Extension of the ParaDiS code to include precipitate interactions, and code optimisation to run on HPC environment

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Here present two featured software modules of the month:

  1. ParaDiS with precipitates
  2. ParaDiS with precipitates optimized to HPC environment

that provide extensions to the ParaDIS Discrete dislocation dynamics (DDD) code (LLNL, http://paradis.stanford.edu/) where dislocation/precipitate interactions are included. Module 2 was built to run the code on an HPC environment, by optimizing the original code for the Cray XC40 cluster at CSC in Finland. Software was developed by E-CAM partners at CSC and Aalto University (Finland).

Practical application and exploitation of the codes

The ParaDiS code is a free large scale dislocation dynamics (DD) simulation code to study the fundamental mechanisms of plasticity. However, DDD simulations don’t always take into account scenarios of impurities interacting with the dislocations and their motion. The consequences of the impurities are multiple: the yield stress is changed, and in general the plastic deformation process is greatly affected. Simulating these by DDD allows to look at a large number of issues from materials design to controlling the yield stress and may be done in a multiscale manner by computing the dislocation-precipitate interactions from microscopic simulations or by coarse-graining the DDD results for the stress-strain curves on the mesoscopic scale to more macroscopic Finite Element Method.

Modules 1 and 2 provide therefore an extension of the ParaDIS code by including dislocation/precipitate interactions. The possibility to run the code on HPC environments is also provided.

Software documentation and link to the source code can be found in our E-CAM software Library here.

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

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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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Mesoscale simulation of billion atom complex systems using thousands of GPGPU’s, an industry success story

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Dr. Jony Castagna, Science and Technology Facilities Council, United Kingdom


Abstract

Jony Castagna recounts his transition from industry scientist to research software developer at the STFC, his E-CAM rewrite of  DL_MESO allowing the simulation of billion atom systems on thousands of GPGPUs, and his latest role as Nvidia ambassador focused on machine learning.

Continue reading…
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Open call for CECAM flagship programme 2020

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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 https://www.cecam.org/submitting/.

Deadline for submission is 16 July 2019.

Good luck!

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DBCSR@MatrixSwitch, an optimised library to deal with sparse matrices

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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 optimized 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.

To carry out calculations in serial mode may be too slow sometimes and a parallelisation strategy is needed. Serial/parallel MatrixSwitch employs Lapack/ScaLapack to perform matrix operations, irrespective of their dense or sparse character. The disadvantage of the Lapack/ScaLapack schemes is that they are not optimised for sparse matrices. DBCSR provides the necessary algorithms to solve this problem and in addition is specially suited to work in parallel.

Direct link to module documentation: https://e-cam.readthedocs.io/en/latest/Electronic-Structure-Modules/modules/MatrixSwitchDBCSR/readme.html

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

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The E-CAM Scoping Workshop “Building the bridge between theories and software: SME as a boost for technology transfer in industrial simulative pipelines”, organised in May 2018 at the Fondazione Istituto Italiano di Tecnologia (IIT), Genoa, brought together top-level scientists of the E-CAM community with expertise in statistical mechanics, multi-scale modeling and electronic structure, 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, and several software vendor SMEs were present at the meeting.

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.

Read the full report here.

Read the workshop scientific report
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Abrupt GC-AdResS: A new and more general implementation of the Grand Canonical Adaptive Resolution Scheme (GC-AdResS)

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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 https://aip.scitation.org/doi/10.1063/1.5031206 (open access version: https://arxiv.org/abs/1806.09870). The main goal of the project is to develop a library or recipe with which GC-AdResS can be implemented in any Classical MD Code.

The current implementation of GC- AdResS in GROMACS has several performance problems. We know that the main performance loss of AdResS simulations in GROMACS is in the neighbouring list search and the generic serial force calculation linking the atomistic (AT) and coarse grained (CG) forces together via a smooth weighting function. Thus, to remove the bottleneck with respect to performance and a hindrance regarding the easy/general implementation into other codes and eliminate the non optimized force calculation, we had to change the neighbourlist search. This lead to a considerable speed up of the code. Furthermore it decouples the method directly from the core of any MD code, which does not hinder the performance and makes the scheme hardware independent[4].

This module presents a very straight forward way to implement a new partitioning scheme in GROMACS . And this solves two problems which affect the performance, the neighborlist search and the generic force kernel.

Information about module purpose, background information, software installation, testing and a link to the source code, can be found in our E-CAM software Library here.

E-CAM Deliverables D4.3[5] and D4.4[6] present more modules developed in the context of this pilot project.

References

[1] L. Delle Site and M. Praprotnik, “Molecular Systems with Open Boundaries: Theory and Simulation,” Phys. Rep., vol. 693, pp. 1–56, 2017

[2] H.Wang, C. Schütte, and L.Delle Site, “Adaptive Resolution Simulation (AdResS): A Smooth Thermodynamic and Structural Transition fromAtomistic to Coarse Grained Resolution and Vice Versa in a Grand Canonical Fashion,” J. Chem. Theory Comput., vol. 8, pp. 2878–2887, 2012

[3] H. Wang, C. Hartmann, C. Schütte, and L. Delle Site, “Grand-Canonical-Like Molecular-Dynamics Simulations by Using an Adaptive-Resolution Technique,” Phys. Rev. X, vol. 3, p. 011018, 2013

[4] C. Krekeler, A. Agarwal, C. Junghans, M. Prapotnik and L. Delle Site, “Adaptive resolution molecular dynamics technique: Down to the essential”, J. Chem. Phys. 149, 024104

[5] B. Duenweg, J. Castagna, S. Chiacchera, H. Kobayashi, and C. Krekeler, “D4.3: Meso– and multi–scale modelling E-CAM modules II”, March 2018 . [Online]. Available: https://doi.org/10.5281/zenodo.1210075

[6] B. Duenweg, J. Castagna, S. Chiacchera, and C. Krekeler, “D4.4: Meso– and multi–scale modelling E-CAM modules III”, Jan 2019 . [Online]. Available: https://doi.org/10.5281/zenodo.2555012

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E-CAM related work labeled as “Excellent Science” by the EC Innovation Radar Initiative

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The Innovation Radar aims to identify high-potential innovations and innovators. It is an important source of actionable intelligence on innovations emerging from research and innovation projects funded through European Union programmes.

E-CAM is associated to the following Innovations (Innovation topic: excellence science):

    1. Improved Simulation Software Packages for Molecular Dynamics (see link)
    2. Improved software modules for Meso– and multi–scale modelling (see link)

Related to the work of our E-CAM funded Postdoctoral researchers supervised by scientists in the team, working on:

  • Development of the OpenPathSampling package to study rare events  (Universiteit van Amsterdam). Link1
  • Implementation of GPU version of DL_MESO_DPD (Hartree Centre (STFC)). Link
  • Development of polarizable mesoscale model for DL_MESO_DPD (Hartree Centre (STFC)). Link

  • Development of the GC-AdResS scheme (Freie Universitaet Berlin). Link

  • Implementation of hierarchical strategy on ESPResSO++ (Max Plank Institute for Polymer Research, Mainz). Link
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New E-CAM publication is out: “Molecular Dynamics of Open Systems: Construction of a Mean‐Field Particle Reservoir”

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New publication from E-CAM partners working at the Institute of Mathematics of the Freie Universität Berlin:

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

Authors: Luigi Delle Site, Christian Krekeler, John Whittaker, Animesh Agarwal, Rupert Klein, and Felix Höfling

Adv. Theory Simul. 2019, 1900014, DOI: 10.1002/adts.201900014 (Open access)

Synopsis

A procedure for the construction of a particle and energy reservoir for the simulation of open molecular systems is presented. The reservoir is made of non‐interacting particles (tracers), embedded in a mean‐field. The tracer molecules acquire atomistic resolution upon entering the atomistic region, while atomistic molecules become tracers after crossing the atomistic boundary.

Abstract

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.

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Open Postdoctoral Position in Mesoscale Modeling in Nanostructured Materials

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In the context of the EU H2020 project E-CAM we are seeking a highly qualified post-doctoral researcher for an exciting collaborative project on the fundamental challenges of  driven transport in complex media. 

Increasingly, modern technology is addressing problems where fluid transport takes place in submicron sized channels, or in pores. The physical laws of transport in such channels are qualitatively different from those that determine bulk flow; they are poorly understood and, importantly, barely exploited. 

The postdoctoral position will  address complementary aspects related to the fundamental challenges of thermodynamic driving on systems of potential industrial interest. In this respect, the  project will be developed in close contact with an industrial partner. 

The project will involve both algorithmic and scientific developments. The candidate will benefit from existing in-house expertise in lattice Boltzmann methods for non-equilibrium soft materials and will contribute to its extension and use on complex materials out of equilibrium. The project will go  beyond the state-of-the-art macroscopic descriptions of phoresis to capture the effects of solute and surface specificity, solute flexibility, surface wettability and heterogeneity, fluctuations and correlations.

We seek motivated researchers, with theoretical and computational expertise. Candidates should have a background in computer simulation, statistical mechanics, biophysics and/or soft condensed matter.

The project will be carried out at the University of Barcelona, under the supervision of Prof. Ignacio Pagonabarraga, for an initial period of 20 months. Candidates with an appropriate background, who are interested in a cutting-edge research at the interface between physics and the biological sciences, are invited to apply.

We look forward to receiving a CV and 1 referee letter. You can address these  documents, or any additional information you require, to Prof. I. Pagonabarraga by email ipagonabarraga@ub.edu. Review of applications will continue until the position is filled.

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