commits)
Vec: document when InsertMode cannot change between reassemblies
VecAssembly BTS: allow reassembly with proper subsets of comm
BuildTwoSided: distinguish events BuildTwoSided vs BuildTwoSidedF
MPI: check for MPIX_Ibarrier (e.g., BG/Q)
VecAssembly BTS: enable by default, use -vec_assembly_bts 0 to disable
VecAssembly BTS: allow proper subsets with VEC_SUBSET_OFF_PROC_ENTRIES
VecAssembly BTS: VEC_SUBSET_OFF_PROC_ENTRIES elides global synchronization
VecAssembly BTS: elide sending empty scalar/block stashes
VecAssembly BTS: separate pending count for scalar and block stashes
VecAssembly BTS: use PetscCommBuildTwoSidedFReq and MPI_Waitsome
VecAssembly BTS: avoid copying data on receive by using pointer frames
Sys BuildTwoSidedFReq: generalization to return requests
VecAssembly: add more scalable implementation, -vec_assembly_bts
Vec_MPI: remove unused members conflated with VecStash
Sys: add PetscMergeMPIIntArray
Sys PetscMergeIntArrayPair: fix PetscFunctionBegin and comment
Sys BuildTwoSidedF_Ibarrier: less synchronous dynamic sparse data exchange
Sys BuildTwoSidedF: build two-sided network with functions in rendezvous
Sys BuildTwoSided test: extract datatype construction
Sys BuildTwoSided: update test for non-contiguous types and verbose output
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Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c
src/sys/threadcomm/interface/threadcomm.c

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