Re: [slurm-users] Slurm and available libraries

[Elisabetta Falivene]

So EasyBuild + Lmod seems the best solution. I'll try. :)
Thank you all!
betta

2018-01-17 17:53 GMT+01:00 Christopher Samuel :

> On 18/01/18 03:50, Patrick Goetz wrote:
>
> Can anyone shed some light on the situation?  I'm very surprised that
>> a module script isn't just an explicit command that comes with the
>> lmod package, and am curious as to why this isn't completely
>> standard.
>>
>
> The module command needs to be able to manipulate the environment in
> the current shell, so it can't just be run as an external command,
> it's output has to be evaluated in the current shell.
>
> It looks like the second machine you mention is using Environment
> Modules, not Lmod.
>
>
> All the best,
> Chris
> --
>  Chris Samuel  :  http://www.csamuel.org/  :  Melbourne, VIC
>
>

Re: [slurm-users] Slurm and available libraries

[Christopher Samuel]

On 18/01/18 02:53, Loris Bennett wrote:


This is all very OT, so it might be better to discuss it on, say, the
OpenHPC mailing list, since as far as I can tell Spack, EasyBuild and
Lmod (but not old or new 'environment-modules') are part of OpenHPC.


Another place might be the Beowulf list, all about Linux HPC (started by
Don Becker many moons ago), now maintained by yours truly.

http://www.beowulf.org/

Happy to add people to the list if they wish, just email me directly.

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

Re: [slurm-users] Slurm and available libraries

[Loris Bennett]

Hi Ole,

Ole Holm Nielsen  writes:

> John: I would refrain from installing the old default package
> "environment-modules" from the Linux distribution, since it doesn't
> seem to be maintained any more.

Is this still true? Here

  http://modules.sourceforge.net/

there is a version 4.1.0 which is two days old.  Does anyone have any
experience of this and how it compares to the old version and/or Lmod?

> Lmod, on the other hand, is actively maintained and solves some
> problems with the old "environment-modules" software.
>
> There's an excellent review paper on different module tools: "Modern
> Scientific Software Management Using EasyBuild and Lmod",
> http://dl.acm.org/citation.cfm?id=2691141

Thanks for the link.  I would also be interested in how EasyBuild and
Spack compare in practice.

This is all very OT, so it might be better to discuss it on, say, the
OpenHPC mailing list, since as far as I can tell Spack, EasyBuild and
Lmod (but not old or new 'environment-modules') are part of OpenHPC.

Cheers,

Loris

-- 
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de

Re: [slurm-users] Slurm and available libraries

[Vanzo, Davide]

Hi Bill!

Always glad to contribute to the Lmod cause! ;)

Back to the discussion, I simply gave my contribution based on how we set up 
our system. In no way I intended to say that that is the only way to deploy 
software. Yours is definitely a valid alternative, although it requires a 
deeper experience in software packaging and deployment.

To solve the problem of users overloading the login nodes we are experimenting 
with cgroups, but here we are going a little too much off topic.

PS: Now that I am in San Antonio I have no more excuses to come and visit you 
guys at TACC.

--
Davide Vanzo, PhD
Application Developer
Adjunct Assistant Professor of Chemical and Biomolecular Engineering
Advanced Computing Center for Research and Education (ACCRE)
Vanderbilt University - Hill Center 201
(615)-875-9137
www.accre.vanderbilt.edu


On 2018-01-17 08:01:10-06:00 slurm-users wrote:

I’d go slightly further, though I do appreciate the Lmod shout-out!: In some 
cases, you may not even want the software on the frontend nodes (hear me out 
before I retract it).

If it’s a library that requires linking against before it can be used, then you 
probably have to have it unless you require users to submit interactive jobs to 
some dedicated build nodes to do their compilation. You’ll find that when users 
have all their software needs in one place on the frontend nodes, that 
sometimes they try to run it there, taking away resources from others. Now, a 
quick test run to make sure that their build is correct is probably no big 
deal, but some users will run their full-on science experiments (or pre- and 
post-processing steps) on the login nodes! We like to encourage those folks to 
submit jobs to the compute nodes. You could, but they probably wouldn’t like, 
cripple or not install some libraries on the login nodes to prevent this, but 
we just watch those systems like a hawk, given that we do want users to be able 
to build their programs on the login nodes.

We don’t use EB, but we do collaborate with them to make it and Lmod 
compatible. We use something like OpenHPC to push RPMs we build in-house to 
manage software on our login and compute nodes. Sometimes, we also just install 
a binary package (like an ISV code like ANSYS or MATLAB) into a shared 
filesystem (one of our Lustre filesystems, usually) when making our own RPM is 
too cumbersome, and then use Lmod to make it available and visible to our 
users. There are more strategies for this than you can imagine, so settle on a 
few and keep it simple for you!

Best,
Bill.

--
Bill Barth, Ph.D., Director, HPC
bba...@tacc.utexas.edu|   Phone: (512) 232-7069
Office: ROC 1.435|   Fax:   (512) 475-9445



On 1/17/18, 7:48 AM, "slurm-users on behalf of Vanzo, Davide" 
slurm-users-boun...@lists.schedmd.com on="" behalf="" of="" 
davide.va...@vanderbilt.edu="" wrote:

Ciao Elisabetta,

I second John's reply.
On our cluster we install software on the shared parallel filesystem with 
EasyBuild and use Lmod as a module front-end. Then users will simply load 
software in the job's environment by using the module command.

Feel free to ping me directly if you need specific help.


--
Davide Vanzo, PhD
Application Developer
Adjunct Assistant Professor of Chemical and Biomolecular Engineering
Advanced Computing Center for Research and Education (ACCRE)
Vanderbilt University - Hill Center 201
(615)-875-9137

https://na01.safelinks.protection.outlook.com/?url=www.accre.vanderbilt.eduamp;data=02%7C01%7Cdavide.vanzo%40vanderbilt.edu%7Ca55a733721e34284029d08d55db2bfa4%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636517944686221529amp;sdata=4qU%2FqW28JoTtmWYE9Jyjc1VeKOT7U4aiMQdsjXnAVYg%3Damp;reserved=0


On 2018-01-17 07:28:31-06:00 slurm-users wrote:

Hi,
let's say I need to execute a python script with slurm. The script require 
a particular library installed on the system like numpy.
If the library is not installed to the system, it is necessary to install 
it on the master AND the nodes, right? This has to be done on each machine 
separately or there's a way to install it one time for all the machine (master 
and nodes)?
Elisabetta







/slurm-users-boun...@lists.schedmd.com

Re: [slurm-users] Slurm and available libraries

[Bill Barth]

I’d go slightly further, though I do appreciate the Lmod shout-out!: In some 
cases, you may not even want the software on the frontend nodes (hear me out 
before I retract it). 

If it’s a library that requires linking against before it can be used, then you 
probably have to have it unless you require users to submit interactive jobs to 
some dedicated build nodes to do their compilation. You’ll find that when users 
have all their software needs in one place on the frontend nodes, that 
sometimes they try to run it there, taking away resources from others. Now, a 
quick test run to make sure that their build is correct is probably no big 
deal, but some users will run their full-on science experiments (or pre- and 
post-processing steps) on the login nodes! We like to encourage those folks to 
submit jobs to the compute nodes. You could, but they probably wouldn’t like, 
cripple or not install some libraries on the login nodes to prevent this, but 
we just watch those systems like a hawk, given that we do want users to be able 
to build their programs on the login nodes.

We don’t use EB, but we do collaborate with them to make it and Lmod 
compatible. We use something like OpenHPC to push RPMs we build in-house to 
manage software on our login and compute nodes. Sometimes, we also just install 
a binary package (like an ISV code like ANSYS or MATLAB) into a shared 
filesystem (one of our Lustre filesystems, usually) when making our own RPM is 
too cumbersome, and then use Lmod to make it available and visible to our 
users. There are more strategies for this than you can imagine, so settle on a 
few and keep it simple for you!

Best,
Bill.

-- 
Bill Barth, Ph.D., Director, HPC
bba...@tacc.utexas.edu|   Phone: (512) 232-7069
Office: ROC 1.435|   Fax:   (512) 475-9445
 
 

On 1/17/18, 7:48 AM, "slurm-users on behalf of Vanzo, Davide" 
 wrote:

Ciao Elisabetta,

I second John's reply.
On our cluster we install software on the shared parallel filesystem with 
EasyBuild and use Lmod as a module front-end. Then users will simply load 
software in the job's environment by using the module command.

Feel free to ping me directly if you need specific help.
 

-- 
Davide Vanzo, PhD
Application Developer
Adjunct Assistant Professor of Chemical and Biomolecular Engineering
Advanced Computing Center for Research and Education (ACCRE)
Vanderbilt University - Hill Center 201
(615)-875-9137
www.accre.vanderbilt.edu

 
On 2018-01-17 07:28:31-06:00 slurm-users wrote:

Hi,
let's say I need to execute a python script with slurm. The script require 
a particular library installed on the system like numpy.
If the library is not installed to the system, it is necessary to install 
it on the master AND the nodes, right? This has to be done on each machine 
separately or there's a way to install it one time for all the machine (master 
and nodes)?
Elisabetta

Re: [slurm-users] Slurm and available libraries

[John Hearns]

I should also say that Modules should be easy to install on Ubuntu. It will
 be the package named "environment-modules"

You probably will have to edit the configuration file a little bit since
the default install will assume al lModules files are local.
You need to set your MODULESPATH to include a shared directory where you
will keep all your Modules files.
This really is a lot easier than it sounds.

On 17 January 2018 at 14:48, Vanzo, Davide 
wrote:

> Ciao Elisabetta,
>
> I second John's reply.
> On our cluster we install software on the shared parallel filesystem with
> EasyBuild and use Lmod as a module front-end. Then users will simply load
> software in the job's environment by using the module command.
>
> Feel free to ping me directly if you need specific help.
>
> --
> *Davide Vanzo, PhD*
> Application Developer
> Adjunct Assistant Professor of Chemical and Biomolecular Engineering
> Advanced Computing Center for Research and Education (ACCRE)
> Vanderbilt University - Hill Center 201
> (615)-875-9137 <(615)%20875-9137>
> www.accre.vanderbilt.edu
>
>
> On 2018-01-17 07:28:31-06:00 slurm-users wrote:
>
> Hi,
> let's say I need to execute a python script with slurm. The script require
> a particular library installed on the system like numpy.
> If the library is not installed to the system, it is necessary to install
> it on the master AND the nodes, right? This has to be done on each machine
> separately or there's a way to install it one time for all the machine
> (master and nodes)?
> Elisabetta
>
>

Re: [slurm-users] Slurm and available libraries

[Ole Holm Nielsen]

I can highly recommend EasyBuild as an easy way to provide software 
packages as "modules" to your cluster.  We have been very pleased with 
EasyBuild in our cluster.


I made some notes about installing EasyBuild in a Wiki page:
  https://wiki.fysik.dtu.dk/niflheim/EasyBuild_modules
We use CentOS 7 Linux.

Also, if you want information about Slurm setup, I have written another 
set of Wiki pages:

  https://wiki.fysik.dtu.dk/niflheim/SLURM

/Ole

On 01/17/2018 02:39 PM, John Hearns wrote:
Hi Elisabetta.  No, you normally do not need to install software on all 
the compute nodes separately.


It is quite common to use the 'modules' environment to manage software 
like this

http://www.admin-magazine.com/HPC/Articles/Environment-Modules

Once you have numpy installed on a shared drive on the cluster, and have 
a Modules file in place, your users put this at the start of their job 
scripts:

module load numpy

You might also want to look at Easybuild 
http://easybuild.readthedocs.io/en/latest/Introduction.html

There are Easybuild 'recipes' for numpy. We use them where I work.



On 17 January 2018 at 14:28, Elisabetta Falivene 
> wrote:


Hi,
let's say I need to execute a python script with slurm. The script
require a particular library installed on the system like numpy.
If the library is not installed to the system, it is necessary to
install it on the master AND the nodes, right? This has to be done
on each machine separately or there's a way to install it one time
for all the machine (master and nodes)?

Elisabetta

Re: [slurm-users] Slurm and available libraries

[Vanzo, Davide]

Ciao Elisabetta,

I second John's reply.
On our cluster we install software on the shared parallel filesystem with 
EasyBuild and use Lmod as a module front-end. Then users will simply load 
software in the job's environment by using the module command.

Feel free to ping me directly if you need specific help.

--
Davide Vanzo, PhD
Application Developer
Adjunct Assistant Professor of Chemical and Biomolecular Engineering
Advanced Computing Center for Research and Education (ACCRE)
Vanderbilt University - Hill Center 201
(615)-875-9137
www.accre.vanderbilt.edu


On 2018-01-17 07:28:31-06:00 slurm-users wrote:

Hi,
let's say I need to execute a python script with slurm. The script require a 
particular library installed on the system like numpy.
If the library is not installed to the system, it is necessary to install it on 
the master AND the nodes, right? This has to be done on each machine separately 
or there's a way to install it one time for all the machine (master and nodes)?
Elisabetta

Re: [slurm-users] Slurm and available libraries

[John Hearns]

Hi Elisabetta.  No, you normally do not need to install software on all the
compute nodes separately.

It is quite common to use the 'modules' environment to manage software like
this
http://www.admin-magazine.com/HPC/Articles/Environment-Modules

Once you have numpy installed on a shared drive on the cluster, and have a
Modules file in place, your users put this at the start of their job
scripts:
module load numpy

You might also want to look at Easybuild
http://easybuild.readthedocs.io/en/latest/Introduction.html
There are Easybuild 'recipes' for numpy. We use them where I work.



On 17 January 2018 at 14:28, Elisabetta Falivene 
wrote:

> Hi,
> let's say I need to execute a python script with slurm. The script require
> a particular library installed on the system like numpy.
> If the library is not installed to the system, it is necessary to install
> it on the master AND the nodes, right? This has to be done on each machine
> separately or there's a way to install it one time for all the machine
> (master and nodes)?
>
> Elisabetta
>

[slurm-users] Slurm and available libraries

[Elisabetta Falivene]

Hi,
let's say I need to execute a python script with slurm. The script require
a particular library installed on the system like numpy.
If the library is not installed to the system, it is necessary to install
it on the master AND the nodes, right? This has to be done on each machine
separately or there's a way to install it one time for all the machine
(master and nodes)?

Elisabetta