Merge branch 'stefano_zampini/allow-unassembled-computeijacobian' into maint

Merge branch 'shri/fixes-for-step-restart'

ts: fix nightlybuild failure with moab example src/ts/examples/tutorials/ex35

Reviewed-by: "Abhyankar, Shrirang G." <abhyshr@anl.gov>

Program received signal SIGSEGV, Segmentation fault.
0x00007fff

ts: fix nightlybuild failure with moab example src/ts/examples/tutorials/ex35

Reviewed-by: "Abhyankar, Shrirang G." <abhyshr@anl.gov>

Program received signal SIGSEGV, Segmentation fault.
0x00007ffff760974e in TSClone (tsin=0x8149e0, tsout=0x7fffffffe0b8) at /sandbox/balay/petsc/src/ts/interface/ts.c:8060
8060 t->event->refct++;
(gdb) p t->event
$1 = (TSEvent) 0x0

balay@stomp^/sandbox/balay/petsc/src/ts/examples/tutorials(next=) $ valgrind --tool=memcheck -q ./ex35
==2811== Invalid read of size 4
==2811== at 0x5789FED: TSClone (ts.c:8060)
==2811== by 0x57AFDA3: TSStep_ARKIMEX (arkimex.c:734)
==2811== by 0x577D6D8: TSStep (ts.c:3963)
==2811== by 0x577EB2B: TSSolve (ts.c:4218)
==2811== by 0x404DBE: main (ex35.cxx:185)
==2811== Address 0xcc is not stack'd, malloc'd or (recently) free'd

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Fixes for next nightly examples breakage 11/22/16 for TS.

Code fixes for TS step restarting (used in ARKIMEX)

i) TSClone() in ARK step-restart was not copying over the event and
trajectory data structures.
ii) When TSDestroy() is called at the end of ARK s

Code fixes for TS step restarting (used in ARKIMEX)

i) TSClone() in ARK step-restart was not copying over the event and
trajectory data structures.
ii) When TSDestroy() is called at the end of ARK step-restart, the event
and trajectory structs were getting destroyed.
iii) ARK step-restart calls TSSolve() that resets ts->steps and
ts->total_steps. This caused the filenames created by TSTrajectory to be
overwritten and thus the saved solutions in the file were not matching
with the correct step numbers.

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TS: allow unassembled mats in compute IJacobian.

Merged in jand42/petsc (pull request #594)

Add .vtu to the -ts_monitor_solution_vtk documentation

Add .vtu to the -ts_monitor_solution_vtk documentation.

Merge branch 'master' into tisaac/dmplex-feature-real-to-ref

I need updated PetscFE interfaces in what I'm going to do

* master: (603 commits)
parmetis: fix typo in testsuite
Added PETSC_HAVE_A

Merge branch 'master' into tisaac/dmplex-feature-real-to-ref

I need updated PetscFE interfaces in what I'm going to do

* master: (603 commits)
parmetis: fix typo in testsuite
Added PETSC_HAVE_ATTRIBUTEALIGNED flag to makefile
PCSetUp_SVD() used incorrect matrix for matrix size in parallel, also need to skip LAPACK call if matrix size is zero
strumpack: update to latest version 1.0.4
Remove valgrind warning about MPI_Allreduce() with uninitialized data
sed for test output that has atol convergence with quad precision
updated ex1_nest tests
fixed incorrect key value
fix: bad merge a69d34a
test: move runex78 to TESTEXAMPLES_C_NOTSINGLE
build: fix warnings
sys: update test to produce same result - irrespective of debug/opt build - and presence of ~/.petscrc
sys: src/sys/examples/tests/ex30.c -> src/sys/examples/tests/ex32.c to avoid conflict in master
Sed output, since quad precision reduces below atol on these tests
remove automatically generated matrix names from test output files since can be different
Fixes for MatMPIXXXSetPreallocation(), they were not reentrant, since they kept the information used for matrix-vector products
GAMG: fix PCView_GAMG() format - and update output/ex56_0.out
superlu_dist: 64-bit-indices fix https://github.com/xiaoyeli/superlu_dist/issues/4
Add SNESSetDivergenceTolerance / -snes_divergence_tolerance.
fixed unit read in Plex
...

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Merge branch 'stefano_zampini/feature-convert-matnest-matis' into stefano_zampini/feature-pcbddc-saddlepoint

I have to merge it here, since there's an API addition for MatIS in stefano_zampini/featu

Merge branch 'stefano_zampini/feature-convert-matnest-matis' into stefano_zampini/feature-pcbddc-saddlepoint

I have to merge it here, since there's an API addition for MatIS in stefano_zampini/feature-pcbddc-saddlepoint
that prevents me to smoothly merge stefano_zampini/feature-convert-matnest-matis into next.

This will also facilitate merging stefano_zampini/feature-pcbddc-saddlepoint into master

Conflicts:
src/docs/website/documentation/changes/dev.html

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Merge branch 'emil/ts-glee'

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

Merge branch 'shri/ts-post-evaluate'

TSPostEvaluate: Add TSPostEvaluate() in TSSolve() and TSRollBack() so that all methods can use it.

fix clang warnings

FIX TS adapt for the global error and to use atol and rtol separatelly

Added new TS eror norms that use the error directly, added new example ODE in ex31, fixed interface comments/doc. Fixed TSAdapt glee.

FIX adapt error when atol and rtol are both zero; fixed order for glee wen used in adapt

FIX error in TSAdapt glee and renaming variables

modified TSGetTime error to include an index that indicates when to estimate the error.

extended the TS weighted error norm to compute the norms relative to absolute and relative tolerances separatelly

TS, TSGLEE: added error messages

TS: Created an interface to initialize the time integrator error to a specific value (for restarts)
TSGLEE: Implemented the initialization of the error/auxiliary solution

TS: Fix in TSGetTimeError and TSGetAuxSolution so that it doesn't crash for TSTypes that don't have them.

TS: created interfaces for TSGetAuxSolution, and TSGetTimeError
TSGLEE: Implemented TSGetAuxSolution, and TSGetTimeError, also TSGetSolutionComponents return all r components, not r-1