Migration process

Which users?

In the current migration phase (Q4 2022) only GPU node users from specific institutes will be migrated. The reason for this is that these institutes have co-invested in Snellius GPU nodes, in order to provide continued GPU access to their users. As part of this investment 36 extra GPU nodes are added to Snellius, to accommodate for the extra users coming from Lisa.

The timetable below specifies the impact on GPU users (planning for CPU users follows in 2023):

Steps

1. SURF will create an account on Snellius for you, and provide you with access details by e-mail
2. If needed register your IP address with our Service Desk, as Snellius uses IP allow-listing. This means that unless your IP is registered you will not be able to log in on Snellius through SSH. By default we already allow certain IP ranges, so please try to log in first before contacting the Service Desk. See this FAQ entry for more information.
   

3. Once you have access to Snellius, you won't have access to Lisa anymore. You will then have to adapt your personal configuration to the Snellius environment (.bashrc, scratch locations, etc.).

   Don't copy your .bashrc and/or.bash_profile from your Lisa directory to your Snellius home directory, without checking them and updating where needed.

4. Logged in on Snellius, you can migrate your Lisa data to your new personal directory. The Lisa file systems will be mounted on Snellius as a read-only mount until 31-3-2023. You can copy your Lisa data to your Snellius homedir or project space. See below for details.
5. Check and adapt your batch scripts to the Snellius Slurm configuration (mainly the partition names and the cores-per-node parameters).
6. User-defined ACLs need to be reconfigured on Snellius, if necessary
   
7. Once your Lisa account expires the data on Lisa will be deleted after 15 weeks (in accordance with our data retention policy)

Time table

This is a provisional timeline, that will be updated as the migration planning in finalized. Please note that users of the Lisa GPU partitions are migrated first, followed by the users of the Lisa CPU partitions.

Transferring your data from Lisa to Snellius

To facilitate date migration the home filesystems of Lisa will be mounted on Snellius in "read-only" mode. So, once you have access to Snellius, you can copy the files that you want to retain from the Lisa read-only mount (/lisa_migration/home/$USER) to your regular Snellius homedir. For the copying you can use the usual Linux commands (like cp or rsync). This is also a good opportunity to clean up your home directory, to reduce the amount of storage used.

A number of Lisa users also had access to a project space on Lisa. These project spaces are also mounted (read-only) on Snellius in the location /lisa_migration/project/<project-space-name>

Note that we still have to work out an (administrative) solution for requesting project space with read-write access on Snellius. This implies that for the time being you can only use the Lisa project spaces for reading input files and copying to Snellius scratch and use it in your computations. You should copy from the mounted Lisa project directory to /scratch-shared/$USER on Snellius using an interactive node, to prepare job input files. The resulting job output has to be stored elsewhere, for instance on your home directory. Note that the home directory has a quota of 200GB. If you expect to have (much larger) data output sizes then please contact the Service Desk for discussing a (temporary) solution.

Any ACLs you had set on Lisa data will need to be re-created on Snellius.

Frequently Asked Questions

curl http://ipecho.net/plain; echo

Snellius compared to Lisa

Environment

The user environment on Snellius is very similar to that on Lisa. Both use the Linux operating system, and they both provide very similar software stacks that can be accessed via the modules environment (see Software).  Slurm is used on both systems to manage the batch queues (see SLURM batch system). So in most cases your existing workflow on Lisa used for creating and running batch jobs can be applied directly on Snellius. Minor changes to job scripts might be needed, for example due to the different set of Slurm partitions on Snellius.

Concurrent with the migration a new set of GPU nodes is added to Snellius, called Phase1A. See below for more details. One difference of these new nodes compared to the existing GPU nodes in Snellius is that they contain a local SSD disk, to be used as fast scratch space. If you want to use the new GPU nodes with the local scratch disk feature, you have to specify this with the --constraint=scratch-node option for Slurm.

On Snellius you can check your current disk quota details with the myquota command.

Phase1A GPU extension of Snellius

The UvA and the VU, the most important stakeholders in the GPU partition of Lisa, are partaking in Snellius. As a result, the GPU capacity of Snellius will been increased considerably in November-December 2022 (the Phase1A and Phase1B extensions). This is an upgrade with nodes that are almost identical to the existing Phase1 GPU nodes. The only difference is the local SSD disks on the additional GPU nodes, that can be used as a very fast local scratch space. The new GPU nodes will be integrated into the existing Slurm partitions on Snellius, and they can be used by every Snellius user that has access to the GPU partition.

Here is a comparison between the existing Phase 1 GPU nodes and the new Phase 1A extension:

System comparison between Lisa and Snellius

GPU partitions on Snellius

For regular users only 2 GPU partitions are visible on Snellius:

See Snellius usage and accounting for all details on these partitions, including how they are accounted.

Getting access to Snellius

For those users who already have an account and username on Lisa, SURF will create the same username/account on Snellius. Also, the Unix uid of your username will remain the same, so you can still access your Lisa files on Snellius.

Users who already have an account on Snellius, will be given the choice to get an additional username/account on Snellius, or to use the existing username/account.

Users who haven't used Lisa yet can request access to Snellius in the same way as for Lisa in the past (see Obtaining an account).