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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Merge branch 'maint'

Merge remote-tracking branch 'origin/balay/fix-prefix-install-relpath/maint' into maint

install: remove usage of os.relpath() - appears to break with some installs

Reported-by: Brad Aagaard <baagaard@usgs.gov>

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/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/jed/futurize-stage-1'

python: futurize stage 1 (modernize python-2 code)

This should have no behavioral change. It was generated by running

futurize -1 -nw config lib setup.py src systems

followed by reverting some

python: futurize stage 1 (modernize python-2 code)

This should have no behavioral change. It was generated by running

futurize -1 -nw config lib setup.py src systems

followed by reverting some "from . import" relative imports (PEP 328
without 366) and fixing up RDict.py __contains__ to not cause recursion.

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Merge branch 'jed/faster-pipelines' [PR #908]

* jed/faster-pipelines:
petsc_testrun: remove watchtime.sh in favor of ulimit -St
petsc_testrun: use exit code even when no job control
make: use

Merge branch 'jed/faster-pipelines' [PR #908]

* jed/faster-pipelines:
petsc_testrun: remove watchtime.sh in favor of ulimit -St
petsc_testrun: use exit code even when no job control
make: use and recommend "make check" instead of "make test" for the brief check
config make: MAKE_TEST_NP default to MAKE_NP for with-mpi=0
travis: update (deactivated) alltests for consistency with bitbucket-pipelines
pipelines: use COPTFLAGS=-O
pipelines: use -check_pointer_intensity 0 -malloc_test

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Merge branch 'jed/gmakefile-paths' [PR #885]

* jed/gmakefile-paths:
makefile: add + to recursive recipes so that "make test" does not warn about -j
gmakefile: use absolute path for SL_LINKER_FUN

Merge branch 'jed/gmakefile-paths' [PR #885]

* jed/gmakefile-paths:
makefile: add + to recursive recipes so that "make test" does not warn about -j
gmakefile: use absolute path for SL_LINKER_FUNCTION
gmakefile: avoid replication of shared library recipe
makefile: use + in common recursive make invocations
gmakegentest: support localrunfiles naming individual files in subdirectories
gmake: remove src/ from build (PETSC_ARCH/obj) and test paths
gmake tests: enable testing prefix install without write access

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petsc_testrun: remove watchtime.sh in favor of ulimit -St

I was having problems with zombie processes when watchtime.sh kills the
subshell. watchtime.sh also suffers from a race condition and thus

petsc_testrun: remove watchtime.sh in favor of ulimit -St

I was having problems with zombie processes when watchtime.sh kills the
subshell. watchtime.sh also suffers from a race condition and thus is a
fundamentally broken approach. Fortunately, ulimit -St offers what I
believe to be more desirable behavior. The soft (-S) versus hard (-H)
limit is needed for some systems (e.g., Linux) to deliver SIGXCPU (24)
instead of SIGKILL (9).

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Merge remote-tracking branch 'origin/balay/fix-pip-install-destdir'

install.py: set a default --destDir='' value - when this option is not specified

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

Merge remote-tracking branch 'origin/balay/prefix-uninstall'

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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install: do not copy over 'RDict.db', 'testfiles', '*.pyc' [along with '*.o'] during install - they are not useful

Also fix bug with comparing file extensions 'DSYM' vs '.DSYM'

And remove 'DIR=' li

install: do not copy over 'RDict.db', 'testfiles', '*.pyc' [along with '*.o'] during install - they are not useful

Also fix bug with comparing file extensions 'DSYM' vs '.DSYM'

And remove 'DIR=' listing from petscvariables - its not used [and affects reproduceable builds]

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uninstall: also delete prefixdir. And avoid os.listdir() as its expensive
[and break out (of deleting parent dirs ) - if the delete of child fails]

uninstall: fix to track [and remove] test related files installed in share/petsc

uninstall: remove build path listing for installed files from uninstall script
Also attept to delete dirs that were crated by the installer
Also remove soft links and the uninstall script

destdir: current code was installing in $DESTDIR - but we should be installing in $DESTDIR/$prefix

https://www.gnu.org/software/make/manual/html_node/DESTDIR.html#DESTDIR

Reported-by: Jed Brown <je

destdir: current code was installing in $DESTDIR - but we should be installing in $DESTDIR/$prefix

https://www.gnu.org/software/make/manual/html_node/DESTDIR.html#DESTDIR

Reported-by: Jed Brown <jed@jedbrown.org>

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Revert "Issue 208 Set PETSC_DIR appropriately in petscconf.h for --prefix installs"

This reverts commit b1eb7ee26dbb340bd2efa99afe69902d7ccba07a.

Revert "Need to fix generated conf files in destination directory not install directory"

This reverts commit deb554b7b8dbbe2d2409a6e24b6228637e583dbc.

gmake: remove src/ from build (PETSC_ARCH/obj) and test paths

This yields shorter targets to type, since formerly src/ was the only
directory in these paths.