PRACE/E-CAM successful collaboration produces task scheduling library for optimising time-scale molecular dynamics simulations

Challenge

E-CAM is interested in the challenge of bridging up timescales. To study molecular dynamics with atomistic detail, timesteps must be used on the order of a femto-second. Many problems in biological chemistry, materials science, and other ends involve events that only spontaneously occur after a millisecond or longer (for example, biomolecular conformational changes, or nucleation processes). That means that around 1012 time steps would be needed to see a single millisecond-scale event. This is the problem of “rare events” in theoretical and computational chemistry. Modern supercomputers are beginning to make it possible to obtain trajectories long enough to observe some of these processes, but to fully characterize a transition with proper statistics, many examples are needed. And in order to obtain many examples, the same application must be run thousands of times with varying inputs. To manage this kind of computation, a task scheduling library is needed

Solution and benefits

The development of a python library, in collaboration with PRACE. This library builds on top of the scalable analytics framework Dask and enables it to resiliently manage multi-node and multiarchitecture environments. This offers exciting possibilities in the areas of interactive supercomputing and burst supercomputing. A white paper focused on the library was written in collaboration with PRACE and is available here.

The main elements of the mentioned scheduling library are: task de definition, a task scheduling (handled in Python) and task execution (facilitated by the MPI layer). While traditionally an HTC workload is looked down upon in the HPC space, the scientific use case for extreme-scale resources exists and algorithms that require a coordinated approach make efficient libraries that implement this approach increasingly important in the HPC space. The 5 Peta op booster technology of JURECA is an interesting concept with respect to this approach since the offloading approach of heavy computation marries perfectly to the concept outlined here.

Reference

Alan O’Cais, David Swenson, Mariusz Uchronski, & Adam Wlodarczyk. (2019, August 14). Task Scheduling Library for Optimising Time-Scale Molecular Dynamics Simulations. Zenodo. http://doi.org/10.5281/zenodo.3527643

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A Conversation on The Fourth Industrial Revolution: Opportunities & Trends for Particle Based Simulation

 

Abstract

In the margins of a recent multiscale simulation workshop a discussion began between a prominent  pharmaceutical industry scientist, and E-CAM and EMMC regarding the unfolding Fourth Industrial Revolution and the role of particle based simulation and statistical methods there.  The impact of simulation  is predicted to become very significant.  This discussion is intended to create awareness of the general public, of how industry 4.0 is initiating in companies, and  how academic research will support that transformation.

Authors: Prof. Pietro Asinari (EMMC and Politecnico di Torino, denoted below as PA) and Dr. Donal MacKernan (E-CAM and University College Dublin, denoted below as  DM) , and a prominent  pharmaceutical industry scientist (name withheld at author’s request as  the view expressed is a personal one, denoted below as  IS)

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Upcoming event: Extended Software Development Workshop in Mesoscopic simulation models and HPC


E-CAM partners at Aalto University (CECAM Finish Node) in collaboration with the HPC training experts from the CSC Supercomputing Centre, are organizing a joint Extended Software Development Workshop from 15-19 October 2019 , aimed at people interested in particle based methods, such as the Discrete Element and Lattice Boltzmann Methods, and on their massive parallelization using GPU architectures. The workshop will mix three different ingredients: (1) workshop on state-of-the-art challenges in computational science and software, (2) CSC -run school, and (3) coding sessions with the aid of CSC facilities and expertise.

How to Apply

Follow the instruction at the CECAM website for the event: https://www.cecam.org/workshop1752/

Organizers

  • Mikko Alava
    Aalto University, Finland
  • Brian Tighe
    TU Delft, The Netherlands
  • Jan Astrom
    CSC It center for science, Finland
  • Antti Puisto
    Aalto University, Finland

Location

CECAM-FI Node, Aalto University, Finland

Dates

October 15 – 19, 2019

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