Biostatistics Cluster Quickstart Guide

This guide will help you get your account, login, and run your first job.

  1. Requesting an account
  2. Logging in
  3. Copy code(s) and data to login node
  4. Creating a batch script
  5. Submitting your job
  6. Checking the status of your job

Requesting an account

The Biostatistics cluster is a paid service. The current cost for cluster access is $1000 per user per year. To request an account on the cluster, please complete the account request form.

Logging in

Using a terminal program (eg; PuTTY, secure shell, ssh from a terminal) connect to host biostat-login.sph.umich.edu using your uniqname for the login name and your SPH Kerberos/IFS password. You will also need to complete Duo two-factor authentication.

The following is an example of opening a session from a Mac or Linux computer

uniqname$ ssh uniqname@biostat-login.sph.umich.edu
Password:
Duo two-factor login for uniqname

Enter a passcode or select one of the following options:

1. Duo Push to iOS
2. Phone call to XXX-XXX-9332

Passcode or option (1-2): 1
Success. Logging you in...

uniqname@bajor ~$

 The following is an example of opening a session from a Windows computer using PuTTY

PuTTY

In the above image enter biostat-login.sph.umich.edu in the Host Name field and then click Open. A terminal will open where you will login using your uniqname, kerberos password and Duo two-factor.

terminal

Copy code(s) and data to login node

Using scp/sftp from the terminal or your secure shell application upload any programs, scripts and data files you will need to run your code. Alternately, if all your files are in IFS you could copy them to your cluster home directory with the following comment

$ cp ~/ifs/script.R ~/

Creating a batch script

Create a text file that you will use to submit your job. You can upload this as in step 3 or create in place in the terminal with a text editor. An easy to use editor is nano. Here is a quick sample batch script for running a single job with a default resource allocation of 1 cpu core and 1000MB of memory running for 1 day.

#!/bin/sh
#SBATCH --mail-type=ALL
#SBATCH --mail-user=uniqname@umich.edu
#SBATCH --job-name=my_first_job
#SBATCH --time=1-00:00:00

srun R CMD BATCH ./script.R

Submitting your job

Assuming you saved the above batch script to job.txt in your home directory you can submit the job with sbatch like this:

$ sbatch ./job.txt

You will see the job id for the job you just submitted and will receive an email when the job starts, when it ends, and if it should fail.

Checking the status of your job

You can check the status of your job in the queue with the squeue command:

$ squeue -u $USER