Added ignore

Merge branch 'scott/test-datafiles-fix' of https://bitbucket.org/petsc/petsc into scott/test-datafiles-fix

Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
ini

Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
initialize ap as complained by the nightly tests
Plex ex3: Update to new point function API
initialize some variables as complained by nightly tests
SNES ex12: Mix misnaming Nf --> Nc
update tests
add tests
add MatView_SeqXAIJ_ASCII_structonly(); enable A->structure_only in MatSetValuesBlocked_SeqBAIJ
typo
fill-in some references
Bib: Fixed ref
Plex: Added PLY to file support
Plex: Adding PLY support
PetscDS: Turn off Fortran bindings for Constants
Plex tests: Updated to new point function API
SNES ex56: Moved tests to new format
DM: Allow field projection functions to take an array of scalars - This will allow us to pass in user data to kernels without void *, more efficiency than aux fields
...

Conflicts:
config/builder.py
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex1.c
src/dm/impls/plex/plexcreate.c
src/dm/impls/plex/plexgmsh.c
src/snes/examples/tutorials/ex63.c

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Merge branch 'master' into stefano_zampini/feature-fetidp-ex69

Merge branch 'knepley/fix-dm-coord-dim'

* knepley/fix-dm-coord-dim:
Ignore generated files
DM: Fix default for coordinate dimension

Merge branch 'knepley/fix-dm-coord-dim' into maint

* knepley/fix-dm-coord-dim:
Ignore generated files
DM: Fix default for coordinate dimension

Ignore generated files

Add Shashi's meth_ethanol mechanism

PETSc TS fails on this, sundials bdf produces unrealistically large final tempature
Commit-type: feature
Funded-by: IMEX
Project: chemistry
Thanks-to: "Aithal, Sh

Add Shashi's meth_ethanol mechanism

PETSc TS fails on this, sundials bdf produces unrealistically large final tempature
Commit-type: feature
Funded-by: IMEX
Project: chemistry
Thanks-to: "Aithal, Shashikant M." <aithal@cels.anl.gov>

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

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes

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

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes
add help menu for MatCreateSubMatricesMPI()
rename struct Mat_SubMat -> Mat_SubSppt
add a little information to the manual about using tchem
rename MatCreateSubMatrixComposite -> MatCreateSubMatrixVirtual; Mat_SubMatrix -> Mat_SubVirtual
need to protect the \ passed on the makefile on my Mac
Bib: Updated ref
update src/mat/examples/tests/output/ex23_#.out
rename MatGetSubMat -> MatCreateSubMat
Mark MatCreateMPIAIJWithSplitArrays() and MatMPIAIJSetPreallocationCSR() with MAT_NO_OFF_PROC_ENTRIES
superlu: libray is installed in PREFIX/lib64 - fix this to use PREFIX/lib
backport fixes cc105cc3 2b35c90a - required for 3bf428d - that was backported from master - 80c96bb
'echo -n' fails on opensolaris/osx - so avoid using it.
fix diffs in nightlybuilds due to options in ~/.petscrc
add Kelley03 to src/docs/tex/petsc.bib
build: determine moudles, mpi.h used during buildtime and print in 'info'
fix analyzer warnings
fix build failure on opensolaris - where -lm from flibs is removed due to -lm in cxxlibs. But then - only flib gets used for some configure tests [blaslapack, parms]
config: prefer __restrict over C99 restrict keyword
...

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Merge branch 'balay/add-prefix-test'

test: add a prefix nightlybuild

- require adding PREFIXDIR variable to petsvariables
- cleanup usage of nPETSC_DIR [becaluse PETSC_DIR can change halfway]
- move code that uses PETSC_ARCH up ahead [

test: add a prefix nightlybuild

- require adding PREFIXDIR variable to petsvariables
- cleanup usage of nPETSC_DIR [becaluse PETSC_DIR can change halfway]
- move code that uses PETSC_ARCH up ahead [as PETSC_ARCH can get reset halfway]
- split up 'make all test' to 'make all install' && 'make test' so that PETSC_DIR can be changed inbetween

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Merge branch 'barry/fortran-update'

gitignore: add ftn-auto-interfaces to ignore list

Merge branch 'master' into barry/add-pcfieldsplit-logevent

Merge branch 'master' into barry/add-pcreset-hypre-for-master

Needed to move PCDestroy_HYPRE() added to master to PCReset_HYPRE() since that was introduced
as a bug fix for maint

Merge branch 'master' into barry-allow-vecset-nan-3.6

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

Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

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

Merge branch 'master' into tisaac/dmforest

Get 3.6.2 patches

* master: (1360 commits)
remove nasty memory leak with CUDA code when using block Jacobi with multiple blocks per process
print abs

Merge branch 'master' into tisaac/dmforest

Get 3.6.2 patches

* master: (1360 commits)
remove nasty memory leak with CUDA code when using block Jacobi with multiple blocks per process
print abs in Fortran test example in order to have same result with real and complex builds
changed outdate mpirun and -np to mpiexec and -n
force sqrt to be taken in the precision of PetscReal in fortran examples
continuation line too soon for some compilers
stop configure if user selected C++ clanguage, single precision, complex combination since we do not support it
fixes for Fortran examples to compile cleanly in single precision that do not involve complex numbers
fixes to Fortran examples to compile cleanly in single precision complex
fix previous mistake
must cast 1. to PetscScalar before dividing by a PetscScalar (C++ complex class is terrible)
must cast 0.0 to PetscScalar before comparison with a PetscScalar
changed order of suggested locations of downloadable PETSc to Barry's preference
Increase patchlevel to 3.6.2
remove debug print statement from two commits before
remove debug print statements I accidently left in the last commit
PetscDraw: Fix dummy definition of PetscDrawCollective{Begin|End}()
remove cleanupMumps flag from MatDestroy_Mumps() it should always free the memory it allocated Bug detected while adding features to libMesh
improved viewing of fractional counts in xml nested log viewing fixed bug in output of doubles to xml nested log files
chombo: build only libs - not examples
fix typo. 'gcc-4.8 --with-cxx-dialect=C++11' gives a warning with this line - even though its in a #ifdef thats never enabled.
...

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To refactor the comments to follow petsc style.

Merge remote-tracking branch 'petsc/master' into fixed-comment-space

Conflicts:
include/petsc/finclude/petscmat.h
src/mat/examples/tests/makefile

To refactor the comments to follow petsc style.

Merge remote-tracking branch 'petsc/master' into fixed-comment-space

Conflicts:
include/petsc/finclude/petscmat.h
src/mat/examples/tests/makefile
src/mat/impls/aij/mpi/mpiov.c

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Merge branch 'pr329/master/Fande-Kong/matpartitioning-hierarch' into pr361/master/Fande-Kong/pcgasm-increaseoverlap: need hierarch to build GASM subdomains.

Conflicts:
src/mat/examples/tests/makefi

Merge branch 'pr329/master/Fande-Kong/matpartitioning-hierarch' into pr361/master/Fande-Kong/pcgasm-increaseoverlap: need hierarch to build GASM subdomains.

Conflicts:
src/mat/examples/tests/makefile
src/mat/impls/aij/mpi/mpiaij.h

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Merge branch 'master' into pr352/dmay/pctelescope/master

Merge branch 'master' into pr358/buptphyphy/addmatcreatenormalhermitian/master

Merge branch 'master' into tisaac/plex-feature-tree-fv

Merge in Barry's fix to synchonized print out of plex objects into
updated output files.

* master: (31 commits)
fix %nd for plex printf that

Merge branch 'master' into tisaac/plex-feature-tree-fv

Merge in Barry's fix to synchonized print out of plex objects into
updated output files.

* master: (31 commits)
fix %nd for plex printf that should be %nD
PGI compiler requires cast to char* of this array for some reason
Incorrect use of %d for %D in viewing of PetscSection
update output for suitesparse examples with new KSP view data
changed boomeramg advanced smoother output files to use short format so there are less differences with different systems
fix some issues with PetscViewerFlush() and PetscViewerASCIIPushSynchronized() within the plex object viewing
incorrectly used stride value instead of local size in check that ISSTRIDE has same layout as columns of matrix
try using int(w) for Fortran case to integer instead of int(w,integer) since the latter failed on most systems claiming integer was not a constant. Very unclear to me what that second argument is suppose to be
SNES function evaluations were not counted for certain Jacobian computations
nightlybuilds: fix vec/ex7,ex7f link issue by using the correct LIBS option
nightlybuilds: move location of petsc.clone(s) on bb44 from nfs to /sandbox
nightlybuilds: arch-linux-complex-gcov -> arch-linux-cmplx-gcov to be consistant with other config tests
add __float128 data file neeed by test example 10 otherwise test example crashes with --with-precision=__float128 builds
cast fortran integer that may be 64bit with int() to prevent compiler warning about Warning: Possible change of value in conversion from INTEGER(8) to INTEGER(4) at (1)
removed unneeded definition of Sqr in example since PetscSqr should be used, and was in other parts of the same example!
nightlybuilds: run 'git gc' in the build clones
opensolaris: use 'FFLAGS=-ftrap=%none' this way fortran examples on solaris do not crash in lapack during 'div by zero' Also use the updated path to mpich
when I swapped the role of coulping and rest in fieldsplit I missed a place
cannot use PetscMalloc2() on arrays that will be freed as two seperate arrays
C++ cannot handle [PETSC_RESTRICT]
...

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Merge branch 'master' into mark/eigen-rand