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 <[email protected]> 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 > [email protected] | (613) 759-1228 > ________________________________ > From: [email protected] [[email protected]] on behalf of INKozin [ > [email protected]] > Sent: June 14, 2014 6:18 PM > To: Kandalaft, Iyad > Cc: [email protected] > 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 <[email protected]<mailto: > [email protected]>> 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 [email protected]<mailto: > [email protected]> > 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: [email protected]<mailto: > [email protected]> [mailto: > [email protected]<mailto: > [email protected]>] On Behalf Of INKozin > Sent: Thursday, June 12, 2014 11:35 AM > To: [email protected]<mailto:[email protected]> > > 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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