E-CAM State of the Art Workshop: CHALLENGES IN MULTIPHASE FLOWS

We would like to draw your attention to a school cum workshop on

CHALLENGES IN MULTIPHASE FLOWS

that will run on Dec 9-12, 2019, at the Monash University Prato Center,
see http://monash.it/, in Tuscany. The event is an E-CAM state-of-the-art
workshop, and its aim is to focus on computer
simulation methods for multiphase systems and their dynamics, and
their strengths and shortcomings. This is a topic that is relevant in
physics, mathematics, chemistry, and engineering, and we are trying to
bring these communities together for a fruitful exchange. At the same
time, a set of advanced lectures at the school is intended to provide
a solid foundation of background knowledge. For more information (in
particular, the list of Invited Speakers), see the

Main web site for the event

Registration is now open. Regular participants need to pay a fee of
500 Australian Dollars (roughly 300 Euros) for meals etc.; however the
first 25 students (with proven status) who register may attend for free.

DEADLINE for registration and abstract submission is September 22.

Please do not hesitate to contact the organisers (contact information on the main website for the event) if you feel you need more information beyond what is provided on the web.

The Organisers

Burkhard Duenweg, Mainz
Ravi Prakash Jagadeeshan, Melbourne
Ignacio Pagonabarraga, Lausanne

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Integrating LAMMPS with OpenPathSampling

This module shows how LAMMPS can be used as Molecular Dynamic (MD) engine in OpenPathSampling (OPS) and it also provide a benchmark for the impact of OPS overhead over the MD engine.

Practical application and exploitation of the code

OpenPathSampling uses OpenMM as default engine for calculating the sampled trajectories. Other engines as GROMACS and LAMMPS can be used (despite not yet available in the official release) allowing to exploit different computer architectures like hybrid CPU-GPU and to simulate more complex problems.

In this module we present the source code for the integration of OPS with LAMMPS as well as a benchmark for of a simple test case to show the impact on the performance due to OPS overhead.

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

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FFTXlib, a rewrite and optimisation of earlier versions of FFT related routines inside QE pre-v6

FFTXlib is mainly a rewrite and optimisation of earlier versions of FFT related routines inside Quantum ESPRESSO (QE) pre-v6; and finally their replacement. Despite many similarities, current version of FFTXlib dramatically changes the FFT strategy in the parallel execution, from 1D+2D FFT performed in QE pre v6 to a 1D+1D+1D one; to allow for greater flexibility in parallelisation.

Practical application and exploitation of the code

FFTXlib module is a collection of driver routines that allows the user to perform complex 3D fast Fourier transform (FFT) in the context of plane wave based electronic structure software. It contains routines to initialize the array structures, to calculate the desired grid shapes. It imposes underlying size assumptions and provides correspondence maps for indices between the two transform domains.

Once this data structure is constructed, forward or inverse in-place FFT can be performed. For this purpose FFTXlib can either use a local copy of an earlier version of FFTW (a commonly used open source FFT library), or it can also serve as a wrapper to external FFT libraries via conditional compilation using pre-processor directives. It supports both MPI and OpenMP parallelisation technologies.

FFTXlib is currently employed within Quantum Espresso package, a widely used suite of codes for electronic structure calculations and materials modeling in the nanoscale, based on planewave and pseudopotentials.

FFTXlib is also interfaced with “miniPWPP” module that solves the Kohn Sham equations in the basis of planewaves and soon to be released as a part of E-CAM Electronic Structure Library.

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

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Issue 11 – June 2019

E-CAM Newsletter of June 2019

Get the latest news from E-CAM, sign up for our quarterly newsletter.

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


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


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


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

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

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

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.

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