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Storage Systems within DIAG

You need a VPN connection active to access the shares from home

Overview

The goals of DIAG storage systems are to provide:

  • high-performance shared file-system for cluster computing
  • shared file-system for archiving of data with data redundancy (backups)

The storage systems consist of:

  • central research storage network shares, maintained by the Information Management Group (IM) of the hospital, used for archiving of data
  • DIAG research storage network shares, maintained by the SOL Team, used for experiment data and connected to our cluster computing facilities

Rules

Impetus for the rules set out here is derived from the following causes:

  • medical imaging data-sets can be (very) large
  • archives can grow quickly and uncontrollably (especially with an automatic in-flow of clinical data)
  • storage is neither free (gratis) nor unbounded

Hence, all users of DIAG storage must abide by the following rules and conventions:

  1. always follow the prescribed top-level structure (see Structure section below)
  2. users should be aware, and keep-track, of how much disk-space is consumed by datasets in their possession
  3. do not place large datasets in the 'users' folder, these should go in 'archives' or 'projects' folders

Shares

Overview

Access to file-systems on all storage systems takes place through an exposed network share. An overview of the storage systems provided by DIAG is the following:

Share Description Address
Blissey Share reserved for pathology //blissey.umcn.nl
Chansey Share reserved for radiology //chansey.umcn.nl
Happiny Share reserved for pathology & radiology //happiny.umcn.nl

Passwords and instructions on how to access the shares can be found on Teams.

Important!

Both Chansey, Blissey and Happiny DO NOT HAVE backup, meaning that your files could GET LOST. In order to avoid such problems, try backup your code (e.g. github) and your files (e.g. using the shares managed by IM, which are backed up.)

Mounting a share on your local computer

On Windows

tbd

On macOS

  1. Open the Finder
  2. Type CMD+K
  3. Adapt and enter the following: smb://<username>@<server-name>.umcn.nl/<share-name>

Structure

All shares with backup should follow the following top-level structure convention (it can contain a subset of these folders):

Directory Description
archives contains mother archives
external contains data which needs to be shared with external partners
projects contain project materials, which cannot be reproduced by code
software software deliveries, pipeline versions, binaries, etc
users user-folders for each user

Miscellaneous

Assuming you have configured SSH key authentification on the controller node (SSH Key Authentification), you can mount your home folder of the controller node on your local machine through sshfs. Below you find an example on how to do this.


# Once inside the docker container, make a mount folder
sudo mkdir -p /mnt/oakslab

# Still from within the docker container, mount oaks-lab home folder using SSHFS
sudo sshfs -o allow_other,reconnect <username>@oaks-lab.umcn.nl:/home/<username>/ /mnt/oakslab/