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.
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.
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.
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.
The need to find easily renewable and environmentally friendly energy sources alternative to the traditional fossil fuels is nowadays a global quest. The solar energy is a promising candidate and organic solar cells (OSCs) have attracted attention. In this collaboration with Merck, E-CAM scientists have used electronic structure calculations to study how a key magnitude – the HOMO-LUMO band gap – changes with respect to the molecular disposition of the donor-acceptor molecule pair.
CLstunfti is an extendable Python toolbox to compute scattering of electrons with a given kinetic energy in liquids and amorphous solids. It uses a continuum trajectory model with differential ionization and scattering cross sections as input to simulate the motion of the electrons through the medium.
Originally, CLstunfti was developed to simulate two experiments: A measurement of the effective attenuation length (EAL) of photoelectrons in liquid water  and a measurement of the photoelectron angular distribution (PAD) of photoelectrons in liquid water . These simulations were performed to determine the elastic mean free path (EMFP) and the inelastic mean free path (IMFP) of liquid water .
The EMFP and IMFP are two central theoretical parameters of every simulation of electron scattering in liquids, but they are not directly accessible experimentally. As CLstunfti can be used to determine the EMFP and IMFP from experimental data, and as it can be easily extended to simulate other problems of particle scattering in liquids, it was decided to make the source code publicly available. For this purpose, within the E-CAM module, the necessary steps were taken to make CLstunfti a useful toolbox for other researchers by providing a documentation, examples, and also extensive inline documentation of the source code.
 Suzuki, Nishizawa, Kurahashi, Suzuki, Effective attenuation length of an electron in liquid water between 10 and 600 eV, Phys. Rev. E 90, 010302 (2014)
 Thürmer, Seidel, Faubel, Eberhardt, Hemminger, Bradforth, Winter, Photoelectron Angular Distributions from Liquid Water: Effects of Electron Scattering, Phys. Rev. Lett. 111, 173005 (2013)
 Schild, Peper, Perry, Rattenbacher, Wörner, Alternative approach for the determination of mean free paths of electron scattering in liquid water based on experimental data, J. Phys. Chem. Lett., 11, 1128−1134 (2020)
Traditionally high-throughput computing (HTC) workloads are looked down upon in the HPC space, however the scientiﬁc use case for extreme-scale resources required by coordinated HTC workﬂows exists. For such cases where there may be thousands of tasks each requiring peta-scale computing, E-CAM has extended the data-analytics framework Dask with a capable and eﬃcient library to handle such workloads.
The initial motivation for E-CAM’s High Throughput Library, jobqueue_features library , is driven by the ensemble-type calculations that are required in many scientiﬁc ﬁelds, and in particular in the materials science domain. A concrete example is the study of molecular dynamics with atomistic detail, where timesteps must be used on the order of a femto-second. Many problems in biological chemistry and materials science involve events that only spontaneously occur after a millisecond or longer (for example, biomolecular conformational changes). That means that around 1012 time steps would be needed to see a single millisecond-scale event. This is the problem of “rare events” in theoretical and computational chemistry.
Modern supercomputers are beginning to make it possible to obtain trajectories long enough to observe some of these processes, but to fully characterize a transition with proper statistics, many examples are needed. In such cases the same peta-scale application must be run many thousands of times with varying inputs. For this use case, we were conceptually attracted to the Dask philosophy : Dask is a speciﬁcation that encodes task schedules with minimal incidental complexity using terms common to all Python projects, namely dicts, tuples, and callables.
However, Dask or it’s extensions do not currently support task-level parallelization (in particular multi-node tasks). We have been able to leverage the Dask extension dask_jobqueue  and build upon it’s functionality to include support for MPI-enabled task workloads on HPC systems. The resulting approach, described in the rest of this piece, allows for multi-level parallelization (at the task level via MPI, and at the framework level via Dask) while leveraging all of the pre-existing eﬀort within the Dask framework such as scheduling, resilience, data management and resource scaling.
E-CAM’s HTC library was created in collaboration with a PRACE team in Wrocław, and is the subject of an associated white paper . This effort is under continuous improvement and development. A series of dedicated webinars will happen in the fall of 2020, which will be an opportunity for people to learn how to use Dask and dask_jobqueue (to submit Dask workloads on a resource scheduler like SLURM), and to implement our library jobqueue_features in their codes. Announcement and more information will soon be available at https://www.e-cam2020.eu/calendar/.
The jobqueue features library  is an extension of dask_jobqueue  which in turn utilizes the Dask  data analytics framework. dask_jobqueue is targeted at deploying Dask on several job queuing systems, such as SLURM or PBS with the use of a Python programming interface. The main enhancements of basic dask_jobqueue functionality is heavily extending the conﬁguration implementation to handle MPI runtimes and diﬀerent resource speciﬁcations. This allows the end-user to conveniently create parallelized tasks without extensive knowledge of the implementation details (e.g., the resource manager or MPI runtime). The library is primarily accessed through a set of Python decorators: on_cluster, task and mpi_task. The on_cluster decorator gets or creates clusters, which in turn submit worker resource allocation requests to the scheduler to execute tasks. The mpi_task decorator derives from task and enhances it with MPI speciﬁc settings (e.g. the MPI runtime and related settings).
In Fig. 1 we show a minimal, but complete, example which uses the mpi_task and on_cluster decorators for a LAMMPS execution. The conﬁguration, communication and serialization is isolated and hidden from user code.
Any call to my_lammps_job results in the lammps_task function being executed remotely by a lammps_cluster worker allocated by the resource manager with 2 nodes and 12 MPI tasks per node. The code can be executed interactively in a Jupyter notebook. To overlap calculations one would need to return the t1 future rather than the actual result.
The library can eﬀectively handle simultaneous workloads on GPU, KNL and CPU partitions of the JURECA supercomputer . The caveat with respect to the hardware environment is that you need to be able to have a network that supports TCP (usually via IPoIB) or UCX connections between the scheduler and the workers (which process and execute the tasks that are queued).
With respect to the software stack, this is an issue highlighted by the KNL booster of JURECA. On the booster, there is a diﬀerent micro-architecture and it is required to completely change your software stack to support this. The design of the software stack implementation on JURECA simpliﬁes this but ensuring your tasks are run in the correct software environment is one of the more diﬃcult things to get right in the library. As a result, the conﬁguration of the clusters (which deﬁne the template required to submit workers to the appropriate queue of the resource manager) can be quite non-trivial. However, they can be located within a single ﬁle which will need to be tuned for the available resources. With respect to the tasks themselves, no tuning is necessarily required.
We see ∼90% throughput eﬃciency for trivial tasks, if the tasks executed for any reasonable length of time this throughout eﬃciency would be much higher.
The library is ﬂexible, scalable, eﬃcient and adaptive. It is capable of simultaneously utilising CPUs, KNL and GPUs (or any other hardware) and dynamically adjusting its use of these resources based on the resource requirements of the scheduled task workload. The ultimate scalability and hardware capabilities of the solution is dictated by the characteristics of the tasks themselves with respect to these. For example, for the use case described here these would mean the hardware and scalability capabilities of LAMMMPS with a further multiplicative factor coming from the library for the number of tasks running simultaneously. There is, unsurprisingly, room for further improvement and development, in particular related to error handling and limitations related to the Python GIL.
We use the present module to avoid topology violations in an entangled polymer system. To preserve the topology in a system of entangled polymers we need to determine the minimal distance between two bonds. Once done we can apply either a soft or hard core potential to avoid the crossing of two bonds. Here, we propose to determine the minimal distance between two segments with the help of the Karush-Kuhn-Tucker conditions.
This module is a part of an E-CAM pilot project at the ENS Lyon, focused on the implementation of contact joint to resolve excluded volume constraints