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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Merge branch 'knepley/fix-section-clone'

* knepley/fix-section-clone:
Plex ex3: Test does not work with single precision
Section: Must also copy field symmetries when cloning
Section: Allow NU

Merge branch 'knepley/fix-section-clone'

* knepley/fix-section-clone:
Plex ex3: Test does not work with single precision
Section: Must also copy field symmetries when cloning
Section: Allow NULL argument to PetscSectionSetSym()
Plex ex3: Added tests for Q3
Plex: Added picture for 3D hex interpolation
Section: Copy symmetries when cloning

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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
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Conflicts:
include/petsclog.h

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Merge branch 'psanan/manpages-notes-newlines' [PR #932]

* psanan/manpages-notes-newlines:
A large number of man pages are improperly formatted because of the lack of a newline after "Notes:", "Fortr

Merge branch 'psanan/manpages-notes-newlines' [PR #932]

* psanan/manpages-notes-newlines:
A large number of man pages are improperly formatted because of the lack of a newline after "Notes:", "Fortran Notes:", or "Developer Notes:".
This batch adds those newlines, with 4 spaces of indentation afterwards.
The uniform indentation arguably makes the man pages a little less readable in the source itself,
but overall this hopefully has a large positive impact on the readability of the HTML pages.

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Man pages: add newlines after "Notes:"

This allows for proper formatting from sowing.

On OS X (using gsed, not the default BSD sed), from the PETSc root directory:

find src include -type f \(

Man pages: add newlines after "Notes:"

This allows for proper formatting from sowing.

On OS X (using gsed, not the default BSD sed), from the PETSc root directory:

find src include -type f \( -name "*.c" -or -name "*.h" -or -name "*.cxx" \) | xargs gsed -i 's/Notes\s*:\s*\(\w.*\)/Notes:\n \1/'

This adds a newline and 4 spaces whenever "Notes:" is followed by any "word" character, in any .c, .h, or .cxx file in src/ or include/

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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
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Conflicts:
src/snes/examples/tutorials/ex13.c

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Plex: Added picture for 3D hex interpolation

Merge branch 'stefano_zampini/feature-glvis-homesh-periodic'

DMPlex: Copy over localized coordinates in DMPlexCopyCoordinates

Add a couple of missing checks in DMPlex{Un}Interpolate
Fix documentation for coordinates
ex4: fix output with coordinates
ex1: added

DMPlex: Copy over localized coordinates in DMPlexCopyCoordinates

Add a couple of missing checks in DMPlex{Un}Interpolate
Fix documentation for coordinates
ex4: fix output with coordinates
ex1: added test for periodic case with uninterpolation

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Merge branch 'barry/tao-to-new-test-harness' into barry/all-new-test-harness-branches

Merge branch 'barry/vec-to-test-harness' into barry/all-new-test-harness-branches

Merge branch 'master' into knepley/feature-plex-adjoint-prelim

* master: (60 commits)
petsc4py: update to use latest 3.8 snapshot
petsc4py: update to snapshot that syncs with 276c550
fix warni

Merge branch 'master' into knepley/feature-plex-adjoint-prelim

* master: (60 commits)
petsc4py: update to use latest 3.8 snapshot
petsc4py: update to snapshot that syncs with 276c550
fix warning
Plex ex26: Protect ExodusII stuff
DM: DMCreateSubDM() field argument should be const
TS ex46: Newlines and some numerical jitter
TS ex45: Newlines and some numerical jitter
TS ex11: Fixed indentation and time step numbering
SNES ex12: Update for DM view changes
Plex tests: Update to new DM output
Plex ex23: Use Nc not dim for vector fields
Plex: Default section now ignores cells hanging off boundary meshes
Plex: Viewer now reports the cell Height
Increase patchlevel to 3.8.3
Plex: Fixed DMPlexInterpolate() bugs - Do not copy associated data if we are not interpolating - Do not interpolate if we already have full depth
fix valgrind errors with using PetscObjectGetName()/SetName() with the same object - resulting in a free() before copy.
ex4: fix compile warning and update makefile
Minor fixes
Improving report_tests
PetscDS: Must initialize the default adjacency
...

Conflicts:
include/petsc/private/dmimpl.h
include/petscdm.h
include/petscis.h
src/dm/impls/plex/plexcreate.c

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Merge remote-tracking branch 'origin/knepley/fix-plex-interpolation-consistency'

Plex: Fixed DMPlexInterpolate() bugs
- Do not copy associated data if we are not interpolating
- Do not interpolate if we already have full depth

fix valgrind errors with using PetscObjectGetName()/SetName() with the same object - resulting in a free() before copy.

Merge branch 'master' into knepley/feature-plex-adjoint-prelim

* master: (251 commits)
yaml: add a backup download URL
Fix documentation of MatSetRandom function
Ignore -malloc-hbw option if m

Merge branch 'master' into knepley/feature-plex-adjoint-prelim

* master: (251 commits)
yaml: add a backup download URL
Fix documentation of MatSetRandom function
Ignore -malloc-hbw option if malloc is already set
Plex: Fixed array initialization
pgi: compile fix
knl: update test to use memkind and remove option that worked arround a bug with intel 17
Check the return value for memkind_posix_memalign
Change the default behavour for -malloc_hbw
Bib: More refs
test: remove runex13f90 as its now converted to new test suite
fix win32 crash. This test was previously run with '-n 4' - so restoring it
Fix petscsfgetgraph_ to work for all Fortran compilers by directly using array of PetscSFNodes
bugfix for MatDuplicate_MPIAIJ_PtAP Reported-by: Samuel Lanthaler <s.lanthaler@gmail.com>
strip out dead sundials usage code; change sundials test to only run 5 timesteps to prevent different number of steps on different systems.
Remove extra lines of output file
Example uses C99 constructs so must mark with requires: c99
fix const missmatch for DMDAVecRestoreArrayRead()
remove conflict between function name in example and new PETSc TS function
builds: attempt to do maint/master/next test builds in separate clones
ex62: it turned out that CHACO partioning is not deterministic. Use a prescribed partition instead
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Conflicts:
src/dm/interface/dm.c
src/snes/examples/tutorials/ex13.c

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Plex: DMPlexCopyCoordinates() does nothing if number of coordinate fields is not set

Plex: Now DMPlexInterpolate() copies labels and coordinates
- Removed non-NULL input option which was not useful

Merge branch 'master' into knepley/fix-plex-bc-multiple

* master: (347 commits)
tests: add 'PETSC_HAVE_C99' flag - so that 'requires: c99' can be used in the test suite
PGI: fix build error with

Merge branch 'master' into knepley/fix-plex-bc-multiple

* master: (347 commits)
tests: add 'PETSC_HAVE_C99' flag - so that 'requires: c99' can be used in the test suite
PGI: fix build error with updated 17.10 compilers
Fix for test dirs that are not tutorials/tests
fix use of double in PetscAbsReal() which produces compiler warnings with single precision build
elemental: remove info on conflict of -with-cxx-dialect=C++11 on osx - it works now.
Cleanup .bib files
Fix allfortranstubs rule to rm generated files from correct directory, not outdated location
ierr set but not checked
Remove initial refine so test runs faster and does not time out on some machines
Gail's copyedits for bibtex items
Docs: manual: add further description of 3 different current testing options
DM: check for ops->localtolocalbegin/end before calling
PetscSF: fix typo in tutorial ex1
Vec+HDF5: Fix output for complex - Need to check for empty group name
SNES: SNESDestroy() can be called with snes->dm == NULL
SNES: SNESDestroy() can be called with snes->dm == NULL
Vec+HDF5: Fix output for complex - Need to check for empty group name
Docs: Manual: Update tests section
gmakegentest: also exclude .#filenames created by emacs
DMPlex: Fix output of test ex1 after changes to Gmsh reader
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Merge remote-tracking branch 'origin/barry/remove-petscdatatype-dmgetworkarray'

Merge commit 'd47bf9aaf1e5266cc3f0ff499f934c85788965a9' into jed/fix-matcreatempibaij/maint

Obtain changed (v3.5) handling of MatMPIBAIJSetPreallocationCSR to match
documentation.

Remove use of PetscDataType from DMGetWorkArray() and one absurd usage

Part of process of removing PetscDataType from PETSc since it duplicates MPI_Datatype
Commit-type: style-fix
Thanks-to: Jed Bro

Remove use of PetscDataType from DMGetWorkArray() and one absurd usage

Part of process of removing PetscDataType from PETSc since it duplicates MPI_Datatype
Commit-type: style-fix
Thanks-to: Jed Brown <jed@jedbrown.org>

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Merge branch 'master' into stefano_zampini/feature-gmsh-periodic

* master: (1016 commits)
metis: setself.downloaddirnames for change in 6d90219d8fa4f8b2fd242cc6ff9008358d87c26f
fix compile warni

Merge branch 'master' into stefano_zampini/feature-gmsh-periodic

* master: (1016 commits)
metis: setself.downloaddirnames for change in 6d90219d8fa4f8b2fd242cc6ff9008358d87c26f
fix compile warning: /sandbox/petsc/petsc.clone/src/snes/examples/tests/ex2.c:250:8: warning: ‘pointsAllProcs’ may be used uninitialized in this function [-Wmaybe-uninitialized] ierr = DMInterpolationSetUp(interpolator, dm, pointsAllProcs);CHKERRQ(ierr);
migrate 'build requires: !mpiuni' to new format
migrate 'build requires: !complex' to new format
workarround 'division by zero' compiler warning on windows C:\cygwin64\home\petsc\PETSC~3.CLO\src\ts\examples\TUTORI~1\ex11.c(416): warning #39: division by zero if (uL->h < 0 || uR->h < 0) {for (i=0; i<1+dim; i++) flux[i] = 0./0.; return;} /* SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Reconstructed thickness is negative"); */
dos2unix to prevent warnings on opensolaris "/export/home/petsc/petsc.clone/src/ksp/ksp/examples/tests/ex53.c", line 6: warning: invalid white space character in directive
fix output file - corresponding to code changes in efd4aadf157bf1ba2d80c2be092fcf4247860003
disable test on windows
update log from opensolaris so that the diff is clean on linux aswell
update grep in sync with change in efd4aadf157bf1ba2d80c2be092fcf4247860003
Fixed code that did not correctly set current color for block insertion
Update output files that did not get fixed after previous merges
Change MPIUni to not immediately abort on operations it cannot perform, instead return error code
Add filter for example that can produce 1 different iteration count
Example add system calloc, bad formating of %d in print, commented out code
Always use (void) for functions that take no arguments, never ()
always need to caste PetscReal variables to (double) in print statements
updates to manual page for clarity
update help menu for MatRARt() -- MatRARt_mpiaij_mpiaij is supported now, but not efficient.
fix nightlybuild error with c1cbb1def3f8ddca04c3998b9c06618fd1ffef35 on arch-linux-IPL64 src/ksp/pc/examples/tests ex5_1
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Conflicts:
include/petscdm.h
src/dm/impls/plex/plexcreate.c
src/dm/impls/plex/plexgmsh.c
src/dm/impls/plex/plexhdf5.c

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Merge branch 'scott/test-datafiles-fix' of https://bitbucket.org/petsc/petsc into scott/test-datafiles-fix