FAQs - High Performance Computing

 

  1. What High Performance Computing resources are available at U of A?

    The U of A CCIT group maintains High Performance Computing systems for use in research applications. A shared memory supercomputer and a Beowulf Linux cluster 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.

    There is also a grid computing system available, which may be better suited for single processor applications – see the Condor/Grid FAQs for more information.

  2. Who can use the UA supercomputer?

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

  3. How much disk space comes with a supercomputer account?
    The default disk quota is 1Gb.  You can set up larger temporary allocations using the xdisk utility.  See the High Performance Computing web site for more information on xdisk. To receive notification that your temporary quota is about to expire, create a file named .forward in your home directory on the supercomputer and put your email address in the .forward file.
  4. 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.

  5. What applications are available on the supercomputer?

    Applications and utilities installed on the supercomputer include perl, mathematica, the NCBI BLAST suite of applications, and fasta.

    Contact us to find out if a particular application can be installed on the supercomputer.

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

    Jobs are submitted to the Portable Batch System (PBS) via C shell scripts. Some example scripts can be found at http://www.super.arizona.edu/batch-util.shtml. There is a sample BLAST submission script on Amadeus in /etc/hpc. Use ssh to log into the supercomputer, and use sftp to transfer your data and script to the supercomputer.

    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.

  7. 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.

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

    Use the command ‘qstat -a’.

  9. How can I stop my supercomputer job?

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

  10. 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.

  11. What is a likely cause of errors such as:

    ‘/pbs/mom1/mom_priv/jobs/1754.aura.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.

  12. 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@hpc.arizona.edu (then enter password)
    put   file.gz
    quit

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

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

  14. How can I get help tracking down errors?

    Email us or the HPC Help Desk consult@hpc.arizona.edu. Include the exact error messages generated by your job and the locations of your script and data files.

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

    Please email us to report any answers that are not clear or any errors that may be present in this document.

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