Infrastructure for Structural Biology
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.
Availability: The cluster is available free of charge for pilot usage (up to 1 TB), with scalable project quotas (seats of 20 TB). View pricing details →
Quick Facts
- Location MBG, Aarhus University
- Primary Use Cryo-EM / Structural Bio
- Storage 3.2 PB CephFS
- GPU Compute 40+ (A100/L40S/V100)
- Access SSH, VDI, VPN
- Backup Off-site + Snapshots
- Graphics Room 13 Workstations
Supported Workflows
Optimized software stacks and dedicated hardware for each research domain.
Your Workflow?
Contact us to discuss custom pipeline integration and software installation.
Cryo-EM
Single-particle analysis, reconstruction, refinement, and high-throughput processing.
Tomography
Tomogram processing, subtomogram averaging, and cryo-ET pipeline orchestration.
Crystallography
X-ray data processing, phasing, refinement, and validation.
Protein Design
Deep-learning driven prediction and de novo design workflows.
LLM & AI
Open-source assistants, RAG pipelines, and scientific chatbots.
Access & Connection
Connect via VDI for a managed desktop, SSH for terminal workflows, or mount your storage locally.
VDI Desktop
Virtual desktop environment. No VPN required.
To use vdi.au.dk you need to contact Rune Kidmose to have your AUID added to the VDI database. This is a one-time setup.
-
1
Go to vdi.au.dk
In your browser, click "Install VMware Horizon Client" which will download an OS specific version (Windows, macOS, or Linux).
-
2
Install & Launch Omnissa Horizon Client
Run the installer. On first launch, you need to fil out the server address:
vdi.au.dk. -
4
Select vdi.au.dk
Double-click the "vdi.au.dk" button. Then login with your EMCC credentials (not your AU credentials).
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4
Login with AU Credentials (AUID) - Not your EMCC Credentials
Use
au123456@uni.au.dk+ your AU password and 2FA. -
5
Select a public workstation
Double-click on any of the public (non privat or designated) workstations to start a remote connection. In the login window use your EMCC credentials (not your AU credentials).
SSH Connection
Connect via submit hosts: yeti, orc, mephisto
Works in Terminal (macOS/Linux) or PowerShell/Command Prompt (Windows)
Mount Storage Locally (SSHFS)
Access your /emcc/ project directory directly from your local machine. Off-campus requires AU VPN.
Requires macFUSE.
Unmount with umount ~/emcc_home
Off-campus access requires AU VPN. See vpn.au.dk for setup instructions.
About the Mount Path
This mounts your project directory at /emcc/<username> . Your Linux home directory at /u/<username> is not included in this mount. To mount another folder modify the above command accordingly.
Compute Infrastructure
GPU and CPU nodes for heterogeneous workloads.
| Node | GPUs | GPU Memory | CPU | System RAM | Network |
|---|---|---|---|---|---|
| Snoke 4 | 4× Tesla V100S | 32 GB | Xeon Gold 6226 | 384 GB DDR4 | 100 GbE |
| Snoke 5–7 (3 nodes) | 4× Tesla A100 | 40/82 GB | Intel Platinum / AMD EPYC | 512–768 GB | 100 GbE |
| Snoke 8–10 (3 nodes) | 4× Tesla L40S | 46 GB | Xeon Platinum / Gold | Up to 1 TB DDR5 | 100 GbE |
Pricing & Access Tiers
Flexible options from free pilot access to full production environments. All paid tiers include snapshot backup, off-site redundancy, and minimum 20 TB base allocation.
Academic Use Only
EMCC is available strictly for academic research. Commercial or industrial use is not permitted. External academic researchers (non-AU) must have an active collaboration agreement with an Aarhus University faculty member to access EMCC resources.
Pilot Tier
Evaluate workflows and test EMCC capabilities before committing.
- 1 TB storage quota
- Limited CPU compute time
- Standard support & Graphics Room access
- No GPU processing
- Individual access only
Storage Only Seat
Raw storage capacity without compute resources. Minimum 20 TB required.
- Minimum 20 TB storage
- Priority support & Graphics Room access
- Snapshot & off-site backup included
- No processing (CPU/GPU)
- Expandable: 4000 DKK per additional 10 TB
CPU-Only + Storage Seat
CPU compute nodes with storage for CPU-only workflows. Minimum 20 TB required.
- Minimum 20 TB storage
- CPU processing
- No GPU processing
- Priority support & Graphics Room access
- Expandable: 6000 DKK per additional 10 TB
Full Project Seat
Full production access with GPU & CPU processing for all workloads. Includes 20 TB storage.
- 20 TB storage: increases in 20TB intervals (number of seats)
- GPU processing
- CPU processing
- Shareable with project members
- Priority support & Graphics Room access
All prices exclude VAT. Additional storage for Project Seat priced on request. Contact us for custom configurations.
AU Internal Documentation & Resources
Internal tools and documentation for EMCC users. AU network or VPN required.
LabBook Wiki
Software documentation and tutorials
Requires AU-user & VPN off-campus
EMCC Chatbot
AI assistants for workflow support
Requires third party account & VPN off-campus
Acknowledge EMCC
If you use EMCC resources in your research, please include this citation in your publications.
The computational resources used in this project were carried out on the EMCC cluster (https://emcc.au.dk). We gratefully acknowledge EMCC for providing the computational resources and support that made these research results possible.
Need Assistance?
Support for software installation, workflow optimization, and access issues.
support.emcc@au.dkAarhus University, Denmark