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

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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Merge branch 'maint'

doc: fix LOCDIR wrt broken URL from MatHYPRESetPreallocation.html

Reported-by: Fande Kong <fdkong.jd@gmail.com>

Tested with:
make ACTION=sourcelist BASE_DIR=$PWD alltree_makefile
ls `cat files` > /

doc: fix LOCDIR wrt broken URL from MatHYPRESetPreallocation.html

Reported-by: Fande Kong <fdkong.jd@gmail.com>

Tested with:
make ACTION=sourcelist BASE_DIR=$PWD alltree_makefile
ls `cat files` > /dev/null

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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 'master' into knepley/fix-superdm-is

* master: (123 commits)
Fix a few more Fortran objects to have their NULL value match the C NULL value
remove dead code
Add variable point blo

Merge branch 'master' into knepley/fix-superdm-is

* master: (123 commits)
Fix a few more Fortran objects to have their NULL value match the C NULL value
remove dead code
Add variable point block Jacobi for MPIAIJ matrix.
should not pass user contexts through CHKFORTRANNULLOBJECT in Fortran stubs
fix mpiuni test
Remove CHKFORTRANNULLOBJECTDEREFERENCE since it is no longer needed with Fortran null equal to C null
PETSCFEOPENCL: declare PetscFEGetTabulation_Basic as external
PETSCFEOPENCL: declare PetscFESetUp_Basic as external
Change Fortran null pointer to match C null pointer
one more fix
jenkins: run 'cleantest' after examples are run - to recover diskspace
logical order bug in diagbrdn update fixed, tests updated again
replace new -petscspace_order instances with -petscspace_degree
PETSCSPACETENSOR: clear up naming confusion of subspaces
regression.py: remove configure code related to old test suite - now that SLEPc no longer needs it
PetscSpaceSetup_Poly(): make idempotent
Plex ex3: update tests
Lift changes to defunct dtfe.c from [PR #1074]
PetscSpace_Tensor: clarification of vector-valued
PetscSpace_Tensor: allow height subspaces, fixes tabulation initialization
...

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

* master: (131 commits)
fix mpiuni test
PETSCFEOPENCL: declare PetscFEGetTabulation_Basic as external
PETSCFEOPENCL: declare PetscFESetUp_Ba

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

* master: (131 commits)
fix mpiuni test
PETSCFEOPENCL: declare PetscFEGetTabulation_Basic as external
PETSCFEOPENCL: declare PetscFESetUp_Basic as external
one more fix
jenkins: run 'cleantest' after examples are run - to recover diskspace
logical order bug in diagbrdn update fixed, tests updated again
replace new -petscspace_order instances with -petscspace_degree
PETSCSPACETENSOR: clear up naming confusion of subspaces
regression.py: remove configure code related to old test suite - now that SLEPc no longer needs it
PetscSpaceSetup_Poly(): make idempotent
Plex ex3: update tests
Lift changes to defunct dtfe.c from [PR #1074]
PetscSpace_Tensor: clarification of vector-valued
PetscSpace_Tensor: allow height subspaces, fixes tabulation initialization
PetscSpace: add a dimension member
PetscSpaceSetDegree(): now take maxDegree argument
-petscspacepoly_tensor -> -petscspace_type tensor
PetscSpaceEvaluate_Polynomial(): fix temp array dependencies
PETSCSPACETENSOR: A generic tensor product of spaces.
PetscSpace: -petscspace_order -> -petscspace_degree
...

Conflicts:
src/dm/dt/interface/dtfe.c
src/snes/examples/tutorials/ex13.c
src/snes/examples/tutorials/ex17.c
src/snes/examples/tutorials/ex62.c
src/snes/examples/tutorials/output/ex62_bddc_quad.out
src/snes/examples/tutorials/output/ex62_fetidp_2d_quad.out
src/snes/examples/tutorials/output/ex62_fetidp_2d_tri.out
src/snes/examples/tutorials/output/ex62_fetidp_3d_hex.out
src/snes/examples/tutorials/output/ex62_fetidp_3d_tet.out

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Merge remote-tracking branch 'origin/tisaac/feature-space-tensor'

PetscFE: create directory structure

It's becoming necessary, as we try to do more complex things,
to sharpen the interface between the things in dtfe, and make
extension more approachable. It's tim

PetscFE: create directory structure

It's becoming necessary, as we try to do more complex things,
to sharpen the interface between the things in dtfe, and make
extension more approachable. It's time.

show more ...