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 'knepley/fix-distribute-check' [PR #1152]

Plex: Fixed argument check

Merged petsc/petsc into master

Merged petsc/petsc into master

Merge from 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'

Merge remote-tracking branch 'origin/jed/fix-dmplexdistribute-fortran' into maint

Merged petsc/petsc into master

DMPlexDistribute: fix man page

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'

Plex: In balanced partition, real ranks are finally communicated

Plex: Fix case of implicit local leaves in SF

Merged petsc/petsc into master

Plex + ex12: Fix for partition balance
- Update test output

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

* master: (455 commits)
bib: spell out some names for format consistency with related refs
bib: two 2018 pubs now appeared
cleaning up analyze

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

* master: (455 commits)
bib: spell out some names for format consistency with related refs
bib: two 2018 pubs now appeared
cleaning up analyzer warnings
compile fixes (workarround PGI bug?):
undoing the branch's changes to leastsquares outputs
more fixes for complex builds
compile error fix for complex builds
1) Look for 64 bit integer MKL BLAS if 64 bit indices are used with PETSc 2) Fix Pardiso code to only compile pardiso_init64 when needed, otherwise can generate warnings/errors
jenkins: run 'cleantest' before 'allgtest-tap' - an attempt to fix errors of type:
cuda: protect cuda includes
fix cuda warnings.
fix complex compile error
Revert "Improved polymorphism of interfaces for MatSetValuesBlocked()"
Bib: Updated ref
Doc: More function documentation
petscvec: move PetscSFCreateFromZero from vscat to vec sources
Fixed an uninitialized variable and got rid of an unused one.
memleak fixed and output files updated
fixing build errors on some archs
Mat: obey options prefix of Mat in MatNullSpaceTest
...

Conflicts:
include/petsc/private/dmpleximpl.h
src/dm/interface/dmi.c

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

* master: (281 commits)
compile fixes (workarround PGI bug?):
1) Look for 64 bit integer MKL BLAS if 64 bit indices are used with PETSc 2) Fix

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

* master: (281 commits)
compile fixes (workarround PGI bug?):
1) Look for 64 bit integer MKL BLAS if 64 bit indices are used with PETSc 2) Fix Pardiso code to only compile pardiso_init64 when needed, otherwise can generate warnings/errors
jenkins: run 'cleantest' before 'allgtest-tap' - an attempt to fix errors of type:
cuda: protect cuda includes
fix cuda warnings.
fix complex compile error
Revert "Improved polymorphism of interfaces for MatSetValuesBlocked()"
Bib: Updated ref
Doc: More function documentation
petscvec: move PetscSFCreateFromZero from vscat to vec sources
Mat: obey options prefix of Mat in MatNullSpaceTest
Plex+SNES: Must pass user context through
vscat: move ftn-custom to correct location remove custom vecscatterdestroy_()
vscat: move interface routines to correct location
vscat: delete dead code
fix compile error
FE: Correct coordinates in IntegrateBd
Bib: Added refs
SNES ex17: 3D tests must require a 3D grid generator
Plex+TS: We cannot run the check with the same vector that is the TS solution
...

Conflicts:
include/petsc/private/dmpleximpl.h
src/docs/website/documentation/changes/dev.html
src/snes/examples/tutorials/ex13.c
src/snes/utils/dmplexsnes.c

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

* master: (249 commits)
Bib: Added refs
Netcdf should always build netcdf-4 (needed for example by exodusii.
trivial fixes of incor

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

* master: (249 commits)
Bib: Added refs
Netcdf should always build netcdf-4 (needed for example by exodusii.
trivial fixes of incorrect formatting in SNES linesearch routines
ISSetBlockSize_General: removed blockwise contiguity check.
netcdf: set zlib as optional dependency corretly [wrt --enable-netcdf-4] - otherwise netcdf configure errors out
config prefix: avoid ad-hoc path substitutions
config/install: no need to rename paths for installBinDir
rules: fix path in (evidently unimportant) uncrustify target
config pkgconfig: use ${prefix} in PETSc.pc and do not modify in install
fix gcov obj path
Improved polymorphism of interfaces for MatSetValuesBlocked()
-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
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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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