NAMD Wiki: NamdAtIndiana

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NAMD is installed on Indiana's Big Red cluster .

Big Red uses Linux, dual-core PowerPC 970MP processors, and Myrinet.

To add NAMD to your path, edit the .soft file in your home directory to add the line "@namd-ibm-64", then type "resoft". The installed namd2 binary uses mpirun, and should but run the same as any other MPI program on the machine.

The script ~tg-jim/NAMD_scripts/runbatch automates submitting a NAMD run. If you can't access this script, look at the example in . If, in using this example, you run into errors with namd2 not being found, use which namd2 to get the absolute path, and specify the absolute path in the mpirun line e.g.

mpirun -np $LOADL_TOTAL_TASKS -machinefile $LOADL_HOSTFILE /N/soft/linux-sles9-ppc64/namd-ibm-64/bin/namd2 ubq_ws_eq.conf > ubq_ws_eq.log

NAMD (sometimes) Seg Faults on BigRed

The current version of NAMD on BigRed seg faults during the startup phase if restraints are active. Similar behavior is observed when trying to do a pressure profile calculation. So the common denominator seems to be that it crashes when you have enabled options that require it to read information from the beta column of a PDB file.