Merge branch 'tisaac/dmlabel-fix-clear-bt'

* tisaac/dmlabel-fix-clear-bt:
Plex tests ex6: remove bad semicolons
DMLabel: add regression test for clearing label values
DMLabel: Clear PetscBT wh

Merge branch 'tisaac/dmlabel-fix-clear-bt'

* tisaac/dmlabel-fix-clear-bt:
Plex tests ex6: remove bad semicolons
DMLabel: add regression test for clearing label values
DMLabel: Clear PetscBT when clearing point (fix regression)

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DMLabel: Clear PetscBT when clearing point (fix regression)

Reported-by: Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk>

Thanks to Lawrence for this patch. Here is his report:

Dear all (but

DMLabel: Clear PetscBT when clearing point (fix regression)

Reported-by: Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk>

Thanks to Lawrence for this patch. Here is his report:

Dear all (but mostly Toby),

some recent changes in DMLabel changed the semantics of DMLabelHasPoint.

In particular, after ad8374f (DMLabel: switch internal storage from
array to IS), clearing a label value produces bad results. Consider
the following:

int main(int argc, char **argv)
{
PetscErrorCode ierr;
DMLabel label;
PetscInt val;
PetscBool flg;
PetscInitialize(&argc, &argv, NULL, NULL);

ierr = DMLabelCreate("foo", &label);CHKERRQ(ierr);

ierr = DMLabelCreateIndex(label, 0, 1);CHKERRQ(ierr);
ierr = DMLabelSetValue(label, 0, 1);CHKERRQ(ierr);
ierr = DMLabelHasPoint(label, 0, &flg);CHKERRQ(ierr);
ierr = DMLabelGetValue(label, 0, &val);CHKERRQ(ierr);
PetscPrintf(PETSC_COMM_WORLD, "Label has point %d, value is %d\n",
flg, val);CHKERRQ(ierr);

ierr = DMLabelClearValue(label, 0, 1);CHKERRQ(ierr);
ierr = DMLabelHasPoint(label, 0, &flg);CHKERRQ(ierr);
ierr = DMLabelGetValue(label, 0, &val);CHKERRQ(ierr);
PetscPrintf(PETSC_COMM_WORLD, "Label has point %d, value is %d\n",
flg, val);CHKERRQ(ierr);

PetscFinalize();
return 0;
}

Before this change:

$ ./bork
Label has point 1, value is 1
Label has point 0, value is -1

After the change:

$ ./bork
Label has point 1, value is 1
Label has point 1, value is -1

So you can see that although the point has been cleared from the point
of view of GetValue, it has not if I use HasPoint.

The problem appears to be that the invalidation of the label after
ClearValue no longer clears the PetscBT entry that exists if an index
has been created.

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Merge branch 'tisaac/dm-label-use-is'

* tisaac/dm-label-use-is:
IS: fix ISLocate(): ex7 passes
IS: added test for ISLocate()
IS: added ISLocate implementations for block and stride
ISGeneral

Merge branch 'tisaac/dm-label-use-is'

* tisaac/dm-label-use-is:
IS: fix ISLocate(): ex7 passes
IS: added test for ISLocate()
IS: added ISLocate implementations for block and stride
ISGeneral: add locate implementation
DMLabel: use ISLocate()
IS: added ISLocate() interface and default implementation
change regression logs for increased number of index sets
DMLabel: added DMLabelSetStratumIS()
DMLabel: switch internal storage from array to IS

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DMLabel: use ISLocate()

DMLabel: added DMLabelSetStratumIS()

DMLabel: switch internal storage from array to IS

This is intended to allow for more efficient storage of common label types, such as the depth label,
where each stratum is contiguous. In the long

DMLabel: switch internal storage from array to IS

This is intended to allow for more efficient storage of common label types, such as the depth label,
where each stratum is contiguous. In the long view, I think this will be useful when making DA and
Plex use the same interface. For a DA, it might be convenient to specify a subset (for, e.g.,
boundary conditions), using an ISStride or some kind of tbd ISSlice.

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Merge branch 'master' into tisaac/ts-ex11-amr

* master: (141 commits)
chombo: fix dirname in tarball and update to use snapshot with gcc-6.1 compile fix
petsc4py: fix tarball url [for arbitary c

Merge branch 'master' into tisaac/ts-ex11-amr

* master: (141 commits)
chombo: fix dirname in tarball and update to use snapshot with gcc-6.1 compile fix
petsc4py: fix tarball url [for arbitary commitid] - and dirname in tarball
Plex: Moved ReconstructGradients_Internal() and ApplyLimiter_Internal() to Plex from SNES
CUDA: Added external declaration for cuBLAS handle.
docs: fix reference to KSP_Create in parent commit
Add information on PETSC_EXTERN and PETSC_INTERN to developers manual
Plex: Symbol is shared between DM and SNES, so must be EXTERN
Plex: Remove unused variables
Configure: Fix check for spaces in PETSC_DIR
Plex: Updated examples to new DMPlexCreateBoxMesh()
sick of failure due to incorrect master branch
SNES ex12: Fixed unstructured GMG test
SNES ex12: Added another unstructured GMG test
petsc4py: use the snapshot with the fix for dmplex change
Examples that require Fortran to compile but were listed in tests that did not require Fortran
Plex ex19: Added DMSetFromOptions()
Plex: Store a flag indicating whether the boundary should change during remeshing - Set using -dm_plex_remesh_bd - Changed Remesh_Internal() signature
Always coarsen boundaries.
Plex: Fixed option name
Plex: Protect unused variables
...

Conflicts:
src/dm/impls/plex/makefile
src/snes/utils/dmplexsnes.c

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Merge branch 'knepley/feature-parallel-mesh-load'

* knepley/feature-parallel-mesh-load:
Plex ex18: Small fixes - Use DMBOUNDARY_NONE correctly, document partition edges
Plex ex18: Added simplex

Merge branch 'knepley/feature-parallel-mesh-load'

* knepley/feature-parallel-mesh-load:
Plex ex18: Small fixes - Use DMBOUNDARY_NONE correctly, document partition edges
Plex ex18: Added simplex 3D tests
fix compile warnings
Plex: Removed unused variable
DMLabel: Fixed DMLabelGather() - The leaves are not compact, but rather follow the local numbering, so we need to allocate nroots space
Plex: Fix for parallel interpolation
Plex-ex18: Enabling 2D simplex tests with interpolation
Plex: Create pointSF for edge/facet points after interpolation
Plex-ex18: Add another test for 2D simplices on 3 ranks
Plex: Fix hash usage in DMPlexBuildFromCellList_Parallel_Private
Plex ex18: Added test for parallel mesh loads - Interpolation test is broken
Plex: Fixed static declaration of some functions
Plex: Added DMPlexCreateFromCellListParallel() - This directly creates a parallel mesh from pieces

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DMLabel: Fixed DMLabelGather()
- The leaves are not compact, but rather follow the local numbering, so we need to allocate nroots space

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

Merge branch 'tisaac/sf-fix-multi-sf-leaves' into tisaac/dmp4est-feature-injection

* tisaac/sf-fix-multi-sf-leaves: (174 commits)
PetscSF: fix PetscSFGetMultiSF() for sparse leaves
PetscSF: make

Merge branch 'tisaac/sf-fix-multi-sf-leaves' into tisaac/dmp4est-feature-injection

* tisaac/sf-fix-multi-sf-leaves: (174 commits)
PetscSF: fix PetscSFGetMultiSF() for sparse leaves
PetscSF: make regression test that fails
few more clang static analyzer fixes
many issues detected by clang static analyzer
Update hypre to its release version
Updates for xSDKTrilinos builds
Added --download-xsdktrilinos
Communicator passed to VecCreateSeq should be PETSC_COMM_SELF
PCMG man page: fix typo in options name
Bib: Added refs
DMLabel: Removed unused variable
Metis tries to use backtrace which requires -lexecinfo on some systems such as freebsd Remove -lexecinfo from freebsd configure files since it is only needed by metis
add alternative output that occurs on some systems due to use of random number generator in partitioner
Plex: When creating cohesive submeshes, fix memory leak
Plex ex11: Updated output for new distribution algorithm
Plex: When explicitly distributing the depth label, we must recreate empty strata
Plex: When partitioning, the cell numbering should include hybrid points
Plex: Allow cell and vertex numberings to include hybrid points
need to show diffs of ex22 if it fails
Support two different output for test example, since due to roundoff this example can produce slightly different convergence history
...

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Merge branch 'master' into sanderarens/fix-plex-neumann-bc

* master: (28 commits)
few more clang static analyzer fixes
many issues detected by clang static analyzer
Update hypre to its release

Merge branch 'master' into sanderarens/fix-plex-neumann-bc

* master: (28 commits)
few more clang static analyzer fixes
many issues detected by clang static analyzer
Update hypre to its release version
Updates for xSDKTrilinos builds
Added --download-xsdktrilinos
DMLabel: Removed unused variable
Plex: When creating cohesive submeshes, fix memory leak
Plex ex11: Updated output for new distribution algorithm
Plex: When explicitly distributing the depth label, we must recreate empty strata
Plex: When partitioning, the cell numbering should include hybrid points
Plex: Allow cell and vertex numberings to include hybrid points
Plex ex1: Fixed output for empty strata
DMLabel: Added DMLabelHasStratum()
Minor changes and fix to bugs introduced in 82f73ecaa
Modified makefile to fix aijcusparse tests
Add missing code for the case PETSC_HAVE_VECCUDA
Fix bugs introduced in 82f73ecaa
Use VECCUDA with MATAIJCUSPARSE
CUDA: Fixed visibility and disabled Fortran bindings for VecScatters on GPU.
Replace kernels with thrust
...

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Merge branch 'knepley/fix-plex-examples'

* knepley/fix-plex-examples:
DMLabel: Removed unused variable
Plex: When creating cohesive submeshes, fix memory leak
Plex ex11: Updated output for new

Merge branch 'knepley/fix-plex-examples'

* knepley/fix-plex-examples:
DMLabel: Removed unused variable
Plex: When creating cohesive submeshes, fix memory leak
Plex ex11: Updated output for new distribution algorithm
Plex: When explicitly distributing the depth label, we must recreate empty strata
Plex: When partitioning, the cell numbering should include hybrid points
Plex: Allow cell and vertex numberings to include hybrid points
Plex ex1: Fixed output for empty strata
DMLabel: Added DMLabelHasStratum()

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DMLabel: Removed unused variable

DMLabel: Added DMLabelHasStratum()

Merge branch 'knepley/fix-plex-distribute-label'

* knepley/fix-plex-distribute-label:
Plex ex11: Added another test of label distribution
Plex: Determination of stratum indices from strum values

Merge branch 'knepley/fix-plex-distribute-label'

* knepley/fix-plex-distribute-label:
Plex ex11: Added another test of label distribution
Plex: Determination of stratum indices from strum values was flawed

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

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

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Plex: Determination of stratum indices from strum values was flawed

Merged petsc/petsc into master

Merge remote-tracking branch 'origin/knepley/fix-plex-hdf5-label' into tisaac/dmforest

* origin/knepley/fix-plex-hdf5-label: (50 commits)
Plex: Fixed HDF5 output for DMLabel - The ISAllGather() wa

Merge remote-tracking branch 'origin/knepley/fix-plex-hdf5-label' into tisaac/dmforest

* origin/knepley/fix-plex-hdf5-label: (50 commits)
Plex: Fixed HDF5 output for DMLabel - The ISAllGather() was being called with an IS that had COMM_SELF - Also, we needed to protect for empty index arrays
superlu_dist: install target should first make sure prefix/[include,lib] dirs exist - similar to superlu
dm: add DMRemoveLabel() fortran interface
nightlybuilds: allocate more time to run arch-linux-xsdk-dbg build...
Remove superfluous information messages
Cannot have rank 1 print before parallel print since it may end up before or after the print from process 0. There change to have rank 0 print the sequential matrix
Bib: Added ref
Plex: Update ex12_5 with correct level-2 overlap
DMLabel: Add missing cleanup for DMLabelGather()
mpiuni: check for "long_long" before checking for "__int64" [as "typedef __int64" gives error with icc] Note: cannot use 'int64_t' as 'typedef unsigned int64_t foo' gives eror with icc
Add filter for solaris linker scope warning to master since that is used in nightly tests of next
Previous commit did not correctly handle downloading from --with-packages-dir
Use special error code of 10 for output list of needed downloaded package tarballs otherwise the outer configure.py script converts the error code to an error message we do not want.
Have ./configure return a nonzero exit code when --with-packages-dir detects missing packages so that calling scripts know this is occurred simplify some code
Completed support for --with-packages-dir=directory that allows --download-xxx features to be cleanly used behind firewalls etc also updated to docs to indicate this new feature
Adding supporting for --download-xxx to reported needed downloads when off line or behind a firewall and using local copies when available with the --with-packages-dir=directory option
Fix typos in linesearch impls:armijo, morethuente, owarmijo.
PetscDraw: Explicitly save draw in KSP/SNES/TS monitors
PetscViewerDraw: Propagate prefix from viewer to draw contexts
PetscDraw: Explicitly save draw in {Vec|Mat|DMDA}View() routines
...

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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
...

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DMLabel: Add missing cleanup for DMLabelGather()

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 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