Beginners Guide to MCNP with Torque

(Thanks to John Pevey )

Note: Please DELETE runtape files if you don't need them!

Your first MCNP Input on the NE Cluster

To begin on Windows you must have Putty and WinSCP. Follow the guides available online to set these up and get connected to the NE cluster.

1. Load the required modules using these commands:
module load openmpi
module load MCNP5
2. Upload your input file to your target directory in the cluster using scp/WinSCP/Filezilla/....
3. Create a unique .sh file that will be used to describe the job. Instructions and notes on this file can be found in the wiki.
4. You have to make your new .sh file executable.
   • Type chmod +x filename.extension
   • After doing this type ls to list the files in the directory. Executable files have a green font.
5. After you have your .sh you need to submit it to the queue. This can be done with this command:qsub filename.sh
   • The output file will be put into the directory that the input file is in.
   • Remember to delete the file ending in ‘r’ after you’re done. This is a recovery file that just takes up space after the run is complete.
6. To check on the job type qstat -a this prints all current jobs. Next, time checkjob (your job#) This will tell you about your job.

Commands to remember:

• Adding executable status to a file: chmod +x filename.extension
• Editing a file in the editor on the cluster: nano filename.extension
• Submitting a .sh to the cluster queue: qsub filename.sh
• Cooking at all jobs running on the cluster: qstat –a
• Checking a job: checkjob –v (job #)
• Deleting a job: qdel (job #)

MCNP6

Much like the above, but in the first step load these modules:
module load intel/12.1.6
module load openmpi/1.6.5-intel-12.1
module load MCNP6