SearcharxivSearch

arXiv subjects

Andrew Emerson

Publications and source records attributed to Andrew Emerson.

2 recordsLinked to original sources

Tunable and Portable Extreme-Scale Drug Discovery Platform at Exascale: the LIGATE Approach

Today digital revolution is having a dramatic impact on the pharmaceutical industry and the entire healthcare system. The implementation of machine learning, extreme-scale computer simulations, and big data analytics in the drug design and development process offers an excellent opportunity to lower the risk of investment and reduce the time to the patient. Within the LIGATE project, we aim to integrate, extend, and co-design best-in-class European components to design Computer-Aided Drug Design (CADD) solutions exploiting today's high-end supercomputers and tomorrow's Exascale resources, fostering European competitiveness in the field. The proposed LIGATE solution is a fully integrated workflow that enables to deliver the result of a virtual screening campaign for drug discovery with the highest speed along with the highest accuracy. The full automation of the solution and the possibility to run it on multiple supercomputing centers at once permit to run an extreme scale in silico drug discovery campaign in few days to respond promptly for example to a worldwide pandemic crisis.

cs.DC

Efficient and Eventually Consistent Collective Operations

Collective operations are common features of parallel programming models that are frequently used in High-Performance (HPC) and machine/ deep learning (ML/ DL) applications. In strong scaling scenarios, collective operations can negatively impact the overall application performance: with the increase in core count, the load per rank decreases, while the time spent in collective operations increases logarithmically. In this article, we propose a design for eventually consistent collectives suitable for ML/ DL computations by reducing communication in Broadcast and Reduce, as well as by exploring the Stale Synchronous Parallel (SSP) synchronization model for the Allreduce collective. Moreover, we also enrich the GASPI ecosystem with frequently used classic/ consistent collective operations -- such as Allreduce for large messages and AlltoAll used in an HPC code. Our implementations show promising preliminary results with significant improvements, especially for Allreduce and AlltoAll, compared to the vendor-provided MPI alternatives.

cs.DC