FAQ

Frequently asked questions

General

How do I get access to the cluster?

Contact Lukas to request an account. You’ll receive your username and initial password. See Connecting to the Cluster for setup instructions.

Why can’t I install packages on compute nodes?

Compute nodes don’t have internet access. Install packages on the head node, which has internet. Since your home directory is shared via NFS, packages installed there are available on all nodes.

My SSH connection keeps dropping. What can I do?

Use tmux to maintain persistent sessions:

tmux new -s work
# ... do your work ...
# If disconnected, reconnect with:
tmux attach -t work

Also check your SSH client settings for keepalive options.

Jobs and Slurm

Why is my job stuck in “pending”?

Check the reason with:

squeue --me --long

Common reasons: - Resources: Waiting for CPUs/memory to free up - Priority: Other jobs are ahead in the queue - QOSMaxJobsPerUserLimit: You’ve hit your job limit

My job failed with “OUT_OF_MEMORY”. What now?

Your job exceeded its memory allocation. Request more memory:

#SBATCH --mem=16G  # or higher

Check how much memory your previous job actually used:

sacct -j <jobid> --format=JobID,MaxRSS

My job hit the time limit. How do I fix it?

Request more time:

#SBATCH --time=12:00:00  # or longer

Or use a QoS that allows longer jobs:

#SBATCH --qos=long

How do I cancel a job?

scancel <jobid>       # Cancel one job
scancel --me          # Cancel all your jobs

Can I run jobs that continue after I log out?

Yes, use batch jobs (sbatch) instead of interactive sessions. Batch jobs run independently of your terminal session.

R

R can’t find my packages in a batch job

Make sure you: 1. Load the same R version you used when installing packages 2. Installed packages on the head node

#SBATCH ...
module load R/4.5.2  # Same version as when you installed
Rscript my_script.R

How do I use multiple cores in R?

Request multiple cores and use parallel or future:

salloc --cpus-per-task=8 --mem=16G --time=02:00:00

library(parallel)
ncores <- as.integer(Sys.getenv("SLURM_CPUS_PER_TASK", "1"))
mclapply(data, my_function, mc.cores = ncores)

Should I use renv?

Yes, if you care about reproducibility. renv creates isolated package environments per project, ensuring your analysis can be reproduced later or by collaborators.

Python

Should I use conda or uv?

We recommend uv for most use cases – it’s faster and simpler. Use conda/micromamba if you need non-Python dependencies (like CUDA libraries) that are easier to install via conda.

My Python script can’t find modules

Make sure you’re running within your environment:

uv run python script.py
# or
source .venv/bin/activate && python script.py

Getting help

Something isn’t working. Who do I contact?

Contact the system administrator with: - What you were trying to do - The exact commands you ran - Any error messages - Your job ID (if applicable)