Infrastructure and Resources

Curnagl

Kesako?

Curnagl (Romanche), or Chocard à bec jaune in French, is a sociable bird known for its acrobatic exploits and is found throughout the alpine region. More information is available here

It's also the name of the HPC cluster managed by the DCSR for the UNIL research community.

A concise description if you need to describe the cluster is:

Curnagl is a 96 node HPC cluster based on AMD Zen2/3 CPUs providing a total of 4608 compute cores and 54TB of memory. 8 machines are equipped with 2 A100 GPUs and all nodes have 100Gb/s HDR Infiniband and 100Gb/s Ethernet network connections in a fat-tree topology. The principal storage is a 2PB disk backed filesystem and a 150TB SSD based scratch system. Additionally all nodes have 1.6 TB local NVMe drives.

If you experience unexpected behaviour or need assistance please contact us via helpdesk@unil.ch starting the mail subject with DCSR Curnagl.

How to connect

For full details on how to connect using SSH please read the documentation.

Please be aware that you must be connected to the VPN if you are not on the campus network. Then simply ssh username@curnagl.dcsr.unil.ch where username is your UNIL account.

The login node must not be used for any form of compute or memory intensive task apart from software compilation and data transfer. Any such tasks will be killed without warning.

You can also use the cluster thourgh the OpenOnDemand interface.

Hardware

Compute

The cluster is composed of 96 compute nodes:

12 nodes with 1024 GB of memory, 512 GB otherwise.

Network

The nodes are connected with both HDR Infiniband and 100 Gb Ethernet. The Infiniband is the primary interconnect for storage and inter-node communication.

Cluster partitions

There are 3 main partitions on the cluster:

interactive

The interactive partition allows rapid access to resources but comes with a number of restrictions, the main ones being:

For example:

CPU cores requested Memory requested GPUs requested Run Time Allowed (h)
4 32 1 8
8 64 1 4
16 128 1 2
32 256 1 1

We recommend that users access this using the Sinteractive command. This partition should also be used for compiling codes.

This partition can also be accessed using the following sbatch directive:

#SBATCH -p interactive

There is one node with GPUs in the interactive partition and in order to allow multiple users to work at the same time these A100 cards have been partitioned into 2 instances each with 20GB of memory for a total of 4 GPUs. The maximum time limit for requesting a GPU is 8 hours with the CPU and memory limits applying. For longer jobs and to have whole A100 GPUs please submit batch jobs to the gpu partition.

Please do not block resources if you are not using them as this prevents other people from working.

If you request too many resources then you will see the following error:

salloc: error: QOSMaxCpuMinutesPerJobLimit`  
salloc: error: Job submit/allocate failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)`

Please reduce either the time or the cpu / memory / gpu requested.

cpu

This is the main partition and includes the majority of the compute nodes. Interactive jobs are not permitted. The partition is configured to prevent long running jobs from using all available resources and to allow multi-node jobs to start within a reasonable delay.

The limits are:

Normal jobs are restricted to ~2/3 of the resources which prevents the cluster being blocked by long running jobs.

In exceptional cases wall time extensions may be granted but for this you need to contact us with a justification before submitting your jobs!

The cpu partition is the default partition so there is no need to specify it but if you wish to do so then use the following sbatch directive

#SBATCH -p cpu

gpu

This contains the nodes equipped with Nvidia A100 GPUs. To request resources in the gpu partition please use the following sbatch directive:

#SBATCH -p gpu

The limits are:

Normal jobs are restricted to ~2/3 of the resources which prevents the cluster being blocked by long running jobs.

--gres=gpu:N

where N is 1 or 2.

gpu-gh

This contains the Nvidia GH200 nodes. You should use --gres=gpu:1.

gpu-l40

This contains the node with the Nvidia L40S. You can use --gres=gpu:N where N could be 1 to 8. To have access to this partition you have to ask us by sending an email to helpdesk@unil.ch with 'DCSR' on the subject.

Software

For information on the DCSR software stack see the following link:

https://wiki.unil.ch/ci/books/high-performance-computing-hpc/page/dcsr-software-stack

Storage

This storage is accessible from within the UNIL network using the SMB/CIFS protocol. It is also accessible on the cluster login node at /nas (see this guide)

The UNIL HPC clusters also have dedicated storage that is shared amongst the compute nodes but this is not, in general, accessible outside of the clusters except via file transfer protocols (scp).

This space is intended for active use by projects and is not a long term store.

Cluster filesystems

The cluster storage is based on the IBM Spectrum Scale (GFPS) parallel filesystem. There are two disk based filesystems (users and work) and one SSD based one (scratch). Whilst there is no backup the storage is reliable and resilient to disk failure.

The role of each filesystem as well as details of the data retention policy is given below.

How much space am I using?

The quotacheck command allows you to see the used and allocated space:

$quotacheck 
------------------------------------------user quota in G-------------------------------------------
Path                     Quota   Used    Avail   Use% | Quota_files  No_files      Use%
/users/cruiz1            50.00   17.78   32.22    36% | 195852       202400         97%
------------------------------------------work quotas in T------------------------------------------
Project                              Quota   Used    Avail   Use% | Quota_files  No_files      Use%
pi_rfabbret_100222-pr-g              3.00    2.11    0.89     70% | 7098428      9990000        71%
cours_hpc_100238-pr-g                0.19    0.00    0.19      2% | 69713        990000          7%
spackbuild_101441-pr-g               1.00    0.00    1.00      0% | 1            9990000         0%

Users

/users/<username>

This is your home directory and can be used for storing small amounts of data. The per user quota is 50 GB and 100,000 files.

There are daily snapshots kept for seven days in case of accidental file deletion. See here for more details.

Work

/work/FAC/FACULTY/INSTITUTE/PI/PROJECT>

The work space is for storing data that is being actively worked on as part of a research project. This space can, and should, be used for the installation of any research group specific software tools including python virtual environments.

Projects have quotas assigned and while we will not delete data in this space there is no backup so all critical data must also be kept on the DCSR NAS. This space is allocated per project and the quota can be increased on request by the PI as long as free space remains.

Scratch

/scratch/<username>

The scratch space is for intermediate files and the results of computations. There is no quota and the space is not charged for. You should think of it as temporary storage for a few weeks while running calculations.

In case of limited space files will be automatically deleted to free up space. The current policy is that if the usage reaches 90% files, starting with the oldest first, will be removed until the occupancy is reduced to 70%. No files newer than two weeks old will be removed.

There is a quota of 50% of the total space per user to prevent runaway jobs wreaking havoc

$TMPDIR

For certain types of calculation it can be useful to use the NVMe drive on the compute node. This has a capacity of ~400 GB and can be accessed inside a batch job by using the $TMPDIR variable.

At the end of the job this space is automatically purged.

Urblauna

Kesako?

Urblauna (Romanche), or Lagopède Alpin in French, is a bird known for its changing plumage which functions as a very effective camouflage. More information is available at https://www.vogelwarte.ch/fr/oiseaux/les-oiseaux-de-suisse/lagopede-alpin

It's also the name of our new sensitive data compute cluster which replaced the Jura cluster.

Information on how to connect to Urblauna can be found here.

The differences between Jura and Urblauna are described here

Hardware

Compute

The cluster is composed of:

Storage

The storage is based on IBM Spectrum Scale / Lenovo DSS and provides 1PB of space in the /data filesystem.

Whilst reliable this space is not backed up and all important data should also be stored on /archive

/data

The /data filesystem is structured in the same way as on Curnagl

/data/FAC/FACULTY/INSTITUTE/PI/PROJECT

This space is on reliable storage but there are no backups or snapshots.

If you wish to increase the limit then just ask us. With 1PB available all resonable requests will be accepted.

/scratch

It is considered as temporary space and there is no fee associated.

There are no quotas but in case of the utilisation being greater that 90% then files older than 2 weeks will be removed automatically.

/users

The /users home directory filesystem.

/work

The Curnagl /work filesystem is visible in read-only from inside Urblauna. This is very useful for being able to install software on an Internet connected system.

/reference

This is intended to host widely used datasets

The /db set of biological databases can be found at /reference/bio_db/

/archive

This is an HSM (Hierarchical Storage Management system) meaning that any files written are copied on tape in two copies, after some time the file content is erased from disk and a pointer to the file on tape remains. If you open a file which content is not on disk any more the tape cardridge has to be loaded in a drive, spooled to the right place and then transferred to disk.

It is only for cold data. If you have to retrieve more than 1000 files please send us a ticket at helpdesk@unil.ch with subject "DCSR Urblauna archive retrieve" and the directory path.

It has the same roganization as /data:

/archive/FAC/FACULTY/INSTITUTE/PI/PROJECT

Software

For information on the DCSR software stack see the following link:

https://wiki.unil.ch/ci/books/high-performance-computing-hpc/page/dcsr-software-stack

Slurm partitions

On Urblauna there are two partitions - "urblauna" and "interactive"

$ sinfo

PARTITION   AVAIL  TIMELIMIT  NODES  STATE NODELIST
urblauna*      up 3-00:00:00     17   idle sna[002-016],snagpu[001-002]
interactive    up    8:00:00      4   idle sna[015-016],snagpu[001-002]

There is no separate GPU partition so to use a GPU simply request

#SBATCH --gres=gpu:1

To launch an interactive session you can use Sinteractive as on Curnagl