Merge branch 'master' into knepley/feature-plex-handle-func-failure

* master: (378 commits)
SNES ex5: Fix coordinate determination for empty subdomains
fixed petsc.bib entry
p4est: fix syntax

Merge branch 'master' into knepley/feature-plex-handle-func-failure

* master: (378 commits)
SNES ex5: Fix coordinate determination for empty subdomains
fixed petsc.bib entry
p4est: fix syntax error with error message
SNES ex5: Correct Jacobian handling on patches
SNES ex5: Stupid complex fixes
DMP4est: fix transfer of labels to parents
petsc4py: update to latest snapshot. Fixes da example breakage in petsc4py test suite
Plex: Correct setting of options on refined or coarsened meshes
Plex: Add info for grid hashing
Plex: Add logging in interpolator creation
Plex: Correct use of tabs in ASCII viewer
DM: Shorten long event name
Plex ex12: Create boundary label automatically at all levels of mesh hierarchy
Plex ex12: Change PetscViewerSetFormat --> PetscViewerPushFormat - Fix order of SetMode and SetFilename
Plex ex12: Change all functions to static
Since DMDA with periodic boundary conditions does support P0 interpolation remove checks that error out under those conditions
ascem-io.py and amanzi.py need to handle self.hdf5.include being None correctly
fix MPI Uni to recycle communicators so it won't run out like with the petsc4py tests also fix check for location of python shared library on mac to check all cases each time
Switch back to Sherry's version since she accepted by pull request
PetscDraw: Update help messages for -draw_save* options
...

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

show more ...

PetscDraw X11: Fix coordinate computations and off-by-one-pixel issues

* User coordinates in range [xl,yl]x[xr,yr] map to pixels [0,w-1]x[0,h-1]
* Simplify PetscDrawString_X()
* Simplify and fix off

PetscDraw X11: Fix coordinate computations and off-by-one-pixel issues

* User coordinates in range [xl,yl]x[xr,yr] map to pixels [0,w-1]x[0,h-1]
* Simplify PetscDrawString_X()
* Simplify and fix offsets in PetscDrawStringVertical_X()
* Fix box computation for calls to XFillRectangle()
* Implement drawing of arrow tips for horizontal arrows

show more ...

PetscDraw: Move handling of save on clear/flush to interface level

Merged petsc/petsc into master

Merged in dalcinl/draw-save (pull request #420)

PetscDraw: Reimplement save image/movie

PetscDraw X11: Fix for getting windows position relative to root windows

PetscDraw: Save PNG/GIF/JPG/PPM images

* Built-in support for writing PPM images.
* Support for writing PNG images (requires libpng)
* Support for writing GIF images (requires giflib)
* Support for

PetscDraw: Save PNG/GIF/JPG/PPM images

* Built-in support for writing PPM images.
* Support for writing PNG images (requires libpng)
* Support for writing GIF images (requires giflib)
* Support for writing JPG images (requires libjpeg)
* Get rid of AfterImage (dated, not std, problematic to build)
* Move most of the saving business to PetscDraw interface
* Add a draw->ops->getimage() slot to implement in draw subtypes
* Allow users choose the movie extension (defaults to .m4v)
* Fix movie generation with ffmpeg for non-animated GIF input

show more ...

Merge remote-tracking branch 'origin/knepley/fix-plex-hdf5-label' into tisaac/dmforest

* origin/knepley/fix-plex-hdf5-label: (50 commits)
Plex: Fixed HDF5 output for DMLabel - The ISAllGather() wa

Merge remote-tracking branch 'origin/knepley/fix-plex-hdf5-label' into tisaac/dmforest

* origin/knepley/fix-plex-hdf5-label: (50 commits)
Plex: Fixed HDF5 output for DMLabel - The ISAllGather() was being called with an IS that had COMM_SELF - Also, we needed to protect for empty index arrays
superlu_dist: install target should first make sure prefix/[include,lib] dirs exist - similar to superlu
dm: add DMRemoveLabel() fortran interface
nightlybuilds: allocate more time to run arch-linux-xsdk-dbg build...
Remove superfluous information messages
Cannot have rank 1 print before parallel print since it may end up before or after the print from process 0. There change to have rank 0 print the sequential matrix
Bib: Added ref
Plex: Update ex12_5 with correct level-2 overlap
DMLabel: Add missing cleanup for DMLabelGather()
mpiuni: check for "long_long" before checking for "__int64" [as "typedef __int64" gives error with icc] Note: cannot use 'int64_t' as 'typedef unsigned int64_t foo' gives eror with icc
Add filter for solaris linker scope warning to master since that is used in nightly tests of next
Previous commit did not correctly handle downloading from --with-packages-dir
Use special error code of 10 for output list of needed downloaded package tarballs otherwise the outer configure.py script converts the error code to an error message we do not want.
Have ./configure return a nonzero exit code when --with-packages-dir detects missing packages so that calling scripts know this is occurred simplify some code
Completed support for --with-packages-dir=directory that allows --download-xxx features to be cleanly used behind firewalls etc also updated to docs to indicate this new feature
Adding supporting for --download-xxx to reported needed downloads when off line or behind a firewall and using local copies when available with the --with-packages-dir=directory option
Fix typos in linesearch impls:armijo, morethuente, owarmijo.
PetscDraw: Explicitly save draw in KSP/SNES/TS monitors
PetscViewerDraw: Propagate prefix from viewer to draw contexts
PetscDraw: Explicitly save draw in {Vec|Mat|DMDA}View() routines
...

show more ...

Merge branch 'tisaac/dmforest' into mlange/fix-plex-multi-level-overlap

Merged in dalcinl/fix-draw (pull request #418)

PetscDraw: API and implementation refactoring

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

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

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

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcgraph.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcscalingbasic.c
src/ksp/pc/impls/bddc/bddcschurs.c
src/mat/impls/is/matis.c

show more ...

PetscDraw: Preliminary work to fix the saving business

PetscDraw: Add PetscDrawGetWindowSize() and X11 fixes

* Update ex6 to use PetscDrawZoom() and PetscDrawGetWindowSize()
* X11: Fix PetscDrawResizeWindow() to handle windows and pixmaps
* X11: Rework

PetscDraw: Add PetscDrawGetWindowSize() and X11 fixes

* Update ex6 to use PetscDrawZoom() and PetscDrawGetWindowSize()
* X11: Fix PetscDrawResizeWindow() to handle windows and pixmaps
* X11: Rework window resize check for PetscDrawGetMouseButton()
* X11: Turn off event notifications after X window is mapped

show more ...

PetscDraw: Fixes for singleton draw and popup handling

PetscDraw X11: Native support for writing binary PPM files

PetscDraw X11: Refactor implementation

* Add prototypes for PetscDrawXiXXX() routines in ximpl.h
* Add utility routine to handle pixmap creation/update
* Rework PetscDrawGetMouseButton_X()
* Fix man

PetscDraw X11: Refactor implementation

* Add prototypes for PetscDrawXiXXX() routines in ximpl.h
* Add utility routine to handle pixmap creation/update
* Rework PetscDrawGetMouseButton_X()
* Fix mangling and remove unused routines

show more ...

PetscDraw: Huge API refactoring

* Make PetscDraw{Clear|Flush}() routines collective functions and remove
now redundant PetscDrawSyncronized{Clear|Flush}() routines
* Make PetscDrawSave() collectiv

PetscDraw: Huge API refactoring

* Make PetscDraw{Clear|Flush}() routines collective functions and remove
now redundant PetscDrawSyncronized{Clear|Flush}() routines
* Make PetscDrawSave() collective.
* Make PetscDrawSetTitle() collective.
* Update PetscDraw{Axis|SP|HG|Bar}, make most PetscDrawXXXSetYYY()
routines either collective or logically collective
* Update PetscViewerDraw accordingly
* Update VecView_XXX_Draw[_DA_YYY]() and DMView_DA_XXX() accordingly

show more ...

Merge remote-tracking branch 'origin/knepley/fix-plex-test-partitions' into tisaac/dmforest

* origin/knepley/fix-plex-test-partitions: (151 commits)
Plex ex5: Provide test partitions
Plex ex4: P

Merge remote-tracking branch 'origin/knepley/fix-plex-test-partitions' into tisaac/dmforest

* origin/knepley/fix-plex-test-partitions: (151 commits)
Plex ex5: Provide test partitions
Plex ex4: Provide test partitions
Configure: I really hate exceptions - We should rewrite this to eliminate all exceptions in favor of return codes
Configure: I hate exceptions
fix typo for 'runex19_superlu_dist_2'
Fix for freeing just what needs to be free when SuperLU_Dist factorizations reused
Updated to latest hypre pre-release with fixes for handling blas/lapack libraries
Switch back to petsc fork of SuperLU_Dist that turns of use of findMPI
PCFactorSetUpMatSolverPackage() should not crash but instead produce a useful error message if called before it is in the proper state.
Clarify that SNESGetLinearSolveIterations() does not include failed iterations.
User reported issues with downloading boost using the previous URL but not this one
Configure: Small change to log order
MatFDColoringSetUp_MPIXAIJ: fix broken initialization of colmap
Bib: Missing comma
add support for binary viewer for -ts_monitor that records time at each timestep
superlu_dist: set MPI_C_COMPILER etc options - so that superlu_dist cmake does not look for a different/incompatible mpi compiler. [and its CFLAGS].
remove reference to VecGetValuesBlocked() and VecGetValuesLocal() from manual page since they do not exist.
Stop configure if user builds with threadsafety and debugging on
Added configure option --with-viewfromoptions=0 which will speed up code with many small solves substantially
Only generate list of all PetscFunctionLists generated in debug mode since in some circumstances where many objects are created searching this list is very slow.
...

Conflicts:
src/ts/examples/tutorials/ex11.c

show more ...

Merged in dalcinl/draw-colormap (pull request #414)

Draw Colormap and other fixes and enhancements

Rename local variable name conflicting with C++ keyword

PetscDraw X11: Fix handling of popup windows

* Set prefix "popup_" in the popup object
* Do not open popup when when parent is using -draw_virtual
* Prevent singleton subdraws from opening popups

PetscDraw X11: Assorted cleanups

PetscDraw X11: Better implementation of option -draw_virtual

* Option -draw_virtual do not open windows, just creates a pixmap
* Rework initialization and setup of the PetscDraw_X structure
* Better

PetscDraw X11: Better implementation of option -draw_virtual

* Option -draw_virtual do not open windows, just creates a pixmap
* Rework initialization and setup of the PetscDraw_X structure
* Better sync of window coordinates and sizes
* Support -draw_size w,h with w,h in pixels (requires w,h > 1.0)
* Option -geometry x,y,w,h no supports negative x,y (wrap around)

show more ...

PetscDraw: Remove PetscDrawSynchronizedGetMouseButton()

* Make PetscDrawGetMouseButton() collective
* Fix PetscDrawPause_{X|OpenGL) accordingly
* Remove now unnecesary window resize checks in PetscD

PetscDraw: Remove PetscDrawSynchronizedGetMouseButton()

* Make PetscDrawGetMouseButton() collective
* Fix PetscDrawPause_{X|OpenGL) accordingly
* Remove now unnecesary window resize checks in PetscDrawZoom()

show more ...

PetscDraw X11: Fix PetscDrawGetMouseButton() when window size changes