Re: [scipion-users] problem using queuing system

[Gary S. <gar...@vr...>]

This is what a normal qsub does when you submit a script to UGE...

$ qsub busy.sh
Your job 6836 ("bz") has been submitted
$

From: Jose Miguel de la Rosa Trevin <del...@gm...<mailto:del...@gm...>>
Date: Tuesday, September 12, 2017 at 4:34 PM
To: Vertex <gar...@vr...<mailto:gar...@vr...>>
Cc: "sci...@li...<mailto:sci...@li...>" <sci...@li...<mailto:sci...@li...>>
Subject: Re: [scipion-users] problem using queuing system

Hi Gary,

This error is because Scipion is trying to parse the output from the submission command. It tries to parse a number (the job id) from the output. Can you share the output of a successful submission command to the queue? This could give us a hint about the issue.

Best,
Jose Miguel



On Sep 12, 2017 8:53 PM, "Gary Smith" <gar...@vr...<mailto:gar...@vr...>> wrote:
I'm trying to get Scipion-1.1 running with our Univa Grid Engine setup (aka. SGE).  Scipion appears to be failing to use the launch protocol remotely, even though this works fine outside of Scipion.  Has anyone seen errors like this?

Error during EXECUTE: ** Couldn't parse ouput: [31m
Scipion v1.1 (2017-06-14) Balbino

[0m

Traceback:
Traceback (most recent call last):
  File "/cluster/app/scipion/1.1/pyworkflow/gui/form.py", line 1710, in _close
    message = self.callback(self.protocol, onlySave)
  File "/cluster/app/scipion/1.1/pyworkflow/gui/project/viewprotocols.py", line 1662, in _executeSaveProtocol
    self.project.launchProtocol(prot)
  File "/cluster/app/scipion/1.1/pyworkflow/project.py", line 417, in launchProtocol
    pwprot.launch(protocol, wait)
  File "/cluster/app/scipion/1.1/pyworkflow/protocol/launch.py", line 64, in launch
    jobId = _launchRemote(protocol, wait)
  File "/cluster/app/scipion/1.1/pyworkflow/protocol/launch.py", line 164, in _launchRemote
    raise Exception("** Couldn't parse ouput: %s" % redStr(out))
Exception: ** Couldn't parse ouput: [31m
Scipion v1.1 (2017-06-14) Balbino

[0m



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