Merge branch 'haplav/feature-check-all-option' into 'master'

DMSetFromOptions_Plex: add -dm_plex_check_all option

See merge request petsc/petsc!2269

doc: Make DMSetFromOptions() manpage a hub for all Check functions.

All DMPlex* point to DMSetFromOptions for complete list.

DMPlexCheckConesConformOnInterfaces -> DMPlexCheckInterfaceCones.

Manpage improved.

Merge branch 'master' into 'barry/2019-08-22/fix-fblaslapack-for-nag'

# Conflicts:
# lib/petsc/conf/test

Merge branch 'barry/2019-09-06/fix-dmplexcheckconseconformoninterfaces' into 'master'

Cannot use PetscSequentialPhaseBegin() to try to sequentialize output

See merge request petsc/petsc!2018

Cannot use PetscSequentialPhaseBegin() to try to sequentialize output

Commit-type: bug-fix
Reported-by: gitlab-ci

Merge branch 'haplav/feature-generalize-dmplexgetconerecursive' [PR #1906]

* haplav/feature-generalize-dmplexgetconerecursive:
generalize DMPlexGetConeRecursive

DMPlexCheckConesConformOnInterfaces: fix several missing CHKERRQ

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.

DMPlexGetConeRecursive: Return ISs and sections for all depths.

- Get rid of recursive function calls.
- Add DMPlexGetConeRecursiveVertices which returns just the IS of depth 0.
- Add DMPlexRestoreC

DMPlexGetConeRecursive: Return ISs and sections for all depths.

- Get rid of recursive function calls.
- Add DMPlexGetConeRecursiveVertices which returns just the IS of depth 0.
- Add DMPlexRestoreConeRecursive which deallocates stuff allocated by DMPlexGetConeRecursive.

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DMPlexCheckConesConformOnInterfaces: option for verbose print

Deprecate PetscSFGetRanks with new PetscSFGetRootRanks

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

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

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Merged in haplav/feature-petscsfcomputemultirootoriginalnumbering-return-count (pull request #1645)

PetscSFComputeMultiRootOriginalNumbering: return multiroot count

Approved-by: Matthew Knepley <kn

Merged in haplav/feature-petscsfcomputemultirootoriginalnumbering-return-count (pull request #1645)

PetscSFComputeMultiRootOriginalNumbering: return multiroot count

Approved-by: Matthew Knepley <knepley@gmail.com>
Approved-by: BarryFSmith <bsmith@mcs.anl.gov>
Approved-by: Junchao Zhang <junchao.zhang@gmail.com>

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PetscSFComputeMultiRootOriginalNumbering: add outarg nMultiRoots

Merge branch 'master' into jpusztay/feature-swarm-symplectic-example

Merge branch 'master' into knepley/fix-plex-partition-parallel

* master: (414 commits)
very small updates to users manual
syntax is define(XXX) in examples tests not defined(XXX)
Increase patc

Merge branch 'master' into knepley/fix-plex-partition-parallel

* master: (414 commits)
very small updates to users manual
syntax is define(XXX) in examples tests not defined(XXX)
Increase patchlevel to 3.10.3
petsc4py: updat to latest maint snapshot with SNESTEST updates
Fix link for CUDA example in PETSc from GPUs.html page Minor fixes to installation instructions
Mat: Fixed types in Pardiso interface
Converted example comment to latex
This example crashes (for unknown reasons, probably related to the handling of extended derived types passed as arguments) with the PGI Fortran compiler
Remove outdated requires: from top of several examples
remove outdated test requires: command from top of source file
Fix the documentation for -ksp_gmres_cgs_refinement_type
Commit f20c2d659b168217cb455989f28afe052d71a64c broke lex.py so the users manual was no longer being built. There reverted the changes to lex.py
Plex: Add PetscPartitioner to fort list Suggested-by: Jiaoyan Li <Jiaoyan.Li@inl.gov>
Doc: Fix spelling Suggested-by: Manuel Colera Rico <m.colera@upm.es>
Mat ex88: check in double or quad precision only
Fix error with PetscComplex when PETSc is compiled with C and used in C++
configure: fix typo endwith -> endswith
Sys ex23: Migrated to ts_max_time in yaml file as well.
AO ex5: Fixed missing CHKERRQ();
Mat test ex88: add tests for MatMultAdd and MatMultTranposeAdd
...

Conflicts:
src/dm/impls/plex/examples/tests/ex12.c

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Merge branch 'master' into knepley/feature-snes-patch

Not sure if this has done the right thing because there are no tests
yet. Also, the fortran stubs break (it doesn't know what to do with
SNESCo

Merge branch 'master' into knepley/feature-snes-patch

Not sure if this has done the right thing because there are no tests
yet. Also, the fortran stubs break (it doesn't know what to do with
SNESCompositeType), and I don't know how to fix it.

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Merged petsc/petsc into master

Merged petsc/petsc into master

Merge branch 'master' into haplav/feature-mataij-load-from-hdf5

because I need the test loop fix

Merge branch 'haplav/fix-plex-interpolate-interface-cones' [PR #1227]

* haplav/fix-plex-interpolate-interface-cones:
DMPlexIntepolate: fix orientation of faces in interface
Fixes orientation of face

Merge branch 'haplav/fix-plex-interpolate-interface-cones' [PR #1227]

* haplav/fix-plex-interpolate-interface-cones:
DMPlexIntepolate: fix orientation of faces in interface
Fixes orientation of faces in interface (i.e. order and orientations of the corresponding cones) so that they conform across ranks.

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ExchangeArrayByRank_Private: fix missing MPI_Waitall() call!

Merge branch 'haplav/feature-dmplex-check-interface-cone-conformance' [PR #1164]

* haplav/feature-dmplex-check-interface-cone-conformance:
DMPlex: check for interface cone conformance
New DMPlexChec

Merge branch 'haplav/feature-dmplex-check-interface-cone-conformance' [PR #1164]

* haplav/feature-dmplex-check-interface-cone-conformance:
DMPlex: check for interface cone conformance
New DMPlexCheckConesConformOnInterfaces() checks that cones of points on inter-partition interfaces have conforming order.
This check is now called in DMPlex test ex18.c. To reproduce the failed check, one can remove requires: TODO from tests.
This merge also adds DMGetCoordinatesLocalSetUp() and DMGetCoordinatesLocalNoncollective() as I needed a non-collective version of DMGetCoordinatesLocal(), and fixes several notes on collectiveness in DMPlex documention.

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