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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Man pages: capitalize "notes:" to "Notes:"

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

find src include -type f \( -name "*.h" -or -name "*.c" \) | xargs gsed -i 's/no

Man pages: capitalize "notes:" to "Notes:"

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

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

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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 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 'hongzh/update-ts-adjoint-api' [PR #870]

* hongzh/update-ts-adjoint-api:
Reorganizes TSAdjoint code.
Deprecates TSAdjointSetRHSJacobian() TSAdjointComputeDRDP() TSAdjointComputeDRDY()

Merge branch 'denera/fix-tablevels-for-views' [PR #869]

* denera/fix-tablevels-for-views:
Instead of manual push-pop tab operations, views now inherit tablevels automatically.
This makes views consi

Merge branch 'denera/fix-tablevels-for-views' [PR #869]

* denera/fix-tablevels-for-views:
Instead of manual push-pop tab operations, views now inherit tablevels automatically.
This makes views consistent with default convergence monitors.

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Merge branch 'hongzh/change-vecarray-to-mat-tlm'

* hongzh/change-vecarray-to-mat-tlm:
Uses a dense array instead of multiple vectors to store TLM sensitivity
and removes TSForwardSetRHSJacobianP (us

Merge branch 'hongzh/change-vecarray-to-mat-tlm'

* hongzh/change-vecarray-to-mat-tlm:
Uses a dense array instead of multiple vectors to store TLM sensitivity
and removes TSForwardSetRHSJacobianP (use TSAdjointSetRHSJacobian instead).

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Reorganize TSAdjoint and deprecate some functions

The derivative routines are independent of integration methods, thus can be shared by adjoint and TLM.

Funded-by:
Project: FASTMATH
Time: 1.0 hours

Reorganize TSAdjoint and deprecate some functions

The derivative routines are independent of integration methods, thus can be shared by adjoint and TLM.

Funded-by:
Project: FASTMATH
Time: 1.0 hours
Reported-by:
Thanks-to:

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Wrapping up for a pull request

All views changed to inherit tab levels from associated objects

Merge branch 'barry/fix-ts-view-push-tab'

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

Fixes for TSView to add proper tabbing

1) add PetscViewerASCIIPushTab() PetscViewerASCIIPopTab() for SNESView inside TSView()
2) make sure usessnes is properly set and unset depending on if the TS m

Fixes for TSView to add proper tabbing

1) add PetscViewerASCIIPushTab() PetscViewerASCIIPopTab() for SNESView inside TSView()
2) make sure usessnes is properly set and unset depending on if the TS method uses SNES
3) fix output for two TS examples that do not use SNES

Commit-type: bug-fix
Reported-by: Alp Dener <adener@anl.gov>
Thanks-to: Todd Munson <tmunson@mcs.anl.gov>

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Merge branch 'barry/feature-ts-burgers-spectral'

Add code for automatically checking if shell matrix vector and transpose matrix vector products work with TS

Added MatShellTestMult(), MatShellTestMultTranspose(), TSRHSJacobianTest(), and TSRHSJaco

Add code for automatically checking if shell matrix vector and transpose matrix vector products work with TS

Added MatShellTestMult(), MatShellTestMultTranspose(), TSRHSJacobianTest(), and TSRHSJacobianTestTranspose()

Commit-type: feature

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-ts_monitor_error can now draw error as well as print the 2-norm

Commit-type: feature

Refactor the TLM model

- The forward sensitivities are now stored in dense matrices. ex20fwd is modified to test the change.
- TSForwardSetRHSJacobianP has been removed. TSForward uses the JacobianP

Refactor the TLM model

- The forward sensitivities are now stored in dense matrices. ex20fwd is modified to test the change.
- TSForwardSetRHSJacobianP has been removed. TSForward uses the JacobianP matrix that one provides via the TSAdjoint interface.

Funded-by:
Project: FASTMath
Time: 8.0 hours
Reported-by:
Thanks-to:

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

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

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
...

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

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Merge remote-tracking branch 'origin/barry/ssisc-spectral-adjoint'

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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add TSMonitorError() and -tao_view_solution

Commit-type: feature

Merge branch 'barry/ssisc-spectral-adjoint' of bitbucket.org:petsc/petsc into barry/ssisc-spectral-adjoint