Using the CLUSTER


General use guidelines:



To use the cluster you need to first obtain an account on the cluster. To obtain an account send an email to Mark Klein (mdklein@scl.ameslab.gov) making the request. All accounts will also need approval from Mark Gordon.

To log on to the cluster ssh to dynamo.iprt.iastate.edu. Once logged onto this node you have full access to your home directory and all compilers.

To get between nodes you should use ssh.

To run jobs you must submit them to SGE (the queueing system). In general the submit command is:

qsub -cwd -o [LOGFILE] -j yes -pe mpi [number of nodes] -N [JobName] [YourScript] [arguments]

The high speed nodes names will be within the file 'hostlist' in the scratch directory on the first node in the hostlist.

If your job requires gpus you can place additional flags on the qsub command. -l gpu=# where # is the number of gpus required.

To run GAMESS jobs use the gms command. It will prompt you for the required information. GAMESS is maintained by Mike Schmidt so please send GAMESS related questions to him (mike@si.fi.ameslab.gov).