In order to run benchmarks the memopt build with SMP support is mandatory.
NAMD may be compiled in an experimental memory-optimized mode that utilizes a compressed version of the molecular structure and also supports parallel I/O.
In addition to reducing per-node memory requirements, the compressed structure greatly reduces startup times compared to reading a psf file.
In order to build this version, your MPI need to have level of thread support: MPI_THREAD_FUNNELED
You need a NAMD 2.11 version or newer.
1. Uncompress/tar the source.
2. cd NAMD_Source_BASE (the directory name depends on how the source obtained,
typically : namd2 or NAMD_2.11_Source )
3. untar the charm-VERSION.tar that exists. If you obtained the namd source via
cvs, you need to download separately charm.
4. cd to charm-VERSION directory
5. configure and compile charm :
This step is system dependent. Some examples are :