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

* master:
sys_tutorials-ex19_1: ignore check_pointer_intensity used in bitbucket pipelines
python2.6: provide subprocess.check_output

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

* master:
sys_tutorials-ex19_1: ignore check_pointer_intensity used in bitbucket pipelines
python2.6: provide subprocess.check_output (introduced in python2.7)
ctags: switch to supbrocess in d35930a37ac51e1f78ebfaaf074c663076f75215 results in verbose output on screen
slepc: use slepc-3.10.1 with petsc-3.10
slepc: fix download with prefix
plexexodusii.c: Vec array type changed from PetscReal* to PetscScalar*.
PCPatch: correct logic for setFromOptions calls on subksps
PCPatch: fix setFromOptions for !save_operators
PCPatch: fix getGlobalDofs for !combined
PCPatch: fix patchSection setup for case !combined
*change* added const to input parameters in BLAS method declarations
sowing: add check for cygwin/g++

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

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

Merged petsc/petsc into master

Merge branch 'pr1197/lm/fix-pcpatch-options/master' [PR #1197]

* pr1197/lm/fix-pcpatch-options/master:
PCPatch: fix setFromOptions for !save_operators
If we do not save the patch operators, their cr

Merge branch 'pr1197/lm/fix-pcpatch-options/master' [PR #1197]

* pr1197/lm/fix-pcpatch-options/master:
PCPatch: fix setFromOptions for !save_operators
If we do not save the patch operators, their creation is deferred until PCPatch_Apply (rather than PCPath_Setup).
As a result, we must also defer KSPSetFromOptions on each patch KSP until the operator has been attached.

I think this won’t result in KSPSetFromOptions being called all the time, but we need to delay this call until the KSP has an operator, otherwise the defaults system produces nonsense.

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Merge branch 'pr1195/lm/fix-pcpatch-section-fields/master' [PR #1195]

* pr1195/lm/fix-pcpatch-section-fields/master:
PCPatch: fix patchSection setup for case !combined
If the discretisation info c

Merge branch 'pr1195/lm/fix-pcpatch-section-fields/master' [PR #1195]

* pr1195/lm/fix-pcpatch-section-fields/master:
PCPatch: fix patchSection setup for case !combined
If the discretisation info comes in as one section per field, the logic for computing a combined patchSection is different.
PCPatch: fix getGlobalDofs for !combined
The offset is the sum of the offsets of all the fields I think. This code path is never exercised.

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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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PCPatch: correct logic for setFromOptions calls on subksps

Additionally fix PCSetUpOnBlocks_PATCH for the !save_operators case.

PCPatch: fix setFromOptions for !save_operators

If we do not save the patch operators, their creation is deferred
until PCPatch_Apply (rather than PCPath_Setup). As a result, we must
also defer KSPS

PCPatch: fix setFromOptions for !save_operators

If we do not save the patch operators, their creation is deferred
until PCPatch_Apply (rather than PCPath_Setup). As a result, we must
also defer KSPSetFromOptions on each patch KSP until the operator has
been attached.

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PCPatch: fix getGlobalDofs for !combined

The offset is the sum of the offsets of all the fields I think. This
code path is never exercised.

PCPatch: fix patchSection setup for case !combined

If the discretisation info comes in as one section per field, the
logic for computing a combined patchSection is different.

Complete support for individual PETSc objects to use their own options database with PetscObjectSetOptions()

Commit-type: feature, example
Reported-by: "Blondel, Sophie" <sblondel@utk.edu>

Merged petsc/petsc into master

Merge remote-tracking branch 'origin/stefano_zampini/weakly-symmetric-elasticity-rebased'

Merge branch 'pefarrell/vanka-exclude-subspaces' [PR #1163]

* pefarrell/vanka-exclude-subspaces:
Generalise the exclude_subspace option of Vanka construction in PCPATCH to exclude_subspaces.
This is

Merge branch 'pefarrell/vanka-exclude-subspaces' [PR #1163]

* pefarrell/vanka-exclude-subspaces:
Generalise the exclude_subspace option of Vanka construction in PCPATCH to exclude_subspaces.
This is important if you have more than one constraint, e.g. MHD problems with one multiplier enforcing solenoidality of the velocity and another enforcing solenoidality of the magnetic field.

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Fix for -pc_patch_exclude_subspaces code when the user hasn't yet set
the number of fields of the problem

Do some housekeeping and add missing CHKERRQ calls

C90 fixes

Generalise the exclude_subspace option of Vanka construction in PCPATCH to exclude_subspaces.

This is important if you have more than one constraint, e.g. MHD problems with
one multiplier enforcing

Generalise the exclude_subspace option of Vanka construction in PCPATCH to exclude_subspaces.

This is important if you have more than one constraint, e.g. MHD problems with
one multiplier enforcing solenoidality of the velocity and another enforcing
solenoidality of the magnetic field.

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Merged petsc/petsc into master

Merge branch 'master' into knepley/feature-dm-nearnullspace

* master: (219 commits)
petsc4py: update with VecScatter API changes
remove duplicate code
petsc4py: update to version 3.10.0
fixe

Merge branch 'master' into knepley/feature-dm-nearnullspace

* master: (219 commits)
petsc4py: update with VecScatter API changes
remove duplicate code
petsc4py: update to version 3.10.0
fixed typos in documentation
fixed typos in documentation
Fix some remaining Register()s to call InitializePackage()
Remove memory leaks of XXXRegister() is called but XXX object is never used
Add to PCTFS manual page that it does not work for complex numbers
Stray , in manual page that should be .
Only register MPI3 VecScatter if they are built
clarification of KSPSetComputeInitialGuess()
Add missing makefiles for VecScatter implementations
Changed VecScatterCreate() to take a communicator and return scatter as other first class PETSc objects do. Changed old VecScatterCreate() to VecScatterCreateWithData()
Added VecScatterSetUp() and converted implementations to use it to compute scatter information
Pull "MPI1" and "MPI3" specific code out of common VecScatter impls code This allows future implementations to use the common code also without changing the common code
Seperate VecScatter implementation code into three subdirectories seq, mpi1, and mpi3
doc: fix author list in manual wrt 6402aee
doc: fix LOCDIR wrt broken URL from MatHYPRESetPreallocation.html
ifort: ifx compile error with --with-mpi=0
changes/310.html: merged two TAO sections
...

Conflicts:
src/dm/interface/dm.c

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Merge branch 'master' into knepley/feature-ksp-ex10-transpose

* master: (219 commits)
petsc4py: update with VecScatter API changes
remove duplicate code
petsc4py: update to version 3.10.0
fi

Merge branch 'master' into knepley/feature-ksp-ex10-transpose

* master: (219 commits)
petsc4py: update with VecScatter API changes
remove duplicate code
petsc4py: update to version 3.10.0
fixed typos in documentation
fixed typos in documentation
Fix some remaining Register()s to call InitializePackage()
Remove memory leaks of XXXRegister() is called but XXX object is never used
Add to PCTFS manual page that it does not work for complex numbers
Stray , in manual page that should be .
Only register MPI3 VecScatter if they are built
clarification of KSPSetComputeInitialGuess()
Add missing makefiles for VecScatter implementations
Changed VecScatterCreate() to take a communicator and return scatter as other first class PETSc objects do. Changed old VecScatterCreate() to VecScatterCreateWithData()
Added VecScatterSetUp() and converted implementations to use it to compute scatter information
Pull "MPI1" and "MPI3" specific code out of common VecScatter impls code This allows future implementations to use the common code also without changing the common code
Seperate VecScatter implementation code into three subdirectories seq, mpi1, and mpi3
doc: fix author list in manual wrt 6402aee
doc: fix LOCDIR wrt broken URL from MatHYPRESetPreallocation.html
ifort: ifx compile error with --with-mpi=0
changes/310.html: merged two TAO sections
...

Conflicts:
src/ksp/ksp/interface/itfunc.c

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Merged petsc/petsc into master

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

* master: (345 commits)
Update dev notes for the coming release
Increase patchlevel to 3.9.4
doc fixes
Added some AIJSELL tests t

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

* master: (345 commits)
Update dev notes for the coming release
Increase patchlevel to 3.9.4
doc fixes
Added some AIJSELL tests that mirror the SELL tests.
Bib: More refs
Removed use of hardwired -1 to represent PETSC_NULL_XXX object, since the null value is now 0.
fix memleaks flagged by valgrind
ex62: disable long running test and workaround differences in iteration counts on various builds.
Add FAQ we can point to when users get error messages such as: "PETSc was configured with one OpenMPI mpi.h version but now appears to be compiling using a different OpenMPI mpi.h version"
swith test from mpich to openmpi as mpich ch3:sock is unuserable per PetscShmCommGet()
DM: Forgot to move include statement
fix nightlybuild issues - disable hypre [for openmp] and fix uninitialized variables
tests: enable openmp and hwloc with one of the mumps tests
Default BoomerAMG smoothers
Configure: Revert changes from debb90c, so that we are back to the original Libmesh
Configure: Reverted change for Libmesh from 83cd5d7
Split vecimpl.h into vecimpl.h and vecscatterimpl.h
SNES ex62: Turned off some tests for other precisions and shortened output of sensitive tests
Use mmap to allocate the shared pthread barrier if available
Add configure test for functional mmap
...

Conflicts:
include/petscconvest.h
src/snes/examples/tutorials/ex13.c
src/snes/interface/snes.c
src/snes/utils/convest.c

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Merge branch 'knepley/feature-pc-patch'