Welcome to the EMCC Cluster

The EMCC cluster provides high-performance computing (HPC) resources specifically tailored for Cryo-EM, structural biology, and computational chemistry research at Aarhus University.

It plays a central role in supporting the full Cryo-EM pipeline—from raw image pre-processing and motion correction, to particle picking, 3D reconstruction, and atomic model building using tools such as RELION, cryoSPARC, AlphaFold3, Rosetta, and Phenix.

EMCC includes a diverse array of CPU and GPU nodes optimized for both throughput and memory-intensive workloads. GPU nodes are configured for deep learning–based structure prediction and design tasks, while CPU nodes efficiently handle parallel reconstruction and refinement workflows.

Backed by a fault-tolerant 3.2 PB CephFS storage system with high-speed 100 GbE networking, EMCC enables efficient management of terabyte-scale Cryo-EM datasets and downstream analysis. All project data is regularly backed up to an off-site ZFS-based tier with snapshot recovery, ensuring data integrity and continuity.

Beyond Cryo-EM, EMCC supports protein crystallography, cryo-electron tomography, de novo protein design, molecular dynamics, and large language model applications—including retrieval-augmented generation (RAG) and scientific chatbots trained on in-house datasets.

Access to EMCC is available via secure SSH connections using AU’s jump-host infrastructure, the VDI.au.dk virtual desktop environment, or through AU's VPN service. Researchers can work interactively or submit batch jobs from remote terminals, workstations, or graphical desktop sessions.

In addition, EMCC hosts 13 high-end GPU-accelerated workstations in a dedicated on-site Graphics Room, allowing users to physically access powerful nodes for interactive 3D visualization, structural modeling, and real-time GPU workflows.

The cluster is available free of charge for pilot usage (up to 1 TB), with scalable project quotas (seats of 20 TB) and institutional support.