Most of your question can be answered on the web site NAMD or subscribe to their community supported list
The rest of this page are simple instruction to get you going.
The NAMD binary was compiled against the Topspin libraries, hence can only run on the
imw queue (Infiniband switch). You need to be a member of the “inf_nodes” unix group to successfully run the bianry.
Here is a sample job.
#!/bin/bash #BSUB -q imw #BSUB -R "span[ptile=1]" #BSUB -J namd #BSUB -o out #BSUB -e err #BSUB -n 4 MPIRUN="/share/apps/bin/lsf.topspin.wrapper" PATH=/usr/local/topspin/mpi/mpich/bin:$PATH export PATH # scratch dirs MYSANSCRATCH=/sanscratch/$LSB_JOBID MYLOCALSCRATCH=/localscratch/$LSB_JOBID #cd $MYSANSCRATCH rm -rf err out export LD_LIBRARY_PATH=/usr/local/topspin/mpi/mpich/lib64 $MPIRUN /share/apps/NAMD/NAMD_2.6_Source/Linux-amd64-MPI/namd2 /home/hmeij/1g6r/named-pgm/alanin
You may browse that directory to view the type of output it generates.
Axel's commentary on how to get NAMD to run with OpenMPI.
the way i'm compiling openmpi is the following (with support for infiniband, myrinet, and job launch directly through OpenPBS without host/nodefiles):
./configure --prefix=/cmm/pkg/openmpi-1.2.7 \ --enable-orterun-prefix-by-default \ --with-gm=/opt/gm-2.1.29 \ --with-openib=/opt/ofed-1.3.1 \ --with-tm=/opt make -j8 make install
now i can select what communication to use by default through /cmm/pkg/openmpi/etc/openmpi-mca-params.conf , which has either btl = openib,self or btl = gm,self
if i run on the frontend, i override that with -mca btl tcp,self
the very same charm++ megatest binary works fine on all four clusters and the front end without any other modifications.
one of the nicest things about a (normal) openmpi installation is that the resulting executables only depend on the openmpi libraries and _not_ on any other lowlevel communication libs, so one can actually use the same binary on a different installation of openmpi with different lowlevel protocols, provided it is of the same openmpi version and uses the same gcc/libc and so on.