Merged petsc/petsc into master

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

PetscDraw: API and implementation refactoring

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

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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 shri/add-tsevent-to-powergrid-examples

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

Merge branch 'master' into barry/always-mark-floats

Needed to merge in master to resolve conflicts that will appear when this branch is merged with 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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Merged in dalcinl/petscdraw (pull request #370)

PetscDraw: Various improvements

* Enhancements to PetscDrawLG/SP/HG/Bar
* Add PetscDrawCollectiveBegin/End() to handle X11 I/O errors in parallel
* Update test examples to run in parallel using PETS

PetscDraw: Various improvements

* Enhancements to PetscDrawLG/SP/HG/Bar
* Add PetscDrawCollectiveBegin/End() to handle X11 I/O errors in parallel
* Update test examples to run in parallel using PETSC_COMM_WORLD
* Enhancements to X11 PetscDraw implementation

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Merge branch 'barry/fix-nonew-notcollective/maint' into jed/mat-assembly-perf

Jed this fucking 6+ month running thing in next that is not in master is a royal fucking pain in the ass and
an abuse of

Merge branch 'barry/fix-nonew-notcollective/maint' into jed/mat-assembly-perf

Jed this fucking 6+ month running thing in next that is not in master is a royal fucking pain in the ass and
an abuse of git. I think it is not justified to ever have anything in next for more than a few weeks at most.
Either take it out of next if it is broken or put it in master if it is not broken. Hanging around in next but
not master for ever is not a good policy.

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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
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Conflicts:
config/builder.py

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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 jed/chem
Note merging a branch with good stuff in it for a year and a half is insane!

Conflicts:
src/ts/examples/tutorials/makefile
src/ts/interface/ts.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c
src/sys/threadcomm/interface/threadcomm.c

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Merge branch 'master' into pr252/dmay/PetscViewerBinarySkipHeaderVecViewLoad
Manual merge of makefile

Conflicts:
src/sys/classes/viewer/examples/tutorials/makefile

Merge branch 'master' into knepley/fix-configure-petsc-dep

* master: (210 commits)
error out on special cases where DMLocalToGlobal_DA won't work
remove unneed uses of local DM vectors and DMLoc

Merge branch 'master' into knepley/fix-configure-petsc-dep

* master: (210 commits)
error out on special cases where DMLocalToGlobal_DA won't work
remove unneed uses of local DM vectors and DMLocalToGlobalBegin/End in examples removed to prevent cut and paste repeats of their use
openmpi: update to version 1.8.3
added more movies and pubs
more movies
MatGetDiagonalBlock() can be called before matrix is assembled
added a couple more movies/images
PetscLogEventGetId() was missing public prototype
simply output from make streams benchmark test
c2html: fixup so that C2HTML make variable is set [similar to cmake.py]
chaco: current blas test does'nt work with Cray CC [which automatically links with blas] and linux - where -lm needs to be listed explicitly. Switch the test to check if we are using PETSc modifled chaco
builddist: always install c2html/sowing
argonne logo for users manual cover
Remove PETSC_HAVE_CUSP_SMOOTHED_AGGREGATION, use PETSC_HAVE_CUSP instead.
mpich: use older tarball with cygwin/gnu compilers
updated information about packages PETSc can use in users manual
Updated users manual to latest ANL Report format requirements
mpich: update to mpich-3.1.3.tar.gz - remove -download-mpich-mpe [mpich no longer packages mpe] - remove -download-mpich-shared. It was added as a split from --with-mpi-shared to --known-mpi-shared and --download-mpich-shared in 50237a55163f90ac7341b723c6422dfa1dbce792 removing this gives back the control of shared=0/1 to package.py - remove download_solaris as the new tarball works with both gcov and on solaris - remove MPICHInstall() [and use GNUPackage.Install()] as the new tarball fixes 'make clean' requiring sudo
added more images and PETSc pubs
Doc: More refs
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Merge branch 'barry/add-snes-monitor-ksp'

added graphics monitor of nonlinear residual during linear solve

Merge branch 'master' into stefano_zampini/pcbddc-multilevel-improvement

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bdd

Merge branch 'master' into stefano_zampini/pcbddc-multilevel-improvement

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddcprivate.c

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Merge branch 'master' into shri/ts-events

Conflicts:
src/ts/interface/ts.c