LearnHPC: dynamic creation of HPC infrastructure for educational purposes

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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

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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

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Few software, like DL_MESO, userMESO and LAMMPS, can currently simulate large Dissipative Particle Dynamics (DPD) simulations. In particular, DL_MESO [1, 2] 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”

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

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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 🙂


©2020 This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License (CC BY-NC-SA 4.0).
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The E-CAM Issue of Comics&Science presented at the international comics festival of Lucca 2020

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Following the recent publication of the E-CAM issue of Comics&Science, our Comics will have its first official “outing” this Friday 30 October at the Lucca Comics&Games Festival. The presentation (in Italian) will start at 14:15 CET and will be live on YouTube at https://www.youtube.com/watch?v=BUysRG0zlCk. The presentation can be reviewed after this date at the same location.

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Dask-traj

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For analysis of molecular dynamics (MD) simulations MDTraj is a fast and commonly used analysis. However MDTraj has some restrictions such as (1) the whole trajectory needs to fit into memory, or gathering results becomes inconvenient; (2) the result of the computation also need to fit into memory, and (3) all processes need access to all the memory, preventing out-of-machine parallelisation and HPC scaling.

Dask-traj solves these restrictions by rewriting the MDTraj functions to work with Dask in order to achieve out-of-memory computations. Combined with dask-distributed this allows for out-of-machine parallelisation, essential for HPCs, and results in a (surprising) speed-up even on a single machine.

Source code

The source code for this module, and modules that build on it, is hosted at https://github.com/sroet/dask-traj. 

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E-CAM article on the EU Research Magazine

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An article about E-CAM has just been released with the Autumn edition of the EU Research Magazine. The EU research magazine is Europe’s leader in research dissemination.

The piece consists on an interview to Prof. Ignacio Pagonabarraga, E-CAM technical manager, Dr. Sara Bonella, leader of our work-package focused on quantum dynamics and also of the work-package that deals with the interactions with industry; Dr. Donal Mackernan, leader of our dissemination work-package and Dr. Jony Castagna, programmer in E-CAM.

The interview describes E-CAM’s work in

(1) developing software targeted at the needs of both academic and industrial end-users, with applications from drug development to the design of new materials ;

(2) tuning those codes to run on HPC machines, through application co-design and the provision of HPC oriented libraries and services;

(3) training scientists from industry and academia ; and

(4) supporting industrial end-users in their use of simulation and modelling, via workshops and direct discussions with experts in the CECAM community.

Autumns edition of the EU Research Magazine is available online at  http://www.euresearcher.com/14/eu-research-live. Our article can be seen here.

Interview in PDF format

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Issue 14 – September 2020

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E-CAM Newsletter of September 2020

 

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

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A possible roadmap for the coarse graining and multiscale simulation community

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A community-driven review with contributions from E-CAM “Unfolding the prospects of computational (bio)materials modeling” has just been published in the Journal of Chemical Physics on the history, developments, and challenges facing coarse graining (CG) and multiscale simulation (MS)  and a set of recommendations on how the latter may be addressed. 

Continue reading…
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