Ginsburg: Getting Started

1 Getting Access
2 Introductory HPC Training and Resources
3 Logging In
4 Submit Account
5 Your First Cluster Job
- 5.1 Submit Scripts
- 5.2 Job Submission

Getting Access

Access to the cluster is subject to formal approval by selected members of the participating research groups. See the HPC Service Webpage for more information on access options.

Introductory HPC Training and Resources

If you're not familiar with basic Linux commands and usage, or if you need a refresher on these topics, please refer to the following resources from our workshop series:

Intro to Linux: workshop recording
Intro to Bash Shell Scripting: and workshop recording
Intro to Python for HPC: and workshop recording
Intro to High Performance Computing: and workshop recording

Also useful:

RCS Video Library with past training recordings
Research Computing (RC) Training & Workshop page with calendar of upcoming events across Columbia
RC-training mailing list subscribe page to get email notifications as sessions are scheduled

Logging In

You will need to use SSH (Secure Shell) in order to access the cluster. Windows users can use PuTTY or Cygwin. MacOS users can use the built-in Terminal application.

Users log in to the cluster's submit node, located at ginsburg.rcs.columbia.edu or use the shorter form burg.rcs.columbia.edu. If logging in from a command line, type:

$ ssh <UNI>@ginsburg.rcs.columbia.edu



OR


$ ssh <UNI>@burg.rcs.columbia.edu

where <UNI> is your Columbia UNI. Please make sure not to include the angle brackets ('<' and' >') in your command; they only represent UNI as a variable entity.

Once prompted, you need to provide your usual Columbia password.

Submit Account

You must specify your account whenever you submit a job to the cluster. You can use the following table to identify the account name to use.

Account	Full Name

Account	Full Name
anastassiou	Anastassiou Lab
apam	Applied Physics and Applied Math
asenjo	Asenjo-Garcia Lab
astro	Astronomy and Astrophysics
berkelbach	Berkelbach Group
biostats	Biostats
ccce	Columbia Center for Computational Electrochemistry
cgl	Biomedical Engineering
dslab	Shohamy Lab
dsi	Data Science Institute
edru	Karin Foerde
e3b	Department of E3B
ehsmsph	Environmental Health Sciences Mailman School of Public Health
emlab	Electromagnetic Geophysics Laboratory
gsb	Business School
hblab	Harmen Bussemaker Lab
iicd	Irving Institute for Cancer Dynamics
jalab	Austermann Lab
jhucbsr	Jianhua Hu Biostatistics
kellylab	Shaina Kelly Lab
katt3	Computer Science
millis	Physics
myers	Myers Lab
mjlab	Biological Sciences
morphogenomics-lab	Bianca M. Dumitrascu
ntar_lab	Neurotrauma and Repair Lab (Morrison)
abernathey	Ocean Climate Physics: Abernathey
camargo	Ocean Climate Physics: Camargo
fiore	Ocean Climate Physics: Fiore
glab	Ocean Climate Physics: Gentine
mckinley	Ocean Climate Physics: McKinley
oshaughnessy	Ben O'Shaughnessy, Dept. Chemical Engineering
seager	Ocean Climate Physics: Seager
sobel	Ocean Climate Physics: Sobel
ting	Ocean Climate Physics: Ting
wu	Ocean Climate Physics: Wu
qmech	Quantum Mechanics: Marianetti
rent	Rent
sail	Schiminovich Astronomy & Instrumentation Lab
seasdean	School of Engineering and Applied Science
sscc	Social Science Computing Committee
stats	Statistics
stock	Stockwell Lab
thea	Sironi / Beloborodov
theory	Theoretical Neuroscience: Abbott Lab
tosches	Tosches Lab
urbangroup	Urban Group
vedula	Vijay Vedula
zi	Zuckerman Institute

Your First Cluster Job

When you first login to Ginsburg, you are on a login node. Login nodes are not places where users should do actual work aside from simple tasks like editing a file or creating new folders.

Instead, it is important to move from the initial login node to a compute node before doing most work. Example:

srun --pty -t 0-2:00 -A <ACCOUNT> /bin/bash

Now you have moved from the login node to one of the compute nodes on the cluster. The simple tasks mentioned above can also be done here, but from here is where it is especially important to submit scripts for processing.

If the HPC group notices jobs being run on a login node, such jobs will be terminated and the user notified.

Submit Scripts

This script will print "Hello World", sleep for 10 seconds, and then print the time and date. The output will be written to a file in your current directory.

In order for this example to work you need to replace ACCOUNT with your group account name. If you don't know your account name the table in the previous section might help.

#!/bin/sh
#
# Simple "Hello World" submit script for Slurm.
#
# Replace ACCOUNT with your account name before submitting.
#
#SBATCH --account=ACCOUNT        # Replace ACCOUNT with your group account name 
#SBATCH --job-name=HelloWorld    # The job name
#SBATCH -N 1                     # The number of nodes to request
#SBATCH -c 1                     # The number of cpu cores to use (up to 32 cores per server)
#SBATCH --time=0-0:30            # The time the job will take to run in D-HH:MM
#SBATCH --mem-per-cpu=5G         # The memory the job will use per cpu core

echo "Hello World"
sleep 10
date

# End of script

Job Submission

If this script is saved as helloworld.sh you can submit it to the cluster with:

$ sbatch helloworld.sh

This job will create one output file name slurm-####.out, where the #'s will be replaced by the job ID assigned by Slurm. If all goes well the file will contain the words "Hello World" and the current date and time.

See the Slurm Quick Start Guide for a more in-depth introduction on using the Slurm scheduler.