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/scott/test-harness-perform2' into maint

test harness: simplify code that checks for sequential-only tests

thisfixes bug with processing nsize in loops [they should be skipped for seq test run]

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'

Performance improvements to gmakegentest.py

* Added filter to avoid parsing non-source files.

Didn't realize this was happening and this alone was probably the biggest cause of
performance

Performance improvements to gmakegentest.py

* Added filter to avoid parsing non-source files.

Didn't realize this was happening and this alone was probably the biggest cause of
performance degradation as non-source files are added.

* Improve performance by moving regex compilation

Moved the compilation of regex compilation from _substVars to
getSubstVars to dramatically reduce the number of regex compilations.

* Refactor relpath calls

Profiling revealed that relpath was actually taking up noticable time
so refactor to make fewer calls. This also resulted in fewer lines
of code.

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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/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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Merge branch 'jed/reproducible-builds' [PR #893]

* jed/reproducible-builds:
Allow to override build date
Sort file lists

Merge remote-tracking branch 'origin/scott/test-harness-minorfixes2'

Merge remote-tracking branch 'origin/scott/test-harness-emacsfixes'

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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gmakegentest: support localrunfiles naming individual files in subdirectories

Ignore more emacs temporary files

Fix for args with hyphens and for loops

A regex is used to process arguments when for loops are contained
within the arguments. A negative lookbehind assertion was used to
ignore matches that have

Fix for args with hyphens and for loops

A regex is used to process arguments when for loops are contained
within the arguments. A negative lookbehind assertion was used to
ignore matches that have
<alphabetical character>-<alphabetical character>

Fixes Issue #206. Reported by Vaclav Hapla.

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Sort file lists

so that petsc builds in a more reproducible way
in spite of indeterministic filesystem readdir order
and http://bugs.python.org/issue30461

See https://reproducible-builds.org/ for w

Sort file lists

so that petsc builds in a more reproducible way
in spite of indeterministic filesystem readdir order
and http://bugs.python.org/issue30461

See https://reproducible-builds.org/ for why this is good.

Without this patch, there would be ordering variations in
CMakeLists.txt
libpetsc.so.3.8.3
petscconf.h
lib/petsc/conf/files
and likely some more places

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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.

gmake tests: enable testing prefix install without write access

Standard configurations should work as before, except that test
executables are once again named using relative paths (as documented i

gmake tests: enable testing prefix install without write access

Standard configurations should work as before, except that test
executables are once again named using relative paths (as documented in
"make help-test"). For prefix installs, testing is performed as

export PETSC_DIR=/path/to/prefix PETSC_ARCH=
make TESTDIR=/tmp/petsc-tests -f $PETSC_DIR/share/petsc/examples/gmakefile.test test

where TESTDIR is some location that is writable.

A side-effect of this change is that the generated
$PETSC_ARCH/lib/petsc/conf/testfiles has moved to $TESTDIR/testfiles.

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Merge branch 'barry/fix-bin-install'

Remove/move all items from $PETSC_DIR/bin so that package maintainers don't have to deal with non-standard usage.

Commit-type: style-fix

tests: fix for multiple 'localrunfiles'. i.e support:

localrunfiles: ex1options power/case9.m water/sample1.inp

Merge branch 'scott/test-harness-installfixes'