Amarel Compute Cluster - General

** If you don’t have acces to the VPN, follow instructions on Connecting to Rutgers VPN Tutorial

Help desk: email [email protected]

<aside> 📖 Cluster User Guide: https://sites.google.com/view/cluster-user-guide

</aside>

Setting up AMAREL and Terminal

A. Getting Access for the First Time

B. Launching a job in Slurm

C. Jupyter Notebook Setup

D. Packages in holmesenv (conda environment)

E. Setting up your own an Env in Python/Amarel

<aside> 🛠 Slurm Documentation

</aside>

<aside> 📖 **Amarel User Guide**

</aside>

<aside> <img src="/icons/preview_gray.svg" alt="/icons/preview_gray.svg" width="40px" /> **Amarel Intro and Basics - Video Tutorial (1hr)**

</aside>

Modules in Amarel (2024)

Terminal Commands

Helpful bash script lines

conda activate /projects/community/holmesenv #activate holmesenv conda
cd /home/netID #change working directory
ls #contents of wd
tree #structure of files within wd 
cd .. #goes to parent dir
mkdir dirName #make directory
rm filename #remove file
mv /sourceDir /movingLocation
cat file.extension #displays file contents 
vim file.extension #like cat but with scroll
sacct #see all the jobs you're running
#optional specifications for sacct:
sacct --format=JobId,JobName%50,Partition%15,State,Elapsed,ExitCode,Start,End --starttime=2024-06-08T22:43:21
watch -n 1 squeue -u netID # View in real time all the jobs you're running
			#ctrl+C to exit



#Use terminal packages
module use /projects/community/modulefiles
module load FreeSurfer/7.4.1-ez82
module load fsl/6.0.0-gc563

Notes