Genomics Compute Cluster
The Genomics Compute Cluster (GCC) is a dedicated resource on Quest designed to support computational genomics research at Northwestern. The GCC is funded by the Feinberg School of Medicine and the Weinberg College of Arts and Sciences, providing researchers with extensive compute power, GPU and high memory resources, and scratch storage space.
The GCC enables a wide range of computational genomics applications—including sequence alignment, RNA-Seq, ChIP-seq, single-cell analysis, whole genome analysis, and custom code execution. All genomics researchers at Northwestern are welcome to join the GCC.
The GCC is part of Quest and uses Quest’s high-performance computing infrastructure and file system. Quest is housed in the University Data Center.
Please include the GCC Acknowledgement of Use when publishing research done using the Genomics Compute Cluster on Quest.
How to Access the GCC
Northwestern researchers affiliated with any Northwestern school who are engaged in computational genomics can apply for access to the Genomics Compute Cluster.
To apply, please complete the Genomics Compute Cluster User Registration form.
Approved researchers are added to the b1042 allocation on Quest and must complete a virtual or in-person orientation before using the cluster and annually fill out a membership renewal form. View the GCC Orientation schedule listed on the Workshops and Learning Resources web page.
Compute and Storage Resources
Compute Nodes
The GCC nodes comprise 10,000+ cores, 5 high-memory nodes, and 4 GPU nodes.
- Standard Compute Nodes: The GCC includes 150 compute nodes, distributed across multiple generations of Quest. For specific information about Quest architectures, see Quest Technical Specifications
- Quest 10: 70 nodes
- Quest 11: 42 nodes
- Quest 12: 20 nodes
- Quest 13: 18 nodes
- GPU Nodes:
- Quest 10 GPU nodes with 4 NVIDIA A100 GPUs each: 2 nodes
- Quest 12 GPU nodes with 4 NVIDIA A100 GPUs each: 2 nodes
- High Memory Nodes:
- Quest 11 nodes with 2 TB RAM each: 5 nodes
Storage Resources
The GCC also includes 655 TB of dedicated scratch storage that is shared between all b1042 members, with a hard limit of 40 TB per user.
All Quest users have an 80 GB home directory. GCC users who need additional non-scratch storage should apply for a General Access allocation in addition to joining the GCC allocation. General reference resources, such as those hosted by AWS iGenomes, are stored on Quest so that GCC users do not need to hold their own copies within scratch storage.
Note that Quest is not approved for storing protected health information (PHI), data from NIH Controlled-Access Data Repositories, including dbGaP (see Requirements for NIH Controlled-Access Data Repositories and Users), or other sensitive or restricted data. See the Quest Data Security Guidelines for more information.
Support
Get help. GCC users have access to the same support resources as other Quest users. Email quest-help@northwestern.edu to create an IT help ticket for support, or schedule a consultation with our computational specialists to discuss more complex issues or ask questions.
Online community. GCC users are encouraged to join the GCC Slack channel at https://genomics-rcs.slack.com/ to connect with peers and stay updated on resources.
Documentation and tutorials. GCC users should look to the Quest User Guide for tutorials and documentation. Additional information specific to using GCC is available in the GCC User Guide
Training. In addition to GCC orientation sessions, Research Computing and Data Services hosts regular workshops on Quest, genomics workflows, and other computational topics. See the workshop schedule.
Research working groups. GCC users may be interested in joining quarter-long working groups to connect with other genomics and bioinformatics researchers and receive support from Research Computing and Data Services staff. Learn more about working groups.