HPC Cluster: HERMES

Institute of Crystallography (IC) - Bari

 

The Institute of Crystallography hosts HERMES (High-performance Environment for Research in MolEcular and Structural Biology), a high-performance computing cluster designed to provide support to the scientific community for CryoEM, BioSAXS, X-Ray data storage and processing, as well as to enhance theoretical and computational research in Structural Biology and Drug Discovery. Specifically, the system consists of 5 CPU compute nodes and 4 CPU/GPU compute nodes, each with 4 NVIDIA H100 GPUs capable of delivering high computational power for applications such as image processing, artificial intelligence model training, and biological big data processing. Additionally, the system features a Scale-Out NAS storage system capable of supporting the storage of large amounts of data.

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HPC Cluster Details

 
 
  • N. 5 Compute nodes Dell PowerEdge R760: 2x Intel Xeon Gold 6448Y 2.1G, 32C/64T, 16GT/s, 60M Cache; 1024GB RAM 4800MHz DDR5
  • N. 4 GPU nodes Dell PowerEdge R760XA: 4x GPU Nvidia H100 94GB NVLINK Bridge
  • N. 2 Login/service nodes Dell PowerEdge R760xs
  • Storage: Scale-Out NAS 4x Dell PowerScale Isilon A3000 nodes: 1280 TB raw space

Software Stack

  • Compilers and libraries: C/C++, Fortran, Python, Perl, Julia, MPI, OpenMP, CUDA
  • Molecular Dynamics: Gromacs, NAMD, LAMMPS
  • Structural Biology: MX packages, BioSAXS software, Cryo-EM software, AlphaFold2, Imaging
  • Computational Chemistry: CP2K, Nwchem, Quantum Espresso, DeepMD
  • AI and Deep Learning: Tensorflow, Keras
  • Statistics: R

 

  • Drug discovery: Schrödinger Suite
    1. Docking and Virtual Screening
    2. Molecular Dynamics Simulations
    3. Homology Modelling
    4. QSAR and cheminformatics models

All data generated on our HPC platform are managed in accordance with the FAIR principles (Findable, Accessible, Interoperable, Reusable).

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