The OpenMind computing cluster is operated by the Department of Brain and Cognitive Sciences (BCS) and the McGovern Institute. It provides the MIT brain research community with access to state-of-art computing resources. There will be a series of online tutorials for computing on OpenMind. These tutorials are designed for assisting OpenMind users to utilize high-performance computing resources efficiently. Any BCS researcher is welcomed to attend. If you want to attend but do not have an OpenMind account, email shaohao@mit.edu.

All times are US eastern standard time. To make it convenient for audiences from different time zones, there is a morning session and an afternoon session for each tutorial. The contents in the two sessions are the same. We welcome international students to attend online from outside the US. No registration is required. Slides and recordings will be available online afterwards.

OpenMind Tutorial I: An Introduction

Thursday, September 10

Session 1: 9–11 am: https://mit.zoom.us/j/93528227509 | Meeting ID: 935 2822 7509

Session 2: 2–4 pm: https://mit.zoom.us/j/98406470339 | Meeting ID: 984 0647 0339

In this tutorial, high performance computing (HPC) and the OpenMind computing cluster will be introduced. Attendees will learn HPC knowledge, basic Linux commands, and practical skills for using the cluster, such as using file systems, managing software, and submitting simple batch jobs. Hands-on examples will be demonstrated. This tutorial is designed for new users or beginners, but it is also an opportunity for experienced users to learn about HPC and OpenMind systematically.

UPCOMING TUTORIALS

OpenMind Tutorial II: Applications and Containers

Friday, September 11

Session 1: 9–11am: https://mit.zoom.us/j/98051622693 | Meeting ID: 980 5162 2693

Session 2: 2–4 pm: https://mit.zoom.us/j/92021394092 | Meeting ID: 920 2139 4092

In this tutorial, attendees will learn how to set up applications (such as MATLAB, Python, Anaconda, containers, Jupyter Notebook, R, and Julia) on OpenMind. First, Environment Module will be introduced, followed by setting up Python in Anaconda. Then the left will be focused on using Singularity Container, which is used to support most applications on Openmind. Topics include: exploring useful containers, running user applications in containers, and building user-customized containers. Tensorflow and Pytorch will be used as illustrating examples. 

OpenMind Tutorial III: Slurm Job Scheduler and Best Practices

Monday, September 14

Session 1: https://mit.zoom.us/j/93930718063 | Meeting ID: 939 3071 8063

Session 2: https://mit.zoom.us/j/92809930121 | Meeting ID: 928 0993 0121

In this tutorial, best practices for using Openmind will be covered. The major part will be focused on many aspects of the Slurm job scheduler, including partition, QOS, preemption, priority, request for CPU, memory and GPU resources, job array, and job dependency. Practical bash shell scripting skills will be introduced along with writing batch job scripts. Using Lustre storage will be briefly introduced too.