Completed support for SuiteSparse Cholmod using GPUs

configure: --with-cuda --download-suitesparse-gpu --with-64-bit-indices (SuiteSparse limitation)
Runtime: -mat_cholmod_useGPU 1 or 0 default is 1

Cholmod only uses GPU when 64 bit indices are used
Allow Mac to use rpath to compile in correct locations of dynamic libraries

remove debug print statment; the shame!

added --download-suitesparse-gpu so that SuiteSparse builds to use GPUs

Compiles and runs ok linking in the CUDA stuff, cannot determine if it actually uses the GPU or not at runtime.

Updated to support SuiteSparse 4.4.1
added UMFPACK and CHOLMOD examples to test suite
updated documentation to better unify klu,umfpack, and cholmod
In response to bitbucket issue 88

Did not add CHO

Updated to support SuiteSparse 4.4.1
added UMFPACK and CHOLMOD examples to test suite
updated documentation to better unify klu,umfpack, and cholmod
In response to bitbucket issue 88

Did not add CHOLMOD GPU support usage to --download-suitesparse yet

Reported-by: Sean Farley <sean.michael.farley@gmail.com>

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mpich: add backup URLs for tarballs

Was not checking correctly for --with-environment-variables set by user
also now print boxed message if using environment variable

rebased version of sarich/feature-configure-allow-environment-vars to support previous fix by Barry of printing warning about environmental variables only if they are not overwritten

make real commit this time

Merge branch 'barry/no-warning-for-overwritten-environmental-variable'

Three directory namespace changes for better --prefix install support

1) include/finclude becomes include/petsc-finclude
2) include/mpiuni becomes include/petsc-mpiuni
3) conf (both $PETSC_DIR/conf

Three directory namespace changes for better --prefix install support

1) include/finclude becomes include/petsc-finclude
2) include/mpiuni becomes include/petsc-mpiuni
3) conf (both $PETSC_DIR/conf and $PETSC_DIR/$PETSC_ARCH/conf become) lib/petsc-conf

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name spaced include/petsc-mpiuni and bin/petsc-mpiexec.uni for PETSc --prefix installs

hwloc no longer downloads by default even when not requested

configure: increase timeout for 'make install' [for openmpi on slow disk machine]

Merge branch 'pr234/vasiliy_kozyrev/mkl_cpardiso'

./configure should not report warning about environmental variable when user
has overwritten it from the command line anyways.

Reported-by: Sean Farley <sean.michael.farley@gmail.com>

Merge branch 'knepley/fix-configure-package-check'

* knepley/fix-configure-package-check:
Configure: Fixed misspelling
Configure: libraryOptions has all sorts of crap in it, so pull out indexTyp

Merge branch 'knepley/fix-configure-package-check'

* knepley/fix-configure-package-check:
Configure: Fixed misspelling
Configure: libraryOptions has all sorts of crap in it, so pull out indexTypes.py - Needs to depend on setCompilers since it checks for a symbol - Change refs in all modules to indexTypes
Configure: Require libraryOptions for PETSc module
Configure: Added new providers to do checks for index size and scalar type

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moab: fix configure so that hdf5/netcdf is disabled in moab - when disabled in petsc configure

Configure: libraryOptions has all sorts of crap in it, so pull out indexTypes.py
- Needs to depend on setCompilers since it checks for a symbol
- Change refs in all modules to indexTypes

Merge branch 'maint'

Configure: Added new providers to do checks for index size and scalar type

Intel MKL Cluster Pardiso. Work only Intel(R) Parallel Studio XE 2015

fix to last commit that broke --download-mpich

Barry learns yet again why it is important to make a branch and test before pushing

fix for bug introduced by removing help messages for --with-mpich- etc..
suggest --download-mpich instead of --download-mpi and --download-f2cblaslapack or --download-fblaslapack instead of --downloa

fix for bug introduced by removing help messages for --with-mpich- etc..
suggest --download-mpich instead of --download-mpi and --download-f2cblaslapack or --download-fblaslapack instead of --download-blaslapack

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certain packages such as MPICH do not support --with-.. options
only --download-MPICH therefor help messages should not display --with... options
Make.py, Cmake.py, and c2html.py each printed two set

certain packages such as MPICH do not support --with-.. options
only --download-MPICH therefor help messages should not display --with... options
Make.py, Cmake.py, and c2html.py each printed two sets of help messages, changed code to display all help messages for each together

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