Skip to main content

Genomics Compute Cluster on Quest

The Feinberg School of Medicine, in an initiative spearheaded by the Office of the Dean, the Center for Genetic Medicine, and the Department of Biochemistry and Molecular Genetics, provides over 4,000 cores on Quest’s Genomics Compute Cluster to Northwestern’s genomics community to foster and empower computational genomics research at Northwestern.

The Genomics Compute Cluster (GCC) continues to support different areas in computational genomics research including aligning sequencing data, RNA-Seq, ChIP -seq, single-cell analysis, whole genome analysis, running custom code, and many more. All genomics researchers at Northwestern are invited to join the GCC.

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 formProspective users will be prompted to provide a brief statement of research to be performed on the GCC.

Once requests are approved, researchers will be added to the GCC buy-in group on Quest, allocation b1042, and may begin using the GCC after attending an orientation .  

Genomics Compute Cluster Compute and Storage Resources

Compute Nodes

4,040 cores across 80 compute nodes: 

For specific information about Quest architectures, see Quest Technical Specifications  

Partitions for GCC Compute Nodes  

Job priority for the GCC is assigned by partition and depends on the researcher’s affiliation with Feinberg School of Medicine. The number of nodes in each partition prioritizes resource availability for Feinberg researchers and jobs that are 48 hours or less.  

Feinberg Researchers

Partition Name Nodes/Cores Maximum Job Duration
genomics 76/3,880 2 days 
genomicslong 60/3,048 10 days
genomics-gpu 2/104 2 days, see GPUs on Quest for job submission guidelines
genomics-himem 2/56 7 days 
genomics-burst 76/3,880 project-based access, email quest-help@northwestern.edu 

Weinberg, McCormick, and other Non-Feinberg Researchers

Partition Name Nodes/Cores Maximum Job Duration
genomicsguest 60/3,048 2 days
genomicsguestex 10/448 10 days or less
genomicsguest-gpu 2/104 2 days, see GPUs on Quest for job submission
genomicsguest-himem 2/56 7 days 

Scratch Storage Space  

The Genomics Compute Cluster provides researchers with 216 TB, shared scratch storage space in /projects/b1042 for short term storage.  For maximum flexibility, this scratch space is open to all users of the Genomics Compute Cluster with no space limitations for individual researchers.   

To keep this shared scratch storage available for everyone’s use, files more than 30 days old are deleted through a purge process on a monthly schedule, but may be purged earlier if /projects/b1042 is getting full. Researchers will receive an email notification prior to their files being deleted from the scratch space.  

Researchers may not run “touch” commands or similar commands for the purpose of altering their files' timestamps to circumvent this file deletion policy. Research Computing will impose strict storage limits on researchers who violate this policy.   

Any files that need to be kept longer than 30 days should be moved to the researcher’s own storage in their project or home directory, or  transferred to other storage services such as RDSS or FSMResfiles .  

Researchers are requested to use this scratch storage space conscientiously by deleting files that they no longer need in /projects/b1042 as soon as they're done with them, rather than occupying storage for the full 30 days unnecessarily.

Shared Library Space

Shared reference files are available to the genomics research community in the  20 TB, read-only storage space in /projects/genomicsshare . To see a list of files, look in /projects/genomicsshare/README. To request files be added to the shared genomics reference library, email   and include "genomicsshare" in the subject line. To request files be added to the shared genomics reference library,  email quest-help@northwestern.edu   and include "genomicsshare" in the subject line.

Genomics Compute Cluster Community

Genomics researchers at Northwestern are invited to join the GCC slack channel at genomics-rcs.slack.com, as a way to connect with other GCC researchers and stay informed about the GCC.  

To request help, email quest-help@northwestern.edu .  

 

Last Updated: 2 April 2021

Get Help Back to top