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December 12, 2019

PBS batch file format Log Out | Topics | Search
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John Keller
Unregistered guest
Posted on Wednesday, June 20, 2012 - 3:43 pm:   

Hi all,
I have installed the TORQUE batch file system (2.5.11) on openSUSE server, and have it communicating with a compute node. WebMO 12.1 and g09 are installed in the default locations. What should the PBS script look like to test the batch file system? I.e., what would the user webmo be creating as it submits a job?
JR Schmidt
Moderator
Username: Schmidt

Post Number: 257
Registered: 11-2006
Posted on Wednesday, June 20, 2012 - 3:48 pm:   

Go ahead and set up WebMO to interface with PBS ("System Manager" and "Batch Queue Manager"). Then submit a WebMO job.

You will see that WebMO creates a "pbs_script.sh" in the job directory (i.e. <userbase>/<username>/<jobnumber>/pbs_scripts.sh). This is the shell script that is actually sent to PBS via qsub.

Obviously, before doing any of the above make sure that you can submit a simple script to PBS and have it execute on the command line! You might try:

#!/bin/bash

echo `hostname`
echo SUCCESS!
John Keller
Unregistered guest
Posted on Wednesday, June 20, 2012 - 4:23 pm:   

Nope - the output for the simple test is placed in /undelivered folder on the compute node. When I do "qstat -f" the error message says among other things "key verification failed" Looks like passwordless SSH is necessary? The firewalls have been turned off on both these machines.
JR Schmidt
Moderator
Username: Schmidt

Post Number: 258
Registered: 11-2006
Posted on Wednesday, June 20, 2012 - 4:29 pm:   

Yes, password less SSH is typically necessary for Torque/PBS. I am not an expert (anymore) on getting Torque set up, so you might trying searching for a Torque HOWTO guide. There should be many. We have an OLD, outdated guide here:
https://www.webmo.net/support/pbs.html
and some of these ideas may still be useful.

Once Torque is working fine on the command line, it should be simple to get it working with WebMO.
John Keller
Unregistered guest
Posted on Friday, June 22, 2012 - 4:10 am:   

Yes, SSH is necessary, and the setup is covered in the admin manual. The test script you suggested now works. Webmo can install the compute node as a remote server, and jobs run. However, when I switch over to PBS, the same job fails. Webmo is installed in /home/keller. keller is also a user on the compute node, and is the destination user for SSH. The firewall hole has been created and you can access this server at

http://chemlinux5.cns.uaf.edu/~keller/cgi-bin/webmo/login.cgi

The errors file in the webmo directory of the webmo server contains many references to a perl time function issue.
Any suggestions for my next step?
JR Schmidt
Moderator
Username: Schmidt

Post Number: 259
Registered: 11-2006
Posted on Friday, June 22, 2012 - 10:11 am:   

Have you followed the entirity of the instructions for setting up WebMO to work with PBS, as outlined in:

https://www.webmo.net/support/enterprise.html

If so, and you are still experiencing problems, please set me up with command-line and WebMO access to that cluster and I will take a look (email account info to schmidt@webmo.net).
John Keller
Unregistered guest
Posted on Friday, June 22, 2012 - 2:34 pm:   

I have been following that, kinda. Although I can run the simple test script, a script to run g09 does not go. I put h2o.com input file and run_h2o.cmd script file in /home/keller and did qsub run_h2o.cmd. The output file run_h2o.cmd.o60 was produced. Somehow torque is still broken.
application/octet-streamg09 input
h2o.com (0.2 k)
application/octet-streamscript file
run_h2o.cmd (0.3 k)
application/octet-streamoutput file
run_h2o.cmd.o60 (0.6 k)
JR Schmidt
Moderator
Username: Schmidt

Post Number: 260
Registered: 11-2006
Posted on Friday, June 22, 2012 - 2:48 pm:   

add a line for:

hostname
pwd

to your run_h2o.cmd file so you can see what node it is running on, and what directory it is running in.
John Keller
Unregistered guest
Posted on Friday, June 22, 2012 - 3:02 pm:   

new file
chemlinux2
/home/keller
Unable to open input file "h2o.com".
Error: segmentation violation
rax 0000000000000000, rbx 00007fff47366ab8, rcx ffffffffffffffff
rdx 0000000000002769, rsp 00007fff47362c68, rbp 00007fff473669b0
rsi 000000000000000b, rdi 0000000000002769, r8 00002b2008af8260
r9 0000000000000000, r10 00007fff47362a00, r11 0000000000000202
r12 ffffffffffffffff, r13 00007fff47366ab0, r14 0000000000000000
r15 0000000000000000
--- traceback not available
/var/spool/torque/mom_priv/jobs/61.chemlinux5.cns.uaf.edu.SC: line 18: 10089 Aborted g09 h2o.com h2o.out
John Keller
Unregistered guest
Posted on Friday, June 22, 2012 - 3:04 pm:   

(Sorry this is garbled. I have about a 1/3 chance of the security graphic showing correctly...)
chemlinux2 is the compute node. chemlinux5 is the webmo server. webmo is installed in /home/keller/public_html

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