23 months ago by
Well, with PBS you submit everything in the header, here's my header for the University of Queensland's PBS server on barrine, it could be that your local server is slightly differently set up. For example, UQ has four types of possible values for server type, "any", "medium", "xl", "large". You'd have to ask your sys admins what your values are.
#PBS -N copy
#PBS -l select=1:ncpus=1:mem=12G:NodeType=medium
#PBS -l walltime=23:00:00
#PBS -A your_group_id
Submit using "qsub scriptname.sh"
-N is the name, that one is just to keep track of your jobs more easily. -l is the various parameters, how much memory requested, how many CPUs, which node type. In your case you have a maximum mem of 240G, don't know how much you actually need. The less you use, the more likely your job is to crash, but the more memory is left for others. Lastly, -l walltime is important for you; in this case, it's set to 23 hours, in your case you probably need more. Try setting it to something large like 100 hours, but again, your system administrators set the maximum allowed time, which also depends on your node type.
your_group_id is your group ID for billing purposes, depends on how your local server handles that.