PRACE Autumn School 2012 on Massively Parallel Architectures and Molecular Simulations

The National Centre for Supercomputing Applications in Sofia, Bulgaria is organizing a PRACE Autumn School on Massively Parallel Architectures and Molecular Simulations that will take place in Sofia from 24 to 28 September 2012.

The school will introduce multi scales/ multi physics molecular simulation methods and software for high performance computing applications in molecular biology, biochemistry, microbiology, pharmacology research, cell medicine, immunology, chemical synthesis, atomic level material damage investigations and investigation of clusters of billions of nanoparticles.

Тhe school will cover the following topics:

  • DL POLY;
  • Long-Range Interactions calculations;
  • GROMACS;
  • Massively Parallel Computers.

DL_POLY offers access to a generic implementation of molecular dynamics/mechanics, that is a theoretical tool for modelling the detailed microscopic behavior of many different types of systems, including; gases, liquids, solids, polymers, surfaces and clusters. This software is an efficient tool for solving numerically the classical equations of motion governing the microscopic time evolution of a many body system, subject to the boundary conditions appropriate for the geometry or symmetry of the system and well defined force – fields. Following the dynamics of a model system one can monitor the microscopic mechanisms of energy and mass transfer in chemical processes, and dynamical properties such as absorption spectra, rate constants and calculate transport properties. Furthermore, it can be employed as a means of sampling from a statistical mechanical ensemble, determining equilibrium properties, including average thermodynamic quantities (pressure, volume, temperature, etc.), structure, and free energies along reaction paths.

Long-Range Interactions are an essential part of molecular simulations. In practice they often involve important physical forces: gravity and the electromagnetic interaction, the basis for the propagation of light, electricity, chemical reactions and the structure of solids, molecules and atoms. Since in such systems, each particle interacts with all other particles, the calculations that need to be carried out increase to extremely big numbers. For example, if a super computer such as JUGENE with its 294 912 processors were to calculate the interactions between three trillion particles directly, it would require more than 32,000 years. One of the methods, which swingeing cuts the calculation times is the fast multipole method (FMM). With the help of the FMM distant particles may be combined into clusters, which are described by the so-called multipole moments. Thus one no longer needs to calculate each interaction individually. On the basis of FMM Jülich scientists Ivo Kabadshow and Holger Dachsel created a new algorithm and solved the same task on the JUGENE supercomputer with its 294 912 processors for less than 695 seconds.

GROMACS is a software package for molecular simulations. Using the Newtonian equations of motion it models the aggregate of hundreds to millions of particles. This software is primarily designed for dynamics simulation of bio molecules like proteins, lipids and nucleic acids and bio molecular interactions. The last version of GROMACS is suitable for calculating non-bonded interactions and is also used for research on non-biological systems, such as polymers.At the school the new massively parallel supercomputer Blue Gene/Q and multi node system EURORA, based on Multi-Core and Many Integrated Core (MIC) Intel processors will be presented.

Program committee:

  • David Henty (EPCC)
  • Giovanni Erbacci (CINECA)
  • Thomas Eickermann (JSC)
  • Svetozar Margenov (BAS)
  • Stoyan Markov (NCSA)

Organizing Committee:

  • Georgi Prangov
  • Krasimir Georgiev
  • Nedi Karaivanov

The number of participants is limited to 50 students. The courses are designed for master and PhD students, postdoctoral students and researchers in academia and industrial research and development organizations, who want to deepen their knowledge in molecular modeling. They need to be acquainted with Linux and programming languages C/C++ or FORTRAN at a basic level and have some experience with molecular simulations.

The school’s schedule can be found here.

Please register online via the registration portal.

The application deadline expires on: August 20, 2012

The list of admitted applicants will be published on September 5, 2012

Accommodation: PRACE Autumn School 2012 will be in “Hotel Expro“, Sofia.

On-line Booking: It is possible to prepare your booking here. Please, indicate the way of payment in the form. The payment will be made at the hotel. Please, send the booking form to hotel’s e-mail.

Please contact the school secretariat for further information.

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