IOSS: Remove duplicate file check; too many false positives; will reimplement in a better way

(From Sierra)

Build/Test Cases Summary
Enabled Packages: SEACASIoss
Disabled Packages: Panzer,PyTrilinos,SEACASExo2mat,SEACASMat2exo
Enabled all Forward Packages
0) MPI_DEBUG => Skipped configure, build, test due to no enabled packages! => Does not affect push readiness! (-1.00 min)
1) SERIAL_RELEASE => Skipped configure, build, test due to no enabled packages! => Does not affect push readiness! (-1.00 min)
2) MPI_DEBUG_SS => passed: passed=21,notpassed=0 (22.41 min)
3) SERIAL_RELEASE_SS => passed: passed=22,notpassed=0 (23.86 min)
Ifpack2: fixed a warning

NestedPreconditioner had virtual functions, but not virtual destructor.
Trilinos: MueLu: enable testing of MPI builds

The purported MPI builds on typhon weren't actually enabling MPI.  The problem
was is that many of the TrilinosCTestDriverCore.* scripts contain the following:

  #Ensuring that MPI is on for all parallel builds that might be run.
  IF(COMM_TYPE STREQUAL MPI)
    SET(TPL_ENABLE_MPI ON)
  ENDIF()

and this got propagated to this file.  The above code does *not* enable MPI.

Instead, it should be

  IF(COMM_TYPE STREQUAL MPI)
    SET( EXTRA_SYSTEM_CONFIGURE_OPTIONS
         ${EXTRA_SYSTEM_CONFIGURE_OPTIONS}
         "-DTPL_ENABLE_MPI:BOOL=ON"
       )
  ENDIF()

Optionally, the MPI installation directory can be specified in the SET,
as well:
         "-DMPI_BASE_DIR:PATH=/usr/local/mpich2/1.4.1p1_gcc_4.4.7"
MueLu: prolongator scaling test

Test for prolongator construction in isolation.
MueLu: fix Epetra test

pesky --
Ifpack2:  Fixing weird compiler error with gcc 4.7.2

With gcc 4.7.2 I was getting a compiler error about
Ifpack2::Details::DenseSolver<> being abstract because
Ifpack2::Preconditioner::apply() was not implemented, even though it
was.  Turns out the reason was the definition of apply() used the MV
typedef instead of spelling out Tpetra::MultiVector<...> explicitly.  I
think the reason it didn't work was MV was a private typedef but was
appearing in the function declaration of a public member function.
Ifpack2: Deprecated condition number estimation.

Refer to discussion of Bug 5841 for details.  Apparently nobody uses
this feature, even in Ifpack ("Ifpack1").  It never worked how people
thought it worked, in either Ifpack or Ifpack2.  I'm deprecating it so
nobody else is tempted to use it.

I also fixed the condition number estimation of Diagonal to return -1
(as it should) instead of +1 in the "not yet computed" case.
Ifpack2: RILUK: Fixed Bug 5778 (alpha and beta ignored in apply()).
Ifpack2: Fixed Bug 5460.

I'm not counting Ifpack2_Parameters.cpp in this fix.  That file should
be deprecated in any case.  Each Preconditioner subclass should
implement its own parameter fetching and parsing.

There is one "FIXME" in Chebyshev relating to this bug, but it doesn't
look like a big deal.
Ifpack2: Chebyshev: Now uses TimeMonitor to store timers.
Ifpack2: LocalFilter: Improved public documentation
Ifpack2: LocalFilter: Reformatted code

Build/Test Cases Summary
Enabled Packages: Ifpack2
0) MPI_DEBUG => passed: passed=23,notpassed=0 (1.50 min)
1) SERIAL_RELEASE => passed: passed=18,notpassed=0 (1.09 min)
Other local commits for this build/test group: f6cec97, ad5e9c8, 353c388, 9feb5b6, 2103ff1
Panzer: Initial implementation of an explicit ME decorator

This first version is a bit inefficient, though this is something
I will have to work on. I wanted to get some capability in so we
could start playing around with it.
Panzer: Enabling use of explicit RK through the ME factory

This keys off the stepper type and so it is hard coded to a single
type of time integrator. This primarily serves to provide a way to
test explicit time integration, and the explicit time integrator
in drekar.