We are doing 1 one our clusters.
Like I said elsewhere the problem appears to be in the interaction between
Python DRMAA and LSF DRMAA, not Galaxy.


On 15 June 2014 01:51, Kandalaft, Iyad <iyad.kandal...@agr.gc.ca> wrote:

> If you are running galaxy on a cluster, you can do one of two things:
> 1. install python on every node in your cluster and ensure they are
> identical. <-- I've had problems with this method
> 2. use pyenv to create a python environment that gets sourced before you
> start galaxy and before any galaxy jobs are run.  I usually activate it by
> putting it in .bashrc
>
> Iyad Kandalaft
> Bioinformatics Programmer
> Microbial Biodiversity Bioinformatics
> Science & Technology Branch
> Agriculture & Agri-Food Canada
> iyad.kandal...@agr.gc.ca | (613) 759-1228
> ________________________________
> From: igk...@gmail.com [igk...@gmail.com] on behalf of INKozin [
> i.n.ko...@googlemail.com]
> Sent: June 14, 2014 6:18 PM
> To: Kandalaft, Iyad
> Cc: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] troubleshooting Galaxy with LSF
>
> I'm not sure what you mean. I'm not using python virtual env, anaconda etc
> But I do set all variables which are required to run Galaxy such as DRMAA
> path, PYTHONPATH.
> In addition to the default Python 2.6, I also tried Python 2.7 built from
> source.
>
>
> On 13 June 2014 17:34, Kandalaft, Iyad <iyad.kandal...@agr.gc.ca<mailto:
> iyad.kandal...@agr.gc.ca>> wrote:
> Just for my curiosity, are you running a python environment isolated for
> galaxy or just using a system wide python environment?
>
> Regards,
>
> Iyad Kandalaft
> Microbial Biodiversity Bioinformatics
> Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada
> 960 Carling Ave.| 960 Ave. Carling
> Ottawa, ON| Ottawa (ON) K1A 0C6
> E-mail Address / Adresse courriel  iyad.kandal...@agr.gc.ca<mailto:
> iyad.kandal...@agr.gc.ca>
> Telephone | Téléphone 613-759-1228<tel:613-759-1228>
> Facsimile | Télécopieur 613-759-1701<tel:613-759-1701>
> Teletypewriter | Téléimprimeur 613-773-2600<tel:613-773-2600>
> Government of Canada | Gouvernement du Canada
>
>
>
> From: galaxy-dev-boun...@lists.bx.psu.edu<mailto:
> galaxy-dev-boun...@lists.bx.psu.edu> [mailto:
> galaxy-dev-boun...@lists.bx.psu.edu<mailto:
> galaxy-dev-boun...@lists.bx.psu.edu>] On Behalf Of INKozin
> Sent: Thursday, June 12, 2014 11:35 AM
> To: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>
>
> Subject: Re: [galaxy-dev] troubleshooting Galaxy with LSF
>
>
> The problem seems to be with DRMAA for Python. While it works fine on the
> OpenSuse
>
> 12.1 box, I'm getting a segfault on RH 6.4.
> Surprisingly, the job however gets submitted and run successfully.
>
>
>
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