June 2019

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Industry Success Story

Mesoscale simulation of billion atom complex systems using thousands of GPGPU's


By Dr. Jony Castagna, Science and Technology Facilities Council, UK

Jony Castagna recounts his transition from industry scientist to research software developer at the STFC; his E-CAM rewrite of DL_MESO, an industrially useful package for DPD Dissipative Particle Dynamics simulations, allowing the simulation of billion atom systems on thousands of GPGPUs; and his latest role as Nvidia ambassador focused on machine learning.

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.

Open call for CECAM flagship programme 2020

The CECAM CALL for workshops and schools that will run from April 2020 to March 2021 is now open! This is also the opportunity to submit an E-CAM proposal. The text of the call and information on how to submit a proposal can be found at Deadline for submission is 16 July 2019.

Workshop Scientific report


Software vendor SMEs as a boost for technology transfer in industrial simulative pipelines

This E-CAM workshop brought together top-level scientists of the E-CAM community, and representatives of pharmaceutical and material industries, with the objective to identify the major gaps which still hamper a systematic exploitation of accurate computer simulations in industrial R&D. Special attention was given to the role of SMEs devoted to simulative software development. The meeting highlighted the role of software vendor SMEs as a key link for the uptake of modelling in industry. They can play an increasingly important role not only in translating the science developed in academia into a proper technological transfer process, but also in building a scientific bridge between the industry requirements in terms of automation and the new theories and algorithms developed at an academic level. There was also a consensus that EU funded Centers of Excellence for Computing Applications, such as E-CAM, can provide an opportunity to enhance the expertise and scope of software vendors SMEs.

Featured Software Modules


Abrupt GC-AdResS: A new and more general implementation of the Grand Canonical Adaptive Resolution Scheme

The Grand Canonical Adaptive resolution scheme (GC-AdResS) gives a methodological description to partition a simulation box into different regions with different degrees of accuracy. For more details on the theory see Refs. [1,2,3]. In the context of an E-CAM pilot project focused on the development of the GC-AdResS scheme, an updated version of GC-AdResS was built and implemented in GROMACS, as reported in [4]. The main goal of the project was to develop a library or recipe with which GC-AdResS can be implemented in any Classical MD Code.

Module DBCSR@MatrixSwitch: an optimised library to deal with sparse matrices

MatrixSwitch is a module which acts as an intermediary interface layer between high-level and low-level routines dealing with matrix storage and manipulation. It allows a seamlessly switch between different software implementations of the matrix operations. DBCSR is an optimised library to deal with sparse matrices, which appear frequently in many kind of numerical simulations. In DBCSR@MatrixSwitch, DBCSR capabilities have been added to MatrixSwitch as an optional library dependency.

Porting of electrostatics to the GPU version of DL_MESO

The porting of DL_MESO to graphic cards (GPUs) was reported in deliverables D4.2 of E-CAM (for a single GPU) and deliverable D4.3 (for multiple GPUs), and has now been extended to include electrostatics, with two alternative schemes: Standard Ewald and Smooth Particle Mesh Ewald (SPME) methods. This work was recently reported on deliverable D4.4.

New Publications

Molecular Dynamics of Open Systems: Construction of a Mean‐Field Particle Reservoir

L. Delle Site, C. Krekeler, J. Whittaker, A. Agarwal, R. Klein, F. Höfling
Adv. Theory Simul. 2019, 1900014
DOI: 10.1002/adts.201900014 (Open access)
The simulation of open molecular systems requires explicit or implicit reservoirs of energy and particles. Whereas full atomistic resolution is desired in the region of interest, there is some freedom in the implementation of the reservoirs. Here, a combined, explicit reservoir is constructed by interfacing the atomistic region with regions of point-like, non-interacting particles (tracers) embedded in a thermodynamic mean field. The tracer molecules acquire atomistic resolution upon entering the atomistic region and equilibrate with this environment, while atomistic molecules become tracers governed by an effective mean-field potential after crossing the atomistic boundary. The approach is extensively tested on thermodynamic, structural, and dynamic properties of liquid water. Conceptual and numerical advantages of the procedure as well as new perspectives are highlighted and discussed.

The Fluctuation−Dissipation Theorem as a Diagnosis and Cure for Zero-Point Energy Leakage in Quantum Thermal Bath Simulations

E. Mangaud, S. Huppert, T. Plé, P. Depondt, S. Bonella, F. Finocchi, J. Chem. Theory Comput. 2019, 15, 2863-2880, DOI: 10.1021/acs.jctc.8b01164
Quantum thermal bath (QTB) simulations reproduce statistical nuclear quantum effects via a Langevin equation with a coloured random force. Although this approach has proven efficient for a variety of chemical and condensed-matter problems, the QTB, as many other semiclassical methods, suffers from zero-point energy leakage (ZPEL). The absence of a reliable criterion to quantify the ZPEL without resorting to demanding comparisons with path integral based calculations has so far hindered the use of the QTB for the simulation of real systems. In this work, we establish a quantitative connection between ZPEL in the QTB framework and deviations from the quantum fluctuation-dissipation theorem (FDT) that can be monitored along the simulation. This provides a rigorous general criterion to detect and quantify the ZPEL without any a priori knowledge of the system under study.

Submitted deliverables

D5.4: ESDW Guidelines and Programme IV*

Updated guidelines for format, content and coding styles in the Extended Software Development Workshops (ESDWs), and E-CAM program of events running in 2020/2021.

D7.6: E-CAM Software Porting and Benchmarking Data III*

Technical report on the results of porting and optimisation of E-CAM modules to massively parallel machines and their benchmarking and scaling. The development of the modules was done in the context of E-CAM ESDWs.
*This is a draft document delivered to the European Commission but not yet approved
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This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 676531