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Handle your data

Storage#

Several volumes of data storage are available on the ABiMS Cluster. Use it knowingly.

Usage Quota (default) Backup policy
/shared/home/ Home directory (personal data) 100GB No
/shared/projects/ Scientific and project (common data) 250GB Yes
/shared/scratch/ For temporary processing data. File older than 90 days are automatically deleted. 500GB No
/shared/bank Read-Only. Common banks (UniProt, RefSeq, ...)

If you need or plan to use more storage space, please contact us: support.abims@sb-roscoff.fr

Backup#

ABiMS provides a backup on your project directory located in /shared/projects/

⚠️ To take advantage of this process, you have to follow some rules:

  • Only the subdirectories archive, script and finalresult are backed up.
  • You must place these subdirectories at the root of your project folder.
  • Please be smart in your backups for our finances and the planet.

Example:

/shared/projects/<my_project>/
├── [...]
├── finalresult
├── script
├── archive
├── [...]

Snapshots#

ABiMS also provides snapshots for short term recovery of your data to protect against deletion by error.

Project#

A project is a directory on the storage associated with users who can access it.

In order to have your folder and space on /shared/projects/<myproject\>, you have to request a new project on the IFB Core Cluster Account Manager: https://my.sb-roscoff.fr/manager2/project

You can have multiple projects (and it's recommended).

More information on The project concept at ABiMS

Transfer#

SSH protocol (or SFTP - SSH File Transfer Protocol) is the only protocol available. But, you can also use clients on the cluster to download your data (wget, curl, scp, rsync, wget, ftp, etc.).

You can get/put your data as described below.

Command line#

On your workstation or on the cluster, you can use command line with your favorite client: scp, rsync, etc.

SFTP Graphic client#

Use a graphic client like FileZilla on your workstation.

Or use your file manager directly if it's possible (SFTP support).

SSHFS#

Use your file manager with SSHFS

Editors#

Several editors and tools are available on the cluster:

  • vim
  • emacs
  • nano

Or graphical editors. Graphic tools need some configuration: see Export display.

  • xemacs
  • geany
  • gedit

Or use web interface:

Export display#

Linux / Mac#

Simply use -Y option:

ssh -Y <username>@ssh.sb-roscoff.fr

Windows#

1- Install a X server (for example: VcXsrv Windows X Server)
2- Launch the X server
3- Activate X11 forwarding

> Example with PuTTY
X11 Forwarding with PuTTY

Once connected, you can launch your program with a graphical user interface.

Manage#

Several possibilities to browse, manage and edit or view your data/scripts

  • Directly on the cluster with the command line

  • Get the data back on your workstation (see Transfer) and work locally.

  • Use SSHFS on your workstation (see above: SSHFS)