Merge branch 'master' into knepley/feature-dt-fem

* master: (211 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries

Merge branch 'master' into knepley/feature-dt-fem

* master: (211 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries
Bib: Updates
AO: fix erroneous processing of -ao_view and factor into AOViewFromOptions
doc: fix named argument in {Vec,Mat,DM}ViewFromOptions
Sys: add PetscDataTypeFromString() and test code
Mat: Should say that it has a nullspace in MatView()
parms: update tarball with fix for namespace conflict with metis
fix citation 'Golub_Varga_1961'
parmetis: update tarball to parmetis-4.0.2-p5 which fixes an install issue with cygwin
Sys Logging: revert parent traversal
fixed hdf5.py so that if self.libraries.compression is None the code still runs correctly
DMDA: fix bad cast of DM_DA to PetscObject
MatClique: follow DistMultiVec API changes
MatClique: remove unused variables
config cmakeboot: add C++ flags any time compiler is available
config OpenMP: check for C++ flag any time the compiler is available
replaced all left-over uses of a single PetscMalloc() to allocated multiple arrays: replaced with PetscMallocN() The only ones left are when the second array is set into the first array and one ugly usage in the MUMPS interface that cannot be easily fixed
...

Conflicts:
config/builder.py
src/dm/impls/plex/plexgeometry.c

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Merge branch 'knepley/fix-valgrind-config'

* knepley/fix-valgrind-config:
Configure: Fail early if --with-valgrind-lib is specified

metis/parmetis: update to metis-5.1.0/parmetis-4.0.3
Also update the test output as the partitioning appears to have changed.

Merge branch 'jed/config-openmp-cxx' into maint

* jed/config-openmp-cxx:
config cmakeboot: add C++ flags any time compiler is available
config OpenMP: check for C++ flag any time the compiler is

Merge branch 'jed/config-openmp-cxx' into maint

* jed/config-openmp-cxx:
config cmakeboot: add C++ flags any time compiler is available
config OpenMP: check for C++ flag any time the compiler is available

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debug version of downloaded hypre compiled with --with-print-errors to help debugging

Merge branch 'maint'

parms: update tarball with fix for namespace conflict with metis

Merge branch 'maint'

parmetis: update tarball to parmetis-4.0.2-p5 which fixes an install issue with cygwin

Merge branch 'jed/config-openmp-cxx'

* jed/config-openmp-cxx:
config cmakeboot: add C++ flags any time compiler is available
config OpenMP: check for C++ flag any time the compiler is available

config OpenMP: check for C++ flag any time the compiler is available

Otherwise C++ source files such as matelem.cxx are compiled without the
-fopenmp flag, which causes breakage due to non-TLS varia

config OpenMP: check for C++ flag any time the compiler is available

Otherwise C++ source files such as matelem.cxx are compiled without the
-fopenmp flag, which causes breakage due to non-TLS variables when using
threads.

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new location for CUDA on the Mac

PetscFE: Large reorganization of FEM dispatch
- WARNING: Now DMPlex and PetscFE have a circular dependence. We need to move the FEM methods to PetscFE
- Changed FEMIntegrateResidualBatch() from to Pe

PetscFE: Large reorganization of FEM dispatch
- WARNING: Now DMPlex and PetscFE have a circular dependence. We need to move the FEM methods to PetscFE
- Changed FEMIntegrateResidualBatch() from to PetscFEIntegrateResidualChunk()
- Changed DMPlexComputeResidualFEM() to use new interface
- Changed signature of f_k and g_kl functions
- Added DMPlexResidualFEM event
- Put PetscQuadrature and PetscCellGeometry
- Moved and changed PetscFEM structure

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updated to new /dir1/dir2/variablename scheme for SAWs

Configure: Fix registration of FIAT and Generator packages

update for latest SAWs

Merge branch 'paulmullowney/txpetscgpu-package-removal2'

Removing TXPETSCGPU from the build system.

Removing the main file and a few other places where
--download-txpetscgpu was used. I think I got them all.

Mat: Update to Elemental revision 0.81

Merge branch 'jack/elemental-0.80'

* jack/elemental-0.80:
Mat Elemental: remove -mat_elemental_grid_width from man page
Mat: update to Elemental version 0.80

converted uAMS usage to SAWs usage; starts server but cannot see any published directories

updates to AMS interface include simple bash scripts

Merge branch 'barry/maint-fix-zoltan.py'

X is listed as a required dependency of Zoltan but it is only optional

Merge branch 'maint'