Merge branch 'barry/download-pflowtran' into barry/downloads

Added support for --download-xxx from hg repository
Added --download-pflotran -- does not work with gfortran 5.2 due to pflotran code that passes arguments of different ranks through the same interfa

Added support for --download-xxx from hg repository
Added --download-pflotran -- does not work with gfortran 5.2 due to pflotran code that passes arguments of different ranks through the same interface; will try to Intel Fortran compilers

Funded-by: IDEAS
Time: 1 hour

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Configure: Fix logging for shell calls in retrieval

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 'barry/petscoptions-object' into stefano_zampini/feature-pardiso-schur

Merge branch 'master' into barry/not-single-precision

Merge remote-tracking branch 'petsc/master' into moved-partitioning-to-pcgasmsetup

Merge branch 'master' into barry/all-petscoptionssetvalue-beforepetscinitialize

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

Merge branch 'master' into barry/remove-unneed-tao-tolerances

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

Merge remote-tracking branch 'origin/balay/configure-pkg-git-autoupdate'

configure: improve git repo support for externalpackages
- do a fetch/checkout on each configure invocation so that the git repo builds are never stale.
- also store git commit-id in a config file

configure: improve git repo support for externalpackages
- do a fetch/checkout on each configure invocation so that the git repo builds are never stale.
- also store git commit-id in a config file - and automatically rebuild package when this changes
The above 2 actions are done in updateGitDir()
- use common notation for various 'package' related files:
externalpackages/git.package - name of the git repo
lib/petsc/conf/pkg.conf.package - contains make/configure config info
lib/petsc/conf/pkg.gitcommit.package - contains git commit-id [if git pkg]
- remove circular dependency between getDir() and downLoad()
- attempt to use 'self.package/PACKAGE' consistantly across these routines

Note: previously we sometimes relied on: if externalpackages/package exits - then
configure won't change its contents. This won't be valid anymore for git repos.
This behavior can be restored by using corresponding option: --download-package-commit=HEAD

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Merge remote-tracking branch 'petsc/master' into fix-pcgasm-reuse

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

Merge branch 'barry/improve-git-download'

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

Add support for --download-xxx=directoryname and --download-xxx=git://gitrepository and --download-xxx-commit=commit

Suggested-by: Roscoe Bartlett <bartlettra@ornl.gov>

Merged handling of git and n

Add support for --download-xxx=directoryname and --download-xxx=git://gitrepository and --download-xxx-commit=commit

Suggested-by: Roscoe Bartlett <bartlettra@ornl.gov>

Merged handling of git and non-git lists of download locations (prepend the git repository name with git://) into a single system instead of having two systems clumsily glued together

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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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To add a space to all comments I have made before. Barry pointed out
that a comment without a space right after '/*' may cause bfort to crash

Merge remote-tracking branch 'petsc/master' into fixed-c

To add a space to all comments I have made before. Barry pointed out
that a comment without a space right after '/*' may cause bfort to crash

Merge remote-tracking branch 'petsc/master' into fixed-comment-space

Conflicts:
include/petsc/finclude/petscmat.h
include/petscmat.h
src/mat/examples/tests/makefile
src/mat/impls/aij/mpi/mpiaij.h

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