Merge branch 'barry/list-downloads'

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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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.

Funded-by: IDEA

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.

Funded-by: IDEAS
Project: xSDK
Time: .1 hour

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

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'

--download-ideas now downloads unittest-cpp

Funded-by: IDEAS
Project: xSDK

Allow --download-xxx-commit= to not turn off other download options with --download-xsdk
Work on amanzi install

Funded-by: IDEAS
Project: xSDK

Merge branch 'barry/downloads'

added --download-ascem-io

Funded-by: IDEAS
Project: xSDK
Time: 1 hour including testing

Allow individually setting --download-trilinos etc for options that are automatically
set with --download-xsdk or --download-ideas

Funded-by: IDEAS
Project: xSDK
Time: .75 hours including testing

make --download-pflotran and friends work correctly with --prefix
This means running the make install after make from within pflotran.py

Funded-by: IDEAS
Project: xSDK
Time: .5 hours including testi

make --download-pflotran and friends work correctly with --prefix
This means running the make install after make from within pflotran.py

Funded-by: IDEAS
Project: xSDK
Time: .5 hours including testing

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If --download-xsdk is used allow user to provide some of the packages (such as boost)
already installed so that one does not have to wait forever for it to be installeda

Funded-by: IDEAS
Project: xS

If --download-xsdk is used allow user to provide some of the packages (such as boost)
already installed so that one does not have to wait forever for it to be installeda

Funded-by: IDEAS
Project: xSDK
Time: .2 hours including testing

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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

Add --download-trilinos to --download-xsdk

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

fix typo of --download-mstk and add library name to mstk.py

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

Added --download-xsdk and --download-ideas

Funded-by: IDEAS
Project: xSDK
Time: .1 hours

Merge branch 'master' into hongzh/checkpointing

Manual merges for a couple of PetscOptions changes in master

Merge branch 'master' into pr391/zianekhodja/lilia/tsirm/master

Merge branch 'tisaac/dm-label-promote' into tisaac/dmforest

* tisaac/dm-label-promote: (319 commits)
snes tutorial ex69: give mesh a name for regression purposes
DM: make DMLabel labels a part o

Merge branch 'tisaac/dm-label-promote' into tisaac/dmforest

* tisaac/dm-label-promote: (319 commits)
snes tutorial ex69: give mesh a name for regression purposes
DM: make DMLabel labels a part of all DMs
builder: update regression tests
builder: update some missing package requirements
DM: set coordinate vector name
ts tutorials ex11_sa: make it compile
mark variable as unused so compiler doesn't warn about unused value
configure: use 'git cat-file -e' to check for existance of a commit in localrepo. ['git rev-parse' does not give error for a hash thats not in repo]
petsc4py: revert to manually syncing petsc4py with petsc master changes
configure: revert gitcommit default value to Null. If a pacakge using giturl does not change this value - raise an error
fix: revert change in a44bcdf that breaks with pgf90
update test output for fixed to hypre interface that now actually pass the interp vectors to BoomerAMG
Error message should say use negative threshold value to prevent filtering out zeros
Calls to HYPRE_BoomerAMGSetInterpVectors() did not actually copy the vector data pointer from the PETSc vector to the hypre vector thus resulting in the hypre interp vectors being identically zero and hence not affecting the quality of the AMG hierarchy produced/
DMPlex: Silence overzealous compiler warnings
add row/col orientation to MatConvert_Elemental_Dense
fix formatting error in previous commit [broke nightlybuilds]
fix formating of TSTHETA manual page and add missing command line option
run hwloc with MPIEXEC and binding so it runs on the correct machine
fix: memory leaks [in valgrind test]
...

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Merge branch 'master' into barry-allow-vecset-nan-3.6

Merge branch 'stefano_zampini/feature-pardiso-schur' of https://bitbucket.org/petsc/petsc into stefano_zampini/feature-pardiso-schur

Merge branch 'master' into knepley/fix-examples-plex

* master: (112 commits)
correct expression for implict ODE/DAE in table 11 of users manual
remove warning about deprecated MPI call in exampl

Merge branch 'master' into knepley/fix-examples-plex

* master: (112 commits)
correct expression for implict ODE/DAE in table 11 of users manual
remove warning about deprecated MPI call in examples
rm variables declared in middle of subroutine
tolerance for equality in PETSc test should depend on machine epsilon
tolerance for acccuracy in test example should depend on machine epsilon
increase convergence tolerance to get same result in single precision as double for convergence history
update no change output for gasm test which had not been properly updated
remove C++ // comment
example mistakenly used MPI_COMM_WORLD as if it was rank in print statement thus producing output only with MPI Uni
grep out name of DM object since on some systems the address printed has extra zeros thus producing a false difference in output
increase tolerance for test example
build: revert el6-4 build to cg - as el6 compilers give link errors
fix error type
insure similar convergence history for single, double, quad
fix ex104.c based on Barry's suggestion
increase example convergence tolerance to get matching convergence history in single and double precision
increase convergence tolerance so that test example has similar convergence history in single and double precisions
changed from cg to gmres for eigenestimator since in single precision cg produced a possible indefinite matrix report
change test example tolerance to depend on machine epsilon so as to give correct results in various precisions
loosen convergence tolerance to have similar convergence history with single, double, quad precisions
...

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Merge branch 'master' into shri/add-tsevent-to-powergrid-examples

Merge branch 'master' into stefano_zampini/feature-pardiso-schur

Branch got out of sync with master