IBG 3 Cluster

Compilation on the cluster

CPlantBox: just do

git clone --depth 1 -b stable_v2.1 https://github.com/Plant-Root-Soil-Interactions-Modelling/CPlantBox.git
cmake . && make

and everything should work

Dumux-rosi: Upload and run the script installDumuxRosi_Ubuntu.py. For security, create and activate a specific conda environment before launching the installation script.

How to run a job

Do not run simulations directly on the master node. The master node is only used for installation, compilation, or small tests. The IBG-3 cluster uses slurm as job management.

A job can be started by $ sbatch some_job.sh. The command $ squeue will show all running jobs including job id, $ scancel [jobid], will terminate the job. Two example batch files: job_single.sh to start a single threaded job, and job.sh to start multiple single threaded jobs.

Generally,

• Do not use graphical outputs
• Write out useful simulation results (you need to work with those outputs in post-processing).
• Console outputs are written to slurm-[jobid].out. Don’t write too much to the console if you send many parallel jobs.

Useful tools

• If you need to edit a file in the console and you don’t know how to use vi or emacs use nano (which is simpler)
• Jupyter Lab -> https://ibg3113.ibg.kfa-juelich.de/user/username/lab (you must be connected via VPN)
• rsync (e.g. rsync -avzP [email protected]:/home/username/DUMUX/dumux-rosi/python/coupled/upscaling/results/ results/)
• Mount cluster to have external drive (Windows: sshfs, convert key to rsa)
• FileZilla, WinSCP

Questions and Answers

Please use our groups slack channel, Root Modelling Lab #rosi_technial.