Biowulf High Performance Computing at the NIH
Classes, Seminars & Walk-In Consults

Next Walk-In Consults

While the coronavirus situation is in effect, the Walk-In Consults are being virtualized.

All problems and concerns are welcome, from scripting problems to node allocation, to strategies for a particular project, to anything that is affecting your use of the HPC systems. The Zoom details are emailed to all Biowulf users the week before the consult. If you need the URL for the Zoom Walk-In session, send email to staff@hpc.nih.gov.

Wed Dec 15, 2021, 1 - 3 pm    Zoom-In

Wed Jan 19, 2022, 1 - 3 pm    Zoom-In

Wed Feb 16, 2022, 1 - 3 pm    Zoom-In

If you can't make the Walk-In/Zoom-In, no worries! Send us an email (staff@hpc.nih.gov) requesting a consult. We will schedule a 1-on-1 phone call or webcast session with one of the staff.

There are no additional in-person classes scheduled at this time. We'll send out an email to HPC users when classes are next scheduled.

Online Self-Paced Classes

No registration is required for these classes.

Bash Shell Scripting
A series of short videos (5-15 minutes) that explore various aspects of Bash from shell setup and command line usage to advanced topics in scripting. The videos can be watched in any order although we provide them in somewhat logical order. In development ... new videos coming each week!

Click here to get to the class.

Introduction to Biowulf
Instructors: NIH HPC Staff

Video tutorials and hands-on exercises to learn about all aspects of the NIH Biowulf cluster including submitting and monitoring jobs. New Biowulf users are encouraged to work through the entire class, and experienced Biowulf users can view specific videos to brush up on a particular section.

Click here to get to the class.

A practical introduction to GATK 4 on Biowulf

A tutorial with a case study and benchmark testing on each step that will help Biowulf users run GATK 4 efficiently. The tutorial is based on germline variant discovery with WGS data from a trio. You will learn NGS data preprocessing and how to optimize your scripts.
Qi Yu and Wolfgang Resch, May 27 2021

Click here to get to the GATK 4 tutorial.

Biowulf Seminars

4 Feb 2020:    [Videocast]
   The Kinetics of Gene Transcription
   Carson Chow (NIDDK)


Biowulf 20th Anniversary Seminar Series

Biowulf 2017-2018 Seminar Series

Slides and Handouts from Previous HPC Classes

Apart from the handouts listed below, the NIH HPC staff creates and maintains Training Videos to help users get the most out of our resources.

Deep Learning by Example on Biowulf. A course comprising a series of hands-on biological examples implemented in Keras, one example per class, intended for NIH researchers using Biowulf.
Gennady Denisov, 2019-2021

Julia for Scientific Computing (Slides) (Video)
This is an introductory course to scientific computing in Julia. The class covers: brief history of Julia, trends in recent Julia usage, comparison of Julia with other scientific computing languages, overview of Julia scientific stack, pros and cons of using Julia, Julia's IDEs, Julia package installation, and interactive Julia script execution on Biowulf.
Antonio Ulloa, 7 April 2021

Overview of Revision Control with Git (Slides)
Presentation to the Laboratory of Epidemiology & Population Science
Afif Elghraoui, 19 March 2021

Biowulf Overview and Best Practices (Slides)
Presentation to the NIH Data Science Team
Nitish Narula and Wolfgang Resch, 12 March 2021

Biowulf Overview and Best Practices (Slides) (Video)
Presentation to the NHLBI Data Science and Bioinformatics group
Wolfgang Resch, 8 March 2021

Making Effective Use of Storage (PDF)
Making effective use of the storage systems provided for HPC and how to avoid common pitfalls that can slow down your jobs and cause system problems.
Tim Miller, 21 May 2020

Introduction to Linux Containers with Singularity (Tutorial GitHub repo) (WebEx recording (Day 1)) (WebEx recording (Day 2))
This class was taught in 2, 3-hour sessions. Students were provided with access to disposable virtual machines (Ubuntu 18.04 on GCP). Students learned what a Linux container is, how it is similar to and differs from a virtual machine, and a bit about leading container platforms and their intended usage. This was followed by hands-on instruction on how to install Singularity and use it to run existing containers from Docker Hub and the Sylabs Container Library. Next students learned how to build containers from scratch and publish them so that others can use them. We finished the class with some advanced examples showing how to tightly integrate container environments with the environment on the host system and how to "fake" the installation of an entire application on the host system through Singularity.
David Godlove, 10-11 March 2020

Python in HPC (PDF)
Profiling, optimizing, and executing python in high performance computing.
Wolfang Resch, 20 February 2020

Bash Shell Scripting (PDF) (PPT) (Webex MP4)
The default shell on many Linux systems is bash. Bash shell scripting provides a method for automating common tasks on Linux systems (such as Helix and Biowulf), including transferring and parsing files, creating sbatch and swarm scripts, pipelining tasks, and monitoring jobs. A step-by-step data-driven lesson is available. There is a summary of Linux commands (PDF) and the GNU Bash manual (PDF) available as well.
David Hoover, 17-18 December 2019

Introduction to Linux (PDF)
Course intended for researchers that are new to Linux/Unix. Covers Unix/Linux operating system concepts, a little history, basic file system navigation, text editing, bash (shell) syntax, file transfer, and a number of useful commands and utilities.
Mark Patkus, 3-4 Dec 2019

Managing Personal Software Installations (PDF)
Scientific software can be challenging to get working. This hands-on workshop will cover private software installations, dealing with various package managers and build systems, and organizing software in your personal space on Biowulf.
Afif Elghraoui, 06 August 2019

Scientific Python for Matlab users (PDF) (Video)
An introduction to scientific Python for those with some experience in Matlab. This course contains a comparison of Python and Matlab as well as an overview of Python's scientific stack (numpy, scipy, matplotlib). Also covered are a brief description of IDEs for Python and how to make use of Jupyter notebooks on the Biowulf cluster.
Antonio Ulloa, 9 July 2019

Data Management Best Practices for Groups (PDF) (PPT)
An overview of file storage, access permissions, file transfer, and sociological behaviors to keep your collaborative group functioning.
David Hoover, 24 April 2019

NIH HPC Object Storage System Overview (PDF)
This course introduces users to the concept of object storage - a new technology being used by many large Internet companies that is becoming increasingly popular for scientific use because of its capability to store large-scale, unstructured data. The class describes the NIH HPC object storage system in detail and includes a practical example of its use in a real scientific workflow.
Tim Miller, 9 Oct 2018

Creating and running software containers with Singularity (slides and tutorial)
This was a three hour hands-on workshop on how to user Singularity to create and run containers. Students learned how to install Singularity on a Linux system, create containers with their choice of Linux distribution and software, and use Singularity to run containerized apps.
Afif Elghraoui, 26 July 2018

Building a reproducible workflow with Snakemake and Singularity (Slides and GitHub repo)
Students attending this class will learn how to build a workflow with Snakemake and how to make it more reproducible with Singularity containers. This class will make use of the Biowulf cluster and requires knowledge of the Linux command line as well as Python.
Wolfgang Resch, 21 February 2018

Singularity Demo( Slides |  Demo Readme)
1h intro and demo of Singularity containers for NIMH Reproducible Neuroscience Workshop

Using the HPC Systems Storage Effectively (PDF)
A course that describes the different storage systems available to NIH HPC users along with policies and best practices. Also explains how to avoid storage bottlenecks when running jobs.
Tim Miller, 16 Feb 2017

Parallel MATLAB jobs on Biowulf (PDF) (PPT) (Videos)
Developing MATLAB code for parallel computing, using the MATLAB compiler to deploy license-free code, automating swarm file generation, spawning and monitoring swarms interactively from within the MATLAB environment, and ordering jobs with dependencies to develop an analysis pipeline.
Dave Godlove, 17 Feb 2016

Swarm on the Biowulf Cluster (PDF) (PPT)
Swarm is a script designed to simplify submitting a group of commands to the Biowulf cluster. With the shift from PBS to Slurm, the functionalities and indiosycrasies of swarm have changed.
David Hoover, 22 Sep 2015

Gene Synthesis using DNAWorks (PPT)
David Hoover, 15 Nov 2006

Linux Tutorials

Helix and Biowulf users will make most effective use of the systems if they are familiar with GNU/Linux.

Below are links to some tutorials which cover the basics of GNU/Linux commands.

Introduction to Linux at the TACC, Texas.
Introduction to Linux guide located on the the Linux Documentation Project's website.
A Basic Unix/Linux Tutorial, at Oxford University, UK.
Unix Tutorial for Beginners. Eight simple tutorials which cover the basics of Unix, at U. Surrey, UK.
Command-line crash course
The Linux Command Line, by William Shotts
Learn the Command Line, A web-based GUI tutorial by codeacademy

Other Training at NIH

The Technology Training Program at CIT offers courses relating to computing, networks, and information systems.

The NIH training program offers classes in writing, speaking, grant writing and more.

The FAES Graduate School runs short and long courses.