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 data.cv
-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 anneal.sh containing the following:

#!/bin/tcsh -f
 
cns_solve < anneal2.inp > /dev/null
 
exit

• If you estimate that your job will take less than an hour, submit it to the fast lane:

sbatch -p fast -n4 anneal.sh

• If this is expected to be a really long job, join the queue:

sbatch -n4 anneal.sh

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