Panzer: Adding a few comments (really copying from sub-class)
Teko: Fixing LSC to work with stable discretizations
Panzer: Enabling transient terms in boundary condition worksets

This was not done and was causing problems. Thanks to JNS
for catching this!
switching to zoltan2

change to:

    <ParameterList name="myTransferCoordinatesFact">
      <Parameter name="factory"                             type="string" value="CoordinatesTransferFactory"/>
    </ParameterList>
Xpetra: fix for compile error with icc 11.0.72

Paul Lin reported that under 11.0.72 and GO=long, Xpetra would not compile.  Errors were like the following:

/ufs/home/ptlin/projects/sierra/64bit/sierra-code20130329/TPLs/Trilinos_flat_headers/Xpetra_CrsMatrixWrap.hpp(129):
 error: a nonstatic member reference must be relative to a specific object
      matrixData_ = CrsMatrixFactory::Build(rowMap, colMap, maxNumEntriesPerRow, pftype);
                    ^
          detected during:
            instantiation of "Xpetra::CrsMatrixWrap<Scalar, LocalOrdinal, GlobalOrdinal, Node, LocalMatOps>::CrsMatrixWrap(const Teuchos::RCP<const Xpetra::Map<LocalOrdinal, GlobalOrdinal, Node>> &, const Teuchos::RCP<const Xpetra::Map<LocalOrdinal, GlobalOrdinal, Node>> &, size_t={unsigned long}, Xpetra::ProfileType) [with Scalar=Scalar={double}, LocalOrdinal=LocalOrdinal={int}, GlobalOrdinal=GlobalOrdinal={long}, Node=Node, LocalMatOps=LocalMatOps]" at line 89 of
                      "/ufs/home/ptlin/projects/sierra/64bit/sierra-code20130329/TPLs/Trilinos_flat_headers/Xpetra_MatrixFactory.hpp"

I believe the issue is that some new build methods were not declared static.
MueLu: Creating column map for Ptent.

Ptent is special and we can calculate the column map.  This is a precursor to using
a fast 3-array insertion method.
MueLu:  adding xml deck for conchas uvw problem.
Tpetra: fixing a shadow warning.
MueLu: build Ptent colmap for uncoupled agg. only

For coupled aggregation, we need to communicate information across processors.
So for now I'm only enabling this optimization when using uncoupled aggregation.
Galeri: fixing another compile error for Helmholtz

Build/Test Cases Summary
Enabled Packages: Galeri, MueLu, Tpetra, Xpetra
Disabled Packages: MOOCHO
Enabled all Forward Packages
0) MPI_DEBUG => passed: passed=582,notpassed=0 (4.45 min)
1) SERIAL_RELEASE => passed: passed=546,notpassed=0 (2.19 min)
2) MPI_SS_DEBUG => FAILED: passed=267,notpassed=4 => Not ready to push! (2.59 min)
Other local commits for this build/test group: 9a92a38, 44dd3d5, a4596ce, 55a097d, 06ab728
WARNING: Forced the push!
Stokhos:  Add includes of expression traits headers

This is for codes that might not include Stokhos_Sacado.hpp.
Tpetra: Map: Defer Directory creation until first use.

The Map's Directory object is only used in getRemoteIndexList().  That
method must be called collectively over all processes in the Map's
communicator, just like creation of the Directory.  Thus, we do not need
to create the Directory in Map's constructor; we can defer Directory
creation to (the first call to) getRemoteIndexList().

This optimization saves the communication cost of creating the
Directory, for some Maps which are never involved in an Import or Export
operation.  For example, a nonsquare sparse matrix (CrsMatrix) with
identical row and range Maps would never need to construct an Export
object.  This is a common case for the prolongation or restriction
operators in algebraic multigrid.  Thus, this commit may reduce MueLu's
setup time.  Note, however, that it does not make the Directory creation
time go away if one actually needs to create an Import or Export with
that Map; it merely shifts the Directory creation time away from Map's
constructor.

Thanks to Chris Siefert for pointing out this optimization.

Build/Test Cases Summary
Enabled Packages: Teuchos, Tpetra, Belos, Ifpack2, Xpetra, MueLu
0) MPI_DEBUG => Test case MPI_DEBUG was not run! => Does not affect push readiness! (-1.00 min)
1) SERIAL_RELEASE => Test case SERIAL_RELEASE was not run! => Does not affect push readiness! (-1.00 min)
2) MPI_DEBUG_SS => passed: passed=272,notpassed=0 (4.61 min)
3) SERIAL_RELEASE_SS => passed: passed=254,notpassed=0 (10.39 min)
MueLu: removed incorrect header from Zoltan2 interface

For some reason, we included Zoltan 1 header in the Zoltan2 interface,
which caused problems when one compiles trilinos with Zoltan 2 but
without Zoltan1.
Teuchos: Fixed pointer errors in templated implementations of
equilibration routines. These only showed up when building the code
with qdlib types. I've wanted to update the Teuchos dense solver
tests to use qdlib types when available for some time. This would be
appropriate since the Teuchos dense solver classes support qdlib
types now.

Build/Test Cases Summary
Enabled Packages: Teuchos
Enabled all Forward Packages
0) MPI_DEBUG => passed: passed=1274,notpassed=0 (34.31 min)
1) SERIAL_RELEASE => passed: passed=1230,notpassed=0 (13.18 min)
Use mesh interface for getting coordinates and connectivity.

EPIC: part of SD transition to Toolkit

(From Sierra)
SEACAS: suplib - fix compilation error with gcc-4.1 in previous fix

(From Sierra)
SEACAS: Update cmake build files

A change to the name of one of the files in the CMakeLists.txt for suplib was
necessary to reflect the name change of one of the files.

Build/Test Cases Summary
Enabled Packages: SEACASIoss, SEACASSuplib
Disabled Packages: Panzer,PyTrilinos
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 (24.70 min)
3) SERIAL_RELEASE_SS => passed: passed=22,notpassed=0 (26.83 min)
Other local commits for this build/test group: dd6279a, 2a79525
MueLu: Xpetra: fixed a problem with a reference to a temporal object

MueLu Tpetra adapter implements the interface of the Tpetra Operator. As
such, the calls to getDomainMap() and getRangeMap() must return
references to RCP. That means, that we have to cast the corresponding
Xpetra::Map to the const reference. However, this was impossible due to
the fact that the corresponding cast function could also deal with zero
maps, which obviously cannot be referenced.
I solved the problem by adding an extra function to Xpetra which returns
the reference, but assumes that the map is not zero.
Trilinos: fix for some compiler warnings

This patch fixes some of the compilation warnings for some packages on
my path of compilation. Specifically, it got rid of most
[-Wunused-local-typedefs] warnings, aka typedef "X" locally defined but
not used; and in couple places added braces for nested dangling else.
Allow TriKota to get information of Dakota's link directories for linking its binaries.  Change likely has to propagate to Albany and other clients of TriKota.