Merge branch 'hzhang/matptap-noreuse'

Merge branch 'barry/improve-matshift-seqaij'

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

Optimized MatShift() for SeqAIJ matrices

Commit-type: performance
Reported-by: Hong Zhang <hongzhang@anl.gov>

Merge branch 'haplav/fix-guard-MatlabEnginePut_SeqAIJ' [PR #1322]

* haplav/fix-guard-MatlabEnginePut_SeqAIJ:
minor fix MatlabEngine{Get,Put}_SeqAIJ declaration
- guard MatlabEngine{Get,Put}_SeqAIJ(

Merge branch 'haplav/fix-guard-MatlabEnginePut_SeqAIJ' [PR #1322]

* haplav/fix-guard-MatlabEnginePut_SeqAIJ:
minor fix MatlabEngine{Get,Put}_SeqAIJ declaration
- guard MatlabEngine{Get,Put}_SeqAIJ() declaration in aij.h with #if defined(PETSC_HAVE_MATLAB_ENGINE)
- don't declare it in aij.c redundantly

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Merge branch 'master' into knepley/feature-multiple-ds

* master: (156 commits)
Added missing CHKERRQ()
KSP ex56: Added alt output file for ex56_2.
Revert "KSP ex56: Updated test output and dom

Merge branch 'master' into knepley/feature-multiple-ds

* master: (156 commits)
Added missing CHKERRQ()
KSP ex56: Added alt output file for ex56_2.
Revert "KSP ex56: Updated test output and domain size for test _2."
DMStag tutorial ex4: fix stencil errors
Hierarchical partitioner: added an alt output file
Add support for DMGetMatrix() with periodic boundary conditions in one dimension for DMDA.
Fixed incorrect 'ntext' argument in PetscOptionsEList call in SNES ex12.c
ISCreateSubIS: Initialize variables owner and lidx to avoid compiler warnings
metis: provide -download-metis-use-doubleprecision option
KSP ex56: Updated test output and domain size for test _2.
Hierarchical partitioner: add a bit documentation
ISCreateSubIS: Added checkers for parameters
Added a test for hierarchical partitioning vertex weights
Plex+Doc: Document options for DMPlexCreateBoxMesh()
Hierarchical partitioner supports vertex weights
Create an API ISCreateSubIS that extracts
Add an alt output file
Plex: Can now give bounds to DMPlexCreateBoxMesh() from options - Use -dm_plex_box_lower and dm_plex_box_upper
PCMG: These methods should be optional
PCMG: Make PCMGGet/SetLevels() proper member functions - Also need to compose them in GAMG
...

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

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guard MatlabEngine{Get,Put}_SeqAIJ declaration in aij.h; don't declare it in aij.c

rename Mat_PtAP -> Mat_AP because they save data structure for A*P

Merge branch 'maint'

Merge branch 'hzhang/fix-submats-memleak/maint' into maint

fix memory leak of MatCreateSubMatrices_MPIAIJ

Merged petsc/petsc into master

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

Merge branch 'haplav/feature-mataij-load-from-hdf5' [PR #1232]

* haplav/feature-mataij-load-from-hdf5:
MatLoad() implementation for HDF5.
This PR done with cooperation with @Mari Pecha brings the HD

Merge branch 'haplav/feature-mataij-load-from-hdf5' [PR #1232]

* haplav/feature-mataij-load-from-hdf5:
MatLoad() implementation for HDF5.
This PR done with cooperation with @Mari Pecha brings the HDF5 matrix loader.
Its impact is twofold:
- It introduces a truly parallel reader where each rank reads its chunk of the matrix.
- It can directly read MATLAB's native MAT-file format (version 7.3) which is in fact an HDF5 flavor.

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add MatLoad_AIJ_HDF5 skeleton; called from MatLoad_{MPI,Seq}AIJ for HDF5 load

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

Merge branch 'master' into jpustay/feature-swarm-example

Merged petsc/petsc into master

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (393 commits)
Bib: Update reference
Mat: Doc fix
Bib: Updated ref
PetscDS: Doc fixes
PC+LU: Do not try to refactor an

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (393 commits)
Bib: Update reference
Mat: Doc fix
Bib: Updated ref
PetscDS: Doc fixes
PC+LU: Do not try to refactor an already factored matrix
Mat: Small fix for checking and docs
Mat: Added MatSetFactorType() - Needed it when making a shell matrix look factored
PetscDS: Added PetscDSUpdateBoundary() - Lets the user change the boundary condition
single precision produces different convergence history
p4est: has a dependency on zlib - so handle it correctly
Add -mat_mffd_complex to use the Lyness complex number trick to compute J_u * v instead of differencing.
Replace VecWAXPY by VecAXPY if needed
Revert "Replace VecWAXPY by VecAXPY if needed"
Replace VecWAXPY by VecAXPY if needed
MatHermitianTransposeGetMat and MatCreateVecs
ex19: Updated test filter to avoid false positives.
DM: Improved Global-To-Natural docs Suggested-by: Josh L <ysjosh.lo@gmail.com>
Do not build shared openblas when doing static build
Upgrade OpenBLAS to 0.3.3
test: add alt output file for changes in OSX-10.14 and Xcode-10.0 [perhaps related to ML]
...

Conflicts:
src/vec/is/utils/vsectionis.c

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Merged petsc/petsc into master

Merge branch 'pr1144/a_selinger/feature-rowmerge-matmatmult' [PR #1144]

* pr1144/a_selinger/feature-rowmerge-matmatmult:
Added another sequential MatMatMult algorithm
This is an extension of the Row

Merge branch 'pr1144/a_selinger/feature-rowmerge-matmatmult' [PR #1144]

* pr1144/a_selinger/feature-rowmerge-matmatmult:
Added another sequential MatMatMult algorithm
This is an extension of the RowMerge algorithm by @Karl Rupp , which enables the multiplication of matrices with an arbitrary number of nonzeros in the left matrix.
It is faster than the default implementation ("sorted") for very sparse matrices.
MatMatMult: Fixed a bug with mem size overflow and reformatted code
Fixed a bug in the "combined"-algorithm, where the variable c_maxmem for memory requiremments could overflow for relatively dense matrices.

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MatMatMult: Added rowmerge algorithm

Merged petsc/petsc into master