AztecOO: Added missing AZ_STOP_TIMER calls for gmres.

See bug #5960 for details.

Signed-off-by: Roger Pawlowski <rppawlo@sandia.gov>
NOX: reenable timers in testing for aztec issue

See ticket #5960.

Signed-off-by: Roger Pawlowski <rppawlo@sandia.gov>

Build/Test Cases Summary
Enabled Packages: AztecOO, NOX
Disabled Packages: SEACAS,Sundance,PyTrilinos,Didasko,Stokhos,TrilinosCouplings,MueLu,STK
Enabled all Forward Packages
0) MPI_DEBUG => passed: passed=512,notpassed=0 (37.68 min)
1) SERIAL_RELEASE => passed: passed=483,notpassed=0 (12.23 min)
2) MPI_DEBUG_SS => passed: passed=690,notpassed=0 (25.39 min)
Other local commits for this build/test group: b36fdba
Reduce processes used to build on Zan for cuda build

This build is consistently running out of memory while compiling tpetra.
Hopefully reducing the number of simultaneous builds will allow the build to
complete.
Ifpack2: fixing issue with Teuchos::Comm

The comm object was being created on the global ordinal type, rather than int.
Also cleaned up formatting (!tabs).

Build/Test Cases Summary
Enabled Packages: Ifpack2
Disabled Packages: MOOCHO
Enabled all Forward Packages
0) MPI_DEBUG => passed: passed=22,notpassed=0 (4.72 min)
1) SERIAL_RELEASE => passed: passed=18,notpassed=0 (3.13 min)
2) MPI_SS_DEBUG => passed: passed=125,notpassed=0 (14.03 min)
3) SERIAL_SS_DEBUG => passed: passed=109,notpassed=0 (11.57 min)
Kokkos: Fixed build issue with gcc 4.2.1 version of std::pair.

gcc 4.2.1 is the version of gcc used by default on Mac OS X, so this
could be considered a Mac fix.  Apparently, with that version of the C++
Standard Library, "std::pair<unsigned, unsigned> (0u, 0u)" as a default
argument of a constructor doesn't work, but "std::make_pair (0u, 0u)"
does work.
Kokkos: Added ad-hoc build scripts for Mac.
MueLu: fix nightly testing of epetra/tpetra only

This commit explicitly disables packages by passing options of the form "-DTrilinos_ENABLE_Foo:BOOL=OFF" to the cmake line.

Previously, the scripts to test MueLu with only Epetra or with only Tpetra were incorrect, and not doing what was intended.
They were using the variable EXTRA_EXCLUDE_PACKAGES.  However, this variable instructs the testing system to not enable package
FOO *directly*, but FOO can still be enabled through an optional dependency on an enable package.

Thanks to Brent P. for setting me straight on this.
Stokhos: Change Dakota Pecos::RealMatrixList to RealMatrixArray
to to reflect a change in Dakota Pecos headers.

Build/Test Cases Summary
Enabled Packages: Stokhos
Enabled all Forward Packages
0) MPI_DEBUG => passed: skipped configure, build, test due to no enabled packages (0.00 min)
1) SERIAL_RELEASE => passed: skipped configure, build, test due to no enabled packages (0.00 min)
2) MPI_RELEASE_SS => passed: passed=60,notpassed=0 (6.63 min)
Removed CHOLMOD test in cmake files since it isn't implented. Fixed Ifpack2_AdditiveSchwarz timers which were not being reset and changed the indexBase of some of the maps to that of the input matrix.

Build/Test Cases Summary
Enabled Packages: Amesos2, Ifpack2
Enabled all Forward Packages
0) MPI_DEBUG => passed: passed=22,notpassed=0 (28.39 min)
1) SERIAL_RELEASE => passed: passed=18,notpassed=0 (11.55 min)
Kokkos Examples: Add commentary in preparation for tutorial walk-through.
Kokkos: Fix Cuda device initialization bug.
Kokkos: Revised build scripts for example