June 16-20, 2013

Leipzig, Germany

Presentation Details

Name: Efficient & Scalable Bio-Molecular Simulations on HPC Systems
Time: Wednesday, June 19, 2013
9:30 AM - 10:00 AM
Room:   Hall 2
CCL - Congress Center Leipzig
Speakers:   Rossen Apostolov, KTH Royal Institute of Technology & ScalaLife
Abstract:   Rapid developments in High Performance Computing infrastructures offer ever-greater opportunities to Life Science researchers for tackling previously unattainable problems. Although it is normal that software development lags behind the hardware one in terms of efficient usage of the available power, the problem is specifically more pronounced in the Life Science domain where many users come from non-computational disciplines. The EU funded ScalaLife project ( has developed new techniques for improving the scalability of several popular Life Science codes on multi-core, streaming and hybrid architectures as well as novel ensemble and high-throughput frameworks for efficient sampling of small-to-medium system. The techniques are implemented in three code bases: GROMACS (Molecular Dynamics simulations), DALTON (Quantum Mechanical and hybrid-QM/MM simulations) and DISCRETE (Discrete Molecular Dynamics simulations). The development work resulted in much improved hard-scaling limits for single run simulations along with very efficient utilization of resources for sampling runs.  
Program may be subject to changes.