gtspring2009:howto:pace
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gtspring2009:howto:pace [2009/06/29 07:03] gibson |
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| ====== How to use the PACE cluster ====== | ====== How to use the PACE cluster ====== | ||
| - | |||
| - | FIXME This document is a mere stub of what it ought to be. | ||
| The Georgia Tech Public Access Cluster Environment (PACE) is a cluster of | The Georgia Tech Public Access Cluster Environment (PACE) is a cluster of | ||
| Line 14: | Line 12: | ||
| cluster using scp (the Unix secure copy utility). It ain't always pretty but it | cluster using scp (the Unix secure copy utility). It ain't always pretty but it | ||
| keeps your laptop from melting. | keeps your laptop from melting. | ||
| + | |||
| ====== PACE documentation ====== | ====== PACE documentation ====== | ||
| Line 30: | Line 29: | ||
| {{:gtspring2009:pc.png|}} Your PACE login ID is your GTID, but I have to create an account for each user, because CNS gets charged for PACE usage. --- //[[predrag.cvitanovic@physics.gatech.edu|Predrag Cvitanovic]] 2009-02-22 16:46// | {{:gtspring2009:pc.png|}} Your PACE login ID is your GTID, but I have to create an account for each user, because CNS gets charged for PACE usage. --- //[[predrag.cvitanovic@physics.gatech.edu|Predrag Cvitanovic]] 2009-02-22 16:46// | ||
| - | |||
| ====== ssh tunneling ====== | ====== ssh tunneling ====== | ||
| - | The denizens of CNS have written [[http://www.cns.gatech.edu/CNS-only/index.html|a bunch of shell scripts]] that simplify the | + | The denizens of CNS have written shell scripts that simplify the process of logging in to the CNS machines and the PACE cluster from outside Georgia |
| - | process of logging in to the CNS machines and the PACE cluster from outside Georgia | + | Tech, and using the svn repositories. You will probably want to install these: [[http://www.cns.gatech.edu/CNS-only/fetchTunnel.html|"Fetch CNS ssh tunneling scripts"]]. |
| - | Tech. You will probably want to install these and figure out how to use them. Ask oldtimers you do not know the CNS webpages password. | + | |
| + | Ask old-timers if you do not know the CNS webpages password. | ||
| + | |||
| + | If you run into a problem and then manage to solve it, please edit [[http://www.cns.gatech.edu/CNS-only/fetchTunnel.html|"Fetch CNS ssh tunneling scripts"]] in svn wwwcns repository accordingly, so the next person has less trouble figuring this out... | ||
| + | |||
| + | Channelflow is hosted at [[http://svn.channelflow.org]], so you can access it directly with svn commands from anywhere --no ssh tunneling required. See the [[docs:install|Installation instructions]]. | ||
| ====== install channelflow ====== | ====== install channelflow ====== | ||
| Line 50: | Line 54: | ||
| Below are two sets of instructions for submitting jobs to the queue. The first describes direct use of the | Below are two sets of instructions for submitting jobs to the queue. The first describes direct use of the | ||
| - | PBS ''qsub'' command. The second uses a shell script I wrote to simplify to | + | PBS ''qsub'' command. The second uses a shell script named ''qsubmit'' I wrote to enable one-line |
| + | queue submissions. | ||
| For further information see the ''qsub'' and ''qstat'' man pages on pacemaker.gatech.edu (type ''man qsub'' at the command-line) | For further information see the ''qsub'' and ''qstat'' man pages on pacemaker.gatech.edu (type ''man qsub'' at the command-line) | ||
| and [[http://www.pace.gatech.edu/facilities/pacecc/starting.php?section=developing&topic=Submitting+Your+Jobs|The official | and [[http://www.pace.gatech.edu/facilities/pacecc/starting.php?section=developing&topic=Submitting+Your+Jobs|The official | ||
| PACE documentation]]. | PACE documentation]]. | ||
| - | |||
| ===== using the PBS qsub command ===== | ===== using the PBS qsub command ===== | ||
| Line 62: | Line 66: | ||
| 1. Log on to pacemaker.pace.edu. | 1. Log on to pacemaker.pace.edu. | ||
| - | 2. Create a ''.pbs'' file with a text editor (e.g. xemacs, vi), using the following as a template | + | 2. Create a PBS job description file with a text editor (e.g. xemacs, vi) |
| + | and with a ''.pbs'' filename extension. I'll use the filename ''foo.pbs''. | ||
| + | Use the following as a template. | ||
| <code> | <code> | ||
| Line 83: | Line 89: | ||
| - | 4. Submit the job using ''qsub'' (assuming the ''.pbs'' file is named ''foo.pbs'') | + | 4. Submit the job using ''qsub'' |
| <code> | <code> | ||
| jg356@pacemaker$ qsub foo.pbs | jg356@pacemaker$ qsub foo.pbs | ||
| </code> | </code> | ||
| - | |||
| ===== using the qsubmit shell script ===== | ===== using the qsubmit shell script ===== | ||
| - | 1. Put the following bash function definition in your ''~/.bash_alias'' or ''~/.bashrc'' file | + | 1. Put the following bash function definition in your ''~/.bash_aliases'' or ''~/.bashrc'' file |
| on PACE. | on PACE. | ||
| Line 129: | Line 134: | ||
| etc and then submitting that file to ''qsub''. Modify it to your liking. | etc and then submitting that file to ''qsub''. Modify it to your liking. | ||
| + | ====== view the results ====== | ||
| - | + | The standard output and standard error streams of your process (what is normally printed in | |
| - | http://www.pace.gatech.edu/facilities/pacecc/starting.php?section=developing&topic=Submitting+Your+Jobs | + | a terminal) will be saved in the files ''~/jobname.oXXXX'' and ''~jobname.eXXXX'' where XXXX |
| - | + | is a job ID number set by the PBS queueing system. Any data saved to disk will be placed in the | |
| - | ====== view the results ====== | + | directory where the job was started. |
gtspring2009/howto/pace.1246284181.txt.gz · Last modified: 2009/06/29 07:03 by gibson
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