Merge branch 'master' into knepley/feature-error-logging

* master: (324 commits)
DT: Reverting the tgamma change broke MPFR - I guess we need a nightly build with it in
Revert "tgamma: icc on wi

Merge branch 'master' into knepley/feature-error-logging

* master: (324 commits)
DT: Reverting the tgamma change broke MPFR - I guess we need a nightly build with it in
Revert "tgamma: icc on windows requires mathimf.h for tgamma."
setup routine no longer calls PetscCalloc5 if the arrays have already been allocated in a previous setup call
clarify SNESGetFunction()
Move MOAB docs to submansec so as not to clutter DM mansec
doc: remove matlab from doc generation dependency - i.e remove 'alldoc3' and use 'html' to generate corresponding '*.m.html' files.
Remove matlab pounders related cruft that is not required. Document the matlab code better and include an appropriate message in the help text.
Fixed typo.
Remove the inclusion of matlab in testing.
Finalizing comments and the work for the test problems.
Finished the testing and generation of plots. Some simple bug fixes addressed.
Set -Wl,-rpath for Mac OS Matlab mkl directory; don't pass -nojvm to matlab since it causes crashes on Barry's machine and is not needed
Added list of known problems with the code.
Added a comment on ignoring the return from Tao.
Finish with initial implementation of matlab interface to test TAO pounders.
Working through the matlab interface for pounders testing.
Fix typo in manual Reported-by: Jaroslaw Piwonski (CAU) <jpi@informatik.uni-kiel.de>
Fixed mkl_sparse_sypr() calls that were using an unsupported value in the matrix descriptor.
test harness: simplify code that checks for sequential-only tests
Fix the doc for call-backs drdyf drdpf
...

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Cannot directly print complex numbers

Commit-type: bug-fix
Reported-by: pipeline tests

MAT_NEW_NONZERO_LOCATIONS flag did not work correctly for MPIAIJ matrices

Commit-type: bug-fix, example
Reported-by: Marius Buerkle <mbuerkle@web.de>

Merge branch 'maint'

Fix typo in manual
Reported-by: Jaroslaw Piwonski (CAU) <jpi@informatik.uni-kiel.de>

Merge remote-tracking branch 'origin/stefano_zampini/feature-matis-ptap-aij'

MatIS: added implementation for PtAP operation

supported P are {Seq|MPI}(B)AIJ and HYPRE
Interface for {MPI|Seq}BAIJ and HYPRE code works, however:
- local PtAP ops are missing for BAIJ
- MatCreateS

MatIS: added implementation for PtAP operation

supported P are {Seq|MPI}(B)AIJ and HYPRE
Interface for {MPI|Seq}BAIJ and HYPRE code works, however:
- local PtAP ops are missing for BAIJ
- MatCreateSubMatr* ops are missing for HYPRE (will be added in a separate branch)

If requested, carry over the l2l representation of P by attaching it to the resulting mat
This is needed by the MFEM constructor for BDDC

added few more tests to ex23.c
L2L storage is disabled because of a bug in MatDestroySubMatrices that will be fixed in a separate branch

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Merge branch 'master' into knepley/feature-error-logging

* master: (221 commits)
dashboard: count and list example compile failures like:
fix fix-pr879-jczhang-optimize-vecscatter-multi-copy
a

Merge branch 'master' into knepley/feature-error-logging

* master: (221 commits)
dashboard: count and list example compile failures like:
fix fix-pr879-jczhang-optimize-vecscatter-multi-copy
add manual page cross links for SNESLineSearchSetPostCheck() and related routines
fix help manual of MatCreateSubmatrices() Reported-by: Tim Steinhoff <kandanovian@gmail.com>
Add manual pages for PetscRealPart() and PetscImaginaryPart()
fix compile error with missing MPI_C_DOBULE_COMPLEX
fix typo Reported-by: Febrian Setianto <febrian.setianto@gmail.com>
plex tutorial ex5: updated test requirements
DMPlexLoad_HDF5_Xdmf_Internal: fix for complex PetscScalar.
DMPlexLoad_HDF5_Xdmf_Internal: fix for 64-bit PetscInt.
DMPlexBuildFromCellList_Internal: use DMPlexInvertCell_Internal (with PetscInt* arg)
petscviewer.h: removed notice which is no longer relevant
DMPlexCreateFromFile: document option
check only if PETSC_USE_DEBUG
DMPlexBuildFromCellList_Internal optionally inverts cells.
ex5: new test 4 with -compare without repartitioning
ex5: new test 3 using -compare
ex5: HDF5 write+read moved to separate function
ex5: option -format processed in ProcessOptions()
ex5: added missing hdf5 requirement
...

Conflicts:
include/petsclog.h

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Merge branch 'psanan/manpages-notes-newlines' [PR #932]

* psanan/manpages-notes-newlines:
A large number of man pages are improperly formatted because of the lack of a newline after "Notes:", "Fortr

Merge branch 'psanan/manpages-notes-newlines' [PR #932]

* psanan/manpages-notes-newlines:
A large number of man pages are improperly formatted because of the lack of a newline after "Notes:", "Fortran Notes:", or "Developer Notes:".
This batch adds those newlines, with 4 spaces of indentation afterwards.
The uniform indentation arguably makes the man pages a little less readable in the source itself,
but overall this hopefully has a large positive impact on the readability of the HTML pages.

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Man pages: add newlines after "Notes:"

This allows for proper formatting from sowing.

On OS X (using gsed, not the default BSD sed), from the PETSc root directory:

find src include -type f \(

Man pages: add newlines after "Notes:"

This allows for proper formatting from sowing.

On OS X (using gsed, not the default BSD sed), from the PETSc root directory:

find src include -type f \( -name "*.c" -or -name "*.h" -or -name "*.cxx" \) | xargs gsed -i 's/Notes\s*:\s*\(\w.*\)/Notes:\n \1/'

This adds a newline and 4 spaces whenever "Notes:" is followed by any "word" character, in any .c, .h, or .cxx file in src/ or include/

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Merge branch 'master' into knepley/feature-snes-ex13-spectral

* master: (2350 commits)
migrate warning fix from next-tmp
Revert "Remove dead code."
clarifying comment in the code
Remove dead

Merge branch 'master' into knepley/feature-snes-ex13-spectral

* master: (2350 commits)
migrate warning fix from next-tmp
Revert "Remove dead code."
clarifying comment in the code
Remove dead code.
Add JuMP citation
Copyedits and updates to developers manual
Add more protection to intrinsics
MPI: protect arguments in MPI macros
Add the missing conditionals for 64-bit build
Plex+VTK: Fix field type determination
Fix bug in name cleanup
Bib: Added ref
Plex+VTK: Fix field type determination
Plex: Updated test output - I am now hating this shit
forgot to save file after moving prototypes to petscsys.h
update Apple example project settings per Xcode
Two functions should actually be public, used, for example from Apple MacOS and iOS programs
includes should always be included relative to include directory
Apple removed old locations of docsets
SNES ex12: Updated test output
...

Conflicts:
src/snes/examples/tutorials/ex13.c

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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'

Merge remote-tracking branch 'origin/knepley/fix-snes-ex69' into tisaac/feature-dmfield

* origin/knepley/fix-snes-ex69: (311 commits)
PetscFECreateDefault: fix custom Fortran interface to use MPI_

Merge remote-tracking branch 'origin/knepley/fix-snes-ex69' into tisaac/feature-dmfield

* origin/knepley/fix-snes-ex69: (311 commits)
PetscFECreateDefault: fix custom Fortran interface to use MPI_Comm
SNES ex69: Updated test output
SNES ex69: Removed all mantle stuff and change fields to constants - Also use dsymutil for executables
SNES ex69: Removed special partition
SNES ex69: Fixed null space creation - Null space locks its vectors
PetscFE: PetscFECreateDefault() now takes MPI_Comm instead of DM
cleanup very ugly PCGAMG manual page
minor clarifications for VecScatterCreate() manual page
gcov: PETSC_ARCH is required onlyfor -run_gcov - and not for -merge_gcov [where it doesn't exist]
make clearer in help statements what --with-external-packages-dir is for.
Website: Added news entry for PETSc User Meeting 2018 on main page.
CUDA: Further test output fixes for mat_tests-ex2
Turn off elemental test for parmetis running since this does not work on batch systems.
3.8 Changes: KSPCHEBYSHEV
CUDA: Fixed most test errors due to MatMultTranspose*
website: update urls
website: fix Jason's name to match pic. Also add Todd's pic
Dev manual: copyedit
DMPlexDistributeLabels: Propagate the output flag
cuda/cusp: update minimum supported versions of cuda to 7.5 and cusp to 0.5.0
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Merge remote-tracking branch 'origin/maint'

Merge remote-tracking branch 'origin/maint' into stefano_zampini/fix-matis-dmda-l2g

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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MatMPIAIJSetPreallocationCSR_MPIAIJ: fix for empty processes

Merge branch 'maint'

Merge branch 'barry/show-load-balance/maint' into maint

Updates for viewing Load Balance information

Don't display for sequential objects. Label all values with "Load Balance"
Want to display load balance for petsc ordering for vectors, not using natural

Updates for viewing Load Balance information

Don't display for sequential objects. Label all values with "Load Balance"
Want to display load balance for petsc ordering for vectors, not using natural ordering

Commit-type: feature

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Add viewer format object for displaying load imbalance of vectors and nonzeros in sparse MPIAIJ matrices

Could be extended to DMs include DMDA and DMPlex

Commit-type: feature
Thanks-to: Fande Kong

Add viewer format object for displaying load imbalance of vectors and nonzeros in sparse MPIAIJ matrices

Could be extended to DMs include DMDA and DMPlex

Commit-type: feature
Thanks-to: Fande Kong <fande.kong@inl.gov>

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

fix: compile error with --with-errorchecking=0

/home/balay/petsc/src/mat/impls/aij/mpi/mpiaij.c: In function ‘matsetvaluesmpiaij_’:
/home/balay/petsc/src/mat/impls/aij/mpi/mpiaij.c:5734:11: error: ‘

fix: compile error with --with-errorchecking=0

/home/balay/petsc/src/mat/impls/aij/mpi/mpiaij.c: In function ‘matsetvaluesmpiaij_’:
/home/balay/petsc/src/mat/impls/aij/mpi/mpiaij.c:5734:11: error: ‘else’ without a previous ‘if’

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Merge branch 'maint'