Hi,

The drmaa library seems suspect here, I am not sure what the current state
of the Platform/IBM-supplied libdrmaa is but the vendor versions have given
me problems in the past. Could you try FedStage DRMAA for LSF?:

    http://sourceforge.net/projects/lsf-drmaa/files/lsf_drmaa/

This does look a bit older than FedStage/PSNC's other DRMAA implementations
but the FedStage/PSNC implementations have been known to work well in the
past, and this library can also have debugging output enabled (./configure
--enable-debug) if you get segfaults with it (and would be useful for
producing cores).

--nate


On Sun, Jun 15, 2014 at 10:15 AM, INKozin <i.n.ko...@googlemail.com> wrote:

> 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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