Merge branch 'pr1305/prj-/update-hypre-matrix-initialization/master' [PR #1343]

* pr1305/prj-/update-hypre-matrix-initialization/master:
Changes how BoomerAMG matrices are initialized.

Fix c89 error

MatAXPY_Basic routines: realloc temporary storage if needed

MatAXPY_Basic is now called in parallel by MatHYPRE, so N may be large

MatAXPY: added basic fallback when DIFFERENT_NONZERO_PATTERN is requested

Merge branch 'jed/fix-matconvert-shell/maint' into maint [PR #1352]

* jed/fix-matconvert-shell/maint:
MatConvert_Shell: fix for non-square and parallel matrices
MatComputeExplicitOperator: use MatCo

Merge branch 'jed/fix-matconvert-shell/maint' into maint [PR #1352]

* jed/fix-matconvert-shell/maint:
MatConvert_Shell: fix for non-square and parallel matrices
MatComputeExplicitOperator: use MatConvert_Shell

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Merge branch 'jed/fix-matconvert-shell/maint' [PR #1352]

* jed/fix-matconvert-shell/maint:
MatConvert_Shell: fix for non-square and parallel matrices
MatComputeExplicitOperator: use MatConvert_Shell

MatComputeExplicitOperator: use MatConvert_Shell

Avoids maintaining a near-verbatim copy of the code.

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Remove outdated requires: from top of several examples
remove outdated test requires: command from top of source file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 'pr1233/tkonolige/fix-diagonalset-increase-state/maint' into maint [PR #1233]

* pr1233/tkonolige/fix-diagonalset-increase-state/maint
Increment matrix state in MatDiagonalSet and MatShi

Merge branch 'pr1233/tkonolige/fix-diagonalset-increase-state/maint' into maint [PR #1233]

* pr1233/tkonolige/fix-diagonalset-increase-state/maint
Increment matrix state in MatDiagonalSet and MatShift
MatDiagonalSet and MatShift do not call PetscObjectStateIncrease on the matrices they are called with.
This causes the PC using them to not rebuild its internal state.
This PR fixes the issue.

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Merge branch 'pr1233/tkonolige/fix-diagonalset-increase-state/maint'

* pr1233/tkonolige/fix-diagonalset-increase-state/maint:
Increment matrix state in MatDiagonalSet and MatShift
MatDiagonalSet and

Merge branch 'pr1233/tkonolige/fix-diagonalset-increase-state/maint'

* pr1233/tkonolige/fix-diagonalset-increase-state/maint:
Increment matrix state in MatDiagonalSet and MatShift
MatDiagonalSet and MatShift do not call PetscObjectStateIncrease on the matrices they are called with.
This causes the PC using them to not rebuild its internal state.
This PR fixes the issue.

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Increment matrix state in MatDiagonalSet and MatScale

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 'barry/have-veccuda-to-have-cuda'

Change outdated HAVE_VECCUDA macro to simply HAVE_CUDA for clarity/ease of maintenance.

Commit-type: style-fix

Merge branch 'master' into knepley/feature-plex-functionals

* master: (984 commits)
netcdf: set zlib as optional dependency corretly [wrt --enable-netcdf-4] - otherwise netcdf configure errors out

Merge branch 'master' into knepley/feature-plex-functionals

* master: (984 commits)
netcdf: set zlib as optional dependency corretly [wrt --enable-netcdf-4] - otherwise netcdf configure errors out
fix gcov obj path
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
configure: fix F2003 test
Dev manual: remove duplicate entry
Plex test ex5: Removed "future" test, as it resulted in issues in the nightly tests.
Some minor typos in TS
Add ADIOS2.py which I forgot to git add in the past
Plex ex5: Disable test
Doc: Added note for interface change
KSPLSQRMonitorDefault fixed for quad precision
Tao: Added alternative output for chwirut2 test.
TS ex45,ex46: Removed overly refined tests for faster nightly tests.
KSP ex72: Fixed needlessly long-running PCTFS tests.
SNES ex56: Reduced test size to speed up nightly test suite.
KSPSolve_LSQR: don't compute unused norm of rhs
SNES ex13: Reduced problem sizes for nightly tests.
PetscOptionsDeprecated(): fix for NULL prefix
PetscOptionsDeprecated(): add option to print additional info
SNES ex12: Reduced sizes for BDDC tests.
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Merge branch 'master' into knepley/feature-plex-elasticity-test

* master: (1553 commits)
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
config

Merge branch 'master' into knepley/feature-plex-elasticity-test

* master: (1553 commits)
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
configure: fix F2003 test
Plex test ex5: Removed "future" test, as it resulted in issues in the nightly tests.
Some minor typos in TS
Add ADIOS2.py which I forgot to git add in the past
Plex ex5: Disable test
Doc: Added note for interface change
KSPLSQRMonitorDefault fixed for quad precision
Tao: Added alternative output for chwirut2 test.
TS ex45,ex46: Removed overly refined tests for faster nightly tests.
KSP ex72: Fixed needlessly long-running PCTFS tests.
SNES ex56: Reduced test size to speed up nightly test suite.
KSPSolve_LSQR: don't compute unused norm of rhs
SNES ex13: Reduced problem sizes for nightly tests.
PetscOptionsDeprecated(): fix for NULL prefix
PetscOptionsDeprecated(): add option to print additional info
SNES ex12: Reduced sizes for BDDC tests.
PetscFileRetrieve(): Suppress output to STDERR when downloading a file.
MatMatMult: Fixed unused variable pN.
DMDestroy: Guard call to dm->ops->destroy * Similar guards are in place in many other methods (IS,Vec,Mat) and permit the DM to be destroyed even if DMSetType() was never called.
...

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