SHARK Cluster

Last modified by Kerwin Olfers on 2024/03/15 14:21

Introduction

UPDATES:

02-03-2022: 
Login node 1 is no longer available, instead a new login node 4 has been added (145.88.76.219)

The SHARK SLURM cluster is maintained and hosted by the LUMC. It is currently the cluster that most FSW users are working on1618997548843-165.png.

Resources

Original SHARK Wiki:  see here. This Wiki is maintained by the LUMC and contains most of the general information needed to use the cluster.

New ALICE & SHARK Wiki: this is the new Wiki shared for both HPC clusters. While the available information here may be more up to date compared to the Original SHARK wiki, not all information has been transferred there yet.

FSW specific issues:  For FSW specific topics, i.e. fMRI analysis, Matlab usage, data-transfer etc, we provide additional information on the page below.

Contact: for all questions about SHARK usage please contact SOLO: labsupport@fsw.leidenuniv.nl, only for password reset contact SHARK admin directly:  ITenDI_Infra-Linux@lumc.nl

Data Management

  • All FSW users share a total of 40TB of spaces of the cluster, 80 compute nodes and have 10GB of personal space on their home directories.
  • Once the shared space is full,  the output of any jobs will not be saved (and will be discarded instead). So always keep an eye on the current status of the shared folder /exports/fsw/  and the expected output size of your jobs.
  • Never have your important data (e.g. raw) or scripts only on the cluster! Remember that none of the data on the exports folder or personal folder is back-upped. That means, if the data gets corrupted, is overwritten, or there is a failure in the drives, the data may be lost permanently.
  • Files can be transferred for long-term & secure storage to FSW using sftp (see here).
  • For shared access (within) research/project groups to data on the Export, project groups can be requested via the LUMC Topdesk.

F.A.Q.

TopicQuestionAnswer
Wiki not accessibleI can't access the Shark Wiki: https://git.lumc.nl/shark/shark-centos-slurm-user-guide/-/wikis/homeThe official Shark wiki is sometimes locked behind the LUMC network (due to hacking attempts), and accessible only from the researchlumc network. After logging into researchlumc or shark slurm, you can open a browser instance and navigate to the wiki. Normally the wiki becomes publicly available again after a few days, if the issue persists however, please contact us.
Log in from FSWI can't log in to Shark from my university computer? 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@145.88.76.217 (for log in node 2) or user@145.88.76.201 (for log in node 3). Login node 1 is no longer available. Note that if you are using MobaXterm, X2Go or Putty, you will also need to disable the jump-server settings.
Data Transfer How do I transfer files from the cluster to the FSW J-drive or P-drive?The "old" method of transferring data via the Vito/Corleone server is no longer working, instead see the required steps here.
Matlab LicensesHow can I use the FSW Matlab license on Shark, as the LUMC does not have a campus license?

There is an install of Matlab 2018  specifically for FSW users, made available in the FSW Exports folder. To access it from the terminal:

PasswordI forgot my password and/or my password is outdated.Please send an email to the SHARK administrators: ITenDI_Infra-Linux@lumc.nl
X11 on MacsX11 / OpenGL is not working on my Mac when I try to run programs with graphical interfaces

This is likely an issue with the XQuartz service on your Mac. The solution seems to be to run the following command in the terminal (on your own machine):

defaults write org.xquartz.X11 enable_iglx -bool true

And then reboot your machine.

Data Transfer to FSW

For migrating your project data from SHARK to FSW, please see the manual here.

Data Migration ALICE

For migrating your project from SHARK to ALICE, please see the manual here.

Getting MobaXTerm

  • If you don't have MobaxTerm yet, download the portable edition version of MobaxTerm (https://mobaxterm.mobatek.net/download-home-edition.html) and unzip it, e.g. to a folder on the desktop
  • Start the MobaxTerm client from the folder by double-clicking the .exe file in the extracted folder.
  • If it is the first time you started MobaxTerm, go to Settings > Configuration >General.
    • For Persistant home directory, enter:  _MobaFolder_
    • For Persistant root, enter: _MobaFolder_\slash
    • Press OK at the bottom and restart MobaxTerm if asked. You can ignore any warnings about network drive speed
      .1627987731297-585.png
  • Start a new local session in MobaxTerm, using the "Start local terminal" button on the home screen, or go the "Session" in the top left then select "Shell" and press OK.
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