FAQ

Frequently asked questions about the DCSR facilities and services

I'm a PI and would like to use the clusters - what do I do?

It's easy! Please fill in the request form at https://conference.unil.ch/research-resource-requests/ and we'll get back in touch with you as soon as possible.

How do I get an account on the clusters?

Your PI needs to add you to the project group.

Once this is done your account will be created - normally this is done the next day but it can occasionally take longer.

Note that if you work for the CHUV then you do not automatically have a UNIL account and will need to create one before you can access the clusters. The procedure is explained at: https://www.unil.ch/ci/ui/ext-hosp

 

How do I ask for help?

Before asking for help please take the time to check that your question hasn't already been answered in our FAQ.

To contact us please send an e-mail to the UNIL Helpdesk at helpdesk@unil.ch starting the subject with DCSR 

From:    user.lambda@unil.ch

To:      helpdesk@unil.ch

Subject: DCSR Cannot run CowMod on Axiom

Dear DCSR,
I am unable to run the CowMod code on Axiom - please see job number 1234567 for example.

The error message is "No grass left in field - please move to alpage"

You can find my input in /users/ulambda/CowMod/tests/hay/

To reproduce the issue on the command line the following recipe works (or rather doesn't work)

module load CowMod
cd /users/ulambda/CowMod/tests/hay/
CowMod --input=Feedtest 

Thanks

Dr Lambda

It helps us if you can provide all relevant information including how we can reproduce the problem and a Job ID if you submitted your task via the batch system.

Once we have analysed your problem we will get in touch with you.

Access to the old Vital-IT archive data

The data which were present on the old Vital-IT archive will remain available in READ ONLY for the forseeable future.

This page describes various ways to get access to these data, however keep in mind that most of them are stored on tape, therefore if you need large quantities of files (> 1000) it is more efficient to send a e-mail to helpdesk@vital-it.ch with DCSR retrieve Vital-IT data in the subject.

From linux or Mac

From archive to system: $ scp <username>@dexvital.unil.ch:/vital-it/archive/path/to/fileToCopy /path/to/dest

Where:

<username> your Vital-IT username

From Windows

Windows users can use WinSCP.

Step 1: create a new session to dexvital.unil.ch with your Vital-IT username

Screenshot 2021-05-12 at 12.06.42 .png

 

Accept the ssh key

 

Then navigate to your directory

 

Screenshot 2021-08-10 at 16.34.49.png

Select the file to transfer and the destination in the following popup

Screenshot 2021-08-10 at 16.37.25.png

Screenshot 2021-08-10 at 16.37.44.png

Then wait for the completion of the transfer

How do I move data to and from the UNIL NAS?

The documentation can be found at:

https://wiki.unil.ch/ci/books/service-de-calcul-haute-performance-%28hpc%29/page/data-management

 

 

I accidentally deleted a file - can I get it back?

This depends on where the file was and when it was created and deleted.

/scratch

There is no backup and no snapshots so the file is gone forever. 

/users

If it was in your home directory /users/<username>  then you can recover files from up to 7 days ago using the built-in snapshots by navigating to the hidden .snapshot directory as follows:

[ulambda@login1 ~]$ pwd
/users/ulambda

[ulambda@login1 ~]$ date
Tue Jan 14 12:00:00 CET 2020

[ulambda@login1 ~]$ cd .snapshot

[ulambda@login1 .snapshot]$ ls
2020.01.08.01.00.02.HPCU_user  
2020.01.09.01.00.01.HPCU_user  
2020.01.10.01.00.01.HPCU_user  
2020.01.11.01.00.01.HPCU_user  
2020.01.12.01.00.01.HPCU_user  
2020.01.13.01.00.01.HPCU_user  
2020.01.14.01.00.01.HPCU_user

[ulambda@login1 .snapshot]$ cd  2020.01.10.01.00.01.HPCU_user

[ulambda@login1 2020.01.10.01.00.01.HPCU_user]$ ls
..
my_deleted_file
..
..


If the file was in a subdirectory then you can also open .snapshot directly in the affected directory.

The snapshots are taken at 1am in the morning so if you created a file in the morning and deleted it the same afternoon then we can't help.

Beyond 7 days the file is lost forever.

Can you install package X for me?

 

The answer is maybe.

General interest tools and libraries

 

If it's a general purpose tool that may be useful to multiple groups then we can do so but will require the following information:

Until we have all the above information no work will be carried out.

 

Domain or group specific codes

 

If the code is only for use by one researcher or research group then we will provide assistance to install it but will not install it centrally.

 

Why are my jobs waiting due to QOSGrpCpuLimit?

On the DCSR clusters long jobs (more that one day) are only allowed to occupy 2/3 of the CPUs at any one time.

This is for the following reasons:

When you submit a job it is automatically assigned a Quality of Service (QoS) policy which is used to apply this restriction.

If you see your jobs pending with the reason QOSGrpCpuLimit then it means that long running jobs are currently occupying all the available CPU slots and it will not run until some long tasks complete.

 

 

How to provide an external collaborator with an account on HPC clusters?

There are three steps:

  1. The PI and the external collaborator must ask an account to UNIL using this form
  2. the PI to whom the external collaborator is related must use this application to add the collaborator into the appropriate project. Log into the application if necessary on the top right, and click on the "Manage members list / Gérer la liste de membres" icon for your project. The usernames always have 8 characters (e.g. Greta Thunberg username would be: gthunber)
  3. the external collaborator needs to use the UNIL VPN:

    https://www.unil.ch/ci/fr/home/menuinst/catalogue-de-services/reseau-et-telephonie/acces-hors-campus-vpn/documentation.html

The external collaborator under VPN can then login to the HPC cluster as if he was inside the UNIL.

Why is there a DCSR GitLab service and what is it?

What is it?

The DCSR hosted version control service (https://gitlab.dcsr.unil.ch) is primarily intended for the users of the "sensitive" data clusters which do not have direct internet access. It is not an official UNIL wide version control service!

It is accessible from both the sensitive data services and the UNIL network. From outside the UNIL network a VPN connection is required. It is open to all registered users of the DCSR facilities and is hosted on reliable hardware.

Should I use it?

If you are a user of the sensitive data clusters/services then the answer is yes.

For other users it may well be more convenient to use internet accessible services such as c4science.ch or GitHub.com as these allow for external collaborations and do not require VPN access or an account on the DCSR systems.

Groups may wish to use it to host a copy (mirror) of publicly hosted repositories (especially GitHub.com) to ensure that their code remains available in the case of changes to the free service.

How to give access to my files on the UNIL NAS to an external collaborator

There are two administrative steps:

  1. the PI and the external collaborator must ask an account to UNIL using this form
  2. the PI (Principal Investigator) to whom the external collaborator is related must use this application to add the collaborator into the appropriate project. Log into the application if necessary on the top right, and click on the "Manage members list / Gérer la liste de membres" icon for your project. The usernames always have 8 characters (e.g. Greta Thunberg username would be: gthunber)

The external collaborator can then access the data of the project stored on the UNIL NAS using VPN:

How to install and use the UNIL VPN:

https://www.unil.ch/ci/fr/home/menuinst/catalogue-de-services/reseau-et-telephonie/acces-hors-campus-vpn/documentation.html

How to access the NAS from a laptop:

https://wiki.unil.ch/ci/link/239#bkmrk-laptop-%3C-%3E-nas