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WebMO Support Forum » WebMO Installation » Other » Connection refused for pipe to qsub in daemon_pbs.cgi « Previous Next »

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Jack Smith
Unregistered guest
Posted on Monday, February 06, 2012 - 11:39 pm:   

We recently switched from PBS to SGE, and I've made all the documented changes (plus a fix for $PBS_NODEFILE in the generated pbs_script.sh file), but I still get the following errors:

[Mon Feb 6 20:52:58 2012] gamess.cgi: error: commlib error: got select error (Connection refused) at daemon_pbs.cgi line 415.
error: commlib error: got select error (Connection refused)
error: unable to send message to qmaster using port 6444 on host "biggreen.local": got send error

However, I can manually execute the pbs_script.sh file with qsub just fine.

Using WebMO 10.1, Perl 5.8.8, and SGE 6.2u5, Rocks+ 6.0
JR Schmidt
Moderator
Username: Schmidt

Post Number: 226
Registered: 11-2006
Posted on Tuesday, February 07, 2012 - 10:40 am:   

When you manually qsub the script, does the job queue and run?

The "connection refused" issue sounds like a possible firewall problem on the host. If you google the error, it comes up several times. I'm not sure this is a WebMO issue per se. Make sure SGE itself is running fine on the command line.
Jack Smith
Unregistered guest
Posted on Tuesday, February 07, 2012 - 12:07 pm:   

Yes, I can manually run (qsub) pbs_script.sh just fine - it queues up and executes successfully, from the very same directory and logged in as webmo. I was wondering if it could be an issue with Perl or Apache (httpd/CGI). I will try to run the CGI script manually to see if that has a different effect.
Jack Smith
Unregistered guest
Posted on Tuesday, February 07, 2012 - 12:37 pm:   

It turns out that I can run the run_gamess.cgi script manually just fine. Could there be a problem with the Apache (httpd) configuration that's preventing qsub from being run (or communicating with qmaster) within a CGI Perl script?
JR Schmidt
Moderator
Username: Schmidt

Post Number: 227
Registered: 11-2006
Posted on Tuesday, February 07, 2012 - 1:16 pm:   

The run_gamess.cgi script isn't the issue. The submission to SGE doesn't happen at that point.

Make sure the sge_qmaster port is set in /etc/services, as described in https://www.webmo.net/support/enterprise.html.
Jack Smith
Unregistered guest
Posted on Tuesday, February 07, 2012 - 6:57 pm:   

I realize that qsub is executed in daemon_pbs.cgi, but I needed to high enough in the CGI hierarchy to have a complete and valid job to submit (using a previously aborted job and remaking the appropriate tmp directory). Yes, the sge_qmaster port is set in /etc/services, and I had followed the instructions in the provided link. I can submit jobs manually fine, just not from the web interface.
JR Schmidt
Moderator
Username: Schmidt

Post Number: 228
Registered: 11-2006
Posted on Tuesday, February 07, 2012 - 7:41 pm:   

The only thing I can think of is that perhaps some SGE related environmental variables are defined in a login script, such that it works on the command line but not from HTTP.

Does "biggreen.local" resolve to an actual IP address? Is this the machine where SGE is running?

I have never seen this issue before with WebMO/SGE and normally no additional environmental variables are needed.

Is there anything
Jack Smith
Unregistered guest
Posted on Tuesday, February 07, 2012 - 7:53 pm:   

Yes, "biggreen.local" (also biggreen.marshall.edu) is the master node where SGE runs, and it does resolve to an IP address. I'll continue to do some exploring. I mainly wanted to make sure it wasn't something obvious from your perspective. By the way, does v12.0 fix the $PBS_NODEFILE problem in daemon_pbs.cgi for SGE? I had to co-opt it into using $pe_hostfile (or $TMPDIR/machines) for SGE.

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