Amarel Compute Cluster - General

Notes:

When making files, sure the ‘group owner’ is the Holmes Lab group, g_ah1491_1. To change the group owner, run in the terminal $ chgrp g_ah1491_1 /path/to/file.ext (or for a folder, $chgrp -R g_ah1491_1 /path/to/folder)
- To see who the group owner is, run $ls -l. The file/folder will be listed as rwxrwxrwx author group ...
1-2 days a month Amarel does maintenance- you can’t connect to the compute nodes, see or edit your files, and any running jobs will be paused (though they won’t be stopped). You can see when maintenance days are scheduled here: https://oarc.rutgers.edu/amarel-system-status

Add THIS to your .bashrc to use Holmes Lab Conda for slurm scripts

Log into Amarel
Make sure your profile is set up to automatically activate the Holmes Lab Conda environment.
- Go to your terminal, and run:
```
$ nano ~/.bashrc
```
- Add the following lines to your bashrc– this will mean that every time you sign into Amarel, your account will automatically activate the Holmes Lab Conda. Thus, any slurm scripts will also use the Holmes Lab Conda

# Set up for conda
. /projects/community/py-data-science-stack/5.1.0/kp807/etc/profile.d/conda.sh

# Activate conda
source /projects/community/py-machine-learning/intel18/cuda12/pgarias/etc/profile.d/conda.sh
conda activate /projects/community/holmesenv

Permissions

For new files and folders (using umask) The umask command determines the default permissions for new files and directories.

Set the umask to 000:
    Open your shell configuration file (e.g., ~/.bashrc or ~/.profile).
    Add the line umask 000 and save the file.
    Restart your shell or run source ~/.bashrc for the change to take effect. 

This sets the default permissions such that new files will be created with rw-rw-rw- (666) and new directories with rwxrwxrwx (777).

Example: Using getfacl to view the current permissions for ‘examplescript’. Using setfacl to provide user ‘netID’ read, write, and execute (rwx) permissions to ‘examplescript’.

getfacl examplescript
setfacl -m u:netID:rwx examplescript

To see what permissions you have in a directory, you can do

ls -ld /home/netID

OARC Resources:

Granting access to files and folders for other users

Help desk: email help@oarc.rutgers.edu

Amarel Info:

Amarel OS: CentOS Linux release 7.9.2009 (Core)

Resources from OARC:

How to use Amarel:

Applications (Conda, Singularity, Python, R)
User Guide (Policies, Storage, Slurm, File transferring)
Beginner Information Hub - Linux, Bash, Code Editors, etc
Getting access (requesting an account)
User environment

Using Compute Notes

Using Software

FAQ