Jan K. Labanowski: Computational Portals for Chemistry  

Example 1 files (cont.)

Under example1 directory you find the following files:
-rw-r--r--   1 tomcat4  tomcat4      818 Nov 14 10:25 description
-rw-r--r--   1 tomcat4  tomcat4      254 Nov 11 10:34 example1.in
-rw-r--r--   1 tomcat4  tomcat4      992 Nov 13 11:06 example1.script
-rw-r--r--   1 tomcat4  tomcat4     3203 Nov 11 09:41 example1.xyz
-rw-r--r--   1 tomcat4  tomcat4     2606 Nov 13 04:10 input-files.xml
-rw-r--r--   1 tomcat4  tomcat4     3567 Nov 13 11:23 output-files.xml
-rw-r--r--   1 tomcat4  tomcat4     2513 Nov 17 08:18 status.xml
The actual script after tags were replaced by the actual data.

wget -- GNU utility to retrieve Web pages, but used here to send status "messages" to the server. Option -O - sends the file retrieved to standard ouput. Note that the content of batch script is only known to Web server and to someone who can read it on the compute host (user who owns the account). It is assumed that the script is securely copied from Web server to the compute server (in this case ssh is used). The HTTP GET requests, however, are sent in the open and have to be protected against impersonation. Each message contains a password, which has to match the one in status.xml file. Password is only good for one use, and subsequent messages with this password are ignored. This could be easy to replace with the JAXM message (or other SOAP client), provided that it runs on the compute server.

#PBS -S /bin/sh
#PBS -N example1
#PBS -l nodes=1:ppn=1
#PBS -l cput=01:00:00
#PBS -l walltime=01:00:00
#PBS -r n
#PBS -eo
#PBS -m ae

sleep 2

wget -O - 'http://heechee.ccl.net:8080/listener/RunEvent.jsp?\
user=jkl@asdn.net&project=example1&event=JobStarted\
&password=uqiQoLVr0O7CFzK&message="The+example1+is+running' > event4.log 2>&1

sleep 2

cd /f/portal/PortalRuns/jkl@asdn.net/example1
mpiexec /home/osu2661/cmt/pse/ohmms-v1.1.x example1.in

sleep 2

wget -O - 'http://heechee.ccl.net:8080/listener/RunEvent.jsp?\
user=jkl@asdn.net&project=example1\
&event=CopyOutputFiles&password=t5GBECPzArrSYVI\
&message="The+example1+files+copied'  > event5.log 2>&1

sleep 2

wget -O - 'http://heechee.ccl.net:8080/listener/RunEvent.jsp?\
user=jkl@asdn.net&project=example1
&event=JobFinished&password=NwFnozEUq0fu1I5\
&message=The+example1+files+copied' > event6.log 2>&1
sleep 2