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

Generate an error if the PETSC_DIR or prefix path has spaces in it

Reported-by: Robert Burry <robertburryxa@gmail.com>

Print clear completion message if PETSc is installed by ./configure

Funded-by: IDEAS
Project: xSDK
Time: 0 hours

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

Merge branch 'master' into barry/fix-private-functions

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

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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

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Merge branch 'barry/fixes-for-release-1'

Added configure option --with-viewfromoptions=0 which will speed up code with many small solves
substantially

Reported-by: Amneet Pal S Bhalla <amneetb@live.unc.edu>

Merge branch 'master' into barry/add-pcfieldsplit-logevent

Merge branch 'knepley/fix-configure-relative-installdir'

Merge branch 'master' into tisaac/dmforest

* master: (87 commits)
fixed --download-xxx=/directory to not mistake other options such as --download-mpich-pm=hydra etc
Correct spelling for Autotool

Merge branch 'master' into tisaac/dmforest

* master: (87 commits)
fixed --download-xxx=/directory to not mistake other options such as --download-mpich-pm=hydra etc
Correct spelling for Autotools libtoolize in commit a0848688a08a6eb150afdc95a2f6ce49cd4cd079
Fix for commit c8b462efbd8e8a5f06df500cf417f3a48f2b88d9 Put back the gitpreReq() check that was needed for MOAB
website: fix Fluidity link
bib/cite: add UMFPACK
nightlybuilds: update test tu use newer intel compiler [detect and use compiler path]
nightlybuilds: fix vec/ex7,ex7f link issue by using the correct LIBS option
Added support for users to provide their own download package installers --download-xxx=/directory where the directory contains the file xxx.py that is a standard PETSc package definition like in config/BuildSystem/config/packages/xxx.py
nightlybuilds: switch default intel compiler [& MKL] from 13.1.3 to 16.0.0.
mkl_pardiso: fix runex125_mkl_pardiso
mkl_pardiso: fix runex2_mkl_pardiso_cholesky
nightlybuilds: switch OSX to use boost from brew [as --download-boost is broken]
trilinos: gitcommit - always specify branch as origin/branch
Add error check to boost.py when running on Mac OS because the shared libraries created do not work since they do not have the proper rpath set
Update output files for mpi matrices that use to be seq
Move PostProcess() runs until after PETSc configure has saved all data to the filesystem so that make install will work correctly.
Switch to Trilinos release candidate for --download-trilinos Tested, failed with unresolved Kokos methods, Issue report to Trilinos team
Some configure packages UnitTest-CPP requires libtoolize to be called before autoreconf on some systems
--download-ideas now downloads unittest-cpp
simplied ./configure packages that need autoreconf to be run first (like moab and unittest-cpp) added unittest-ccp download changed downloadfilename to downloaddirname since that is what it is
...

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

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Merge branch 'barry/downloads'

fixed --download-xxx=/directory to not mistake other options such as --download-mpich-pm=hydra etc

Funded-by: IDEAS
Project: xSDK
Reported-by: nightly tests

Merge branch 'barry/downloads'

Configure: Should use installdir rather than --prefix

Added support for users to provide their own download package installers
--download-xxx=/directory where the directory contains the file xxx.py that
is a standard PETSc package definition like in

Added support for users to provide their own download package installers
--download-xxx=/directory where the directory contains the file xxx.py that
is a standard PETSc package definition like in config/BuildSystem/config/packages/xxx.py

Funded-by: IDEAS
Project: xSDK
Time: .7 hours
Thanks-to: Ethan Coon <ecoon@lanl.gov>

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Merge branch 'barry/downloads'

Move PostProcess() runs until after PETSc configure has saved all data to the filesystem
so that make install will work correctly.

Funded-by: IDEAS
Project: xSDK
Time: .05 hours

Merge branch 'barry/downloads'

Merge branch 'master' into barry/downloads

Merge branch 'maint'

install: fix RDict.db error duing 'make install'

Patch-from: Matthew Knepley <knepley@gmail.com>
Reported-by: Torquil Macdonald Sørensen <torquil@gmail.com>
Reported-by: "Klinvex, Alicia Marie" <amk

install: fix RDict.db error duing 'make install'

Patch-from: Matthew Knepley <knepley@gmail.com>
Reported-by: Torquil Macdonald Sørensen <torquil@gmail.com>
Reported-by: "Klinvex, Alicia Marie" <amklinv@sandia.gov>

*** Using PETSC_DIR=/home/amklinv/PETScDir/petsc PETSC_ARCH=arch-linux2-cxx-debug ***
No cached configure in RDict at arch-linux2-cxx-debug/lib/petsc/conf/RDict.db
Traceback (most recent call last):
File "./config/install.py", line 380, in <module>
Installer(sys.argv[1:]).run()
File "./config/install.py", line 373, in run
self.runsetup()
File "./config/install.py", line 334, in runsetup
self.setup()
File "./config/install.py", line 60, in setup
self.setupModules()
File "./config/install.py", line 51, in setupModules
self.setCompilers = self.framework.require('config.setCompilers', None)
AttributeError: 'NoneType' object has no attribute 'require'
make: *** [install] Error 1

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Merge branch 'tisaac/dmforest' of bitbucket.org:petsc/petsc into tisaac/dmforest

Merge branch 'master' into tisaac/dmforest

* master: (136 commits)
Make error message specific to exactly what matrix is supported
Prevent fblaslapack or f2cblaslapack from being compiled with t

Merge branch 'master' into tisaac/dmforest

* master: (136 commits)
Make error message specific to exactly what matrix is supported
Prevent fblaslapack or f2cblaslapack from being compiled with the -no-prec-dev Intel compiler option since it can produce incorrect results
Fix for PCReset_HYPRE to make it reentrant.
replace default superlu_dist '-mat_superlu_dist_colperm METIS_AT_PLUS_A' with MMD_ATA to avoid different random numbers for nightly tests
fixes for merge from maint patch
Added PCReset_HYPRE() so it may be used with SNESVI solvers
remove Microsoft compiler message for paste macros used for handling Blas/Lapack macro name mangling for example
Increase the number of PetscViewerPushFormat() possible to 25 and use a macro PETSCVIEWERFORMATPUSHESMAX for the value
Configure: Remove redundant logging
Bib: Added ref
nightlybuids: fix permissions of script
MatRegisterDestroy() does not exist but it is listed in manual pages
externalpackages-git: save local changes if any - in git stash - before 'git checkout -f' Useful incase --with-package-commit=HEAD option was msissing [perhaps due to a typo]
nightlybuilds: add xsdk builds
Add architectures for testing xsdk package downloads (Trilinos, Hypre, SuperLU)
create another version of TurnForward() for adaptive time stepping specifically
Configure: Give proper default if HOME is missing from the environment
fix abbreviation
allow zeropivot for MatSOR_SeqAIJ_Inode, node size=1
add test case using adpative time stepping for checkpointing type 'NONE'
...

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