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

Merge branch 'knepley/fix-error-messages'

* knepley/fix-error-messages:
Plex ex2: Removed unused variable
DM: Better error messages

Merged collection routines from dmay/swarm-boundingbox-collect

Merge branch 'dmay/swarm-boundingbox-collect' into dmay/swarm-next

DMGetNeighbors:
* Updated manpage

DM:
* Add method for getneighbors
* Added new DM API
* Added getneighbor support for PLEX and DMDA

DM: Better error messages

DMLocatePoints: change output from an IS to a PetscSF, and allow initial guesses.

A PetscSF is a more natural return value from DMLocatePoints() because:
- In the event that the mesh has overlapping

DMLocatePoints: change output from an IS to a PetscSF, and allow initial guesses.

A PetscSF is a more natural return value from DMLocatePoints() because:
- In the event that the mesh has overlapping cells, it's clearer which
in which process/cell the point is located.
- A natural next step after DMLocatePoints() is to send each point to
its cell for some local computation. With a PetscSF this is easy with
PetscSFGatherBegin()/PetscSFGatherEnd().

show more ...

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

Merge branch 'barry/add-dmshellcreaterestriction'

Merge branch 'master' into knepley/feature-plex-handle-func-failure

* master: (378 commits)
SNES ex5: Fix coordinate determination for empty subdomains
fixed petsc.bib entry
p4est: fix syntax

Merge branch 'master' into knepley/feature-plex-handle-func-failure

* master: (378 commits)
SNES ex5: Fix coordinate determination for empty subdomains
fixed petsc.bib entry
p4est: fix syntax error with error message
SNES ex5: Correct Jacobian handling on patches
SNES ex5: Stupid complex fixes
DMP4est: fix transfer of labels to parents
petsc4py: update to latest snapshot. Fixes da example breakage in petsc4py test suite
Plex: Correct setting of options on refined or coarsened meshes
Plex: Add info for grid hashing
Plex: Add logging in interpolator creation
Plex: Correct use of tabs in ASCII viewer
DM: Shorten long event name
Plex ex12: Create boundary label automatically at all levels of mesh hierarchy
Plex ex12: Change PetscViewerSetFormat --> PetscViewerPushFormat - Fix order of SetMode and SetFilename
Plex ex12: Change all functions to static
Since DMDA with periodic boundary conditions does support P0 interpolation remove checks that error out under those conditions
ascem-io.py and amanzi.py need to handle self.hdf5.include being None correctly
fix MPI Uni to recycle communicators so it won't run out like with the petsc4py tests also fix check for location of python shared library on mac to check all cases each time
Switch back to Sherry's version since she accepted by pull request
PetscDraw: Update help messages for -draw_save* options
...

Conflicts:
src/dm/impls/plex/plexfem.c

show more ...

Merge branch 'tisaac/dmforest'

* tisaac/dmforest: (36 commits)
DMP4est: fix transfer of labels to parents
DMPlexCreateInterpolatorTree: fix handling of global dofs (can be < 0)
DMPlexComputeIn

Merge branch 'tisaac/dmforest'

* tisaac/dmforest: (36 commits)
DMP4est: fix transfer of labels to parents
DMPlexCreateInterpolatorTree: fix handling of global dofs (can be < 0)
DMPlexComputeInterpolatorTree(): fix workspace size
DM: warn when no injection implemented
DMPlexComputeInterpolatorTree(): use row layout to preallocate
DMP4est: all processes agree on root type
DMPlexComputeInterpolatorTree(): valgrind fixes
DMP4est: reset childID if anctecedent is not parent
DMP4est: send labels from children to parents and bcast
DMForest: added DMForestGetAdaptivityPurpose()
DMP4est: enable caching of results of DMPforestGetTransferSF()
Plex: fix empty partition errors
DMPforestGetTransferSF_Internal(): handle different type roots on different processes
DMP4est: broadcast labels when transfering for agreement
PetscSFBasic: fix usage of MPI_Reduce_local
DMPforestLabelsInitialize(): search through parents when finding a point in the closure
DMP4est: try to connect high strata points when transfering
DMP4est: can't use PetscSFCreateSectionSF. It compresses when we don't want to
DMP4est: expand transfer sfs by the CellSF
DMP4est: add DMForestCreateCellSF_p4est
...

show more ...

Merged petsc/petsc into master

fix MPI Uni to recycle communicators so it won't run out like with the petsc4py tests
also fix check for location of python shared library on mac to check all cases each time

Reported-by: Lisandro D

fix MPI Uni to recycle communicators so it won't run out like with the petsc4py tests
also fix check for location of python shared library on mac to check all cases each time

Reported-by: Lisandro Dalcin <dalcinl@gmail.com>

show more ...

More work on complete DMSHELL example that wraps a DMDA1d. It crashes in valgrind with
==80209== Invalid read of size 8
==80209== at 0x100A9E2D5: DMCountNonCyclicReferences (dm.c:500)
==80209==

More work on complete DMSHELL example that wraps a DMDA1d. It crashes in valgrind with
==80209== Invalid read of size 8
==80209== at 0x100A9E2D5: DMCountNonCyclicReferences (dm.c:500)
==80209== by 0x100A8F70A: DMDestroy (dm.c:573)
==80209== by 0x101221BBE: KSPDestroy (itfunc.c:985)
==80209== by 0x1010BCBFC: PCDestroy_MG (mg.c:302)
==80209== by 0x1010E23F7: PCDestroy (precon.c:122)
==80209== by 0x101221C3A: KSPDestroy (itfunc.c:986)
==80209== by 0x100001C4C: main (in ./ex65)
==80209== Address 0x10398fd68 is 5,864 bytes inside a block of size 6,196 free'd
==80209== at 0x10001595D: free (vg_replace_malloc.c:480)
==80209== by 0x1000FE393: PetscFreeAlign (mal.c:72)
==80209== by 0x100100D1E: PetscTrFreeDefault (mtr.c:315)
==80209== by 0x100A91C5A: DMDestroy (dm.c:716)
==80209== by 0x1010E2478: PCDestroy (precon.c:123)
==80209== by 0x101221C3A: KSPDestroy (itfunc.c:986)
==80209== by 0x1010BCBFC: PCDestroy_MG (mg.c:302)
==80209== by 0x1010E23F7: PCDestroy (precon.c:122)
==80209== by 0x101221C3A: KSPDestroy (itfunc.c:986)
==80209== by 0x100001C4C: main (in ./ex65)

I am reporting to Toby who wrote that code because it is difficult for me to figure how to debug

Time: 3 hours

show more ...

Added DMShellSetRestriction() and ability of PCMG to use DMCreateRestriction()

Time: .2 hours
Reported-by: anton <popov@uni-mainz.de>

DM: warn when no injection implemented

Merge branch 'mlange/fix-plex-multi-level-overlap'

* mlange/fix-plex-multi-level-overlap: (259 commits)
Plex: Update ex12_5 with correct level-2 overlap
DMLabel: Add missing cleanup for DMLabelG

Merge branch 'mlange/fix-plex-multi-level-overlap'

* mlange/fix-plex-multi-level-overlap: (259 commits)
Plex: Update ex12_5 with correct level-2 overlap
DMLabel: Add missing cleanup for DMLabelGather()
Plex ex12: Fixed variable initialization and some output
Plex ex11: Added error checking
Plex ex14: Now boundary label does not have cells
Plex ex1: Now boundary label does not have cells
Plex ex1: Fix for VTK format
added some debugging code, getting ready to branch
added some print statements, should be an -info...
smome cleaning up
restructured ex11 to allow for problem specific BCs
DMPlex: Update test ex12_5 with correct level-2 overlap
DMPlex: Use global processSF in DMPlexPartitionInvert
DMPlex: Add remote leaf contributions to roots in DMLabelPropagate
DMPlex: Add DMLabelGather to migrate label values from leafs to roots
DMPlex: Refactor DMLabelDistribute to separate point stratum distribution
DMPlex: Add propagation of remote point donations for multi-level overlap
DMPlex: Fix DMLabelDistribute for all-to-all migrations
Plex: make extern exactly match prototype: semantic match is not enough.
DMP4est: typo fix
...

show more ...

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

show more ...

DM: ignore constraint matrices with out rows

Merge branch 'tisaac/dmforest' into mlange/fix-plex-multi-level-overlap

Conflicts:
src/dm/impls/plex/examples/tests/output/ex12_5.out
src/dm/label/dmlabel.c

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

DM: The BC DM must also get the DS

DM: DMConvert() should be a no-op for the same type

Plex: Fixed coordinate copy

DMGetCoordinatesLocalized(): return false if not periodic