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

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

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 ...

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 shri/ts-events

Conflicts:
src/ts/interface/ts.c

Merge branch 'master' into barry/xcode

Merge branch 'master' into barry/wirth-fusion-materials

Conflicts:
src/ts/examples/tutorials/advection-diffusion-reaction/ex10.c

Merge branch 'barry/dmvecmattypes' into barry/saws

Needed to work with version of PETSc that did not have constant calls to VecSetFromOptions() etc

Conflicts:
src/ksp/ksp/interface/ams/kspams.c
s

Merge branch 'barry/dmvecmattypes' into barry/saws

Needed to work with version of PETSc that did not have constant calls to VecSetFromOptions() etc

Conflicts:
src/ksp/ksp/interface/ams/kspams.c
src/snes/impls/composite/snescomposite.c
src/snes/impls/gs/snesgs.c
src/snes/impls/nasm/nasm.c
src/snes/impls/ngmres/snesngmres.c

show more ...

Merge branch 'master' into knepley/feature-dt-fem

* master: (211 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries

Merge branch 'master' into knepley/feature-dt-fem

* master: (211 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries
Bib: Updates
AO: fix erroneous processing of -ao_view and factor into AOViewFromOptions
doc: fix named argument in {Vec,Mat,DM}ViewFromOptions
Sys: add PetscDataTypeFromString() and test code
Mat: Should say that it has a nullspace in MatView()
parms: update tarball with fix for namespace conflict with metis
fix citation 'Golub_Varga_1961'
parmetis: update tarball to parmetis-4.0.2-p5 which fixes an install issue with cygwin
Sys Logging: revert parent traversal
fixed hdf5.py so that if self.libraries.compression is None the code still runs correctly
DMDA: fix bad cast of DM_DA to PetscObject
MatClique: follow DistMultiVec API changes
MatClique: remove unused variables
config cmakeboot: add C++ flags any time compiler is available
config OpenMP: check for C++ flag any time the compiler is available
replaced all left-over uses of a single PetscMalloc() to allocated multiple arrays: replaced with PetscMallocN() The only ones left are when the second array is set into the first array and one ugly usage in the MUMPS interface that cannot be easily fixed
...

Conflicts:
config/builder.py
src/dm/impls/plex/plexgeometry.c

show more ...

Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (273 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib

Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (273 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries
Bib: Updates
AO: fix erroneous processing of -ao_view and factor into AOViewFromOptions
doc: fix named argument in {Vec,Mat,DM}ViewFromOptions
Sys: add PetscDataTypeFromString() and test code
Mat: Should say that it has a nullspace in MatView()
parms: update tarball with fix for namespace conflict with metis
fix citation 'Golub_Varga_1961'
parmetis: update tarball to parmetis-4.0.2-p5 which fixes an install issue with cygwin
Sys Logging: revert parent traversal
fixed hdf5.py so that if self.libraries.compression is None the code still runs correctly
DMDA: fix bad cast of DM_DA to PetscObject
MatClique: follow DistMultiVec API changes
MatClique: remove unused variables
config cmakeboot: add C++ flags any time compiler is available
config OpenMP: check for C++ flag any time the compiler is available
replaced all left-over uses of a single PetscMalloc() to allocated multiple arrays: replaced with PetscMallocN() The only ones left are when the second array is set into the first array and one ugly usage in the MUMPS interface that cannot be easily fixed
...

Conflicts:
include/petscdmplex.h

show more ...

Merge branch 'master' into knepley/feature-dmda-section

* master: (287 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib e

Merge branch 'master' into knepley/feature-dmda-section

* master: (287 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries
Bib: Updates
AO: fix erroneous processing of -ao_view and factor into AOViewFromOptions
doc: fix named argument in {Vec,Mat,DM}ViewFromOptions
Sys: add PetscDataTypeFromString() and test code
Mat: Should say that it has a nullspace in MatView()
parms: update tarball with fix for namespace conflict with metis
fix citation 'Golub_Varga_1961'
parmetis: update tarball to parmetis-4.0.2-p5 which fixes an install issue with cygwin
Sys Logging: revert parent traversal
fixed hdf5.py so that if self.libraries.compression is None the code still runs correctly
DMDA: fix bad cast of DM_DA to PetscObject
MatClique: follow DistMultiVec API changes
MatClique: remove unused variables
config cmakeboot: add C++ flags any time compiler is available
config OpenMP: check for C++ flag any time the compiler is available
replaced all left-over uses of a single PetscMalloc() to allocated multiple arrays: replaced with PetscMallocN() The only ones left are when the second array is set into the first array and one ugly usage in the MUMPS interface that cannot be easily fixed
...

show more ...

Merge branch 'master' of bitbucket.org:petsc/petsc

Merge branch 'maint'

Documentation and examples from ATPESC 2013 tutorial

* maint:
KSPSetDM docs: fix KSPSetDMActive args, add cross-references
Added shallow water equation mesh (annulus-20.exo

Merge branch 'maint'

Documentation and examples from ATPESC 2013 tutorial

* maint:
KSPSetDM docs: fix KSPSetDMActive args, add cross-references
Added shallow water equation mesh (annulus-20.exo)
cleanup some docs error out if KSPSetDM() is used but not made inactive or DMKSPSetComputeOperators() is not called
docs on KSPSetNullSpace() that KSP auto uses any previously added to the Mat
shallow water examples for tutorial (mesh file annulus-20.exo not included)
tutorials/HandsOnExercise: run jobs with ./ex19; MPICH does not add '.' to path
TS ex11: I believe the default physics is simple advection. I asked Jed to put in shallow water on the annulus. He might be able to do it from Beijing airport.
third case of example 3 had wrong options
handson: update instructions [for ex42]
added <pre> to output files, added text to HandsOnTutorial.html added ex42 example run commands
HandsOn: rename all output files to .html - [to avoid popup on safari]
HandsOn: fix line numbers in URLs to ex*.c.html
added explanation of runs for HandsOnExercises
HandsOn: fix missing html format [from copy/paste]
HandsOn: update some runs
HandsOn: update the run commands
HandsOn: Force Jed to come up with more exciting examples than these
TS ex11: Added shallow water equations
TS ex11: Fixed docs
TS ex11: Added some explanatory text. Need more.
Makefile: Added TS ex11 to EXAMPLESC
Main page: Changed links to petsc-dev website
vis
selected 4 tutorial examples began to cleanup tutorial page introduction on them
added start of Hands on tutorial that works through a few examples bug fix for valgrind broadcasting uninitialized values

show more ...

Merge branch 'karlrupp/august-tutorial-cherry-picked' into maint

Tutorial for ATPESC (http://extremecomputingtraining.anl.gov/)

* karlrupp/august-tutorial-cherry-picked:
Added shallow water equat

Merge branch 'karlrupp/august-tutorial-cherry-picked' into maint

Tutorial for ATPESC (http://extremecomputingtraining.anl.gov/)

* karlrupp/august-tutorial-cherry-picked:
Added shallow water equation mesh (annulus-20.exo)
cleanup some docs error out if KSPSetDM() is used but not made inactive or DMKSPSetComputeOperators() is not called
docs on KSPSetNullSpace() that KSP auto uses any previously added to the Mat
shallow water examples for tutorial (mesh file annulus-20.exo not included)
tutorials/HandsOnExercise: run jobs with ./ex19; MPICH does not add '.' to path
TS ex11: I believe the default physics is simple advection. I asked Jed to put in shallow water on the annulus. He might be able to do it from Beijing airport.
third case of example 3 had wrong options
handson: update instructions [for ex42]
added <pre> to output files, added text to HandsOnTutorial.html added ex42 example run commands
HandsOn: rename all output files to .html - [to avoid popup on safari]
HandsOn: fix line numbers in URLs to ex*.c.html
added explanation of runs for HandsOnExercises
HandsOn: fix missing html format [from copy/paste]
HandsOn: update some runs
HandsOn: update the run commands
HandsOn: Force Jed to come up with more exciting examples than these
TS ex11: Added shallow water equations
TS ex11: Fixed docs
TS ex11: Added some explanatory text. Need more.
Makefile: Added TS ex11 to EXAMPLESC
Main page: Changed links to petsc-dev website
vis
selected 4 tutorial examples began to cleanup tutorial page introduction on them
added start of Hands on tutorial that works through a few examples bug fix for valgrind broadcasting uninitialized values

show more ...

Added shallow water equation mesh (annulus-20.exo)