NAMD on Linux-mvapich-amd64

Hardware: AMD64 Cluster with Infiniband

Software: Openfabrics 1.2 with MVAPICH 0.9.8

Setup: Copy the source, untar the source, untar the charm.tar file.

edit src/arch/mpi-linux-amd64/conv-mach.h change:

#define CMK_MALLOC_USE_GNU_MALLOC 1

#define CMK_MALLOC_USE_OS_BUILTIN 0

to

#define CMK_MALLOC_USE_GNU_MALLOC 0

#define CMK_MALLOC_USE_OS_BUILTIN 1

Otherwise the mvampich will not allocate memory properly.

./build charm++ mpi-linux-amd64

cd tests/charm++/simplearrayhello make <after the build> <create a host file with some machines in it for mvapich to run> ./charmrun -np 2 -machinefile hosts ./hello

Return to the base directory of NAMD. Modify the file Make.charm to indicate the base of the charm directory.

./config Linux-amd64-MPI cd Linux-amd64-MPI make

./charmrun +p2 -np 2 -machinefile hosts ./namd2 src/alanin