High Performance Computing

The Joint High Performance Computing Exchange (J H P C E) is a High-Performance Computing (HPC) facility in the  Department of Biostatistics at the Johns Hopkins Bloomberg School of Public Health. This fee-for-service core is a long-standing collaborative effort between Biostatistics and the  Computational Biology & Research Computing group in the department of Molecular Microbiology and Immunology. The facility is open to all Johns Hopkins affiliated researchers.

The facility is used primarily by labs and research groups in the  Johns Hopkins Bloomberg School of Public Health (SPH), the Johns Hopkins School of Medicine (SOM) and the Lieber Institute for Brain Development (LIBD). We have over 800 user accounts, 400 active users  and approximately 100 unique users per quarter.

The computing and storage systems are optimized for genomics and biomedical research. The cluster has 72 compute nodes, providing over 4000 cores, 30TB of DRAM and over 14 PB of networked mass storage. Networked mass storage uses open-source file systems (ZFS and Lustre-over-ZFS) and custom-built hardware. The latter includes a 5 PB of Lustre file system space that may be the lowest-cost and lowest-power parallel file system on the planet. We also have a 2PB disk-to-disk backup system for backing up more critical data.

The JHPCE cluster is optimized for the embarrassingly parallel applications that are the bread-and-butter of our stakeholders, e.g. genomics and statistical applications, rather than the tightly-coupled applications that are typical in traditional HPC fields, e.g. physics,  fluid-dynamics, quantum simulation etc. The network fabric consists of a 10 Gbps ethernet. The facility is connected via a 40Gbps network to the University’s Science DMZ. Job scheduling is performed with Open Grid Engine (OGE).

The JHPCE operates as a formal Common Pool Resource (CPR) Hierarchy with rights to specific resources based on stakeholder ownership of resources. To benefit the entire research community, excess computing capacity is made available to non-stakeholders on an as-available basis, in exchange for fees that defray the operating costs of the stakeholders.

If your lab is interested in joining the JHPCE community, either as a stakeholder or as a non-stakeholder, please contact the director (jhpce@jhu.edu) to determine whether we can accommodate your needs.

If your lab is already a member, and you need to add new users, then have the users fill out the JHPCE new user request form.

Mark Miller and Brian Caffo
Co-Directors, JHPCE