HPC in Molecular and Atomistic Simulations @ICHEC

Europe/Dublin
Room B003/B002/B004, Computer Science Building (University College Dublin)

Room B003/B002/B004, Computer Science Building

University College Dublin

Belfield, Dublin 4, Ireland
Description

This course aims to provide a general overview of HPC and relevant applications for researchers involved in molecular and atomistic simulations, encompassing areas such as computational and physical chemistry. It is targeted mainly at researchers who may have little to no prior experience in using parallel applications on HPC systems. The course is organised in collaboration with E-CAM, a European Centre of Excellence that support HPC simulations through software development, training and research.

The course initially covers some of the key HPC concepts (e.g. architecture, batch systems), including scripting for pre- and post- processing simulation data. It will then delve into quantum mechanics and molecular dynamics simulations, introducing their respective key concepts and popular applications such as Gaussian, Gromacs and LAMMPS. There will be a heavy emphasis on practical sessions where participants will gain knowledge about best practices on using the simulation packages in parallel and ways to measure and achieve optimum scalability.

Each participant is required to bring his/her own laptop to the course for the practical sessions. Accounts on a HPC system will be allocated during the course.

The course will be held in Room B003 (Weds 13th), B002 (Thurs 14th) and B004 (Fri 15th) in the Computer Science and Informatics Centre (Building #17 on UCD campus map).

    • 09:00 10:30
      Introduction to HPC
    • 10:30 11:00
      Break 30m
    • 11:00 12:30
      HPC environment I
    • 12:30 13:30
      Lunch 1h
    • 13:30 15:00
      HPC environment II
    • 15:00 15:30
      Break 30m
    • 15:30 17:00
      Scripting
    • 09:30 10:30
      Quantum Mechanics: Theory
    • 10:30 11:00
      Break 30m
    • 11:00 12:30
      Quantum Mechanics: Gaussian
    • 12:30 13:30
      Lunch 1h
    • 13:30 15:00
      Quantum Mechanics: Gaussian
    • 15:00 15:30
      Break 30m
    • 15:30 16:30
      Quantum Mechanics: Gaussian
    • 16:30 17:00
      JUBE
    • 09:30 10:30
      Molecular Dynamics: Theory
    • 10:30 11:00
      Break 30m
    • 11:00 12:30
      Molecular Dynamics: Gromacs
    • 12:30 13:30
      Lunch 1h
    • 13:30 15:00
      Molecular Dynamics: LAMMPS
    • 15:00 15:30
      Break 30m
    • 15:30 17:00
      Molecular Dynamics: Benchmarking
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