Merge branch 'master' into knepley/feature-plex-parallel-submesh

* master: (2931 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComp

Merge branch 'master' into knepley/feature-plex-parallel-submesh

* master: (2931 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComplex type is missing from fortran
initialize variables so that static analyzer doesn't mistakenly think they are used uninitialized.
Move access of prefix until it is actually used
Remove DMDASplitComm2d(), used in one example that was not tested
Functions that do not return PetscErrorCode should not use PetscFunctionBegin/End paradgm
remove unneeded reassignment of same value
Missing CHKERRQ(); Mostly in Tao code
Remove clang static analyser warning about passing NULL variable to strncat()
missing newline in -ts_monitor_extreme
minor fixes for integer counters
Configure: Deal with '__func__' in C89 builds with newer Clang and GCC.
Jenkinsfile: Increased timeout for tests to 5 minutes.
3.9 changes: further clarify removal of -pc_factor_mat_solver_package
Options deprecations: add "PETSc" to inline warning
removing unused variable
MatShift support added to MATSUBMAT. Mimics MATSHELL functionality. Needed for matrix-free Hessians in TAO Newton-Line-Search methods.
Add -ts_monitor_extreme
Dev manual: add note on deprecating options database keys
...

Conflicts:
src/dm/impls/plex/examples/tests/ex4.c

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Merge branch 'master' into knepley/fix-plex-submesh-projection

* master: (425 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComplex

Merge branch 'master' into knepley/fix-plex-submesh-projection

* master: (425 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComplex type is missing from fortran
initialize variables so that static analyzer doesn't mistakenly think they are used uninitialized.
Move access of prefix until it is actually used
Remove DMDASplitComm2d(), used in one example that was not tested
Functions that do not return PetscErrorCode should not use PetscFunctionBegin/End paradgm
remove unneeded reassignment of same value
Missing CHKERRQ(); Mostly in Tao code
Remove clang static analyser warning about passing NULL variable to strncat()
missing newline in -ts_monitor_extreme
minor fixes for integer counters
Configure: Deal with '__func__' in C89 builds with newer Clang and GCC.
Jenkinsfile: Increased timeout for tests to 5 minutes.
3.9 changes: further clarify removal of -pc_factor_mat_solver_package
Options deprecations: add "PETSc" to inline warning
removing unused variable
MatShift support added to MATSUBMAT. Mimics MATSHELL functionality. Needed for matrix-free Hessians in TAO Newton-Line-Search methods.
Add -ts_monitor_extreme
Dev manual: add note on deprecating options database keys
...

Conflicts:
src/dm/impls/plex/examples/tests/ex4.c

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Merged petsc/petsc into master

Merge branch 'karlrupp/feature-test-harness-detailed-timings' [PR #1053]

* karlrupp/feature-test-harness-detailed-timings:
Test harness: Display and sort by actual run time rather than total CPU tim

Merge branch 'karlrupp/feature-test-harness-detailed-timings' [PR #1053]

* karlrupp/feature-test-harness-detailed-timings:
Test harness: Display and sort by actual run time rather than total CPU time in summary.
Previous output only reported total CPU time, which does not reflect how long a particular test has actually run.
Now both the test execution time (max of CPU time over all MPI ranks) as well as the total CPU time (sum of CPU time over all MPI ranks) are reported.

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Test harness: Display and sort by actual run time rather than total CPU time.

This gives us a better idea of which tests take long on different machines.

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 '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 branch 'scott/test-harness-timing2'

fix grep usage on solaris [use egrep]

opensolaris: fix errors

fgrep: can't open runex4.err
fgrep: can't open runex4.err

grep: can't open timing.out

Update timer reporting and minor reporting fix

Realized that loops and multiple tests were not having their time
recorded properly when using the time command. This now appends
to the file and then

Update timer reporting and minor reporting fix

Realized that loops and multiple tests were not having their time
recorded properly when using the time command. This now appends
to the file and then uses awk to total all of the times. Went
ahead and switched to user+sys time as well since that seems
more accurate.

Also, fix for the telling the user which tests to rerun when failing
when there is a label_suffix (e.g., snes_tutorials-ex12_restart-b).
Reported by @satish

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fix for osx

/Users/balay/petsc/config/petsc_harness.sh: line 162: [: -v: unary operator expected

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

Use time instead of date %s

Stackoverflow showed how to use the time command within a shell script
while leaving the stdout/stderr streams intact. This captures the
real time and reports. report_t

Use time instead of date %s

Stackoverflow showed how to use the time command within a shell script
while leaving the stdout/stderr streams intact. This captures the
real time and reports. report_tests.py updated to report the new
timing.

While doing this, I removed the sub('_1','') in the failures listing.
Reported by @knepley

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test: another timed out test on stdout and ensure nonzero error code

test: more complete test for timeout and suppress output

Reported-by: Satish Balay <balay@mcs.anl.gov>

tests: use MPIEXEC_TIMEOUT instead of ulimit

Tested with Open MPI, MPICH, and MSMPI.

Thanks-to: Satish Balay <balay@mcs.anl.gov>

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

tests: job control with 'ulimit' does not work on cygwin/windows - so check and disable

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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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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