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

[Miguel Gutiérrez Páez]

Hi,

Home directory are also shared among all nodes (and head one as well). The
base system (that is, local drive, including os, system files, etc) are
identical and cloned based among all the hosts. If I need to install some
light package (dev version of a library for example or similar) I install
it over all the nodes with, for example, ansible, but this is not usual and
99% of apps, libraries or wathever, are installed on a shared location and
managed with lmod.

Regards

El sáb., 12 may. 2018 6:06, Eric F. Alemany <ealemany at stanford.edu>
escribió:

> HI Miguel,
>
> Thank you for your comment. That sounds pretty straight forward.
> you never had issues with programs relying on the system files or relying
> on the home directory location?
>
> Thanks
> 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 11:55 PM, Miguel Gutiérrez Páez <mgutierrez at gmail.com>
> wrote:
>
> 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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