Comics & Science ? The E-CAM issue: an experiment in dissemination

 

The E-CAM issue of Comics & Science has just been released on-line…and it’s just the beginning of the adventure!

Identifying exciting and original tools to engage the general public with advanced research is an intriguing and non-trivial challenge for the scientific community. E-CAM decided to try something unusual, and embarked on an interesting and slightly bizarre experience: collaborating with experts and artists to use comics to talk about HPC and simulation and modelling!

The adventure started when CECAM Deputy Director and E-CAM Work-Package leader Sara Bonella visited the CNR Institute for applied mathematics “Mauro Picone” (Cnr-Iac), in Rome, and became acquainted with the work of Comics&Science, a magazine published by CNR Edizioni to promote the relationship between science and entertainment. The magazine was created in 2013 by Roberto Natalini, Director of the Cnr-Iac, and Andrea Plazzi, author and editor with a scientific background and active in the field of comics.

Adopting the unique language of the comics, Comics&Science communicates science in a funny and understandable way via original stories that are always edited by some of the best authors and cartoonists in town. For the E-CAM issue, we had the good fortune to collaborate with Giovanni Eccher, comics writer and scriptwriter for movies and animations, and Sergio Ponchione, illustrator and cartoonist.

Giovanni and Sergio created for us the unique story of Ekham the wise, a magnificent witch  that – with an accurate model and the help of a High Performance Cauldron (!) – enables Prince Variant to defeat the fearful Dragon that has kidnapped Princess Beauty. As usual, the King had promised the Princess’s hand to the vanquisher of the dragon, but things don’t turn out exactly as expected…

In addition to the comics, the E-CAM issue of Comics&Science  presents several articles  describing – in a language targeted at young adults, and, in general, lay public – what are simulations in advanced research and the role of High Performance Computing. The issue also contains a statement from the European Commission on its vision for HPC. We are very grateful to our authors, that include Ignacio Pagonabarraga, Catarina Mendonça, Sara Bonella, Christoph Dellago, and Gerhard Sutmann, for playing with us.

The issue has been produced in partnership with CECAM, coordinator of E-CAM, and the longest standing institution promoting fundamental research on advanced computational methods.

The E-CAM issue of Comics&Science is freely available on our website at https://www.e-cam2020.eu/e-cam-issue-of-comics-science/. Should you wish to use this new toy to promote modelling and simulation, get in touch at info@e-cam2020.eu and let us know about your plans: we are happy to share the material provided that provenance is acknowledged.

The “first outing” of the E-CAM issue of Comics&Science took place on Friday 30 October at 14:15 CET with a presentation (in Italian) in the on-line programme of the 2020 Lucca Comics&Games Festival. A recording of that moment is available at https://www.youtube.com/watch?v=BUysRG0zlCk.

Enjoy the read and, most importantly, have fun 🙂

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Issue 15 – December 2020

E-CAM Newsletter of December 2020

 

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The ALL Load Balancing Library

 

Abstract

Scalability of parallel applications depends on a number of characteristics, among which is efficient communication, equal distribution of work or efficient data lay-out. Especially for methods based on domain decomposition, as it is standard for, e.g., molecular dynamics, dissipative particle dynamics or particle-in-cell methods, unequal load is to be expected for cases where particles are not distributed homogeneously, different costs of interaction calculations are present or heterogeneous architectures are invoked, to name a few. For these scenarios the code has to decide how to redistribute the work among processes according to a work sharing protocol or to dynamically adjust computational domains, to balance the workload. The A Load Balancing Library (ALL) developed within E-CAM at the Julich Supercomputing Center aims to provide an easy and portable way to include dynamic domain-based load balancing into particle based simulation codes. It provides several schemes to find the ideal split of the workload, from the simplest orthogonal non staggered domain decomposition, to the more fancy Voronoi mesh scheme. Within this text we provide an overview of ALL, its capabilities and current use cases, as well as where to find additional information on the library.

 

Description

Most modern parallelized (classical) particle simulation programs are based on a spatial decomposition method as an underlying parallel algorithm: different processors administrate different spatial regions of the simulation domain and keep track of those particles that are located in their respective region. Processors exchange information

  • in order to compute interactions between particles located on different processors
  • to exchange particles that have moved to a region administered by a different processor.

This implies that the workload of a given processor is very much determined by its number of particles, or, more precisely, by the number of interactions that are to be evaluated within its spatial region.

Certain systems of high physical and practical interest (e.g. condensing fluids) dynamically develop into a state where the distribution of particles becomes spatially inhomogeneous. Unless special care is being taken, this results in a substantially inhomogeneous distribution of the processors’ workload. Since the work usually has to be synchronized between the processors, the runtime is determined by the slowest processor (i.e. the one with the highest workload). In the extreme case, this means that a large fraction of the processors are idle during these waiting times. This problem becomes particularly severe if one aims at strong scaling, where the number of processors is increased at constant problem size: Every processor administrates smaller and smaller regions and therefore inhomogeneities will become more and more pronounced. This will eventually saturate the scalability of a given problem, already at a processor number that is still so small that communication overhead remains negligible.

The solution to this problem is the inclusion of dynamic load balancing techniques. These methods redistribute the workload among the processors, by lowering the load of the most busy cores and enhancing the load of the most idle ones. Fortunately, several successful techniques are known already to put this strategy into practice. Nevertheless, dynamic load balancing that is both efficient and widely applicable implies highly non-trivial coding work. Therefore it has not yet been implemented in a number of important codes. 

The A Load-Balancing Library (ALL) developed within E-CAM at the Simulation Laboratory Molecular Systems of the Juelich Supercomputing Centre, aims to provide an easy and portable way to include dynamic domain-based load balancing into particle based simulation codes. It was created in the context of an Extended Software Development Workshop (ESDW) within E-CAM (see ALL ESDW event details), where code developers of CECAM community codes were invited together with E-CAM postdocs, to work on the implementation of load balancing strategies. The goal of this activity is to increase the scalability of applications to a larger number of cores on HPC systems, for spatially inhomogeneous systems, and thus to reduce the time-to-solution of the applications .

 
Particle system before and after the load balancing. Left: equal domain sizes with bad balance; right: unequal domain sizes and good work load.
 

ALL includes several load-balancing schemes, with additional approaches currently being added. The following list gives an overview about the currently included schemes: 

  1. Tensor-Product method: For the Tensor-Product method, the work on all processes (subdomains) is reduced over the cartesian planes in the systems. This work is then equalized by adjusting the borders of the cartesian planes.
  2. Staggered Grid Method: For the staggered-grid scheme, a 3-step hierarchical approach is applied: work over the Cartesian planes is reduced before the borders of these planes are adjusted; in each of the Cartesian planes the work is reduced for each Cartesian column, these columns are then adjusted to each other to homogenise the work in each column; the work between neighbouring domains in each column is adjusted. Each adjustment is done locally with the neighbouring planes, columns or domains by adjusting the adjacent boundaries.
  3. Unstructured Mesh Method: In contrast to the Tensor-Product method and the Staggered Grid Method, the unstructured mesh method adjusts domains not by moving boundaries but vertices, i.e. corner points, of domains. For each vertex, a force, based on the differences in work of the neighboring domains, is computed and the vertex is shifted in a way to equalize the work between these neighboring domains.
  4. Voronoi Mesh Method: Similar to the topological mesh method (Unstructured Mesh Method), the Voronoi mesh method computes a force, based on work differences. In contrast to the topological mesh method, the force acts on a Voronoi point rather than a vertex, i.e. a point defining a Voronoi cell, which describes the domain. Consequently, the number of neighbors is not a conserved quantity, i.e. the topology may change over time.
  5. Histogram-based Staggered Grid Method: The histogram-based staggered-grid scheme results in the same grid as the staggered-grid scheme (see Staggered Grid Method), this scheme uses the cumulative work function in each of the three cartesian directions in order to generate this grid. Using histograms and the previously defined distribution of process domains in a cartesian grid, this scheme generates in three steps a staggered-grid result, in which the work is distributed as evenly as the resolution of the underlying histogram allows. In contrast to the other schemes this scheme depends on a global exchange of work between processes.

Use cases

ALL is being tested with the HemeLB code[1] from the Centre of Excellence CompBiomed. A recent paper describes how HemeLB’s developments in memory management and load balancing (with ALL) allow near linear scaling performance of the code on hundreds of thousands of computer codes[2]. 

ALL is implemented in the multi-GPU version of DL_MESO_DPD package (see related news item here). The intention of this integration is to allow for better performance when modelling complex systems with DL_MESO_DPD[3], like large proteins or lipid bilayers, redistributing the work load across the GPUs.

 

References

[1] D. Groen, J. Hetherington, H.B. Carver, R.W. Nash, M.O. Bernabeu, and P.V. Coveney. Analysing and modelling the performance of the HemeLB lattice-Boltzmann simulation environment. Journal of Computational Science, 4(5):412 – 422, 2013. doi: https://doi.org/10.1016/j.jocs.2013.03.002. // HemeLB URL: www.hemelb.org

[2] McCullough JWS et al. 2021 Towards blood flow in the virtual human: efficient self-coupling of HemeLB. Interface Focus 11: 20190119. doi: http://dx.doi.org/10.1098/rsfs.2019.0119 

[3] MA Seaton, RL Anderson, S Metz and W Smith, DL_MESO: highly scalable mesoscale simulations, Mol Simul 39 (10), 796–821 (2013) doi: http://dx.doi.org/10.1080/08927022.2013.772297 // https://www.scd.stfc.ac.uk/Pages/DL_MESO.aspx  

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December Module of the Month: Load balancing for multi-GPU DL_MESO

 

Description

This module concerns the implementation of the E-CAM Load Balancing Library (ALL) in the multi-GPU version of DL_MESO_DPD code. The intention is to allow for better performance when modelling complex systems with DL_MESO_DPD, like large proteins or lipid bilayers, redistributing the work load across the GPUs.

ALL provides several schemes to find the ideal split of the work load : Tensor-Product method, Staggered Grid Method, Unstructured Mesh Method, Voronoi Mesh Method and Histogram-based Staggered Grid Method. Due to the orthogonal domain decomposition used in DL_MESO, the Tensor-Product scheme was used, which works well for non-staggered orthogonal meshes.

Practical application

A test case was implemented (see Figure 1 a), b) and c)) that reproduces 32k water beads initially scattered along a regular structure and then slowly agglomerating towards an unique large drop confined between two parallel surfaces. The system is divided across 8 GPUs and, for the purposes of the visualisation, we restrict ourselves to 32k particles. For a larger number of particles it would not be possible to simulate the system without load-balancing, since all the particles agglomerate to a subset of the available GPUs and one or more GPUs would run out of memory having to accommodate a large number of particles. Moreover, such a strong load imbalance drastically reduces the scalability of the application.

In Figure d) we see the time history of the load imbalance for each GPU when using the ALL library. Without load balancing the system would gradually diverge from the ideal value of 12.5%. You can find a video that shows the evolution of the load-balancing for this system in another software module.

Figure 1: Load imbalance in DL_MESO with ALL library for a water drop between two surfaces. Each colour represents different domain assigned to a different GPU: a) top view, b) perspective view, c) front view, d) load balance vs time

Source code

Further details on the implementation of ALL library in DL_MESO and the source code can be found in the E-CAM software repository here.

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Proof of concept : Metamorphosis

 

Abstract 

The transformation of a beautiful idea born via simulation into a commercial opportunity is described as it progresses from proof of concept towards a product. At the heart of this ongoing story is advanced simulation using massively parallel computation and rare-event methods.

Continue reading…
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New article: Quantum Monte Carlo determination of the principal Hugoniot of deuterium

 

A new article from E-CAM partners at the Maison de la Simulation (CEA, CNRS, Univ. Paris-Sud), have published a new article:

Quantum Monte Carlo determination of the principal Hugoniot of deuterium

Michele Ruggeri, Markus Holzmann, David M. Ceperley, and Carlo Pierleoni
Phys. Rev. B2020, 102, 144108
DOI: https://doi.org/10.1103/PhysRevB.102.144108
Open access version

Abstract: We present coupled electron-ion Monte Carlo results for the principal Hugoniot of deuterium together with an accurate study of the initial reference state of shock-wave experiments. We discuss the influence of nuclear quantum effects, thermal electronic excitations, and the convergence of the potential energy surface by wave-function optimization within variational Monte Carlo and projection quantum Monte Carlo methods. Compared to a previous study, our calculations also include low pressure-temperature (P,T) conditions resulting in close agreement with experimental data, while our revised results at higher (P,T) conditions still predict a more compressible Hugoniot than experimentally observed.

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Conversation with the authors of the E-CAM Comics “Ekham the Wise”

During the making-of of the E-CAM Comics the collaboration with the founders and directors of the Comics&Science magazine, Roberto Natalini and Andrea Plazzi, and with the authors of the comics, Giovanni Eccher (writer) and Sergio Ponchione (cartoonist), was remarkable.

In this conversation about how “it all came to be”, Sara Bonella (CECAM Deputy Director), Ignacio Pagonabarraga (CECAM Director) and the Comics&Science team will shed light on how they found a way to explain laypeople about modelling, simulation and HPC through comics.

Short biography of the people involved in this conversation

Extracts from the conversation

FULL VIDEO ON YOUTUBE
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LearnHPC: dynamic creation of HPC infrastructure for educational purposes

 

Abstract

In a newly successful PRACE-ICEI proposal, E-CAM, FocusCoE, HPC Carpentry and EESSI join forces to bring HPC resources to the classroom in a simple, secure and scalable way. Our plan is to reproduce the model developed by the Canadian open-source software project Magic Castle. The proposed solution creates virtual HPC infrastructure(s) in a public cloud, in this case on the Fenix Research Infrastructure, and generates temporary event-specific HPC clusters for training purposes, including a complete scientific software stack. The scientific software stack is fully optimised for the available hardware and will be provided by the European Environment for Scientific Software Installations (EESSI). 

Description 

EU-wide requirements for HPC training are exploding as the adoption of HPC in the wider scientific community gathers pace. However, the number of topics that can be thoroughly addressed without providing access to actual HPC resources is very limited, even at the introductory level. In cases where such access is available, security concerns and the overhead of the process of provisioning accounts make the scalability of this approach questionable.

EU-wide access to HPC resources on the scale required to meet the training needs of all countries is an objective that we attempt to address with this project. The proposed solution essentially provisions virtual HPC system(s) in a public cloud, in this case on the Fenix Research Infrastructure. The infrastructure will dynamically create temporary event-specific HPC clusters for training purposes, including a scientific software stack. The scientific software stack will be provided by the European Environment for Scientific Software Installations (EESSI) which uses a software distribution system developed at CERN, CernVM-FS, and makes a research-grade scalable software stack available for a wide set of HPC systems, as well as servers, desktops and laptops (including MacOS and Windows!). 

The concept is built upon the solution of Compute Canada, Magic Castle, which aims to recreate the Compute Canada user experience in public clouds (there is even a presentation where the main developer creates a cluster just by talking to his phone!). Magic Castle uses the open-source software Terraform and HashiCorp Language (HCL) to define the virtual machines, volumes, and networks that are required to replicate a virtual HPC infrastructure. 

In addition to providing a dynamically provisioned HPC resource, the project will also offer a scientific software stack provided by EESSI. This model is also based on a Compute Canada approach and enables replication of the EESSI software environment outside of any directly related physical infrastructure. 

Our adaption of Magic Castle aims to recreate the EESSI HPC user experience, for training purposes, on the Fenix Research Infrastructure.  After deployment, the user is provided with a complete HPC cluster software environment including a Slurm scheduler, a Globus Endpoint, JupyterHub, LDAP, DNS, and a wide selection of research software applications compiled by experts with EasyBuild.

The architecture of the solution is best represented by the graphic below (taken from the Compute Canada documentation at https://github.com/ComputeCanada/magic_castle/tree/master/docs):

Cloud Cluster Architecture Overview ©Magic Castle (https://github.com/ComputeCanada/magic_castle)

With the resources made available to the project, we plan to run 6 HPC training events from January to July 2021. These training events are connected to the Centres of Excellence E-CAM and FocusCoE and with HPC Carpentry.

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November Module of the Month: PerGauss, Periodic Boundary Conditions for gaussian bases

 

Description

The module PerGauss (Per iodic Gauss ians) consists on an implementation of periodic boundary conditions for gaussian bases for the Quantics program package.

In quantum dynamics, the choice of coordinates is crucial to obtain meaningful results. While xyz or normal mode coordinates are linear and do not need a periodical treatment, particular angles, such as dihedrals, must be included to describe accurately the (photo-)chemistry of the system under consideration. In these cases, periodicity can be taken into account, since the value of the wave function and hamiltonian repeats itself after certain intervals.

Practical application

The module is expected to provide the quantum dynamics community with a more efficient way of treating large systems whose excited state driving forces involve periodic coordinates. When used on precomputed potentials (in G-MCTDH and vMCG), the model can improve the convergence since smaller grid sizes are needed. Used on-the-fly, it reduces considerably the amount of electronic structure computations needed compared to cartesian coordinates, since conformations that seemed far in the spanned space may be closer after applying a periodic transformation.

Source code

Currently PerGauss resides within the Quantics software package available upon request through gitlab. For more information see the PerGauss documentation here.

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Registration open for Extended Software Development Workshop in HPC for Mesoscale Simulation

 

Few software, like DL_MESO, userMESO and LAMMPS, can currently simulate large Dissipative Particle Dynamics (DPD) simulations. In particular, DL_MESO [12] has recently been ported to multi-GPU architectures and runs efficiently up to 4096 GPUs, an effort supported by E-CAM. 

In this E-CAM Extended Software Development Workshop, the developers of the DL_MESO code themselves will provide an introduction to DPD, DL_MESO, its features and functionalities, as well as they will initiate participants to parallel programming of hybrid CPU-GPU systems. Part of the workshop will be dedicated to theory lectures and hands-on sessions on GPU architectures and OpenACC (NVidia DLI course) given by an NVidia DLI Certified Instructor, followed by the practical case of porting DL_MESO to OpenACC. 

Interested in participating? Join us on the 18-22 January for this ONLINE course. Express your motivation to attend the workshop directly through the CECAM website at https://www.cecam.org/workshop-details/8

References

[1] DL_MESO is a general purpose mesoscopic simulation package developed at Daresbury Laboratory by Dr. Michael Seaton : http://www.cse.clrc.ac.uk/ccg/software/DL_MESO/

[2] M. A. Seaton, R. L. Anderson, S.Metz, and W. Smith, “DL_MESO: highly scalable mesoscale simulations,”Molecular Simulation, vol. 39, no. 10, pp. 796–821, Sep. 2013

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|QBN 〉 Webinar on “Quantum Computing for Material Science and Pharma”

 

Quantum Business Network |QBN 〉 manages the collaborative processes within the quantum technology ecosystem. The vision of |QBN〉 is to transform the German and the European quantum community to a strong quantum industry.

To support this, |QBN 〉 is organising an interesting webinar and a series of expert meetings on quantum simulations as follows:

To learn more about |QBN 〉 and register to their events, visit their website at https://quantumbusinessnetwork.de/en/.

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