Re: [scipion-users] problem using queuing system

[Juha H. <ju...@st...>]

Hi Gary,

Please contact me directly if you are still struggling with it and I can
share our host.conf file for Univa Grid Engine with you.

Best wishes,
Juha

On Wed, Sep 13, 2017 at 9:23 AM, Jose Miguel de la Rosa Trevin <
del...@gm...> wrote:

> 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..." <sci...@li...urcefor
>> ge.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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>>
>> This email message and any attachments are confidential and intended for
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>
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