The confluence migration is currently ongoing. Please note that any modifications made right now will not be transferred or preserved in the new instance. Plan your activities accordingly to accommodate this limitation. For details on the migration please click here

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 Linux 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:

For a list of recorded trainings and upcoming research computing workshops and events, please see:

https://www.cuit.columbia.edu/rcs/training



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

anastassiou

Anastassiou Lab

apamApplied Physics and Applied Math

asenjo

Asenjo-Garcia Lab
astroAstronomy and Astrophysics
berkelbachBerkelbach Group
biostatsBiostats
ccceColumbia Center for Computational Electrochemistry
cglBiomedical Engineering
dslabShohamy Lab
dsiData Science Institute
edruKarin Foerde
e3labE3B
ehsmsphEnvironmental Health Sciences Mailman School of Public Health
emlabElectromagnetic Geophysics Laboratory
gsbBusiness School
hblabHarmen Bussemaker Lab
iicdIrving Institute for Cancer Dynamics 
jalabAustermann Lab
jhucbsrJianhua Hu Biostatistics
kellylabShaina Kelly Lab
katt3Computer Science
millisPhysics
myersMyers Lab
mjlabBiological Sciences
morphogenomics-labBianca M. Dumitrascu
ntar_labNeurotrauma and Repair Lab (Morrison)

abernathey

Ocean Climate Physics: Abernathey

camargoOcean Climate Physics: Camargo
fioreOcean Climate Physics: Fiore
glabOcean Climate Physics: Gentine
mckinleyOcean Climate Physics: McKinley
oshaughnessyBen O'Shaughnessy, Dept. Chemical Engineering
seagerOcean Climate Physics: Seager
sobelOcean Climate Physics: Sobel
tingOcean Climate Physics: Ting
wuOcean Climate Physics: Wu
qmechQuantum Mechanics: Marianetti
rentRent
sailSchiminovich Astronomy & Instrumentation Lab
seasdeanSchool of Engineering and Applied Science

sscc

Social Science Computing Committee
statsStatistics
stockStockwell Lab
theaSironi / Beloborodov
theoryTheoretical Neuroscience: Abbott Lab
toschesTosches Lab
urbangroupUrban Group
vedulaVijay Vedula
ziZuckerman 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.

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