Merge branch 'maint'

fix help manual of MatCreateSubmatrices()
Reported-by: Tim Steinhoff <kandanovian@gmail.com>

Man pages: add newlines after "Notes:"

This allows for proper formatting from sowing.

On OS X (using gsed, not the default BSD sed), from the PETSc root directory:

find src include -type f \(

Man pages: add newlines after "Notes:"

This allows for proper formatting from sowing.

On OS X (using gsed, not the default BSD sed), from the PETSc root directory:

find src include -type f \( -name "*.c" -or -name "*.h" -or -name "*.cxx" \) | xargs gsed -i 's/Notes\s*:\s*\(\w.*\)/Notes:\n \1/'

This adds a newline and 4 spaces whenever "Notes:" is followed by any "word" character, in any .c, .h, or .cxx file in src/ or include/

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Add MatGetOperation() and fixes to MATSHELL

Consistent handling of command line options -info_exclude and -log_exclude

Merge branch 'karlrupp/feature-remove-cusp'

* karlrupp/feature-remove-cusp:
Removes VECCUSP vectors and AIJCUSP matrices, because they provide no added benefit over VECCUDA and AIJCUSPARSE.
Also rem

Merge branch 'karlrupp/feature-remove-cusp'

* karlrupp/feature-remove-cusp:
Removes VECCUSP vectors and AIJCUSP matrices, because they provide no added benefit over VECCUDA and AIJCUSPARSE.
Also removes the CUSP-based preconditioners for now.
SACUSP will be re-added later, after the new release is out.

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GPUs: Allow ViennaCL and VECCUDA to be used concurrently.

This also gets rid of the weird veccuda.py.

Merge branch 'stefano_zampini/fix-matis-dmda-l2g'

CUSP: Removed VECCUSP and AIJCUSP as well as preconditioners.

SA-AMG from CUSP will be re-added in a follow-up commit,
made to work with AIJCUSPARSE and VECCUDA.

Merge branch 'pr838/haplav/haplav/feature-petscpartitionermatpartitioning-rb/master'

* pr838/haplav/haplav/feature-petscpartitionermatpartitioning-rb/master:
Implemented wrapper of MatPartitioning i

Merge branch 'pr838/haplav/haplav/feature-petscpartitionermatpartitioning-rb/master'

* pr838/haplav/haplav/feature-petscpartitionermatpartitioning-rb/master:
Implemented wrapper of MatPartitioning into PetscPartitioner.

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Merge branch 'stefano_zampini/feature-factor-sell' [PR #860]

* stefano_zampini/feature-factor-sell:
This branch adds LU factorization support to MATSEQSELL via MUMPS and SuperLU.

Change PetscStrncat() to PetscStrlcat() to match BSD API where l represents total length

Update many uses of PetscStrcpy() and PetscStrcat() to the safer PetscStrncpy() and PetscStrlcat()

Commit-ty

Change PetscStrncat() to PetscStrlcat() to match BSD API where l represents total length

Update many uses of PetscStrcpy() and PetscStrcat() to the safer PetscStrncpy() and PetscStrlcat()

Commit-type: style-fix, feature
Thanks-to: Jed Brown

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get rid of unneeded PC_ApplyOnMproc, fix manual page for parallel blocks for PCBJACOBI

Commit-type: style-fix, documentation

Mat: relax the erroring condition

if a matrix is hermitian and symmetric then the imaginary part is zero

Begin refactorization of MatShell to make the code more straightforward and extensible

Introduce MatSetOperation() for changing operations on non-MATSHELLs
Introduce two modes for MATSHELL
1) MAT

Begin refactorization of MatShell to make the code more straightforward and extensible

Introduce MatSetOperation() for changing operations on non-MATSHELLs
Introduce two modes for MATSHELL
1) MATSHELL manages scalings and shifts automatically
2) Creator of MATSHELL can provide their own code for managing scaling and shifts
This is used by MatCreateADA() and MatCreateSubMatrixFree()

The extensibility is so that a MatShell can be easily used in as many places as possible as other matrices,
for example,

/* A = diag(u) G */
ierr = MatCopy(appctx->SEMop.grad,A,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatDiagonalScale(A,globalin,NULL);CHKERRQ(ierr);
/* A = A + diag(Gu) */
ierr = VecDuplicate(globalin,&Gglobalin);CHKERRQ(ierr);
ierr = MatMult(appctx->SEMop.grad,globalin,Gglobalin);CHKERRQ(ierr);
ierr = MatDiagonalSet(A,Gglobalin,ADD_VALUES);CHKERRQ(ierr);
ierr = VecDestroy(&Gglobalin);CHKERRQ(ierr);
/* A = K - A */
ierr = MatScale(A,-1.0);CHKERRQ(ierr);
ierr = MatAXPY(A,1.0,appctx->SEMop.keptstiff,SAME_NONZERO_PATTERN);

Commit-type: feature

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cosmetic fixes

Merge branch 'maint'

fix location of checking of format

Commit-type: bug-fix

Present load balance information for Mat in PETSc ordering not natural ordering

Commit-type: bug-fix

Updates for viewing Load Balance information

Don't display for sequential objects. Label all values with "Load Balance"
Want to display load balance for petsc ordering for vectors, not using natural

Updates for viewing Load Balance information

Don't display for sequential objects. Label all values with "Load Balance"
Want to display load balance for petsc ordering for vectors, not using natural ordering

Commit-type: feature

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fix matlufactorsymbolic_()


not ok mat_tests-ex126f_2
# ==30264== Invalid read of size 4
# ==30264== at 0x59C46A0: MatLUFactorSymbolic (matrix.c:3033)
# ==30264== by 0x5A31CC

fix matlufactorsymbolic_()


not ok mat_tests-ex126f_2
# ==30264== Invalid read of size 4
# ==30264== at 0x59C46A0: MatLUFactorSymbolic (matrix.c:3033)
# ==30264== by 0x5A31CC6: matlufactorsymbolic_ (zmatrixf.c:751)
# ==30264== by 0x40C6CC: MAIN__ (ex126f.F:91)
# ==30264== by 0x40C8E9: main (ex126f.F:8)
# ==30264== Address 0xffffffffffffffff is not stack'd, malloc'd or (recently) free'd

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Merge branch 'maint'

* maint:
PetscCheckPointerSetIntensity(): document -check_pointer_intensity
MatGetRowIJ man page: minor cleanup

MatGetRowIJ man page: minor cleanup

Fix doc typo and add formula for MatMultTranspose

Merge branch 'barry/fix-matdensegetarray'