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

[Eric F. Alemany]

._____________________________________________________________________________________________________

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<tel:1-650-498-7969>  No Texting
Fax:1-650-723-7382<tel:1-650-723-7382>

On May 12, 2018, at 00:08, John Hearns <hearnsj at googlemail.com<mailto:hearnsj at googlemail.com>> wrote:

Eric, I'm sorry to be a little prickly here.
Each node has an independent home directory for the user?
How then do applications update dot files?
How then would as a for instance do the users edit the .bashrc file to bring Anaconda into their paths?

Beofre anyone says it, a proper Modules system is the way forward.
But I know that when you install Anaconda as a user it adds the path to your .bashrc
Which fouls up Gnomes dbus daemon, which is another tale.







On 12 May 2018 at 07:09, Eric F. Alemany <ealemany at stanford.edu<mailto:ealemany at stanford.edu>> wrote:
Hi Chris,

Thank you for your comments. I will look at Easybuild. There are quite a few options to automate the creation of software modules.

I will be doing lots of reading this week-end.

By the way, i signed up to the Beowulf mailing list.

Thank you,

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<tel:1-650-498-7969>  No Texting
Fax:1-650-723-7382<tel:1-650-723-7382>



On May 11, 2018, at 12:56 AM, Chris Samuel <chris at csamuel.org<mailto:chris at csamuel.org>> wrote:

On Friday, 11 May 2018 5:11:38 PM AEST John Hearns wrote:

Eric, my advice would be to definitely learn the Modules system and
implement modules for your users.

I will echo that, and the suggestion of shared storage (we use our Lustre
filesystem for that).  I would also suggest looking at a system to help you
automate building of software packages.   Not only does this help replicate
builds, but it also gives you access to the community who write the recipes
for them - and that itself can be very valuable.

We use Easybuild (which also automates the creation of software modules - and
I would suggest using the Lmod system for that):

https://easybuilders.github.io/easybuild/

But there's also Spack too:

https://spack.io/

As another resource (as we are going off topic from Slurm here), I would
suggest the Beowulf list as a mailing list that deals with Linux based HPC
systems of many different scales.  Disclosure: I now caretake the list, but
it's been going since the 1990s.

http://beowulf.org/

All the best!
Chris
--
Chris Samuel  :  http://www.csamuel.org/  :  Melbourne, VIC




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