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.kozin@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.Kandalaft@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.Kandalaft@agr.gc.ca | (613) 759-1228 ________________________________ From: igko50@gmail.com [igko50@gmail.com] on behalf of INKozin [ i.n.kozin@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.Kandalaft@agr.gc.ca<mailto: Iyad.Kandalaft@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.Kandalaft@agr.gc.ca<mailto: Iyad.Kandalaft@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-bounces@lists.bx.psu.edu<mailto: galaxy-dev-bounces@lists.bx.psu.edu> [mailto: galaxy-dev-bounces@lists.bx.psu.edu<mailto: galaxy-dev-bounces@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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