Submitting a CNS job

CNS v.1.2 understands multithreading, and will automatically spawn four threads on a four-core machine. This means that you are better-off asking directly for -n4 cores (ie. a node) and avoid complications. To submit a job

  • Collect all your files in a directory. For example, a typical list for an annealing job would be :
-rw-r--r-- 1 glykos glykos   39938 Mar 20 16:46 anneal2.inp
-rw-r--r-- 1 glykos glykos  282584 Apr 17  2008 bindividual8.pdb
-rw-r--r-- 1 glykos glykos 1318953 Apr 17  2008
-rw-r--r-- 1 glykos glykos  360248 Apr 17  2008 generate_easy.mtf
  • Make sure your jobs starts without problems keeping in mind that this is CNS v.1.2 :
cns_solve < anneal2.inp
  • Prepare a submission script, let's say containing the following:
#!/bin/tcsh -f
cns_solve < anneal2.inp > /dev/null
  • If you estimate that your job will take less than an hour, submit it to the fast lane:
sbatch -p fast -n4
  • If this is expected to be a really long job, join the queue:
sbatch -n4

Results will appear in the current directory, possible error messages in the file slurm-*.out

research/howto/submitting_a_cns_job.txt · Last modified: 2009/03/20 19:08 (external edit)