Euler Cheat Sheet

November 2025, Nik Zemp, GDC

🔑 Key resources to consider

  • 📁 File System
  • 🔋 Memory (RAM) --mem-per-cpu
  • ⚙️ CPUs --cpus-per-task
  • ⏱️ Runtime --time

🔐 Login

ssh <USER>@euler.ethz.ch

📦 Software Stack

# Source GDC stack
source /cluster/project/gdc/shared/stack/GDCstack.sh
# Show all available tools
module avail
# Load a module
module load <name>

📂 File System

  • Use your $HOME for scripts and own installation.
  • Always use $SCRATCH or $TMPDIR for processing your data.
  • Copy only final data to the GDC home and GDC projects for save keeping.
    • Archive many small files using tar or zip.
    • Compress large outputs.
    • Storage is charged annually.
# Show folder size of mapping
du -sh --si mapping
# Count files in raw_data     
find raw_data | wc -l          		

# Archive folder data1
tar cvzf data1.tar.gz data1    		
# List archive contents
tar ztvf data1.tar.gz 
# Extract all  		
tar xvf data1.tar.gz  
# Extract specific folder         		
tar xvf data1.tar.gz data1/raw 		

#Data transfer
scp -r data <USER>@euler.ethz.ch:/cluster/scratch/<USER>
scp -r <USER>@euler.ethz.ch:/cluster/scratch/<USER>/data ./

# Generate checksums
md5sum *fq.gz > md5sums.txt  
# Verify checksums  		
md5sum --check md5sums.txt

🚀Job Submission

### Submit a job
sbatch < submit.tool.slurm.sh

### Overview of the submitted jobs 
jview

### Kill specific job
scancel <Job-ID>/<Array-ID>

### Kill all running jobs
scancel --user=$USER

Interaktive Job

srun --pty bash

Submission script

#!/bin/bash
#SBATCH --job-name=tool			#Name
#SBATCH --array=1-10%4			#Array length 1-10, 4 at the time
#SBATCH --ntasks=1				#Node (always 1)
#SBATCH --cpus-per-task=2		#2 CPUs
#SBATCH --mem-per-cpu=2G		#Memory per 2 CPU; 4G in total
#SBATCH --time=4:00:00			#Run time
#SBATCH --output=tool_%a.log	#Log-file

source /cluster/project/gdc/shared/stack/GDCstack.sh
module load <name> 

## Array variable (e.g. 1-10) and extract sample names from the index
IDX=${SLURM_ARRAY_TASK_ID}
SAMPLE=$(sed -n ${IDX}p sample.lst)

## Run the array e.g. SAMPLE 1-10 
tool -in ${SAMPLE}.in -out ${SAMPLE}.out

👀Job Monitoring

Running jobs

jeffrun -r 
jeffrun -j <Job-ID>/<Array-ID>

Finished jobs

## Efficency of specific job
jeff <Job-ID>/<Array-ID>
## Get an overview about the last 24 hours
jeff24
## Get an overview about the last week
jefflow

📊 WebGUI