The U of A UITS (formerly CCIT) group maintains High Performance Computing systems for use in research applications. A shared memory supercomputer (marin) and a Linux cluster (ICE) are available for running jobs requiring a large amount of memory, parallel processing, and certain visualization and scientific applications. Details about the hardware and accessing the supercomputer resources are listed on the HPC web page.

NOTE:  In March 2007, a new supercomputer became available, with a front-end machine named 'marin'.  For information on the new system, see: http://www.hpc.arizona.edu/2007/user-guide.shtml .  Be aware that each research group is allocated 1000 hours of CPU time per month and familiarize yourself with how these allocations are charged: You are charged for walltime used (as opposed to walltime requested) multiplied by the number of cpus that you request, regardless of whether or not your job uses all of the requested cpus.   The ICE cluster arrived in March 2008, and on this system, similar limits apply.   For information specific to the ICE cluster, see the separate ICE computing FAQ .  There is also a grid computing system available, which may be better suited for single processor applications and has no limit on cpu time used – see the Condor/Grid FAQs for more information.

Who can use the UA supercomputers?

Accounts are available to UA faculty and faculty-sponsored individuals. A UA NetID is required.

How much disk space comes with a supercomputer account?

How does the supercomputer run jobs?

Jobs are placed in a batch queue until the requested resources are available. When the job finishes, an email notification is sent.

What applications are available on the supercomputer?

Applications and utilities installed on the supercomputer include Perl/BioPerl, the EMBOSS suite, the NCBI BLAST suite of applications, blat, fasta, HMMER, phylip, clustalw, mp34compsw (Smith-Waterman search), mrbayes-MPI, ASGARD and AutoFACT.

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How can I submit a job to run on the supercomputer?

Use sftp to transfer your data files to the supercomputer (See Question 13). To log into the supercomputer use the ssh command: ssh -X This e-mail address is being protected from spam bots, you need JavaScript enabled to view it
Jobs are submitted to the Portable Batch System (PBS) via C shell scripts. Some example scripts can be found in the User Guide. There is a sample BLAST submission script on marin in /genome/marinblast.csh. A sample mrbayesMPI submit file is in /genome/mrbayesMPI.csh, and a sample autoFACT submit file is in /genome/autofact.csh.   Use the cp command to copy one of these sample files to your directory and edit your copy as follows.   On marin, use the va (view allocations) command to identify your group_list setting for the .csh file. Edit your .csh file to specify the JobName, email address, group_list, cpu and time requests (See Question 7), and commands to run.  To submit your job, type the command: ‘qsub script’ (do not type the quotation marks). The qsub command displays the job number assigned to your submission.

What are the #PBS lines in the batch script?

These are directives to the PBS batch system, and need to be in the script. The lines must begin with ‘#PBS’, and you must alter only the jobname (following -N option) and your email address (following the –M option).

The –l options identify requested resources and the –q option requests a particular job queue.

The –m bea directive tells the batch system to send email notifications when your job begins, ends, or aborts. The –W line identifies your work group, which can be found using the va (view allocations) command.

How can I check the status of my job after submission?

Use the command ‘qstat -a’.

How can I stop my supercomputer job?

The command ‘qdel job_number’ will stop your job and remove it from the queue.

If my job fails, where can I find out what happened?

The batch system creates an output file and an error file, named by appending the letter o or e and the job number to the jobname specified in the PBS script. The output file contains the standard output from the job, possibly including the line ‘Warning: no access to tty (Bad file number).’ This warning can be ignored. The error file will contain more specific information about the error that occurred. It also may include the line ‘stty: tcgetattr: Not a typewriter’, which can be ignored.

What is a likely cause of errors such as:

‘/pbs/mom1/mom_priv/jobs/1754...SC: Command not found.’ ?

This type of error can occur if you have edited your script or data files on a PC and transferred them to a Unix system. Check for control-M characters (^M) at the end of lines in your script by using the command: ‘cat –vet script’.

If ^M’s are present, remove them with the command: ‘tr –d “\015” <PCscript >UNIXscript’.

This command reads input from the file ‘PCscript’ and writes output to the file ‘UNIXscript’. Do not try to use the same filename for both input and output or your input file will be corrupted.
Alternatively, this problem can be avoided by using the nedit editor on amadeus for editing your scripts.

Why do I see "qsub: unauthorized request" when I try to submit a job?

One possiblilty is that your group has already used the 1000 cpu hours allocated for the default queue.  The va command will show you the amount of time remaining.  If you have insufficient time remaining in the default queue, you can try submitting your job to the windfall queue.

How do I Transfer Files to the Supercomputer?

On amadeus, use gzip to compress the file (a .gz extension is added by gzip):
gzip   file

Use the sftp command to copy the file to the Supercomputer:
sftp  mylogin@marin.hpc.arizona.edu (then enter first 8 characters of UANetID password)
put   file.gz
quit

How do I run BLAST jobs on the supercomputer?

See the FAQ Running BLAST jobs on the Supercomputer .

Where can I find out more about High Performance Computing at UA?

There are many useful links at the High Performance Computing web site.

How can I get help tracking down errors?

This e-mail address is being protected from spam bots, you need JavaScript enabled to view it or the HPC Help Desk This e-mail address is being protected from spam bots, you need JavaScript enabled to view it . Include the exact error messages generated by your job and the locations of your script and data files.

What if I don’t understand something in this FAQ?

Please This e-mail address is being protected from spam bots, you need JavaScript enabled to view it to report any answers that are not clear or any errors that may be present in this document.