DM{Get|Set}DefaultConstraints: fix typo in docs

Merge branch 'master' into this one.

Merge branch 'barry/2019-09-01/rm-default-language-from-dm' into 'master'

Update public API, and internal naming conventions for DM to eliminate use of...

See merge request petsc/petsc!1998

Update public API, and internal naming conventions for DM to eliminate use of "default" (previously refered to default sections)

Commit-type: style-fix, documentation

DMView should be properly checking viewer input

Merge branch 'jed/deprecate-dmgetdefaultsection' [PR #1969]

* jed/deprecate-dmgetdefaultsection:
DMGetDefaultSection et al: add PETSC_DEPRECATED_FUNCTION
These functions were deprecated in v3.9, but

Merge branch 'jed/deprecate-dmgetdefaultsection' [PR #1969]

* jed/deprecate-dmgetdefaultsection:
DMGetDefaultSection et al: add PETSC_DEPRECATED_FUNCTION
These functions were deprecated in v3.9, but no PETSC_DEPRECATED_FUNCTION was added at that time so many uses crept back into the source code. Here we mark it deprecated and fix all existing uses in PETSc.

DMGetLocalSection/DMSetLocalSection: add explicit names for DMGetSection/DMSetSection
These names are for symmetry with DMGetLocalVector() versus DMGetGlobalVector().

DMGetSection: replace all internal usage with DMGetLocalSection
Same for DMSetSection -> DMSetLocalSection. We retain the interface for DMGetSection/DMSetSection without deprecation warnings (for now).

show more ...

DMGetSection: replace all internal usage with DMGetLocalSection

Same for DMSetSection -> DMSetLocalSection. We retain the interface
for DMGetSection/DMSetSection without deprecation warnings (for n

DMGetSection: replace all internal usage with DMGetLocalSection

Same for DMSetSection -> DMSetLocalSection. We retain the interface
for DMGetSection/DMSetSection without deprecation warnings (for now).

Suggested-by: Barry Smith <bsmith@mcs.anl.gov>

show more ...

DMGetLocalSection/DMSetLocalSection: add explicit names for DMGetSection/DMSetSection

These names are for symmetry with DMGetLocalVector() versus DMGetGlobalVector().

Suggested-by: Barry Smith <bsm

DMGetLocalSection/DMSetLocalSection: add explicit names for DMGetSection/DMSetSection

These names are for symmetry with DMGetLocalVector() versus DMGetGlobalVector().

Suggested-by: Barry Smith <bsmith@mcs.anl.gov>

show more ...

Merge branch 'jczhang/sf-more-opts' [PR #1567]

* jczhang/sf-more-opts:
Add more optimizations in SF and use it as the default for VecScatter.

Merge branch 'dalcinl/fix-headers' [PR #1897]

* dalcinl/fix-headers:
Minor fixes to headers.

Fix a bunch of PetscValidPointer() -> PetscValidXXXPointer()

Deprecate PetscSFGetRanks with new PetscSFGetRootRanks

Since we have PetscSFGetLeafRanks, it is better to have a similar name.

Do not scatter to the same vector at the same time

In vecscatter, the target vector is write-locked

Merged in dalcinl/dm-api (pull request #1850)

DM interface

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

DM: Improve error checking

DM: Deprecate DMCreateAggregates()

* This interface is untested and may be redundant
* DMDA is the only provider, keep it as DMDACreateAggregates()

DMSetType: Clear dm->ops and set type name before calling constructor

DM: Simplify implementation of DMHasCreateInjection()

* Add log event for DMCreateInjection()
* Get rid of DMHasCreateInjection_Default()
* Rename dm->ops->getinjection to dm->ops->createinjection
*

DM: Simplify implementation of DMHasCreateInjection()

* Add log event for DMCreateInjection()
* Get rid of DMHasCreateInjection_Default()
* Rename dm->ops->getinjection to dm->ops->createinjection
* Improve error checking here and there

show more ...

Fixes for doctext update

Merged in barry/cuda-multigrid-test (pull request #1763)

Various improvements for GPUs (mostly for performance and CUDA)

Various improvements for GPUs (mostly for performance and CUDA)

1) Add VecPinToCPU() for CUDA vector and matrices
2) Move initialization of cuBLAS to PetscInitialize() since it takes 1/2 second and

Various improvements for GPUs (mostly for performance and CUDA)

1) Add VecPinToCPU() for CUDA vector and matrices
2) Move initialization of cuBLAS to PetscInitialize() since it takes 1/2 second and distorts timing with -log_view
3) Add logging for DMCreateMatrix (for large meshes this is very large)
4) Add VecGet/RestoreArrayWrite() to prevent unneeded copies from GPU (only implemented so far for CUDA);
added a small number of usages in the source so that snes tutorials ex19 does not do unneeded communication from the GPU
5) Automatically convert MAIJ matrices to AIJ for CUDA since they are not yet supported natively in PETSc's CUDA matrix implementation
6) Pinned objects should still use the CUDA/ViennaCL versions of Destroy to clean up the GPU stuff

Commit-type: feature

show more ...

Merged in balay/fix-snes_tutorials-ex24 (pull request #1815)

fix valgrind errors with snes_tutorials-ex24_2d_bdm1_p0_0 with arch-linux-pkgs-dbg-ftn-interfaces

Approved-by: BarryFSmith <bsmith@mcs.a

Merged in balay/fix-snes_tutorials-ex24 (pull request #1815)

fix valgrind errors with snes_tutorials-ex24_2d_bdm1_p0_0 with arch-linux-pkgs-dbg-ftn-interfaces

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

show more ...

fix valgrind errors with snes_tutorials-ex24_2d_bdm1_p0_0 with arch-linux-pkgs-dbg-ftn-interfaces

==650== Conditional jump or move depends on uninitialised value(s)
==650== at 0x4D38597: MatSetVa

fix valgrind errors with snes_tutorials-ex24_2d_bdm1_p0_0 with arch-linux-pkgs-dbg-ftn-interfaces

==650== Conditional jump or move depends on uninitialised value(s)
==650== at 0x4D38597: MatSetValues_SeqAIJ (aij.c:449)
==650== by 0x4BC7EE5: MatSetValues (matrix.c:1388)
==650== by 0x52F0CBA: DMPlexMatSetClosure (plex.c:5894)
==650== by 0x5860889: DMPlexComputeBdJacobian_Single_Internal (dmplexsnes.c:1813)
==650== by 0x58614DC: DMPlexComputeBdJacobian_Internal (dmplexsnes.c:1879)
==650== by 0x5864173: DMPlexComputeJacobian_Internal (dmplexsnes.c:2096)
==650== by 0x5864759: DMPlexSNESComputeJacobianFEM (dmplexsnes.c:2323)
==650== by 0x584C04C: SNESComputeJacobian_DMLocal (dmlocalsnes.c:125)
==650== by 0x5821FFC: SNESComputeJacobian (snes.c:2643)
==650== by 0x5869329: DMSNESCheckJacobian (dmplexsnes.c:2544)
==650== by 0x586A76F: DMSNESCheck_Internal (dmplexsnes.c:2625)
==650== by 0x586AAB8: DMSNESCheckFromOptions (dmplexsnes.c:2653)
==650== by 0x40435C: main (ex24.c:373)
==650== Uninitialised value was created by a heap allocation
==650== at 0x483B051: memalign (vg_replace_malloc.c:909)
==650== by 0x495C735: PetscMallocAlign (mal.c:49)
==650== by 0x495E8EF: PetscTrMallocDefault (mtr.c:189)
==650== by 0x50723C4: DMGetWorkArray (dm.c:1380)
==650== by 0x52C1CB8: DMPlexGetTransitiveClosure (plex.c:2194)
==650== by 0x52C9A06: DMPlexGetCompressedClosure (plex.c:4064)
==650== by 0x52CA33B: DMPlexVecGetClosure (plex.c:4271)
==650== by 0x53AA5F7: DMPlexComputeLineGeometry_Internal (plexgeometry.c:1116)
==650== by 0x53AD314: DMPlexComputeCellGeometryFEM_Implicit (plexgeometry.c:1538)
==650== by 0x53B0FFE: DMPlexComputeCellGeometryFEM (plexgeometry.c:1799)
==650== by 0x50EF873: PetscFEGetFaceTabulation (fe.c:797)
==650== by 0x514D33B: PetscDSSetUp (dtds.c:374)
==650== by 0x509CDF8: DMCreateDS (dm.c:5102)
==650== by 0x403CC0: SetupDiscretization (ex24.c:341)
==650== by 0x403CC0: main (ex24.c:367)

show more ...

Merge remote-tracking branch 'origin/barry/add-petscarrayxxx-ops' [PR #1771]

Add PetscArraycmp(), PetscArraycpy(), PetscArrayzero(), PetscArraymove(), update code to use new forms

Replace a couple multi-mallocs with a single malloc
Replace backwards loops in MatSetValues_*()

Add PetscArraycmp(), PetscArraycpy(), PetscArrayzero(), PetscArraymove(), update code to use new forms

Replace a couple multi-mallocs with a single malloc
Replace backwards loops in MatSetValues_*() with PetscArraymove()

Commit-type: style-fix, feature

show more ...