Merge branch 'master' into knepley/fix-plex-residual-loop
Warning: This merge includes real changes

* master: (188 commits)
Add JuMP citation
Copyedits and updates to developers manual
Add mor

Merge branch 'master' into knepley/fix-plex-residual-loop
Warning: This merge includes real changes

* master: (188 commits)
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
SNES ex62: Set name of solution vector - Update test output
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html
release: set v3.9 strings
move output file to the correct location. i.e fix 305862f9cd0dc399542ae11dd744508e4b6ad2e3
...

Conflicts:
src/snes/utils/dmplexsnes.c
src/ts/utils/dmplexts.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/dalcinl/mat-getset-ops'

Add MatGetOperation() and fixes to MATSHELL

Merge branch 'karlrupp/feature-remove-cusp'

* karlrupp/feature-remove-cusp:
Removes VECCUSP vectors and AIJCUSP matrices, because they provide no added benefit over VECCUDA and AIJCUSPARSE.
Also rem

Merge branch 'karlrupp/feature-remove-cusp'

* karlrupp/feature-remove-cusp:
Removes VECCUSP vectors and AIJCUSP matrices, because they provide no added benefit over VECCUDA and AIJCUSPARSE.
Also removes the CUSP-based preconditioners for now.
SACUSP will be re-added later, after the new release is out.

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GPUs: Allow ViennaCL and VECCUDA to be used concurrently.

This also gets rid of the weird veccuda.py.

Merge branch 'stefano_zampini/fix-matis-dmda-l2g'

CUSP: Removed VECCUSP and AIJCUSP as well as preconditioners.

SA-AMG from CUSP will be re-added in a follow-up commit,
made to work with AIJCUSPARSE and VECCUDA.

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 branch 'stefano_zampini/feature-factor-sell' [PR #860]

* stefano_zampini/feature-factor-sell:
This branch adds LU factorization support to MATSEQSELL via MUMPS and SuperLU.

Merge branch 'barry/refactor-petscstrncat'

Change PetscStrncat() to PetscStrlcat() to match BSD API where l represents total length

Update many uses of PetscStrcpy() and PetscStrcat() to the safer PetscStrncpy() and PetscStrlcat()

Commit-ty

Change PetscStrncat() to PetscStrlcat() to match BSD API where l represents total length

Update many uses of PetscStrcpy() and PetscStrcat() to the safer PetscStrncpy() and PetscStrlcat()

Commit-type: style-fix, feature
Thanks-to: Jed Brown

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Mat: relax the erroring condition

if a matrix is hermitian and symmetric then the imaginary part is zero

Merge branch 'barry/refactor-matshell'

Begin refactorization of MatShell to make the code more straightforward and extensible

Introduce MatSetOperation() for changing operations on non-MATSHELLs
Introduce two modes for MATSHELL
1) MAT

Begin refactorization of MatShell to make the code more straightforward and extensible

Introduce MatSetOperation() for changing operations on non-MATSHELLs
Introduce two modes for MATSHELL
1) MATSHELL manages scalings and shifts automatically
2) Creator of MATSHELL can provide their own code for managing scaling and shifts
This is used by MatCreateADA() and MatCreateSubMatrixFree()

The extensibility is so that a MatShell can be easily used in as many places as possible as other matrices,
for example,

/* A = diag(u) G */
ierr = MatCopy(appctx->SEMop.grad,A,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatDiagonalScale(A,globalin,NULL);CHKERRQ(ierr);
/* A = A + diag(Gu) */
ierr = VecDuplicate(globalin,&Gglobalin);CHKERRQ(ierr);
ierr = MatMult(appctx->SEMop.grad,globalin,Gglobalin);CHKERRQ(ierr);
ierr = MatDiagonalSet(A,Gglobalin,ADD_VALUES);CHKERRQ(ierr);
ierr = VecDestroy(&Gglobalin);CHKERRQ(ierr);
/* A = K - A */
ierr = MatScale(A,-1.0);CHKERRQ(ierr);
ierr = MatAXPY(A,1.0,appctx->SEMop.keptstiff,SAME_NONZERO_PATTERN);

Commit-type: feature

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cosmetic fixes

Merge branch 'maint'

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

fix location of checking of format

Commit-type: bug-fix

Present load balance information for Mat in PETSc ordering not natural ordering

Commit-type: bug-fix

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

Merge branch 'maint'

* maint:
PetscCheckPointerSetIntensity(): document -check_pointer_intensity
MatGetRowIJ man page: minor cleanup

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

Merged in David-Wobrock/petsc (pull request #849)

Fix doc typo and add formula for MatMultTranspose