channelflow.org

====== Differences ====== This shows you the differences between two versions of the page.

--- gtspring2009:howto:pace [2009/02/22 16:54]
predrag fixed a few PACE links
+++ gtspring2009:howto:pace [2010/02/02 07:55] (current)
@@ Line 1: / Line 1: @@
 ====== 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
@@ Line 16: / Line 14: @@
 ====== PACE documentation ======
+[[http://www.pace.gatech.edu/facilities/pacecc/starting.php|The official PACE documentation page from OIT.]]
 {{:gtspring2009:pc.png|}} temptation to Balkanization is irresistible, but there is a
 [[http://www.cns.gatech.edu/CNS-only/PACE.html|CNS PACE homepage]] on the svn wwwcns repository,
 so please enter general (not channelflow specific) PACE documentation there.  --- //[[predrag.cvitanovic@physics.gatech.edu|Predrag Cvitanovic]] 2009-02-22 16:41//
+{{:gtspring2009:gibson.png?24}} You might be the only person on the planet with enough goodwill,
+patience, and CNS permissions to document via svn checkout, editing html, checkin, and recheckout
+as www on zero. Maybe we can get some contributions by lowering the overhead with dokuwiki editing.
 ====== PACE login ======
 {{: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 ======
-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 ======
@@ Line 35: / Line 45: @@
 Install channelflow on the PACE cluster. This should be straightforward. Follow
 the [[docs:install]] directions.
 ====== submit a job to the queue ======
-====== view the results ======
+The PACE cluster has PBS job-queue software that automatically distributes processes among the nodes (computers)
+in the cluster (e.g. pace1, pace2, ...). You //must// use this system to start long-running jobs (anything that
+runs for more than a few minutes), instead of logging onto a particular node, starting a job on the command-line,
+and backgrounding it. If you do the latter it'll interfere with the queuing system and annoy other users and
+the PACE administrators.
+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 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)
+and [[http://www.pace.gatech.edu/facilities/pacecc/starting.php?section=developing&topic=Submitting+Your+Jobs|The official
+PACE documentation]].
+===== using the PBS qsub command =====
+To submit a job using the PBS queue software,
+. Log on to pacemaker.pace.edu.
+. 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>
+#PBS -N arnoldi-EQ9-Re380
+#PBS -l nodes=1:ppn=1,walltime=72:00:00
+#PBS -q pace-cns
+#PBS -k oe
+#PBS -m abe
+cd /nv/hp1/jg356/simulations/narrowbox/arnoldi-EQ9/Re380
+arnoldi --flow -Na 100 -R 380 ../../continue-EQ9/Re380/ubest.ff
+</code>
+The lines in the above file specify
+  * -N a name for the job
+  * -l how many nodes, processors per node, and wallclock time the jobs is allowed
+  * -q the name of the queue the job should be submitted to
+  * -k save output and error files to ''~/arnoldi-EQ9-Re380.oXXXXX'' and ''.eXXXXX''
+  * -m send email when the job starts, stops, or is terminated
+  * ''cd /nv/hp1/jg356/....'' The Unix commands to execute to start the job
+. Submit the job using ''qsub''
+<code>
+jg356@pacemaker$ qsub foo.pbs
+</code>
+===== using the qsubmit shell script  =====
+. Put the following bash function definition in your ''~/.bash_aliases'' or ''~/.bashrc'' file
+on PACE.
+<code>
+function qsubmit() {
+  tag=$1
+  shift
+  echo "#PBS -N $tag" > tmp.pbs
+  echo "#PBS -l nodes=1:ppn=1,walltime=72:00:00" >> tmp.pbs
+  echo "#PBS -q pace-cns" >> tmp.pbs
+  echo "#PBS -k oe"   >> tmp.pbs
+  echo "#PBS -m abe"  >> tmp.pbs
+  echo "cd $(pwd)"    >> tmp.pbs
+  echo $*             >> tmp.pbs
+  cat tmp.pbs
+  qsub tmp.pbs
+}
+</code>
+. Load the new definition into your current shell (this will happen automatically the next time
+you log in).
+<code>
+jg356@pacemaker$ source ~/.bash_aliases
+</code>
+. Submit a job using the script
+<code>
+jg356@pacemaker$ qsubmit arnoldi-EQ9-Re380 arnoldi --flow -Na 100 -R 380 ../../continue-EQ9/Re380/ubest.ff
+</code>
+The first argument after ''qsubmit'' is the job name and the remaining arguments specify what is to be run,
+i.e. the Unix commands you would type is you were just running the process directly in the shell.
+The ''qsubmit'' script works by creating a ''tmp.pbs'' file with some default values for wallclock time
+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
+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
+directory where the job was started.

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