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Genomics Compute Cluster on Quest

The Feinberg School of Medicine, in an initiative spearheaded by the Feinberg School of Medicine Office of the Dean, the Center for Genetic Medicine, and the Department of Biochemistry and Molecular Genetics provides over 100 nodes on Northwestern’s High Performance Computing Cluster, Quest, to be used for genomics research. This University resource has been made available to the greater genomics community in an effort to foster genomics research and empower the computational genomics community at Northwestern University.

How can I apply to use the Genomics Compute Cluster?

Principle Investigators (PIs) doing genomics research and their graduate students may apply to use the genomics compute cluster by completing the Genomics Compute Cluster User Registration form. Prospective users will be prompted to enter a brief statement of research to be performed on the genomics compute cluster. Once requests have been approved, the user’s NetID will be added to the genomics compute cluster buy-in group, b1042, and the researcher may begin using the nodes.

What is included with access to the Genomics Compute Cluster?

Access to 100 high-throughput nodes

The 100 Nodes each have 24 cores and 128 GB of memory for a combined resource of 2,400 cores.

Access to two high-memory nodes

The high-memory nodes each have 28 cores and 1 TB of memory.

175 TB scratch in /projects/b1042

This shared storage space is intended for temporary files needed and created when genomics jobs are run. Users are requested to create a PI directory under /projects/b1042 to keep scratch files from intermingling with other users’ work. Please keep in mind this is a shared resource and it is important to implement best practices regarding cleaning up these files and using the scratch space in the most efficient way possible, including ending batch files by deleting temporary files that are no longer needed and moving files to your /projects or /home directory when complete.

Files in the scratch space will be deleted after 30 days. You will receive an email reminder before your scratch files are deleted, but it is your responsibility to move files you want to keep into long term storage such as your project directory on Quest or FSMRESfiles. To learn about other research storage options at Northwestern or to increase the space you have available in your project directory, contact quest-help@northwestern.edu for assistance.

10 TB shared library space in /projects/genomicsshare

This storage space is read-only and intended to store shared reference files for the use of the genomics research community. To see a list of files available in genomicsshare, look in /projects/genomicsshare/README. To request files be added to the shared genomics reference library, email quest-help@northwestern.edu and include "genomicsshare" in the subject line.

 

How do I start using the Genomics Compute Cluster?

Once your application to join the Genomics Compute Cluster has been approved you will receive an email with instructions. See Getting Started in the Genomics Compute Cluster for more information on getting started.

Bioinformatics software available on Quest

New software is continually being added to Quest. Please use the command "module avail" for an up-to-date listing of all software packages including genomics software on Quest.

If you would like additional software packages installed on Quest, please see Installing Software on Quest.

Join the Genomics Conversation

The genomics nodes on Quest have a Slack community open to anyone with a Northwestern email address.
Join the Genomics Slack channel to connect with other computataional genomics researchers at Northwestern.

Last Updated: 4 June 2019

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