Institution: Istituto di Cristallografia
Departement: Scienze chimiche e tecnologie dei materiali
Typology: Facility
Location: IC-CNR, Via G. Amendola 122/O 70126 Bari
Contacts:
- Dritan Siliqi (dritan.siliqi@cnr.it)
- Domenico Alberga (domenico.alberga@cnr.it)
Description:
HERMES (High-performance Environment for Research in MolEcular and Structural Biology), is 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 <strong>Software Stack:</strong> <ul> <li>Compilers and libraries: C/C++, Fortran, Python, Perl, Julia, MPI, OpenMP, CUDA</li> <li>Molecular Dynamics: Gromacs, NAMD, LAMMPS</li> <li>Structural Biology: MX packages, BioSAXS software, Cryo-EM software, AlphaFold2, Imaging</li> <li>Computational Chemistry: CP2K, Nwchem, Quantum Espresso, DeepMD</li> <li>AI and Deep Learning: Tensorflow, Keras</li> <li>Statistics: R</li> <li>Drug discovery - Schrödinger Suite: - Docking and Virtual Screening - Molecular Dynamics Simulations - Homology Modelling - QSAR and cheminformatics models</li> </ul>
Team:
- Dritan Siliqi (dritan.siliqi@cnr.it)
- Domenico Alberga (domenico.alberga@cnr.it)
- Giuseppe Felice Mangiatordi (giuseppe.mangiatordi@cnr.it)
- Nicola Corriero (nicola.corriero@cnr.it)
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