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:
- 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.camailto: 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.camailto: Iyad.Kandalaft@agr.gc.ca Telephone | Téléphone 613-759-1228tel:613-759-1228 Facsimile | Télécopieur 613-759-1701tel:613-759-1701 Teletypewriter | Téléimprimeur 613-773-2600tel:613-773-2600 Government of Canada | Gouvernement du Canada
From: galaxy-dev-bounces@lists.bx.psu.edumailto: galaxy-dev-bounces@lists.bx.psu.edu [mailto: galaxy-dev-bounces@lists.bx.psu.edumailto: 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.edumailto: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.