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

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcscalingbasic.c
src/mat/impls/aij/mpi/mumps/mumps.c
s

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

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcscalingbasic.c
src/mat/impls/aij/mpi/mumps/mumps.c
src/mat/impls/is/matis.h

show more ...

Merged master into semihozmen/ksp-fcg-eigen-comp-support

Merge branch 'master' into pr192/Fande-Kong/scalable-matincreaseoverlap/master

Needed to merge master to update to new calling sequence PetscCommBuildTwoSided

Merged petsc/petsc into master

Merge branch 'barry/fix-directory-layout'

updated PETSc directory layout to match standard packaging strategies

include/petsc finclude,private,mpiuni
lib/petsc conf
bin/petsc*

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 ...

removed generation of automatic matrix name when viewing parallel matrices
removed double printing of matrix header when printing matrices associated with DAs

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

some of the DMCreateMatrix_DA* functions did not set the matrix block size

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

set but unused variable removed

Merge branch 'barry/fix-dmda-creatematrix-large-nc'

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

optimized memory usage of DMCreateMatrix_DA_Xd_MPIAIJ_Fill() for memory usage for setting zeros row at a time into the matrix
for the initial nonzero pattern; previously allocated too large a space f

optimized memory usage of DMCreateMatrix_DA_Xd_MPIAIJ_Fill() for memory usage for setting zeros row at a time into the matrix
for the initial nonzero pattern; previously allocated too large a space for large nc

show more ...

Merge branch 'master' into barry/ksp-converged-reason-viewer

Conflicts:
src/sys/objects/options.c

Merge branch 'knepley/fix-iscoloring-create'

* knepley/fix-iscoloring-create:
IS: Fix typo
ISColoring: Added PetscCopyMode argument to create
IS: Create a types header, and moved most structs

Merge branch 'knepley/fix-iscoloring-create'

* knepley/fix-iscoloring-create:
IS: Fix typo
ISColoring: Added PetscCopyMode argument to create
IS: Create a types header, and moved most structs to the impl header - Layout should not be in the main header, but it is needed by some static functions

show more ...

ISColoring: Added PetscCopyMode argument to create

Merge branch 'barry/remove-unneeded-paren-petscmalloc'

Conflicts:
src/mat/impls/baij/seq/baij.c

convert some PetscMalloc() to PetscMalloc1()
remove unneeded () in first argument to PetscMalloc/Calloc1()
fixes for MATLAB examples

Merge branch 'knepley/feature-dm-dimension-handling'

* knepley/feature-dm-dimension-handling:
DM: Fixed DMDASetDim() in examples
Plex: Fix for isoparametric geometry
Plex: Complex fix
TS ex1

Merge branch 'knepley/feature-dm-dimension-handling'

* knepley/feature-dm-dimension-handling:
DM: Fixed DMDASetDim() in examples
Plex: Fix for isoparametric geometry
Plex: Complex fix
TS ex11: Fixed calls to DMSetCoordinateSection()
DM: FIxed DMClone() to copy dimension
Plex+DA: Now cell geometry routine can take a PetscFE in order to evaluate at quadrature points - We evaluate isoparametrically at the quadrature points - Changed DMDAComputeCellGeometry() --> DMDAComputeCellGeometryFEM() - Changed DMPlexComputeCellGeometry() --> DMPlexComputeCellGeometryFEM() - Added DMPlexComputeCellGeometryAffineFEM()
DM: Added a embedding dimension, different from the topological dimension - This can now be set in DMSetCoordinateSection(), or it can be automatically determined
Plex: Fix output for ex4
DM: Added DMGetDimPoints() - This replicates DMPlex/DAGetDepthStratum(), but uses the dimension which people have said is more intuitive
DM: Move dimension up into DM - Both DA and Plex had this and I think it makes sense

Conflicts:
src/dm/impls/plex/plexcreate.c

show more ...

DM: Move dimension up into DM
- Both DA and Plex had this and I think it makes sense