RIS HPC Newsletter

High-Performance Communications – November 7, 2024

Unveiling Innovation

Welcoming new condos and allocations on Storage2

The future of scientific computing at WashU

The RIS team is actively working on the delivery, installation, and configuration of hardware from each vendor. This is crucial in ensuring our cluster infrastructure meets Compute2’s highest performance, security, and reliability standards.

We anticipate that early adopters will have access to the cluster around February 2025. 

Improving performance & increasing security

This month, Washington University in St. Louis is embarking on a major network upgrade. It will replace outdated routers and switches with cutting-edge technology designed to significantly enhance the network’s capacity, speed, and reliability.

Why it matters: The modernization will deliver a 10-fold increase in bandwidth, meeting the university’s growing academic and research demands. These improvements are essential as students and staff use data-heavy applications and cloud services. The upgraded infrastructure will also enhance security features, such as network segmentation, to safeguard sensitive data and mitigate cyber threats. Automation and centralized control will streamline network management, creating a more secure and resilient system.

Check the maintenance schedule to see when your building will be impacted.

For more information, visit the WashU IT Network Modernization Project webpage.

Exploring Frontiers With Computational Power

Research @ WashU with the Turner Lab

Turner T. Precision Genomics [Internet]. Turner Lab. St. Louis, Missouri; [cited 2024]. Available from: https://turnerlab.wustl.edu/research/

Mission:  While not synonymous with Precision Medicine, Precision Genomics plays a crucial role within its broader scope alongside fields like Precision Psychiatry and Precision Imaging. As a research lab, the Turner Lab is dedicated to advancing Precision Genomics by tackling five key challenges(in the above image) that currently limit its application for everyone.

Resulted Success:  In the Turner Lab, success is measured by published papers, the types of grants received, and whether trainees are learning from this research and becoming the next generation to impact the field in new ways.  

Expert Insights: “We’ve done lots of AlphaFold calculations on the RIS. They would have cost millions of dollars if we had run them in Google Cloud. Running them on the RIS made an impossible problem possible because our lab does not currently have millions of dollars to run these computations in the cloud. We do, however, have a nice RIS setup to get the work done.” – Tychele Turner, Assistant Professor of Genetics. – Dr. Tychele Turner, Assistant Professor of Genetics.

“We created a new tool, 3D-Clump, to look at clustering of variants on protein structures, and we were aided by being able to make AlphaFold predictions on the RIS.” – Dr. Tychele Turner, Assistant Professor of Genetics.

Developed Collaboration:  Hare And Tortoise, HAT, are two de novo variant callers developed by the Tychele N. Turner, Ph.D. Lab with the help of Research Infrastructure Services at WashU. Hare, as seen in Ng et al. 2022, uses the software Parabricks, v4.0.0-1, by NVIDIA, that leverages GPUs to accelerate variant calling, specifically for Haplotyecaller GATK 4.2.0 and DeepVariant v1.4.0. Tortoise uses freely available, open-source versions of these variant callers. The lab uses GLnexus to form family-level joint-genotyped files that can be run through their custom de novo variant filter workflow.

By the Number: RIS Resources at Work
2.5 PB  Active storage
1 PB of Archive storage
272 CPUs, 4 GPUs, and 1 Condo server 
4,395,828 jobs consumed 13,391,704 CPU core hours and 216,467 GPU hours

Stay Informed and Inspired

Managing allocations with ColdFront

Welcome to ColdFront RIS’s new tool for managing resource allocations on Storage2. In the near future, it will include a self-service portal for users to request access to resources for their research group.

Why it matters: ColdFront allows institutions to allocate resources efficiently, track usage, and implement policies, all through a centralized web-based interface. It streamlines the process of managing access to valuable computing and storage resources, making it essential for organizations looking to improve transparency, accountability, and efficiency in their research infrastructure.

Expanding capabilities of Globus data management

In the near future, researchers can request the use of Globus Premium Storage Connectors,  which will provide a uniform interface for accessing, moving, and sharing data across cloud storage services such as Box, Amazon S3, Google Cloud Storage, and Microsoft Azure.

Why it matters: Globus Cloud Connectors enable secure, efficient, and scalable data transfers, sharing, and management of cloud-stored data. This makes it easier for researchers and institutions to handle large-scale datasets in collaborative and high-performance computing environments.

Elevate Your Expertise

Join virtual workshops designed to deepen your knowledge, refine your skills, and provide hands-on experience in a dynamic learning environment.