File systems on Noctua[Bearbeiten]
The cluster provides two types of file systems:
- A shared file system located on an external filer. This file system is available on all clusters and on all systems running in the University network.
- A cluster-local parallel file system (Lustre). It provides low-latency access, high bandwidths and parallel file access.
The quota and used storage of your project for the different file systems is shown in the output of pc2status.
|Environment Variable||Source||Purpose||Initial Quota||Backup|
|HOME||Filer||Permanent small data. Per user account.||5 GB||Yes|
|PC2DATA||Filer||Permanent project data (e.g. program binaries, final results). Per project, full path $PC2DATA/<project-acronym> . Mounted read-only on the compute nodes and read-write on the frontends.||Requested at project application||Yes|
|PC2PFS||parallel Lustre file system||Temporary working data. Per project, full path $PC2PFS/<project-acronym> .||Requested at project application||NO|
|PC2SCRATCH||Filer||Temporary working data. Per project, only for legacy projects.||Requested at project application||NO|
|PC2SW||Filer/Cluster||Pre-installed software. Read only.||None||Yes|
|PC2DEPOT||Filer||Long term backup of research data for members of Paderborn University. This filesystem is hosted and maintained by [IMT].||Requested at depot application||Yes|
Depending on you project, some of these file systems might not be available.
File systems on compute nodes of Noctua[Bearbeiten]
There are NO Node-local disks (except on the FPGA-nodes). Compute jobs as well as I/O-intensive jobs should use the Lustre-file system, i.e., PC2PFS.
Please also note, that the temporary directory /tmp on the nodes is a ramdisk. That means that the files written to this directory reside in the main memory of the node and reduce the main memory that is available to your programs. Thus, it is not recommended to use /tmp.
Storing research data at $PC2DEPOT[Bearbeiten]
To be able to store data on $pc2depot you have to apply for a depot at the Center for Information and Media Technologies at the University of Paderborn. The easiest way to do this is to simply send an email with your request to firstname.lastname@example.org.
To access the depot from Noctua you first need a Kerberos ticket. You can get this via
The UNI-PADERBORN.DE must be written in capital letters. The ticket is valid for 10 hours. If you need longer access to $PC2DEPOT, you have to renew the ticket within these 10 hours. Afterwards you can access your depot using the environment variable $PC2DEPOT or the path /upb/depot/. The depot is only mounted on the frontends. Further documentation can be found at https://hilfe.uni-paderborn.de/Netzwerkspeicher.
Export of Lustre File System[Bearbeiten]
The Lustre file system can be mounted on your personal computer on two different ways, by CIFS or NFS4'' protocol. To do this, your computer must be connected to the university network. The address of the gateway is
For both protocols you have to use your IMT credentials to establish the mount.
To access the parallel Filesystem from Windows open the File Explorer and enter \\lus-gw.cr2018.pc2.uni-paderborn.de\scratch\ in the navigation bar.
Password: IMT password
You can access the parallel Filesystem on macOS from the Finder with the menu Go to/Connect with server (shortcut CMD+K).
In the shown window enter the server address smb://lus-gw.cr2018.pc2.uni-paderborn.de/scratch/
Password: IMT password
A sftp like access to the parallel Filesystem is possible by installing smbclient on your computer and issuing the following command:
smbclient //lus-gw.cr2018.pc2.uni-paderborn.de/scratch -U Your-IMT-username -W AD
When asked for a password use your your IMT password
In order to be able to mount the Lustre file system on a Linux computer you need the cifs utilities. They can be installed from the packages of your linux distribution, e.g. on Ubuntu or Debian with "apt install cifs-utils". You can then mount /scratch ($PC2PFS) to your local directory MOUNTPOINT with as root:
mount -t cifs //lus-gw.cr2018.pc2.uni-paderborn.de/scratch MOUNTPOINT -o username=Your-IMT-username,domain=AD.UNI-PADERBORN.DE
You can also add the following to /etc/fstab to make a permanent mount
//lus-gw.cr2018.pc2.uni-paderborn.de/scratch MOUNTPOINT cifs username=Your-IMT-username,domain=ad.uni-paderborn.de 0 0
You will be asked for your password at boot.
To mount the parallel Filesystem via the NFS4 protocol you need a Kerberos Ticket and mount Lustre to MOUNTPOINT
kinit Your-IMT-username@UNI-PADERBORN.DE mount -t nfs -o vers=4,sec=krb5 lus-gw.cr2018.pc2.uni-paderborn.de:/ MOUNTPOINT
Copy files with rsync[Bearbeiten]
Besides the possibility to mount the lustre filesystem on your PC via CIFS or NFS, you can transfer files from and to it via rsync and SSH with ProxyJump:
rsync -azv -e 'ssh -J <your-username>@fe.noctua.pc2.uni-paderborn.de' <your-files> <your-username>@ln-0001:/scratch/<path>
As an alternative to rsync, you can use scp:
scp -o 'ProxyJump <your-username>@fe.noctua.pc2.uni-paderborn.de' <your-files> <your-username>@ln-0001:/scratch/<path>
You can use both of the clusters frontends (ln-0001 and ln-0002) as the target.
Note that on Windows you need to run the scp command from the PowerShell and it will not work from the command prompt (cmd.exe).