[slurm-users] Python and R installation in a SLURM cluster

[Miguel Gutiérrez Páez]

Hi,

I install all my apps in a shared storage, and change environment variables
(path, vars, etc.) with lmod. It's very useful.

Regards.

El vie., 11 may. 2018 a las 6:19, Eric F. Alemany (<ealemany at stanford.edu>)
escribió:

> Hi Lachlan,
>
> Thank you for sharing your environment. Everyone has their own set of
> rules and i appreciate everyone’s input.
> It seems as if the NFS share is a great place to start.
>
> Best,
> Eric
>
> _____________________________________________________________________________________________________
>
> * Eric F.  Alemany *
> *System Administrator for Research*
>
> Division of Radiation & Cancer  Biology
> Department of Radiation Oncology
>
> Stanford University School of Medicine
> Stanford, California 94305
>
> Tel:1-650-498-7969  No Texting
> Fax:1-650-723-7382
>
>
>
> On May 10, 2018, at 4:23 PM, Lachlan Musicman <datakid at gmail.com> wrote:
>
> On 11 May 2018 at 01:35, Eric F. Alemany <ealemany at stanford.edu> wrote:
>
>> Hi All,
>>
>> I know this might sounds as a very basic question: where in the cluster
>> should I install Python and R?
>> Headnode?
>> Execute nodes ?
>>
>> And is there a particular directory (path) I need to install Python and R.
>>
>> Background:
>> SLURM on Ubuntu 18.04
>> 1 headnode
>> 4 execute nodes
>> NFS shared drive among all nodes.
>>
>
>
> Eric,
>
> To echo the others: we have a /binaries nfs share that utilises the
> standard Environment Modules software so that researchers can manipulate
> their $PATH on the fly with module load/module unload. That share is
> mounted on all the nodes.
>
> For Python, I use virtualenv's but instead of activating, the path is
> changed by the Module file. Personally, I find conda doesn't work very well
> in a shared environment. It's fine on a personal level/
>
> For R, we have resorted to only installing the main point release because
> we have >700 libraries installed within R and I don't want to reinstall
> them every time. We do also have packrat installed so researchers can
> install their own libraries locally as well.
>
>
> Cheers
> L.
>
>
>
>
>
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