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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:

  • 72 nodes with 2 x AMD Epyc2 7402
  • 24 nodes with 2 x AMD Epyc3 7443
  • 18 NVIDIA A100 distributed on 8 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:

  • Only one job per user at a time
  • Maximum run time of 8 hours but this decreases if you ask for lots of resources.

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 - 3 days
  • Short jobs - 12 hours

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 GPU equipped nodes.

To request resources in the gpu partition please use the following sbatch directive:

#SBATCH -p gpu

The limits are:

  • Normal jobs - 3 days
  • Short jobs - 12 hours

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.

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 providedaccessible 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 a Lenovo DSS systemprojects and is not a long term store.

Cluster filesystems

The cluster storage is based on the IBM Spectrum Scale (GPFS)GFPS) parallel filesystem.

/There are two disk based filesystems (users

Your home space is at /users/username and work) and one SSD based one (scratch). Whilst there is ano 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 ofis 50 GB and 100,000 files.

WeThere wouldare likedaily tosnapshots remind you that all scripts and code should be stored in a Git repository.

/scratch

The scratch filesystem is the primary working spacekept for runningseven calculations.

The scratch space runs on SSD storage and has an automatic cleaning policy sodays in case of aaccidental shortagefile ofdeletion. freeSee spacehere files older than 2 weeks (starting with the oldest first) will be deleted.

Initially this cleanup will be triggered if the space isfor more than 90% used and this limit will be reviewed as we gain experience with the usage patterns.

The space is per user and there are no quotas (*). Your scratch space can be found at /scratch/username

e.g. /scratch/ulambda

Use of this space is not charged for as it is now classed as temporary storage.

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

Work

/workwork/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 structurescratch is: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 workcase /of FAC / FACULTY / INSTITUTE / PI / PROJECT

Thislimited space can,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 should,can be usedaccessed forinside a batch job by using the installation$TMPDIR variable.

At the end of anythe researchjob groupthis specificspace softwareis toolsautomatically including python virtual environments.purged.

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