Ginsburg: Getting Started
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.eduwhere <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 |
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/bashNow 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.