Merged in hongzh/improve-tstrajectory-folder (pull request #1673)

Generate unique folder names for TSTrajectory

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>
Approved-by: Emil Constantinescu <emcon

Merged in hongzh/improve-tstrajectory-folder (pull request #1673)

Generate unique folder names for TSTrajectory

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>
Approved-by: Emil Constantinescu <emconsta@mcs.anl.gov>
Approved-by: Stefano Zampini <stefano.zampini@gmail.com>

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Generate unique folder names for TSTrajectory

- Added PetscMkdtemp()
- Removed -ts_trajectory_dirname in tests
- The changes are also applied to trajmemory.c

Funded-by:
Project: FASTMATH adjoint
Ti

Generate unique folder names for TSTrajectory

- Added PetscMkdtemp()
- Removed -ts_trajectory_dirname in tests
- The changes are also applied to trajmemory.c

Funded-by:
Project: FASTMATH adjoint
Time: 6.5 hours
Reported-by:
Thanks-to:

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Merged in hongzh/ts-adjoint2 (pull request #1562)

Second-order adjoint ODE solvers

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

Remove PetscRMTree

Funded-by:
Project: FASTMath adjoint
Time:
Reported-by: Stefano Zampini
Thanks-to:

Checkpoint the TLM sensitivity for second-order adjoint

Add TSForwardGetStages to acces the stage values for TLM sensitivities

Funded-by:
Project: FASTMath adjoint
Time: 8 hours
Reported-by:
Thanks

Checkpoint the TLM sensitivity for second-order adjoint

Add TSForwardGetStages to acces the stage values for TLM sensitivities

Funded-by:
Project: FASTMath adjoint
Time: 8 hours
Reported-by:
Thanks-to:

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Fix TSTrajectory problems caused by rebasing to master

This fix is related to the Commit f3334a0

- Add an option to disable the usage of TSHistory

Funded-by:
Project: FASTMath adjoint
Time: 5.0 ho

Fix TSTrajectory problems caused by rebasing to master

This fix is related to the Commit f3334a0

- Add an option to disable the usage of TSHistory

Funded-by:
Project: FASTMath adjoint
Time: 5.0 hours
Reported-by:
Thanks-to:

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Merge branch 'master' into jpusztay/feature-swarm-symplectic-example

Merged petsc/petsc into master

Merge branch 'master' into knepley/fix-plex-partition-parallel

* master: (414 commits)
very small updates to users manual
syntax is define(XXX) in examples tests not defined(XXX)
Increase patc

Merge branch 'master' into knepley/fix-plex-partition-parallel

* master: (414 commits)
very small updates to users manual
syntax is define(XXX) in examples tests not defined(XXX)
Increase patchlevel to 3.10.3
petsc4py: updat to latest maint snapshot with SNESTEST updates
Fix link for CUDA example in PETSc from GPUs.html page Minor fixes to installation instructions
Mat: Fixed types in Pardiso interface
Converted example comment to latex
This example crashes (for unknown reasons, probably related to the handling of extended derived types passed as arguments) with the PGI Fortran compiler
Remove outdated requires: from top of several examples
remove outdated test requires: command from top of source file
Fix the documentation for -ksp_gmres_cgs_refinement_type
Commit f20c2d659b168217cb455989f28afe052d71a64c broke lex.py so the users manual was no longer being built. There reverted the changes to lex.py
Plex: Add PetscPartitioner to fort list Suggested-by: Jiaoyan Li <Jiaoyan.Li@inl.gov>
Doc: Fix spelling Suggested-by: Manuel Colera Rico <m.colera@upm.es>
Mat ex88: check in double or quad precision only
Fix error with PetscComplex when PETSc is compiled with C and used in C++
configure: fix typo endwith -> endswith
Sys ex23: Migrated to ts_max_time in yaml file as well.
AO ex5: Fixed missing CHKERRQ();
Mat test ex88: add tests for MatMultAdd and MatMultTranposeAdd
...

Conflicts:
src/dm/impls/plex/examples/tests/ex12.c

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Merge branch 'master' into knepley/feature-snes-patch

Not sure if this has done the right thing because there are no tests
yet. Also, the fortran stubs break (it doesn't know what to do with
SNESCo

Merge branch 'master' into knepley/feature-snes-patch

Not sure if this has done the right thing because there are no tests
yet. Also, the fortran stubs break (it doesn't know what to do with
SNESCompositeType), and I don't know how to fix it.

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Merged petsc/petsc into master

Merged petsc/petsc into master

Merge branch 'stefano_zampini/cherrypick-from-continuous-adjoint' [PR #1250]

* stefano_zampini/cherrypick-from-continuous-adjoint:
Few improvements from the continuous adjoint branch
This branch ext

Merge branch 'stefano_zampini/cherrypick-from-continuous-adjoint' [PR #1250]

* stefano_zampini/cherrypick-from-continuous-adjoint:
Few improvements from the continuous adjoint branch
This branch extracts few things that are in the continuous adjoint branch that should go into PETSc

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TSTrajectoryBasic: minor fixes

Prevent from calling PetscRMTree when setting up the object
Reuse same viewer, by just changing the filename
Use PETSC_VIEWER_NATIVE to dump and load data (this is ver

TSTrajectoryBasic: minor fixes

Prevent from calling PetscRMTree when setting up the object
Reuse same viewer, by just changing the filename
Use PETSC_VIEWER_NATIVE to dump and load data (this is very very very important)

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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/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 'barry/tao-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 error checking for TSTrajectory dirname and filetemplate

and do not reproduce template on each call.
Also fix makefile for TAO/TS example

Commit-type: bug-fix, portability-fix,style-fix, featur

Add error checking for TSTrajectory dirname and filetemplate

and do not reproduce template on each call.
Also fix makefile for TAO/TS example

Commit-type: bug-fix, portability-fix,style-fix, feature
Thanks-to: Hong Zhang <hongzhang@anl.gov>
Development Tools: Vim, Emacs, Eclipse

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Cleanup of code, making it clearer/simplier, removed use of C++ template keyword

Commit-type: bug-fix, portability-fix, style-fix, example

Fix TSTrajectory handling of directory name and filetemplate

So that TSSetFromOptions() and TSTrajectorySetFromOptions() need not be called and
work directory name and templace still function

Fix b

Fix TSTrajectory handling of directory name and filetemplate

So that TSSetFromOptions() and TSTrajectorySetFromOptions() need not be called and
work directory name and templace still function

Fix badly formated TEST in example that prevented it from being run

Commit-type: bug-fix

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Merge remote-tracking branch 'origin/hongzh/add-tstraj-filename'

Merge remote-tracking branch 'origin/barry/delete-adjoint-trajectory'