HPC cheat sheet

Useful links

HPC application

HPC wiki

[screen wiki][screen]

[myJam website][myJam]

☞ Nota Bene

Connections from outside of the University network are currently disabled for security reasons. You can still connect if you use the VPN. Its setup is described here.

Connect with terminal

You can connect to the HPC login node via SSH.

ssh <username>@hpc.rz.uni-duesseldorf.de

If this is to long for you to type everytime you can open ~/.ssh/config with an editor of your choice and add the lines:

Host hilbert
    User <username>
    HostName hpc.rz.uni-duesseldorf.de

Host hilbert-storage
    User <username>
    HostName storage.hpc.rz.uni-duesseldorf.de

This way you can just type ssh hilbert to connect to the login node. To make it even more convinient, consider adding your ssh public key to your authorized_keys file on hilbert. If you have no clue what this means, just run the following on your local personal machine from where you already can connect using your password. Assuming you use some kind of disk encryption, it should be safe to choose an empty password for your key in the first step.

ssh-keygen -t ed25519
ssh-copy-id hilbert

From then on you can login to hilbert without providing your password.

Other ways of connecting

Mount a directory

If you’re inside the University network, you should connect to the storage backend of hilbert as it’s able to achieve speeds around 100 MB/s.

sshfs hilbert-storage:some/path/on/the/HPC some/path/on/your/system

You can mount a HPC directory to your filesystem from outside the University network by running

sshfs hilbert:some/path/on/the/HPC some/path/on/your/system

but this is discouraged by the ZIM people.

Example:

sshfs hilbert-storage:/gpfs/scratch/joweb106 Documents/hilbert3/
sshfs hilbert:/gpfs/scratch/joweb106 Documents/hilbert3/

You can also use Filezilla, or the file browser of your Linux distribution. Just try to enter sftp://hilbert-storage/gpfs/scratch/<username> into the address bar of your file browser.

Also look at this HPC wiki post

Graphical Session

You can request one here.

Your home directory

You shoud do your work in /gpfs/scratch/username.

Modules

You can load specific software with modules:

module load module-name

List of all modules:

module avail

For conda:

module load Miniconda/3

For conda with Snakemake (different miniconda module):

module load Miniconda/3_snakemake Snakemake/5.10.0

screen

One can use [screen] to start a new screen session