DataScience Workbook / 06. High-Performance Computing (HPC) / 1. Introduction to HPC infrastructure / 1.3 ISU HPC / 1.3.2 Nova Computing Cluster
Introduction
Nodes and storage can be purchased on the Nova cluster for use by the researchers at ISU. For details about the Nova cluster, click here.
Getting Started
Access and Login
Before logging in the first time, check the Loging in section of the Intro to ISU HPC ⤴ page for information about getting started. Install Google Authenticator on Android ⤴, iPhone ⤴ or Windows ⤴ devices for authentication.
Once connected to ISU network, use any Terminal (Terminal on Linux/Mac and Powershell on Windows) and input following command to log in to Nova:
ssh <ISU NetID>@nova.its.iastate.edu
Data Transfer and Jobs
Use the login hostname (@nova.its.iastate.edu) to log in to Nova and submit jobs, but use the data transfer node for data transfers (@novadtn.its.iastate.edu).
# Data transfer example
Login:
ssh Your-ISU-NetID@novadtn.its.iastate.edu
Copy data:
cp /home/$USER/test.txt /myfiles/Users/$USER/
Once logged in you can start using Nova cluster and submit jobs using SLURM Workload Manager ⤴. SLURM is used to allocate memory and processors to an input job on Nova. If not familiar with the script, use this Script generator for Nova ⤴, input your requirements and it will generate a text script. You can then copy this script in a text file, add your commands at the bottom and then submit the job. Check out the SLURM Basics ⤴ to learn about running your job on Nova or any other HPC Cluster.
Example job script
#!/bin/bash
#SBATCH --time=01:00:00 # walltime limit (HH:MM:SS)
#SBATCH --nodes=1 # number of nodes
#SBATCH --ntasks-per-node=36 # 36 processor core(s) per node
#SBATCH --mail-user=netid@iastate.edu
#SBATCH --mail-type=begin
#SBATCH --mail-type=end
# LOAD MODULES, INSERT CODE, AND RUN YOUR PROGRAMS HERE
module load modulename
your code/commands
Copy/paste the above job script into a text file, add your modules and commands, and submit with the following command:
sbatch filename
Check your queued jobs:
squeue -u your_netID
Available Software
Check out the following:
- System and Application Software ⤴ guide for Nova from ISU
- Software Available on HPC ⤴ in this workbook
Further Reading
- 2. Remote Access to HPC Resources
- 3. Setting up Your Home Directory for Data Analysis
- 4. Software Available on HPC
- 5. Introduction to Job Scheduling
- 6. Introduction to GNU Parallel
- 7. Introduction to Containers