Insomnia: Getting Started

1 Getting Access
2 Introductory Linux Training and Resources
3 Logging In
4 Submit Account
5 Your First Cluster Job
- 5.1 An example Submit Script
- 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 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 insomnia.rcs.columbia.edu or use the shorter form som.rcs.columbia.edu. If logging in from a command line, type:

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



OR


$ ssh <UNI>@som.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
5sigma	Biostatistics
astro	Columbia Astrophysics Lab
berkelbach	Chemistry
cboyce	Chemical Engineering (Christopher Boyce)
cklab	IEOR
crislab	Chemical Engineering (Venkat Venkatasubramanian)
db	Computer Science
e3b	Ecology, Evolution and Environmental Biology
esma	SIPA-CGEP
exposomics	MSPH Exposomics
delmore_lab	Ecology, Evolution and Environmental Biology
hill	Physics (Columbia Astrophysics Laboratory)
houlab	Laboratory of Wenpin Hou
ieortang	Industrial Engineering and Operations Research (IEOR)
iicd	Irving Institute for Cancer Dynamics
intelseedfree	Special group with access to a non-NVIDIA GPU seed node from Intel. email hpc-support@columbia.edu if interested in details.
mcilvain	Grace McIlvain Lab
mmsci	Multimessenger Science
morpheus	Bianca Dumitrascu Lab
msph	MSPH IT
neuralctrl	Laboratory for Neural Engineering and Control
ntar_lab	Biomedical Engineering (Morrison)
pas_lab	Biological Sciences
ueil	Biomedical Engineering (Konofagou)
qmech	Quantum Mechanics/Applied Physics and Applied Math: Marianetti
sscc	Social Science Computing Committee (ISERP, Econ, and CPRC)
tekle_smith	Chemistry Dept - Tekle Smith group
xulab	Earth and Environmental Engineering

Your First Cluster Job

While best practice on all Columbia HPC group clusters, it is particularly important on Insomnia 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. While simple things like editing a file or making new folders can be done on a login node, they can also be done on a compute node, and as you run more complicated jobs on Insomnia, some things simply will not work unless you are first on a compute node.

An example Submit Script

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:

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 further documentation we have about submitting jobs. For much more in-depth information, there is a Slurm Quick Start Guide on the web.