Workshop on Basic Computing Services in the Physics Department - subMIT

Kolker Room (26-414)

Kolker Room (26-414)


The subMIT computing facility is a login pool that is designed to provide access to the basic research computing resources of the physics department and beyond.

This one day workshop will provide an overview and updates on the status and plans for the system and project, as well as topical presentations on a range of use cases.

Additionally, there will be tutorial sessions.  Bring your laptop to run the examples in real-time or just sit back and listen to the accompanying instructional talk.

More information on the subMIT project as well as user documentation is available at

The workshop will take place in the Kolker Room and a Zoom connection will be available at

Refreshments will be provided during coffee breaks!

Please note: the details of the schedule of individual talks may change as we work to accommodate new requests for contributions.

    • 9:00 AM 9:30 AM
      Introduction/subMIT Project Overview 30m
      Speaker: Joshua Bendavid (Massachusetts Institute of Technology)
    • 9:30 AM 9:40 AM
      Getting started on subMIT: Available Resources 10m
      • Computational Resources

      • Documentation: Users Guide, GitHub Examples

      • Support: Help Desk & Chat Bot

      Speaker: Zhangqier Wang
    • 9:40 AM 9:55 AM
      Getting started on subMIT: How to Interact with subMIT 15m
      • ssh / terminal
      • JupyterHub
      • X2Go
      • Visual Studio Code (Remote Development)
      • 1-minute summary of batch jobs (see also later tutorial)
      Speaker: Matthew Heine (Massachusetts Institute of Technology)
    • 9:55 AM 10:05 AM
      Getting started on subMIT: Installing / Managing Software 10m
      • native environment
      • installing software with conda
      • software environment management tools
      • containers overview
      Speaker: Chad Freer (Massachusetts Institute of Technology)
    • 10:05 AM 10:20 AM
      Navigating the recent Linux Upgrade 15m

      In this session we will outline key changes in the migration to the new version of Linux as well as how to access the older version via containers. We are also setting aside a portion of time to answer user questions about the upgrade, so please bring any questions you have, general or specific.

      Speaker: Marianne Moore (MIT)
    • 10:20 AM 10:40 AM
      Coffee Break 20m
    • 10:40 AM 11:00 AM
      Experience thus far running a multi-experiment OpenShift Cluster at FNAL 20m
      Speaker: Lindsey Gray (Fermi National Accelerator Laboratory)
    • 11:00 AM 11:30 AM
      Tutorial: Batch Job / Workflow Management: SLURM & HTCondor 30m

      This session will show how to use the batch schedulers/resource-managers SLURM & HTCondor to manage your computational tasks, distributing them across the shared resources. Depending on your workflow, this may provide an easy way to run your calculations in parallel, shortening time-to-result and eliminating some manual tasks.

      Speaker: Chad Freer (Massachusetts Institute of Technology)
    • 11:30 AM 12:30 PM
      Tutorial: GPUs: Introduction to Likelihood-Free Inference with PyTorch Lightning 1h

      This tutorial will give an overview of using pytorch lightning for building and training neural networks. A simple problem in inference: measuring the parameters of a line will be presented. The tutorial will also introduce distributed training with pytorch lightning

      Speaker: Deep Chatterjee (Massachusetts Institute of Technology)
    • 12:30 PM 2:00 PM
      Lunch 1h 30m
    • 2:00 PM 2:15 PM
      Parameter Estimation of Un-modeled Gravitational-wave Signals using Likelihood-free Inference 15m
      Speaker: Deep Chatterjee (Massachusetts Institute of Technology)
    • 2:15 PM 2:35 PM
      DM21cm: a GPU-accelerated simulation of dark matter energy injection in 21cm cosmology 20m
      Speaker: Yitian Sun (Massachusetts Institute of Technology)
    • 2:35 PM 2:45 PM
      Embarrassingly parallel ray-tracing for the Arcus X-ray spectrometer 10m
      Speaker: Hans Guenther (Massachusetts Institute of Technology)
    • 2:45 PM 2:55 PM
      Employing snakemake to perform measurements with the LHCb experiment at CERN 10m
      Speaker: Blaise Delaney (Massachusetts Institute of Technology)
    • 2:55 PM 3:05 PM
      Tutorial: Introduction to the Snakemake workflow manager 10m
      Speaker: Blaise Delaney (Massachusetts Institute of Technology)
    • 3:05 PM 3:30 PM
      Coffee Break 25m
    • 3:30 PM 3:45 PM
      CMS Analysis on subMIT with crab and dask jobqueue 15m
      Speaker: Simon Rothman (Massachusetts Institute of Technology)
    • 3:45 PM 4:00 PM
      Adaptive Brillouin-zone integration for optical conductivity 15m
      Speaker: Lorenzo Van Munoz (Massachusetts Institute of Technology)
    • 4:00 PM 4:10 PM
      Axion and high-frequency gravitational wave searches with ABRACADABRA and DMRadio 10m
      Speaker: Kaliroe Pappas (MIT laboratory for nuclear science)
    • 4:10 PM 4:20 PM
      Training spiking neural networks via adjoint sensitivity analysis 10m
      Speaker: Enrique Toloza (Massachusetts Institute of Technology)
    • 4:20 PM 4:30 PM
      ML for Science: Best Practices 10m
      Speaker: Denis Boyda (Massachusetts Institute of Technology)
    • 4:30 PM 5:00 PM
      Open Discussion & Closing Remarks 30m