Add support to SNESTestJacobian() for viewing the matrices with any standard viewer

Commit-type: feature

Refactor SNESTestJacobian() to display norms of differences first, display both Jacobian and Jacobian for preconditioner

Commit-type: feature

Remove link to nonexistent manual page; comment on routines that don't need manual pages

Commit-type: documentation

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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Man pages: capitalize "notes:" to "Notes:"

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

find src include -type f \( -name "*.h" -or -name "*.c" \) | xargs gsed -i 's/no

Man pages: capitalize "notes:" to "Notes:"

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

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

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Merge branch 'master' into knepley/feature-pc-patch

* master: (440 commits)
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html
release: set v3.9 strings
fix grep us

Merge branch 'master' into knepley/feature-pc-patch

* master: (440 commits)
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html
release: set v3.9 strings
fix grep usage on solaris [use egrep]
opensolaris: fix errors
Update timer reporting and minor reporting fix
Remove redundant if statement. Found by @jedbrown
Fixed problem with order of developer photos on website.
superlu_dist: use correct flag in example [PETSC_HAVE_SUPERLU -> PETSC_HAVE_SUPERLU_DIST]
Bib: PERMON ref
fix for osx
doc: more author fixes
doc: more author fixes
Italicized "orderings" in MPI process placement discussion.
Added Richard to the user manual author list.
Added Richard to the list of active developers on the website.
add string check for MS-MPI and IMPI timeout errors
opensolaris does not have multiple grep utils - but default one does not support -F. So use fgrep instead
Standardizing timeout checks
Report wall clock time of total tests
Use time instead of date %s
...

Conflicts:
include/petscpc.h
src/ksp/ksp/interface/itfunc.c

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SNES: Add nullspace to automatically constructed matrices
- This supports convergence determination

Deprecate DMSet/GetDefaultSection() for DMSet/GetSection()

Revert manual page change per Matt's preference

Commit-type: style-fix
Thanks-to: Matthew Knepley

ConvEst: Now estimate rates for each field
- Option -num_refine --> -convest_num_refine
- Added -convest_monitor

Merge remote-tracking branch 'origin/jed/fix-analyzer-bugs'

PetscAbsScalar(threshold) is called for a PetscReal variable (in snes.c:2362).

You can see the details here:
http://slepc.upv.es/buildbot/builders/linux-clang-c-complex-valgrind/builds/290

Commit-t

PetscAbsScalar(threshold) is called for a PetscReal variable (in snes.c:2362).

You can see the details here:
http://slepc.upv.es/buildbot/builders/linux-clang-c-complex-valgrind/builds/290

Commit-type: bug-fix, portability-fix
Reported-by: Jose E. Roman <jroman@dsic.upv.es>

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Merged in dalcinl/fix-info-log-exclude (pull request #914)

Consistent handling of command line options -info_exclude and -log_exclude

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

Consistent handling of command line options -info_exclude and -log_exclude

double ;; typo

Commit-type: portability-fix
Reported-by: nightly tests

Move logic from -snes_type test to be called instead with each computation of the Jacobian

Introduces the options -snes_test_jacobian -snes_test_jacobian_display -snes_test_jacobian_display_threshol

Move logic from -snes_type test to be called instead with each computation of the Jacobian

Introduces the options -snes_test_jacobian -snes_test_jacobian_display -snes_test_jacobian_display_threshold

Note that this ignores Jed's code that checks the Jacobian at each computation of the Jacobian because
I don't like it.

Commit-type: feature

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Merge branch 'denera/fix-tablevels-for-views' [PR #869]

* denera/fix-tablevels-for-views:
Instead of manual push-pop tab operations, views now inherit tablevels automatically.
This makes views consi

Merge branch 'denera/fix-tablevels-for-views' [PR #869]

* denera/fix-tablevels-for-views:
Instead of manual push-pop tab operations, views now inherit tablevels automatically.
This makes views consistent with default convergence monitors.

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Fix some minor/semantic bugs identified by clang analyzer

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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