Merge branch 'master' into knepley/feature-pc-patch

* master: (440 commits)
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html
release: set v3.9 strings
fix grep us

Merge branch 'master' into knepley/feature-pc-patch

* master: (440 commits)
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html
release: set v3.9 strings
fix grep usage on solaris [use egrep]
opensolaris: fix errors
Update timer reporting and minor reporting fix
Remove redundant if statement. Found by @jedbrown
Fixed problem with order of developer photos on website.
superlu_dist: use correct flag in example [PETSC_HAVE_SUPERLU -> PETSC_HAVE_SUPERLU_DIST]
Bib: PERMON ref
fix for osx
doc: more author fixes
doc: more author fixes
Italicized "orderings" in MPI process placement discussion.
Added Richard to the user manual author list.
Added Richard to the list of active developers on the website.
add string check for MS-MPI and IMPI timeout errors
opensolaris does not have multiple grep utils - but default one does not support -F. So use fgrep instead
Standardizing timeout checks
Report wall clock time of total tests
Use time instead of date %s
...

Conflicts:
include/petscpc.h
src/ksp/ksp/interface/itfunc.c

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Merge remote-tracking branch 'origin/hzhang/vec_node/master-rebased-v2'

VecScatter: reorganization

implement several vecnode routines
rm mpi3 from _p_VecScatter struct -- nolonger useful
rm using native shared memory from src/ksp/ksp/examples/tests/ex56.c

VecScatter: reorganization

implement several vecnode routines
rm mpi3 from _p_VecScatter struct -- nolonger useful
rm using native shared memory from src/ksp/ksp/examples/tests/ex56.c
fix memory bug in VecScatterCreateLocal_PtoS_MPI3()
bugfix for VecScatterCopy() -- copy scattertype
add flg is_duplicate to _p_VecScatter; use it to prevent using StoP in VecScatterEndMPI3Node()
rename VecScatterCreateGeneral_ -> VecScatterCreate_
rename VecScatterCreate_vectype_mpitype() -> VecScatterCreateLocal_vectype_mpitype()
check for duplicate indices when mpi3node scatter is created; update tests
undo the commit bb8026e126c43792cc81c094ed5610e9a92280e3: add an example for testing MatMult() with node vectors
add MPI_Barrier(mscomm) in VecScatterEndMPI3Node for safe, but would lose correctness due to wright to same variable (see run2_5 and run3_5). Until finding an efficient way to deal with variable racing, we may give up this work :-(
add test output files
bugfix for VecScatterEndMPI3Node; update ex2.c
Merge branch 'hzhang/vec_node/master-rebased' of bitbucket.org:petsc/petsc into hzhang/vec_node/master-rebased
add an example for testing MatMult() with node vectors
bugfix for VecScatterEndMPI3Node()
rm checking vec_type in VecScatterCreate_mpi3node()
add winarray to Vec_node struct to avoid calls to MPI_Win_shared_query() in scatterEnd()
optionize a loop for xv -> yv
small bugfix and optimization
implement several Vec routines for node type
using object state counter for vector to rm 2 MPI_Barrier()
small optimization and cleanup
small build fix
add few vector routines for node type
add VecScatterCreate_vectype_private() for cleanup
replace MPI_Barrier(comm) by MPI_Barrier(mscomm)
add tests for StoP scatter
bugfix: src/vec/vscat/examples/ex1 and ex2 are working well now
update ex1 and ex2
reverse scatter PtoS works for bs=1
cleanup; fixed memory bug for bs>1
PtoP and PtoS(forward) scatter work for bs>1
mpi3node works for PtoP
forward scatter, I can read on-core xvalues in VecScatterEndMPI3Node
check vectypes for VecScatterCreate_MPI3Node()
add VecScatterCreate_MPI2Node() -- not done yet
rename VecScatterCreate_StoS() -> xxx_Seq(); add VecScatterCreate_type(); reorganize
cleanup and organization -- all seems working well
cleanup; update VecScatterSetFromOptions()
add VecScatterSetFromOptions()
rm VecScatterCreate_MPI1(); cleanup
cleanup VecScatterCreateGeneral_StoP()
add VecScatterCreateGeneral_StoP()
cleanup VecScatterCreateGeneral_PtoS()
VecScatterCreateGeneral_PtoS() works
bugfix after rebase -- passed local tests for both mpi1 and mpi3

add VecScatterCreate_StoS()
add GetInputISType_private()
update src/vec/vscat/examples/ex1.c and its output
new VecScatterCreate() as an interface function
add src/vec/vscat/interface/dlregisvecscat.c
mv vecscatter routines from src/vec/vec/ to src/vec/vscat/
add src/vec/vscat/interface/vscreate.c
reorganize files: create src/vec/vscat
small fix for mmaij.c
add VecScatterType
rename VecScatterType -> VecScatterFormat
add new VecType VECNODE for creating vector over on-node shared memory

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Merge commit 'd47bf9aaf1e5266cc3f0ff499f934c85788965a9' into jed/fix-matcreatempibaij/maint

Obtain changed (v3.5) handling of MatMPIBAIJSetPreallocationCSR to match
documentation.

Merge branch 'master' into pr263/PierreBdR/ts-domain-error-in-stage/master

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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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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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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Merge branch 'pr192/Fande-Kong/scalable-matincreaseoverlap/master' of https://bitbucket.org/petsc/petsc

Merged petsc/petsc into master

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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Merged master into semihozmen/ksp-fcg-eigen-comp-support

Merge branch 'master' into pr192/Fande-Kong/scalable-matincreaseoverlap/master

Needed to merge master to update to new calling sequence PetscCommBuildTwoSided

Merged petsc/petsc into master

Merge branch 'barry/fix-directory-layout'

updated PETSc directory layout to match standard packaging strategies

include/petsc finclude,private,mpiuni
lib/petsc conf
bin/petsc*

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 '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

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 '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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Merge branch 'master' into pr252/dmay/PetscViewerBinarySkipHeaderVecViewLoad
Manual merge of makefile

Conflicts:
src/sys/classes/viewer/examples/tutorials/makefile

Merge branch 'master' of bitbucket.org:petsc/petsc into mark/gamg-crs-ksp2

manual merge of conflict