Access - Each Time

  1. Connect to VPN

    Screenshot 2024-06-05 at 2.52.31 PM.png

    1. fill in on Cisco anyconnect app:
      1. vpn.rutgers.edu
      2. NetID password
      3. DUO mobile password
    2. or webpage: https://vpn1.rutgers.edu/+CSCOE+/logon.html#form_title_text

  2. Terminal:

    1. On terminal or shell scripting application, Enter ssh [email protected] (replace with your NetID)
    2. prompts for password- Enter NetID password

  3. Environment

    1. conda activate /projects/community/holmesenv

  4. Start a jupyter notebook etc. session https://ondemand.hpc.rutgers.edu

    1. Go to https://ondemand.hpc.rutgers.edu for the GUI

    2. Go to dashboard → interactive apps → Personal Jupyter

      Recommended Settings:

      Partition: main

      Hours: 24 (max is 8064)

      Conda Path: projects/community/holmesenv

      Conda Environment: holmesenv

  5. Launch session

  6. In Jupyter Notebook, if necessary, make sure you’re in the holmesenv conda

    1. Select in toolbar Kernel>Change kernel>holmesenv

Personal Storage

Holmes Lab Storage

Permissions

Slurm Job

Common commands

<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 available in Amarel (2024)

Help desk: email [email protected]

Amarel Info:

Amarel OS: CentOS Linux release 7.9.2009 (Core)

holmesenv modules installed:

BASICS (From **Amarel User Guide)**:

Cluster User Guide:

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