Re: [scipion-users] problem using queuing system

[Jose M. de la R. T. <del...@gm...>]

Hi Gary,

I think I know what the problem is. You need to specify 'localhost' in the
host.conf file.
I know it could be a bit confusing and we may improve this in the future.
It should be able to submit the jobs in your cluster. The _launchRemote
function in the
Python code is not fully working. It will be used for a future idea of
launching jobs
to more than one machines (clusters or not), but this is still not working.

Best,
Jose Miguel



On Tue, Sep 12, 2017 at 10:37 PM, Gary Smith <gar...@vr...> wrote:

> 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...>
> Date: Tuesday, September 12, 2017 at 4:34 PM
> To: Vertex <gar...@vr...>
> Cc: "sci...@li..." <scipion-users@lists.
> sourceforge.net>
> 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...> 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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