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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Merge branch 'barry/use-complex-for-mffd' [PR #1189]

* barry/use-complex-for-mffd:
Add -mat_mffd_complex to use the Lyness complex number trick to compute J_u * v instead of differencing.
Requires c

Merge branch 'barry/use-complex-for-mffd' [PR #1189]

* barry/use-complex-for-mffd:
Add -mat_mffd_complex to use the Lyness complex number trick to compute J_u * v instead of differencing.
Requires complex number build of PETSc

Thanks to: Oana Marin <oanam@mcs.anl.gov>

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Add -mat_mffd_complex to use the Lyness complex number trick to compute J_u * v instead of differencing.

Requires complex number build of PETSc

Commit-type: feature
Reported-by: Oana Marin <oanam@m

Add -mat_mffd_complex to use the Lyness complex number trick to compute J_u * v instead of differencing.

Requires complex number build of PETSc

Commit-type: feature
Reported-by: Oana Marin <oanam@mcs.anl.gov>

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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
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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'

Merge remote-tracking branch 'origin/barry/fix-xxxregister-memory-leaks/maint' into maint

Fix some remaining Register()s to call InitializePackage()

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:
Add variable point block Jacobi for MPIAIJ matrix.
should not pass user contexts through CHKFORTRANNULLOBJECT in Fortran stubs
Rem

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

* master:
Add variable point block Jacobi for MPIAIJ matrix.
should not pass user contexts through CHKFORTRANNULLOBJECT in Fortran stubs
Remove CHKFORTRANNULLOBJECTDEREFERENCE since it is no longer needed with Fortran null equal to C null
Change Fortran null pointer to match C null pointer

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

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Merge remote-tracking branch 'origin/barry/change-fortran-null'

Remove CHKFORTRANNULLOBJECTDEREFERENCE since it is no longer needed with Fortran null equal to C null

Commit-type: feature

Merged petsc/petsc into master

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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Merge branch 'master' into knepley/feature-plex-parallel-submesh

* master: (2931 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComp

Merge branch 'master' into knepley/feature-plex-parallel-submesh

* master: (2931 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComplex type is missing from fortran
initialize variables so that static analyzer doesn't mistakenly think they are used uninitialized.
Move access of prefix until it is actually used
Remove DMDASplitComm2d(), used in one example that was not tested
Functions that do not return PetscErrorCode should not use PetscFunctionBegin/End paradgm
remove unneeded reassignment of same value
Missing CHKERRQ(); Mostly in Tao code
Remove clang static analyser warning about passing NULL variable to strncat()
missing newline in -ts_monitor_extreme
minor fixes for integer counters
Configure: Deal with '__func__' in C89 builds with newer Clang and GCC.
Jenkinsfile: Increased timeout for tests to 5 minutes.
3.9 changes: further clarify removal of -pc_factor_mat_solver_package
Options deprecations: add "PETSc" to inline warning
removing unused variable
MatShift support added to MATSUBMAT. Mimics MATSHELL functionality. Needed for matrix-free Hessians in TAO Newton-Line-Search methods.
Add -ts_monitor_extreme
Dev manual: add note on deprecating options database keys
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Conflicts:
src/dm/impls/plex/examples/tests/ex4.c

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Merge branch 'master' into knepley/fix-plex-submesh-projection

* master: (425 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComplex

Merge branch 'master' into knepley/fix-plex-submesh-projection

* master: (425 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComplex type is missing from fortran
initialize variables so that static analyzer doesn't mistakenly think they are used uninitialized.
Move access of prefix until it is actually used
Remove DMDASplitComm2d(), used in one example that was not tested
Functions that do not return PetscErrorCode should not use PetscFunctionBegin/End paradgm
remove unneeded reassignment of same value
Missing CHKERRQ(); Mostly in Tao code
Remove clang static analyser warning about passing NULL variable to strncat()
missing newline in -ts_monitor_extreme
minor fixes for integer counters
Configure: Deal with '__func__' in C89 builds with newer Clang and GCC.
Jenkinsfile: Increased timeout for tests to 5 minutes.
3.9 changes: further clarify removal of -pc_factor_mat_solver_package
Options deprecations: add "PETSc" to inline warning
removing unused variable
MatShift support added to MATSUBMAT. Mimics MATSHELL functionality. Needed for matrix-free Hessians in TAO Newton-Line-Search methods.
Add -ts_monitor_extreme
Dev manual: add note on deprecating options database keys
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Conflicts:
src/dm/impls/plex/examples/tests/ex4.c

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

* master: (353 commits)
Configure: Pragmatic now requires Cxx11
fix compile warning
mpiuni: build somempifort.o after mpiuni.mod

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

* master: (353 commits)
Configure: Pragmatic now requires Cxx11
fix compile warning
mpiuni: build somempifort.o after mpiuni.mod
Remove use of common block from MPIUNI code
use was in wrong location
Fortran line extends past 72 char
Moved the rest of the PETSc common block variables over to petscsys module
tests: fix breakage due to cd93b0e13c6da70ee1e038f55989cf888bc1d1c5
Need to use petscsys to get PETSC_COMM_SELF defined in example
Mat ex23 and ex40: fix errors reported from nightly tests
Put declaration on too lines because otherwise it generates an error for truncated line
Move PETSC_COMM_WORLD and PETSC_COMM_SELF from common blocks to petscsys module
tests: fix requires - and create out files for seqaijmkl tests
KSP ex72: nested dissection is likely to be different between machines
cmake: downgrade to version 3.9 - as newer versions require cxx11 compiler [which is not universal]. However stick with version 3.11 on opensolaris
Mat ex23: fix memory leaks
Bib: Some new refs
KSP examples: add missing casts to double in printf
updated GAMG KSP tests
PetscRound() should be PetscRoundReal() in __fp16
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Conflicts:
include/petsclog.h
src/sys/logging/plog.c
src/sys/logging/utils/eventlog.c

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Merge branch 'master' into denera/lmvm-mat-and-pc

Merge branch 'master' into knepley/fix-plex-project-tests

* master: (477 commits)
Added correct report number for PETSc Developers Guide
Update PETSc Developers Guide title and final pages to ne

Merge branch 'master' into knepley/fix-plex-project-tests

* master: (477 commits)
Added correct report number for PETSc Developers Guide
Update PETSc Developers Guide title and final pages to new ANL style
Hash: Quick documentation fix
PetscBinaryViewerRead -> PetscViewerBinaryRead
cast in GAMG_HASH so that it works for PetscInt32 near PETSC_INT_MAX without overflow to negative numbers
Add link for DrMemory which may serve as an alternative to valgrind on Windows
Finish Gail's copyedits for developers manual.
openmpi: fix namespace conflict [with static build on ppc64le]
two pages of Gail's edits to developers guide
Another chapter of Gail's copyedits for the developers guide
Gail's copyedits on two more chapters of the developers guide
Fix more %d to %D in GAMG code. Fix code style in GAMG code
DMPlexVTK: vertices is int! need to use %d instead of %D
TS ex18: update outputs (reported by nightly tests)
Use %D in error messages for GAMG hash; fix style issues with GAMG hash
config: Update petsc4py git commit
Fix bad plain extern declaration.
Add Gail's copyedits for the initial portion of the developers guide
Add missing common block to subroutine
fix mpiuni tests with xl compilers
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