Merge branch 'master' into stefano_zampini/pcbddc-adaptive-selection

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.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 'tisaac/simplify-register-all'

Removed the XXXRegisterAll() functions from the public interface. These should now only be handled by the package intialization functions.

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

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

Merge branch 'master' into stefano_zampini/pcbddc-adaptive-selection

Merge branch 'barry/experiment'

updated new XXXSetFromOptions_YYY() methods to take PetscOptionsObjectType

Merge branch 'master' into barry/ksp-converged-reason-viewer

Conflicts:
src/sys/objects/options.c

Merge branch 'barry/fix-damp-not-one-pcapplyrichardson'

-ksp_richardson_scale was ignored when PCApplyRichardson() was used
Fix: turn off PCApplyRichardson() when scale is not 1 and print PetscInfo warning

Reported-by: Mark Adams <mfadams@lbl.gov>

Fixed

-ksp_richardson_scale was ignored when PCApplyRichardson() was used
Fix: turn off PCApplyRichardson() when scale is not 1 and print PetscInfo warning

Reported-by: Mark Adams <mfadams@lbl.gov>

Fixed missing carriage return in uses of PetscInfo() and missing ierr CHKERRQ() usage

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Remove XXXRegisterAllCalled from public interface.

All XXXRegisterAll() methods are now idempotent, so a boolean indicating
whether they can be called or not is no longer necessary.

Merge branch 'master' into mlange/refactor-plex-distribute

Conflicts:
src/dm/impls/plex/examples/tests/output/ex12_1.out
src/dm/impls/plex/examples/tests/output/ex12_2.out

Merge branch 'maint'

Conflicts:
config/BuildSystem/config/packages/ml.py
src/ksp/pc/impls/mg/mg.c

fix formatting of some manual pages
specifically remove use of $ from the middle of parameter or options lists

Merge branch 'barry/fix-options-default'

Conflicts:
src/ksp/ksp/examples/tutorials/ex52.c

update use of PetscOptionsBool() to not rely on default setting automatically

cleanup of use of PetscOptionsInt and friends including use of flag final argument

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 'tisaac/feature-fe-geom-dim' into tisaac/plex-flexible-projection

Use the new PetscFECellGeom

Conflicts:
include/petscdmplex.h
include/petscfe.h
src/dm/impls/plex/plexfem.c

Merge branch 'master' of bitbucket.org:petsc/petsc into mark/ex49-bs

clarify documention on ksp count in history

tao->ksp_its is per iteration, tao->ksp_tot_its is per solve

Merge branch 'adam_qc/add-taogetcurrentfunctionevaluations' of /home/sarich/petsc-remotes into adam_qc/add-taogetcurrentfunctionevaluations

Merge branch 'sarich/tao-add-fortran-stubs'

Merge branch 'sarich/tao-history-store-ksp-its'