Merge commit 'd47bf9aaf1e5266cc3f0ff499f934c85788965a9' into jed/fix-matcreatempibaij/maint

Obtain changed (v3.5) handling of MatMPIBAIJSetPreallocationCSR to match
documentation.

Merge remote-tracking branch 'origin/maint'

Merged in dalcinl/petscsf-include (pull request #730)

Add missing include petscsf.h in petsc.h

Approved-by: Jed Brown <jed@59a2.org>

Add missing include petscsf.h in petsc.h

Merge branch 'master' into pr263/PierreBdR/ts-domain-error-in-stage/master

Merge branch 'barry/fix-nonew-notcollective/maint' into jed/mat-assembly-perf

Jed this fucking 6+ month running thing in next that is not in master is a royal fucking pain in the ass and
an abuse of

Merge branch 'barry/fix-nonew-notcollective/maint' into jed/mat-assembly-perf

Jed this fucking 6+ month running thing in next that is not in master is a royal fucking pain in the ass and
an abuse of git. I think it is not justified to ever have anything in next for more than a few weeks at most.
Either take it out of next if it is broken or put it in master if it is not broken. Hanging around in next but
not master for ever is not a good policy.

show more ...

Merge remote-tracking branch 'petsc/master' into mat-increaseoverlap

Merge branch 'master' into knepley/solkx

* master: (6933 commits)
Bib: Added reference
Includegraph: Updated for compatibility with new folder layout.
Add SNESLineSearchReason to fortran inclu

Merge branch 'master' into knepley/solkx

* master: (6933 commits)
Bib: Added reference
Includegraph: Updated for compatibility with new folder layout.
Add SNESLineSearchReason to fortran includes Also truncate names to fit 32 char fortran limit
fix compile warnings /usr/home/balay/petsc.clone-2/src/vec/vec/interface/vector.c:1944: warning: division by zero in '1.0e+0 / 0.' /usr/home/balay/petsc.clone-2/src/ksp/ksp/interface/itfunc.c:508: warning: 'vec_rhs' may be used uninitialized in this function
updated output for new trust region initial size
initial size of the trust region is set as a percent of the norm of the initial guess, it should not be related to the initial norm of the function (which is kind of nuts).
The default bounds for SNESVISetVariableBounds() in the manual page were reversed from correct values
Bib: Added refs
Bib: Update MPICH webpage
Plex: Forgot to close file
removed nonexistent ex46f from makefile test rule
Revert "fixed bad merge into master"
fixed bad merge into master
fix memory leak in mkl_pardiso fix some formatting in mkl_pardiso code
mv runex111 from TESTEXAMPLES_C to TESTEXAMPLES_DATAFILESPATH
Mat+Doc: More Fortran docs
Plex ex3: Run tests with the correct number of field components
Bib: Added TetGen cite
parmetis: make sure 'ldd libparmetis.so' points to the correct libmetis.so that its linked with.
small fix as reported by the nightly test
...

Conflicts:
config/builder.py

show more ...

Merged petsc/petsc into master

Merge branch 'master' into tisaac/dmforest

directory layout changed again: merging to switching branches back and forth
doesn't cause reconfigure to have a hard time

* master: (357 commits)
remov

Merge branch 'master' into tisaac/dmforest

directory layout changed again: merging to switching branches back and forth
doesn't cause reconfigure to have a hard time

* master: (357 commits)
removed nonexistent ex46f from makefile test rule
Revert "fixed bad merge into master"
fixed bad merge into master
fix memory leak in mkl_pardiso fix some formatting in mkl_pardiso code
mv runex111 from TESTEXAMPLES_C to TESTEXAMPLES_DATAFILESPATH
Mat+Doc: More Fortran docs
Bib: Added TetGen cite
parmetis: make sure 'ldd libparmetis.so' points to the correct libmetis.so that its linked with.
small fix as reported by the nightly test
add a test for MatPtAP()
small cleanup; add tests
cleanup MatPtAPSymbolic_MPIAIJ_MPIAIJ()
Fix nonzerostate tracking in all MATMPI types.
update location of test matrices in faq.html file
unused variable still declared
Fix for MatLoad_MPIDense() from sparsely stored matrix also fix for MatLoad_MPIDense_DenseInFile() when matrix has not had its local sizes preset by user
Preserve the B nonzerostate during disassembly.
TSEvent: Fix arch-mswin nightly errors due to declaring variables in the middle of a function.
Fix error in parallel loading of dense format matrix
removed KSPSetNullSpace() since mat already carries that information and having two locations for it is confusing, unnecessary and prone to error added MatSetTransposeNullSpace() for providing the null space of the transpose of the matrix and added support in KSPSolve() to remove this null space from the right handside of the linear system thus making the system consistent.
...

show more ...

Merge branch 'barry/remove-thread-classes-master'

stripped out all PETSc threadcomm code

stripped out all PETSc threadcomm code

Merge branch 'master' into tisaac/dmforest

If we're going to start developing on this again, the recent changes to the
location of configuration files will make it annoying to switch to and from
thi

Merge branch 'master' into tisaac/dmforest

If we're going to start developing on this again, the recent changes to the
location of configuration files will make it annoying to switch to and from
this branch. Matt's and my fixes in DMPlex will also be relevant.

* master: (1557 commits)
MatLoad_MPIDense() always allocated array space even if it was previously provided
Clarified lumping options for PCFieldSplitSchurPreType SELFP.
fixed up PetscInfo in GAMG
TSErrorWeightedNorm[2|Infinity]: API changes
MatLoad_SeqDense() always allocated new space for the data even if the user already provided it
Fixed DMCompositeGetAccessArray() to support readonly vectors
Fix obviously-wrong aspects of documentation on SNESVINEWTONRSLS and SNESVINEWTONSSLS.
fixed example to compile - demonstrates a bug
var name 'len' was F90 key word
For user provided Jacobian functions they should always assembly into the second matrix, the one from which the preconditioner is built because the first may be used as matrix-free with -snes_mf_operator
Suggest --with-64-bit-indices if users mistakenly use --with-64bit-indices
Fix configure logging of integer size.
missing underscore in #define of vecgetarrayread translation of fortran stub for VECGETARRAYREAD
updated test output files to reflect differences introduced previously in PCView output
-ksp_type preonly does not support -ksp_monitor_short so remove from test line to prevent extranious warning output
missing CHKERRQ; and ugly double declaration of ierr
Plex ex3: For want of a semicolon, the kingdom was lost
MatSetValuesMPISBAIJ will now print correct global indices when error generated due to new nonzero location
completed basic use of MatSetValuesBlocked_SeqBAIJ_Inlined() by MatSetValuesBlocked_MPIBAIJ() to allow proper global indices being printed when error generated by new nonzero locations.
Added inline version of MatSetValuesBlocked_SeqBAIJ() to be used by MatSetValuesBlocked_MPIBAIJ() to print error message for nonzero block with global indices
...

show more ...

Merge branch 'master' into shri/ts-is-for-differential-variables

Conflicts:
include/petsc-private/tsimpl.h
src/ts/impls/eimex/eimex.c
src/ts/interface/ts.c

Merge branch 'master' into jed/chem
Note merging a branch with good stuff in it for a year and a half is insane!

Conflicts:
src/ts/examples/tutorials/makefile
src/ts/interface/ts.c

Merge branch 'master' into stefano_zampini/pcbddc-adaptive-selection

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c
src/sys/threadcomm/interface/threadcomm.c

show more ...

Merge branch 'master' into pr252/dmay/PetscViewerBinarySkipHeaderVecViewLoad
Manual merge of makefile

Conflicts:
src/sys/classes/viewer/examples/tutorials/makefile

Merge branch 'tisaac/feature-gamg-extensible' into barry/experiment

Conflicts:
src/ksp/pc/impls/gamg/gamg.h

Merge branch 'knepley/feature-combined-tabulation'

* knepley/feature-combined-tabulation: (38 commits)
Plex: Fix compiler warning
Plex+SNES: Fixes for nonzero cStart
Plex: Preserve periodicity

Merge branch 'knepley/feature-combined-tabulation'

* knepley/feature-combined-tabulation: (38 commits)
Plex: Fix compiler warning
Plex+SNES: Fixes for nonzero cStart
Plex: Preserve periodicity when adding ghost cells
Plex: Fixed DMPlexGetGlobalFieldOffset_Private() in optimized mode
Plex+SNES: Offset should be into field components, not basis functions
Plex+SNES: Add guards for optional arrays
DS: Added PetscDSGetComponentOffset(), Added to petsc.h
Plex+TS: FVM RHS computation uses a global F
Plex+FV: Corrected accumulation of fluxes to cells and added time derivative term
Plex: Added DMPlexPointGlobalFieldRead/Ref()
Plex+SNES: Fixed DMPlexGetFaceFields() - It returns field values, not coefficients - FE evaluation is now done
FV: In PetscFVIntegrateRHSFunction(), the arguments are field values, not coefficients
FE: Added EvaluateFaceFields() to FE fields at face centroids
Plex: Added DMPlexPointLocalFieldRead()
FE: Have a standard tabulation at face centroids
Plex: Copy BC for hierarchical refinement
FE: Allow P0 over 1D cells
Plex+FV: Fixed BC with gradient calculation
Plex ex1: Move overlap computation after SetFromOptions
Plex: DMPlexDistribute() no longer calls DMSetFromOptions() - Fixed examples
...

show more ...

Merge branch 'knepley/feature-combined-tabulation' into knepley/feature-ts-fem+fvm-example

* knepley/feature-combined-tabulation: (41 commits)
Plex: Fix distribution of uninterpolated meshes - Doe

Merge branch 'knepley/feature-combined-tabulation' into knepley/feature-ts-fem+fvm-example

* knepley/feature-combined-tabulation: (41 commits)
Plex: Fix distribution of uninterpolated meshes - Does SF stratification by depth, not by dimension - The old code numbered cells after vertices
Plex+SNES: Fixes for nonzero cStart
cannot call PetscObjectGetName() on a subset of the MPI processes
MatView() with some matrix formats and ASCII_MATLAB did not print correct matrix name
Plex: Preserve periodicity when adding ghost cells
Plex: Fixed DMPlexGetGlobalFieldOffset_Private() in optimized mode
Plex+SNES: Offset should be into field components, not basis functions
Plex+SNES: Add guards for optional arrays
DS: Added PetscDSGetComponentOffset(), Added to petsc.h
Plex+TS: FVM RHS computation uses a global F
Plex+FV: Corrected accumulation of fluxes to cells and added time derivative term
Plex: Added DMPlexPointGlobalFieldRead/Ref()
Plex+SNES: Fixed DMPlexGetFaceFields() - It returns field values, not coefficients - FE evaluation is now done
FV: In PetscFVIntegrateRHSFunction(), the arguments are field values, not coefficients
FE: Added EvaluateFaceFields() to FE fields at face centroids
Plex: Added DMPlexPointLocalFieldRead()
FE: Have a standard tabulation at face centroids
Plex: Copy BC for hierarchical refinement
FE: Allow P0 over 1D cells
Plex+FV: Fixed BC with gradient calculation
...

Conflicts:
config/builder.py

show more ...

DS: Added PetscDSGetComponentOffset(), Added to petsc.h

Merge branch 'master' into barry/saws-options

Merge branch 'master' into stefano_zampini/pcbddc-multilevel-improvement

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bdd

Merge branch 'master' into stefano_zampini/pcbddc-multilevel-improvement

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddcprivate.c

show more ...