High-Performance Computing at the NIH
GitHub YouTube @nih_hpc RSS Feed
Training, Seminars, Classes

Upcoming HPC classes: Classes taught by the HPC staff are free, but registration is required. Priority is given to Helix/Biowulf users.
Click here to see upcoming NIH HPC classes and register for them.

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 NIH HPC staff creates and maintains Training Videos to help users get the most out of our resources.

Slides and Handouts from Previous HPC Classes

Bash Shell Scripting (PDF)
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. There is a summary of Linux commands (PDF) available as well.
George Fekete, CSRA. 15 May 2017.

The NIH Biowulf Cluster: Scientific Supercomputing (PDF)
This two-morning class is an introduction to the Biowulf Linux cluster for users who have NIH Biowulf accounts or Helix users planning to get one. Topics covered: cluster concepts, accounts, connection, storage, batch system, how to set up and submit a simple batch job, partitions, interactive jobs, swarm jobs, available scientific applications, job monitoring, resource allocation, licensed software.
Steven Fellini and Susan Chacko, 2/3 May 2017

Building a reproducible workflow with Snakemake and Singularity. (course materials)
Hands-on introduction to snakemake. Also included a demonstration on how to integrate singularity containers with snakemake to create a reproducible workflow.
Wolfgang Resch, May 1, 2017

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.
George Fekete, CSRA, 26/27 Apr 2017

Creating and running software containers with Singularity (course materials)
This was a three hour hands-on (no slides) 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. The file course materials link above is simply a snapshot of the instructors home directory after demonstrating commands and editing files. The file history_commands contains a transcript of the training session. To extract the contents of the compressed archive after downloading it, use the command: tar xvf singularity_class_2017-04-24.tar.gz
Dave Godlove, 24 April 2017

NIH HPC Object Storage System Overview (PDF) (PPT)
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, 28 Feb 2017

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

Biowulf: A Beowulf for Bioscience (PDF) (PPT)
An introduction to the Biowulf2 Linux cluster for new Biowulf users or Helix users planning to get a Biowulf account. Topics covered: cluster concepts, accounts, connection, storage, batch system, how to set up and submit a simple batch job, partitions, interactive jobs, swarm jobs, available scientific applications, job monitoring, resource allocation, licensed software.
Steven Fellini & Susan Chacko, 17-18 Oct 2016

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 Biowulf2 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

Biowulf2 training session (PDF)
Introductory talk for current Biowulf users about the expanded Biowulf cluster, including description of hardware, Slurm batch system, and monitoring tools.
Steven Fellini, Susan Chacko, David Hoover, 9 July 2015.

Imputing Big Data from GWAS (PDF) (PPT)
A discussion of imputation and large scale meta-analyses of GWAS data on the biowulf cluster featuring hands on examples and experienced instruction.
Michael Nalls (NIA), 10 Sep 2014, 1 Oct 2014

Rosetta Workshop
Tutorials and presentations from the Rosetta Design Group, hosted by Helix Systems. (NIH only)
Xavier Ambroggio and Monica Berrondo, 19-21 May 2009

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