TS: Refactor TSStep() and TSRollBack()

* TSStep() handles the step counter increment, and not TSStep_XXX().
* TSRollBack() handles the step counter decrement.
* Removed ``time_step_prev`` from the T

TS: Refactor TSStep() and TSRollBack()

* TSStep() handles the step counter increment, and not TSStep_XXX().
* TSRollBack() handles the step counter decrement.
* Removed ``time_step_prev`` from the TS structure. New code should use
ts->ptime - ts->ptime_prev to determine the previous time step size.
* Removed unused ``time_step_orig`` from the TS structure.
* Removed unused ``time_step_since_decrease`` from the TS structure.
* Minor update bouncing ball test examples.
* Regenerate some test examples output.

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TS: Fix TSView() for TSTHETA and TSALPHA to view the TSAdapt context

Merged in dalcinl/fix-ts-declarations (pull request #450)

TS: Fix function declarations and visibility

TS: Fix function declarations and visibility

* Most of these fixes where spotted by GCC -Wmissing-declarations

Fixes for issues found with clang static analyzer,
mostly set but unused variables

Time: 1 hour

Merged in dalcinl/fix-tsadapt (pull request #441)

TSAdapt and related improvements

TSAdapt: Rework implementation

* Simplify handling of TSAdapt in TSALPHA
* Remove broken adaptivity in TSTHETA and use the same backward difference
aproach from TSALPHA
* Update TSEULER to use TSA

TSAdapt: Rework implementation

* Simplify handling of TSAdapt in TSALPHA
* Remove broken adaptivity in TSTHETA and use the same backward difference
aproach from TSALPHA
* Update TSEULER to use TSAdapt (TODO: rejections and adaptivity)
* Update TSSSP to use TSAdapt (TODO: rejections and adaptivity)

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TS: Move calls to TSPreStep() from implementation to interface

* Make the semantics symmetric with TSPostStep()
* Handle rolled back steps appropriately
* If a callback is ever needed to run at the

TS: Move calls to TSPreStep() from implementation to interface

* Make the semantics symmetric with TSPostStep()
* Handle rolled back steps appropriately
* If a callback is ever needed to run at the begining of each TSStep()
(including rolled back steps and step rejections), we can add a new API
to support this particular need (BTW, patches welcome!)

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Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcgraph.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/imp

Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcgraph.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcscalingbasic.c
src/ksp/pc/impls/bddc/bddcschurs.c
src/mat/impls/is/matis.c

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Merge remote-tracking branch 'origin/knepley/fix-plex-test-partitions' into tisaac/dmforest

* origin/knepley/fix-plex-test-partitions: (151 commits)
Plex ex5: Provide test partitions
Plex ex4: P

Merge remote-tracking branch 'origin/knepley/fix-plex-test-partitions' into tisaac/dmforest

* origin/knepley/fix-plex-test-partitions: (151 commits)
Plex ex5: Provide test partitions
Plex ex4: Provide test partitions
Configure: I really hate exceptions - We should rewrite this to eliminate all exceptions in favor of return codes
Configure: I hate exceptions
fix typo for 'runex19_superlu_dist_2'
Fix for freeing just what needs to be free when SuperLU_Dist factorizations reused
Updated to latest hypre pre-release with fixes for handling blas/lapack libraries
Switch back to petsc fork of SuperLU_Dist that turns of use of findMPI
PCFactorSetUpMatSolverPackage() should not crash but instead produce a useful error message if called before it is in the proper state.
Clarify that SNESGetLinearSolveIterations() does not include failed iterations.
User reported issues with downloading boost using the previous URL but not this one
Configure: Small change to log order
MatFDColoringSetUp_MPIXAIJ: fix broken initialization of colmap
Bib: Missing comma
add support for binary viewer for -ts_monitor that records time at each timestep
superlu_dist: set MPI_C_COMPILER etc options - so that superlu_dist cmake does not look for a different/incompatible mpi compiler. [and its CFLAGS].
remove reference to VecGetValuesBlocked() and VecGetValuesLocal() from manual page since they do not exist.
Stop configure if user builds with threadsafety and debugging on
Added configure option --with-viewfromoptions=0 which will speed up code with many small solves substantially
Only generate list of all PetscFunctionLists generated in debug mode since in some circumstances where many objects are created searching this list is very slow.
...

Conflicts:
src/ts/examples/tutorials/ex11.c

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Merge branch 'master' into barry/add-pcfieldsplit-logevent

Merge branch 'maint'

Merge branch 'emil/to-maint-fix-ts-reporting-nonembedded' into maint

ts: add a more complete error message for methods that do not have embedded counterparts and are used with ts_adapt

Reported-by: https://bitbucket.org/petsc/petsc/issues/121/non-embedded-rk-types-gi

ts: add a more complete error message for methods that do not have embedded counterparts and are used with ts_adapt

Reported-by: https://bitbucket.org/petsc/petsc/issues/121/non-embedded-rk-types-give-unhelpful-error

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Merge branch 'master' into tisaac/dmforest

* master: (87 commits)
fixed --download-xxx=/directory to not mistake other options such as --download-mpich-pm=hydra etc
Correct spelling for Autotool

Merge branch 'master' into tisaac/dmforest

* master: (87 commits)
fixed --download-xxx=/directory to not mistake other options such as --download-mpich-pm=hydra etc
Correct spelling for Autotools libtoolize in commit a0848688a08a6eb150afdc95a2f6ce49cd4cd079
Fix for commit c8b462efbd8e8a5f06df500cf417f3a48f2b88d9 Put back the gitpreReq() check that was needed for MOAB
website: fix Fluidity link
bib/cite: add UMFPACK
nightlybuilds: update test tu use newer intel compiler [detect and use compiler path]
nightlybuilds: fix vec/ex7,ex7f link issue by using the correct LIBS option
Added support for users to provide their own download package installers --download-xxx=/directory where the directory contains the file xxx.py that is a standard PETSc package definition like in config/BuildSystem/config/packages/xxx.py
nightlybuilds: switch default intel compiler [& MKL] from 13.1.3 to 16.0.0.
mkl_pardiso: fix runex125_mkl_pardiso
mkl_pardiso: fix runex2_mkl_pardiso_cholesky
nightlybuilds: switch OSX to use boost from brew [as --download-boost is broken]
trilinos: gitcommit - always specify branch as origin/branch
Add error check to boost.py when running on Mac OS because the shared libraries created do not work since they do not have the proper rpath set
Update output files for mpi matrices that use to be seq
Move PostProcess() runs until after PETSc configure has saved all data to the filesystem so that make install will work correctly.
Switch to Trilinos release candidate for --download-trilinos Tested, failed with unresolved Kokos methods, Issue report to Trilinos team
Some configure packages UnitTest-CPP requires libtoolize to be called before autoreconf on some systems
--download-ideas now downloads unittest-cpp
simplied ./configure packages that need autoreconf to be run first (like moab and unittest-cpp) added unittest-ccp download changed downloadfilename to downloaddirname since that is what it is
...

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

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Merge branch 'hongzh/fix-bug-for-cost-integral'

fix cost integral for rk methods and update the examples

Merge branch 'master' into barry/add-pcreset-hypre-for-master

Needed to move PCDestroy_HYPRE() added to master to PCReset_HYPRE() since that was introduced
as a bug fix for maint

Merge branch 'master' into hongzh/checkpointing

Manual merges for a couple of PetscOptions changes in master

Merge remote-tracking branch 'origin/knepley/feature-plex-add-time' into tisaac/dmforest

Both branches changeds DM projection behavior, so I wanted to sort it
out before merging

* origin/knepley/fe

Merge remote-tracking branch 'origin/knepley/feature-plex-add-time' into tisaac/dmforest

Both branches changeds DM projection behavior, so I wanted to sort it
out before merging

* origin/knepley/feature-plex-add-time: (59 commits)
SNES ex69: Updated to new function API, fixed test output
SNES ex75: Fixed for new function API
add fortran stub for TSMonitorLGSetTransform() and fix TSMonitorLG for multiple fields but no names provided for fields
add -binary_write_double so __float128 precision can save as double to binary files
TSClone() did not clone Fortran function pointers hence some TS methods would fail if functions provided in Fortan
petsc4py: update to snapshot with 'barry/petscoptions-object' changes
fix bad merge that introduced 2 copies of the MPI_Comm_free()
update example to use MAT_INPLACE_MATRIX, not REUSE
incorrect addition of float to PetscInt
update for new PetscOptions API
TS ex18: Fixed function API and test output
Function now takes PetscOptions as first argument, this was missed during the first round of updates
bugfix for MatSetOption_Elemental()
fix test example no change output that was missing a line
fixes for new PetscOptions.. API that are needed based on problems with nightly build
Plex ex3: Use new function API
SNES ex62: Use new function API
SNES ex12: Use new function API
Plex: Fixed unused options in examples
Plex+DMDA: Add time to signatures
...

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Merge branch 'master' into pr391/zianekhodja/lilia/tsirm/master

Merge branch 'master' into knepley/feature-plex-add-time

* master: (57 commits)
add fortran stub for TSMonitorLGSetTransform() and fix TSMonitorLG for multiple fields but no names provided for fie

Merge branch 'master' into knepley/feature-plex-add-time

* master: (57 commits)
add fortran stub for TSMonitorLGSetTransform() and fix TSMonitorLG for multiple fields but no names provided for fields
add -binary_write_double so __float128 precision can save as double to binary files
TSClone() did not clone Fortran function pointers hence some TS methods would fail if functions provided in Fortan
petsc4py: update to snapshot with 'barry/petscoptions-object' changes
fix bad merge that introduced 2 copies of the MPI_Comm_free()
update example to use MAT_INPLACE_MATRIX, not REUSE
incorrect addition of float to PetscInt
update for new PetscOptions API
Function now takes PetscOptions as first argument, this was missed during the first round of updates
bugfix for MatSetOption_Elemental()
fix test example no change output that was missing a line
fixes for new PetscOptions.. API that are needed based on problems with nightly build
mark variable as unused so compiler doesn't warn about unused value
configure: use 'git cat-file -e' to check for existance of a commit in localrepo. ['git rev-parse' does not give error for a hash thats not in repo]
petsc4py: revert to manually syncing petsc4py with petsc master changes
configure: revert gitcommit default value to Null. If a pacakge using giturl does not change this value - raise an error
fix: revert change in a44bcdf that breaks with pgf90
update test output for fixed to hypre interface that now actually pass the interp vectors to BoomerAMG
fixes for merge from Jed's branch that should have been merged into master months ago!
Add to changes dev.html file the change to the PetscOptions routines
...

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Merge branch 'master' of bitbucket.org:petsc/petsc

Merge remote-tracking branch 'petsc/master' into moved-partitioning-to-pcgasmsetup

Merge branch 'tisaac/dm-label-promote' into tisaac/dmforest

* tisaac/dm-label-promote: (319 commits)
snes tutorial ex69: give mesh a name for regression purposes
DM: make DMLabel labels a part o

Merge branch 'tisaac/dm-label-promote' into tisaac/dmforest

* tisaac/dm-label-promote: (319 commits)
snes tutorial ex69: give mesh a name for regression purposes
DM: make DMLabel labels a part of all DMs
builder: update regression tests
builder: update some missing package requirements
DM: set coordinate vector name
ts tutorials ex11_sa: make it compile
mark variable as unused so compiler doesn't warn about unused value
configure: use 'git cat-file -e' to check for existance of a commit in localrepo. ['git rev-parse' does not give error for a hash thats not in repo]
petsc4py: revert to manually syncing petsc4py with petsc master changes
configure: revert gitcommit default value to Null. If a pacakge using giturl does not change this value - raise an error
fix: revert change in a44bcdf that breaks with pgf90
update test output for fixed to hypre interface that now actually pass the interp vectors to BoomerAMG
Error message should say use negative threshold value to prevent filtering out zeros
Calls to HYPRE_BoomerAMGSetInterpVectors() did not actually copy the vector data pointer from the PETSc vector to the hypre vector thus resulting in the hypre interp vectors being identically zero and hence not affecting the quality of the AMG hierarchy produced/
DMPlex: Silence overzealous compiler warnings
add row/col orientation to MatConvert_Elemental_Dense
fix formatting error in previous commit [broke nightlybuilds]
fix formating of TSTHETA manual page and add missing command line option
run hwloc with MPIEXEC and binding so it runs on the correct machine
fix: memory leaks [in valgrind test]
...

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