High Performance Computing

Overview

Bigelow Laboratory for Ocean Sciences's High Performance Computer Cluster (HPCC), Charlie, is designed to handle a diverse range of scientific data processing needs. Charlie consists of six high performance nodes with a combined 576 processor cores, 6 TB of memory (RAM) and access to 250 TB of onsite storage.

Features

Compute Nodes

Charlies currently features six Dell R840s, each with four Intel Xeon Platinum 8168 processors (2.7GHz, 24C, 33MB cache) and one terabyte of memory. One node is dedicated to development and one hosts an NDVIA A100 GPU (80GB 1935GBps memory).

Network

Charlie's nodes are interconnected using a 10Gbps network. They are connected to the internet using a fast 1Gbps fiber network. Bigelow is also connected to the national Internet 2 and the local MaineREN networks that link research and educational institutions directly together in order to reduce latency and increase speed/performance when sharing resources.

Software

At the heart of Charlie's Rocky Linux-based software environment is PBS Pro. PBS Pro is a scheduling system that allocates resources to HPCC jobs based on availability, priority, and permissions. Charlie uses environment modules to provide access to many bioinformatics tools, including BLAST, VirSorter, and dada2, in addition to general applications such as R, Python, and OpenMPI.

Funding

Charlie has been supported by multiple grants, including from the National Science Foundation's Division of Biological Infrastructure and the Simons Foundation.