Submitting an NAMD job to Norma

  • Transfer all files needed for your job to Norma using ftp or sftp.
  • Organise your files in a sensible way (use mkdir).
  • If you working with a completely new system (see the benchmarks page), consider the possibility of tuning the simulation parameters for Norma. If you do not know how, ask for advice.
  • cd to the directory containing the NAMD files and make sure that everything you need for the run is there.
  • Submitting the job to the queue using the provided NAMDjob script is a piece of cake. Say, for example, that you need 8 cores, that the name of the NAMD script is equi.namd and that you want your log file to be named mylog. All you have to do is to type:

# NAMDjob 8 equi.namd mylog

  • Use squeue or sview to verify that your job appeared in the primary slurm queue (NAMD jobs never go to the fast queue for obvious reasons).
  • That's it.

Submitting an CUDA-enabled NAMD job to Norma

Piece of cake :

# setenv CUDA 1            
# NAMDjob 8 equi.namd mylog

… and you should see something like ”… This will be a CUDA run …”

research/howto/submitting_a_namd_job.txt · Last modified: 2011/09/28 16:14 by glykos