Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (353 commits)
Configure: Pragmatic now requires Cxx11
fix compile warning
mpiuni: build somempifort.o after mpiuni.mod

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (353 commits)
Configure: Pragmatic now requires Cxx11
fix compile warning
mpiuni: build somempifort.o after mpiuni.mod
Remove use of common block from MPIUNI code
use was in wrong location
Fortran line extends past 72 char
Moved the rest of the PETSc common block variables over to petscsys module
tests: fix breakage due to cd93b0e13c6da70ee1e038f55989cf888bc1d1c5
Need to use petscsys to get PETSC_COMM_SELF defined in example
Mat ex23 and ex40: fix errors reported from nightly tests
Put declaration on too lines because otherwise it generates an error for truncated line
Move PETSC_COMM_WORLD and PETSC_COMM_SELF from common blocks to petscsys module
tests: fix requires - and create out files for seqaijmkl tests
KSP ex72: nested dissection is likely to be different between machines
cmake: downgrade to version 3.9 - as newer versions require cxx11 compiler [which is not universal]. However stick with version 3.11 on opensolaris
Mat ex23: fix memory leaks
Bib: Some new refs
KSP examples: add missing casts to double in printf
updated GAMG KSP tests
PetscRound() should be PetscRoundReal() in __fp16
...

Conflicts:
include/petsclog.h
src/sys/logging/plog.c
src/sys/logging/utils/eventlog.c

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Merge branch 'master' into knepley/fix-plex-project-tests

* master: (477 commits)
Added correct report number for PETSc Developers Guide
Update PETSc Developers Guide title and final pages to ne

Merge branch 'master' into knepley/fix-plex-project-tests

* master: (477 commits)
Added correct report number for PETSc Developers Guide
Update PETSc Developers Guide title and final pages to new ANL style
Hash: Quick documentation fix
PetscBinaryViewerRead -> PetscViewerBinaryRead
cast in GAMG_HASH so that it works for PetscInt32 near PETSC_INT_MAX without overflow to negative numbers
Add link for DrMemory which may serve as an alternative to valgrind on Windows
Finish Gail's copyedits for developers manual.
openmpi: fix namespace conflict [with static build on ppc64le]
two pages of Gail's edits to developers guide
Another chapter of Gail's copyedits for the developers guide
Gail's copyedits on two more chapters of the developers guide
Fix more %d to %D in GAMG code. Fix code style in GAMG code
DMPlexVTK: vertices is int! need to use %d instead of %D
TS ex18: update outputs (reported by nightly tests)
Use %D in error messages for GAMG hash; fix style issues with GAMG hash
config: Update petsc4py git commit
Fix bad plain extern declaration.
Add Gail's copyedits for the initial portion of the developers guide
Add missing common block to subroutine
fix mpiuni tests with xl compilers
...

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

* master: (562 commits)
fix clang-analyzer warning
Developers manual never use system randomizers in PETSc and example source code.
missing

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

* master: (562 commits)
fix clang-analyzer warning
Developers manual never use system randomizers in PETSc and example source code.
missing CHKERRQ()
DT: Reverting the tgamma change broke MPFR - I guess we need a nightly build with it in
Add a test for ex21
Fix error in ex21
Add missing fortran interface that handles null objects
DMComposite: add missing guards
MatPreallocate: fix overpreallocation of local rows
style fixes
MatView_MPI_DA: do not print twice the class prefix
MatSetOperation: stash the original MatView_XXX in the viewnative function pointer
DMCreateInterpolation_DA gracefully error instead of catching FPE signals
MatIncreaseOverlap: preserve communicator of index sets
MatMPIAIJ: fix indentation and missing CHKERRQ
ISBuildTwoSided: remove tabs and fix style
Fix documentation
PetscViewerDraw: fix unininitialized warning from valgrind
MatConvert_SeqAIJ_SeqBAIJ: remove error for non square matrices and add MAT_REUSE_MATRIX case
Mat: MAT_INPLACE_MATRIX can be used for transposition with rectangular matrices
...

Conflicts:
src/dm/dt/interface/dtfe.c
src/dm/impls/plex/plex.c
src/dm/impls/plex/plexfem.c
src/snes/examples/tutorials/ex13.c
src/snes/examples/tutorials/ex62.c
src/snes/examples/tutorials/makefile
src/snes/examples/tutorials/output/ex62_18.out
src/snes/examples/tutorials/output/ex62_19.out
src/snes/examples/tutorials/output/ex62_20.out
src/snes/examples/tutorials/output/ex62_20_parmetis.out
src/snes/examples/tutorials/output/ex62_21.out
src/snes/examples/tutorials/output/ex62_22.out
src/snes/examples/tutorials/output/ex62_23.out
src/snes/examples/tutorials/output/ex62_24.out
src/snes/examples/tutorials/output/ex62_25.out
src/snes/examples/tutorials/output/ex62_26.out
src/snes/examples/tutorials/output/ex62_27.out
src/snes/examples/tutorials/output/ex62_28.out
src/snes/examples/tutorials/output/ex62_29.out
src/snes/examples/tutorials/output/ex62_2d_p3_1.out
src/snes/examples/tutorials/output/ex62_30.out
src/snes/examples/tutorials/output/ex62_31.out
src/snes/examples/tutorials/output/ex62_32.out
src/snes/examples/tutorials/output/ex62_33.out
src/snes/examples/tutorials/output/ex62_34.out
src/snes/examples/tutorials/output/ex62_35.out
src/snes/examples/tutorials/output/ex62_36.out
src/snes/examples/tutorials/output/ex62_pc_simple.out
src/snes/examples/tutorials/output/ex62_pc_simplec.out
src/snes/examples/tutorials/output/ex62_quad_q2p1_full.out
src/snes/examples/tutorials/output/ex62_quad_q2q1_full.out
src/snes/utils/dmplexsnes.c

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Merge branch 'maint'

Merge branch 'stefano_zampini/cherrypick/maint' into maint

Merge branch 'knepley/feature-error-logging' of bitbucket.org:petsc/petsc into knepley/feature-error-logging

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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Fixes for annoying warnings from GNU (-Wmaybe-uninitialized)

Merge remote-tracking branch 'origin/hzhang/update-example-ts-pipes1'

fixbug for DMNetworkHasJacobian() when nVertices=0;
add cases of using user Jacobian elements to src/ts/examples/tutorials/network/wash/pipes1.c

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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Deprecate DMSet/GetDefaultSection() for DMSet/GetSection()

Revert manual page change per Matt's preference

Commit-type: style-fix
Thanks-to: Matthew Knepley

Merge remote-tracking branch 'origin/shri/dmnetwork-subnetworks-rebased'

Fix last commit to properly pass int cell lists to DMPlex from DMNetwork

Network examples now work with 64 bit indices

Commit-type: bug-fix

Git rid of int argument for edgelist with DMNetwork, replace with PetscInt

The DMNetwork examples now don't work with 64 bit indices probably due to some place in
DMPlex that uses int instead of Pet

Git rid of int argument for edgelist with DMNetwork, replace with PetscInt

The DMNetwork examples now don't work with 64 bit indices probably due to some place in
DMPlex that uses int instead of PetscInt. But this means that DMPlex needs to be fixed to
not have this one crazy location with int instead of PetscInt.

Commit-type: style-fix, feature

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fix warnings reported from regression tests

rm old DMNetworkLayoutSetUp()

change API of DMNetworkSetEdgeList() to DMNetworkSetEdgeList(DM dm,int *edgelist[],int *edgelistCouple[])

replace DMNetworkSetSizes() with DMNetworkSetSizesCoupled()

cleanup

implement DMNetworkSetSizesCoupled()

access coupling vertices

bugfix: ex3.c works now

add coupling vertices