Cluster Computing

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Introduction

Cluster computing allows researchers the opportunity to perform computationally intense operations (e.g. fMRI analysis) on dedicated 'high performance computing' HPC clusters. These clusters often have many available CPU's, GPU's en RAM storage, allowing for much faster (parallel) computing than is possible on personal / work computers.

Currently FSW users have three HPC options available:

  • Shark OLD: This HPC is maintained by the LUMC and is considered end-of-life, current users are encouraged to move to Shark SLURM
  • Shark SLURM: This is the LUMC's newer version of Shark, which is currently fully operational. FSW users can use this cluster until the new Alice cluster is fully functional
  • Alice: This is the new university-wide HPC cluster. The goal is for FSW users to exclusively use this cluster in the future. However, currently, the hardware and software needed for typical FSW use-cases (e.g. fMRI analysis) is not yet available.

For questions, account requests and other issues, please contact the HPC support at SOLO: Kerwin Olfers

Shark

F.A.Q.

Shark Wiki Q I can't access the Shark Wiki: https://git.lumc.nl/shark/shark-centos-slurm-user-guide/-/wikis/home
A The official Shark wiki is accessible only from the researchlumc network. After logging into researchlumc or shark slurm, you can open a browser instance and navigate to the wiki. Alternatively: solowiki hosts a copy of the Shark LUMC Wiki. Please note this may not always be the most current version.
Shark Log In Q I can't log in to Shark from my university computer?
A The FSW network is directly connected to the Shark network, that means you do not need to use the jump-server (RESEARCHLUMC). Additionally, dns-routing does not work at the moment for Shark SLURM, meaning you have to use the ip-address instead of the network name. Therefore, for shark old ssh to: user@shark.researchlumc.nl, for Shark SLURM ssh to: user@145.88.76.243 (for log in node 1) or user@145.88.76.217 (for log in node 2). Note that if you are using MobaXterm, X2Go or Putty, you will also need to disable the jump-server settings.
File Transfer Q File transfer from Shark to the FSW J-drive does not seem to work (e.g. no access to the vito server).
A This is a known problem, we are currently working on a solution.

Alice

Alice is the new university-wide HPC cluster that is currently in development. In addition to research, Alice can also be used for courses and by students. Currently Alice does not yet support all the features that Shark does (e.g.: graphical remote desktop, hardware accelerated graphics, large storage, fMRI analysis software), however implementation of these is planned for the near future. Users who need less specific software (e.g. R, Matlab) or can work from Singularity containers and have relatively low storage requirements, may consider switching already.

The best source of information on Alice is the official Alice Wiki.