See NamdAtNICS for information on Kraken, a Cray XT5 with compute node Linux (officially called Cray Linux Environment or CLE).

The XT5 uses Opteron processors, runs Linux. and requires and MPI-based NAMD. The only strange thing is that there is no mpicc/mpiCC, you just use cc and CC. Usually pathcc, pgcc, and gcc are available, and you use modules to select which one is mapped to cc/CC. If it works gcc will probably give the best performance. The Intel compiler would probably be better but is usually not available.

To build Charm++ (from the charm source directory):

env MPICXX=CC MPICC=cc ./build charm++ mpi-linux-x86_64 --no-build-shared -O -DCMK_OPTIMIZE=1

To build NAMD use arch CRAY-XT-pgcc for the PGI compilers or CRAY-XT-g++ for the GNU compilers.

For NAMD 2.7b1 you will need to change the CXX definition in arch/CRAY-XT-pgcc.arch to:

CXX = CC -D'nearbyint(X)'='floor((X)+0.5)'