Re: [slurm-users] Environment modules

[Mariano.Maluf]

Thank you all for your suggestions, comments and for your time.
I will try Lmod.
All the best.
Mariano

Re: [slurm-users] Environment modules

[Steven Dick]

lmod can mark modules as deprecated, so users are warned.  I think you
might also be able to get it to collect statistics on module usage or
something.

lmod also has the advantage of being much more complicated and much less
efficient if set up incorrectly.

On Sun, Nov 24, 2019 at 9:20 PM Brian Andrus  wrote:

> Is there something besides versioning that lmod shines at?
>
>

Re: [slurm-users] Environment modules

[Brian Andrus]

I never understood the benefit of lmod vs environment modules, although 
I see a push to use lmod. Particularly for versioning, but I always 
managed versions by using directory hierarchies. For instance, OpenMPI:


mpi/openmpi/3.2.3
mpi/openmpi/4.0.2

Then set a conflict on the top path (mpi/openmpi), which forces only one 
version to be able to be loaded. I also set paths so specific versions 
of libraries become available depending on what environment you select 
(gcc vs intel for example).


Is there something besides versioning that lmod shines at?

Brian Andrus


On 11/24/2019 12:48 AM, Yair Yarom wrote:
We also use lmod here. Very useful when different versions are needed 
or for any software installations outside the distribution.


However, our environment is heterogenous, and the software modules 
might have different versions/paths on different nodes. This creates 
an issue when users run 'module load something' on the submission 
node, and then run srun/sbatch and the wrong module is loaded (or just 
the wrong PATH is kept).
To solve this (in an overly complicated manner..) we have a taskprolog 
plugin and a spank plugin that: a. resets the modules at submission, 
and b. let the user add "--module " to the srun/sbatch so 
that the appropriate module will be loaded on the nodes.


On Sat, Nov 23, 2019 at 11:55 AM William Brown 
mailto:will...@signalbox.org.uk>> wrote:


Agreed, I have just been setting up Lmod on a national compute
cluster where I am a non-privileged cluster and on an internal
cluster where I have full rights.  It works very well, and Lmod
can read theTcl module files also.  The most recent version has
some extra features specially for Slurm.  An I use EasyBuild,
saves hundreds of hours of effort.   I do quite often have to hand
create simple module files for software with no EasyConfig but I
can just copy the structure from module files created by EasyBuild
so it has never been a great problem.

The best bit of modules is being able to offer multiple
conflicting versions of software like Java, Perl, R etc.

William

On Sat, 23 Nov 2019 at 03:57, Chris Samuel mailto:ch...@csamuel.org>> wrote:

On 22/11/19 9:37 am, Mariano.Maluf wrote:

> The cluster is operational but I need to install and configure
> environment modules.

If you use Easybuild to install your HPC software then it can
take care
of the modules too for you.  I'd also echo the recommendation
from
others to use Lmod.

Website: https://easybuilders.github.io/easybuild/
Documentation: https://easybuild.readthedocs.io/

All the best,
Chris
-- 
  Chris Samuel  : http://www.csamuel.org/  : Berkeley, CA, USA




--
   /||
   \/|Yair Yarom | Senior DevOps Architect
   []|The Rachel and Selim Benin School
   []  /\ |of Computer Science and Engineering
   []//\\/   |The Hebrew University of Jerusalem
   [//   \\   |T +972-2-5494522 | F +972-2-5494522
   // \   |ir...@cs.huji.ac.il 
  // |

Re: [slurm-users] Environment modules

[Yair Yarom]

We also use lmod here. Very useful when different versions are needed or
for any software installations outside the distribution.

However, our environment is heterogenous, and the software modules might
have different versions/paths on different nodes. This creates an issue
when users run 'module load something' on the submission node, and then run
srun/sbatch and the wrong module is loaded (or just the wrong PATH is kept).
To solve this (in an overly complicated manner..) we have a taskprolog
plugin and a spank plugin that: a. resets the modules at submission, and b.
let the user add "--module " to the srun/sbatch so that the
appropriate module will be loaded on the nodes.

On Sat, Nov 23, 2019 at 11:55 AM William Brown 
wrote:

> Agreed, I have just been setting up Lmod on a national compute cluster
> where I am a non-privileged cluster and on an internal cluster where I have
> full rights.  It works very well, and Lmod can read theTcl module files
> also.  The most recent version has some extra features specially for
> Slurm.  An I use EasyBuild, saves hundreds of hours of effort.   I do quite
> often have to hand create simple module files for software with no
> EasyConfig but I can just copy the structure from module files created by
> EasyBuild so it has never been a great problem.
>
> The best bit of modules is being able to offer multiple conflicting
> versions of software like Java, Perl, R etc.
>
> William
>
> On Sat, 23 Nov 2019 at 03:57, Chris Samuel  wrote:
>
>> On 22/11/19 9:37 am, Mariano.Maluf wrote:
>>
>> > The cluster is operational but I need to install and configure
>> > environment modules.
>>
>> If you use Easybuild to install your HPC software then it can take care
>> of the modules too for you.  I'd also echo the recommendation from
>> others to use Lmod.
>>
>> Website: https://easybuilders.github.io/easybuild/
>> Documentation: https://easybuild.readthedocs.io/
>>
>> All the best,
>> Chris
>> --
>>   Chris Samuel  :  http://www.csamuel.org/  :  Berkeley, CA, USA
>>
>>

-- 

  /|   |
  \/   | Yair Yarom | Senior DevOps Architect
  []   | The Rachel and Selim Benin School
  [] /\| of Computer Science and Engineering
  []//\\/  | The Hebrew University of Jerusalem
  [//  \\  | T +972-2-5494522 | F +972-2-5494522
  //\  | ir...@cs.huji.ac.il
 //|

Re: [slurm-users] Environment modules

[William Brown]

Agreed, I have just been setting up Lmod on a national compute cluster
where I am a non-privileged cluster and on an internal cluster where I have
full rights.  It works very well, and Lmod can read theTcl module files
also.  The most recent version has some extra features specially for
Slurm.  An I use EasyBuild, saves hundreds of hours of effort.   I do quite
often have to hand create simple module files for software with no
EasyConfig but I can just copy the structure from module files created by
EasyBuild so it has never been a great problem.

The best bit of modules is being able to offer multiple conflicting
versions of software like Java, Perl, R etc.

William

On Sat, 23 Nov 2019 at 03:57, Chris Samuel  wrote:

> On 22/11/19 9:37 am, Mariano.Maluf wrote:
>
> > The cluster is operational but I need to install and configure
> > environment modules.
>
> If you use Easybuild to install your HPC software then it can take care
> of the modules too for you.  I'd also echo the recommendation from
> others to use Lmod.
>
> Website: https://easybuilders.github.io/easybuild/
> Documentation: https://easybuild.readthedocs.io/
>
> All the best,
> Chris
> --
>   Chris Samuel  :  http://www.csamuel.org/  :  Berkeley, CA, USA
>
>

Re: [slurm-users] Environment modules

[Chris Samuel]

On 22/11/19 9:37 am, Mariano.Maluf wrote:

The cluster is operational but I need to install and configure 
environment modules.


If you use Easybuild to install your HPC software then it can take care 
of the modules too for you.  I'd also echo the recommendation from 
others to use Lmod.


Website: https://easybuilders.github.io/easybuild/
Documentation: https://easybuild.readthedocs.io/

All the best,
Chris
--
 Chris Samuel  :  http://www.csamuel.org/  :  Berkeley, CA, USA

Re: [slurm-users] Environment modules

[Ree, Jan-Albert van]

Jan-Albert van Ree  | Linux System Administrator | Digital Services
MARIN | T +31 317 49 35 48 | mailto:j.a.v@marin.nl | http://www.marin.nl

Just install the default CentOS RPM package environment-modules and play with 
it. If you're at home in bash you'll pick it up in minutes.

All default modules will be put in /usr/share/Modules/modulefiles or 
/etc/modulefiles for CentOS but you can add new locations (in a cluster you'd 
put it on the shared filesystem, so all nodes can have immediate access after 
installing it there)

For the correct syntax for environment modules , just check out some default 
modulefiles ; install the CentOS openmpi package and look at the file 
/etc/modulefiles/mpi/openmpi-x86_64 for some of the possibilities with 
modulefiles , although there's a lot more possible, such as automatically 
loading of dependent modules

Hope this helps
--
Jan-Albert



From: slurm-users  on behalf of 
Mariano.Maluf 
Sent: Friday, November 22, 2019 18:37
To: slurm-users@lists.schedmd.com
Subject: [slurm-users] Environment modules

Hi all

I am setting up for the first time a cluster with Slurm in Centos7 with
1 headnode and 12 nodes.

The cluster is operational but I need to install and configure
environment modules.

Could you advise me some documentation about it?

Thanks in advance.

Regards,
Mariano.

--
Lic. Mariano Maluf
Universidad Nacional de San Martín
2033-1400 int. 6046

Re: [slurm-users] Environment modules

[Nguyen Dai Quy]

On Fri, Nov 22, 2019 at 6:37 PM Mariano.Maluf 
wrote:

> Hi all
>
> I am setting up for the first time a cluster with Slurm in Centos7 with
> 1 headnode and 12 nodes.
>
> The cluster is operational but I need to install and configure
> environment modules.
>
> Could you advise me some documentation about it?
>
>
Nothing to see with Slurm :-)
But it's not so hard to setup. Just define your path to modulefiles, the
same for headnode & nodes. Put your module files on shared folder for all
nodes. That's all :-)





> Thanks in advance.
>
> Regards,
> Mariano.
>
> --
> Lic. Mariano Maluf
> Universidad Nacional de San Martín
> 2033-1400 int. 6046
>
>
>

Re: [slurm-users] Environment modules

[Wiegand, Paul]

We use TACC's lmod system.  It is pretty straightforward to setup and 
reasonably well documented:

https://www.tacc.utexas.edu/research-development/tacc-projects/lmod

Paul.


> On Nov 22, 2019, at 12:37 PM, Mariano.Maluf  wrote:
> 
> Hi all
> 
> I am setting up for the first time a cluster with Slurm in Centos7 with 1 
> headnode and 12 nodes.
> 
> The cluster is operational but I need to install and configure environment 
> modules.
> 
> Could you advise me some documentation about it?
> 
> Thanks in advance.
> 
> Regards,
> Mariano.
> 
> -- 
> Lic. Mariano Maluf
> Universidad Nacional de San Martín
> 2033-1400 int. 6046
> 
> 

[slurm-users] Environment modules

[Mariano.Maluf]

Hi all

I am setting up for the first time a cluster with Slurm in Centos7 with 
1 headnode and 12 nodes.


The cluster is operational but I need to install and configure 
environment modules.


Could you advise me some documentation about it?

Thanks in advance.

Regards,
Mariano.

--
Lic. Mariano Maluf
Universidad Nacional de San Martín
2033-1400 int. 6046