Interviews feature scientists who use the supercomputers at IT4Innovations.
Andrea Nedělníková: „A supercomputer is the bridge between equations and the behaviour of biomolecules“
Andrea Nedělníková is a PhD student in Informatics and Computational Science at VSB – Technical University of Ostrava and works at CATRIN – Czech Advanced Technology and Research Institute in Olomouc, where she focuses on biomolecular simulations. While she once imagined her future in a laboratory, she now uses computational chemistry as an atomic-scale ‘microscope’ to help develop new drugs and nanomaterials. With the Karolina and LUMI supercomputers, she can obtain results in days rather than weeks.
In my research, I focus on the study of biostructures – specifically nucleic acids, lipids, and proteins; in short, the molecules that make up our bodies – and their interactions with drugs or nanomaterials. Before a new drug or material can be used in medicine, it is essential to thoroughly investigate both its therapeutic effects and its potential adverse impacts.
In my work, I use the computer as a “microscope” at the atomic level. Using computational chemistry methods, I observe how molecules behave and interact with one another. And it is the supercomputer that performs these extensive calculations.
The difference is fundamental. When I was calculating on not so powerful machines, I had to wait weeks for results; now, with the help of supercomputers, I can analyse them after just a few days. This opens up possibilities for more complex research. A SUPERcomputer delivers calculation results SUPERfast. Which is simply SUPER.
Before entering university, I knew almost nothing about supercomputers. I first encountered them in the context of computational chemistry during one of the introductory lectures. As an enthusiastic chemist back then, I imagined my future exclusively in a laboratory wearing a white coat—the idea of a chemist sitting at a computer seemed almost absurd to me. However, the school closures during the COVID-19 pandemic shifted my career path. Today, I can no longer imagine my work without a supercomputer.
While basic chemical calculations can be handled by a standard laptop or desktop, a supercomputer performs them much faster and allows us to work with larger and more complex systems. This not only yields results more quickly but also enables me to run a higher volume of simulations, significantly enhancing both the quality and depth of the research.
Insight into the behaviour of atoms – the fundamental building blocks of matter – helps me better understand processes occurring in living organisms. This can contribute to the development of more effective or entirely new drugs, as well as the preparation of novel materials. For example, we have studied the behaviour of doxorubicin (a drug used in cancer treatment) in interaction with DNA and polymyxin (an antibiotic) with bacterial membranes. Currently, I am also studying graphene for use in electrodes designed for deep brain stimulation in patients with Parkinson's disease. In these research projects, I am supported not only by the Ostrava-based Karolina supercomputer but also by LUMI, located in Kajaani, Finland.
Debora Lančová: „A supercomputer is like a laboratory that we cannot build on Earth, but we can model it this way“
Debora Lančová works at the Research Centre for Computational Physics and Data Processing (Astrocomp) within the Institute of Physics at the Silesian University in Opava. She is currently on a two-year research fellowship at the Nicolaus Copernicus Astronomical Center in Warsaw, funded by the Czech Science Foundation postdoctoral grant. Her research focuses on the behaviour of matter in the immediate vicinity of black holes, where she searches for traces of this behaviour in data from bright X-ray stars.
I model the flow of magnetised gas – plasma, in the immediate vicinity of black holes, where Einstein's General Theory of Relativity applies. In these regions, the plasma reaches extreme temperatures, and the gravity is so intense that an immense amount of energy is released. This energy is then captured by space-based X-ray telescopes. At the same time, this is the only way to learn anything about black holes at all—since the black hole itself cannot be observed directly, we can only see how it influences the matter surrounding it.
To model what happens in the vicinity of a black hole, we must simultaneously solve a vast number of equations—covering the movement of matter, magnetic fields, and the radiation effect. The method I use involves dividing the entire space around the black hole into millions of small cells and calculating how everything flows between them. This type of computation is perfectly suited for a supercomputer, as it can be naturally distributed across the immense number of compute cores it provides.
I first encountered a supercomputer during my MSc studies at the Institute of Physics. I was assigned a seminar project to simulate the movement of several thousand particles around a black hole. When I launched the code on my laptop back then, I realised I would be waiting over a week for the results. We applied for computational resources at IT4Innovations, and witnessing that immense power was incredible. The fact that using a supercomputer is so straightforward and accessible to the scientific community is equally impressive – it is a tremendous advantage.
What surprised me most back then was that working with a supercomputer was not that different from using a classical computer. What never ceases to amaze me, however, is how rapidly the technology evolves and changes.
I study how matter behaves under conditions so extreme that they are impossible to recreate on Earth. However, thanks to modern space observatories, we can compare our simulation results with actual observations from space, allowing us to validate our theories.
Ivana Miháliková: “To me, a supercomputer is like a quantum computer simulator.”
Ivana Miháliková is a researcher at Matej Bel University in Banská Bystrica and at the Slovak Academy of Sciences in Bratislava. Her research focuses on quantum algorithms, utilising supercomputers to simulate their behaviour, as today’s quantum computers are still error-prone and limited.
"Thank goodness for supercomputers," she recalls saying for the first time when she began systematically comparing algorithm performance across various settings and added noise levels. Supercomputers allow her to test scenarios in parallel and safely experiment with quantum algorithms before deploying them into the "real quantum world."
I primarily use supercomputers to simulate the behaviour of a quantum computer. Put simply, I test quantum algorithms that could, in the future, calculate material properties more efficiently and naturally than conventional methods. However, because today's quantum computers are still error-prone and limited, I first need to investigate their behaviour in detail through simulations on supercomputers.
Simulating a quantum computer on a classical machine is extremely demanding because the complexity grows exponentially with the number of qubits. Even relatively small quantum circuits can take a very long time on a standard PC or may not fit into the memory at all. For me, a supercomputer is crucial because it allows me to simulate larger circuits and more qubits, and to compare different algorithm settings and parameters to ensure the results are reliable. With these simulations, we can estimate what quantum algorithms can realistically achieve on today's quantum machines.
‘Thank goodness we have supercomputers,’ I said to myself for the first time when I wanted to systematically compare the behaviour of the algorithm across different settings and with added noise. A single calculation quickly turns into dozens or even hundreds of runs, and it becomes clear that without a supercomputer, this project would take not just a few days, but an unreasonably long time.
What surprised me most was that a supercomputer isn't just about “a lot of power,” but mainly about an efficient workflow. It allows you to test scenarios in parallel, compare results, and systematically advance your research without waiting months for a single output.
I am trying to find out how quantum computers will help in material design and technology development in the future. Since today's quantum computers still make errors, I use supercomputers to simulate them so that we can already know today which approaches have real potential to bring specific practical applications.
Martin Vrábel: “For me, a supercomputer is a time accelerator.”
Martin Vrábel has been with IT4Innovations since 2017, focusing on research into the fluid and gas flow in various engineering systems.
Supercomputers help him to create detailed computational models, which in turn allow him to study devices in various configurations and operating states. They enable him to solve complex problems in a matter of days rather than months.
I am a graduate of the Slovak University of Technology in Bratislava and VSB – Technical University of Ostrava. At IT4Innovations, I primarily use supercomputers for research into fluid and gas flow in various engineering systems and devices. I create detailed computational models that combine specialised simulation software with the high computing power of supercomputers. During my time at IT4Innovations, I have participated in projects focused on water pumps, turbines, combustion systems, electrolysers, and fuel cells, among others.
Supercomputers are crucial for me because they allow me to study these devices in various geometric configurations and operating states. Theoretically, similar simulations can also be performed on a standard workstation, but the computing power of supercomputers gives me significantly more freedom in setting up models, working with detailed physical descriptions, and, above all, saves time. This allows me to compare multiple variants in a short period of time and reach relevant results faster.
In the beginning, I used supercomputers one step at a time – from setting up access to working with a larger number of compute nodes. At that stage, the support of my colleagues was crucial, as they helped me greatly to find my way around and understand the entire computing ecosystem. Even today, I cannot imagine my work without supercomputers.
The most significant milestones for me were projects implemented in cooperation with companies such as Sigma Lutín and Siemens, as well as those carried out as part of university-wide research activities. It was during these projects that I fully realised the vital role supercomputers play – they enable us to solve complex problems that would otherwise be impossible to tackle effectively. I therefore see all the achieved results, publications, and projects as a collective team success and, at the same time, as confirmation that ‘it's a good thing we have supercomputers’.
When working with supercomputers, I was surprised at how efficiently this infrastructure can be used to solve very complex problems in a relatively short time. In the past, I used the Salomon and Barbora supercomputers, and currently I am running my calculations on the Karolina supercomputer.
I see the greatest contribution of my work to society in optimising industrial machinery and equipment and in designing them in digital form. Thanks to computer simulations, these models can be verified and fine-tuned using experimental data even before they are put into real operation.
Michael Komm and tokamak research
Michael Komm is the Head of the High-Temperature Plasma Physics Department at the Institute of Plasma Physics, Czech Academy of Sciences in Prague. His research focuses on nuclear fusion - specifically, how to protect the first wall of future fusion reactors from extreme heat fluxes from hot plasma. In addition to experiments on tokamaks, he is also involved in modelling the interaction of plasma with first wall components. To do this, he uses the services of a number of supercomputers, including those of IT4Innovations (IT4I).
Do you remember when and how you first encountered a supercomputer?
The first and only supercomputer I ever visited was at IT4I in Ostrava on the occasion of its commissioning. The IT4I building and the equipment of its data room left me with a very positive impression. Touring the data room in a reduced oxygen atmosphere was a bit of an adrenaline rush :)
Which supercomputers at IT4Innovations have you used?
I have been using the IT4I supercomputers for years. So far, I have used the Anselm, Salomon, and Karolina supercomputers. When it comes to foreign supercomputers, I am currently performing my computations on Italian Marconi located in Cineca and Japanese JFRS.
Which IT4Innovations supercomputer are you currently using for your research, and how important is it for your work?
I am currently using the Karolina machine for particle-in-cell simulations of fusion plasma-first wall interactions. I strive for thorough characterisation of the effect of collisions between plasma particles on the incident heat and particle fluxes and on the thermionic electron flux that can be emitted into the plasma by tungsten components when heated to temperatures near the melting point. This scenario may occur in the future, for example, on the ITER tokamak if the heat fluxes to its tungsten plates exceed a nominal rate. It is important to investigate what would happen in such a case and what the consequences would be for the lifetime of the plates and the quality of the plasma discharge.
Can you reflect on an achievement you are particularly proud of?
Last year, in collaboration with colleagues from several European fusion laboratories, I was able to experimentally demonstrate on the German ASDEX Upgrade tokamak that heat fluxes originating from plasma edge instabilities (edge-localised modes, ELMs) can be significantly reduced by injecting argon into the plasma. This approach has long been considered unfeasible in the community due to the predictions of numerical modelling. However, in plasma physics, it is still true that experiments are one step ahead of modelling. :)
A few years ago, my Swedish colleagues and I were able to augment a predictive model of thermionic flux escaping from a hot wall (e.g. tungsten) for plasmas with magnetic fields. This required a series of computationally intensive simulations, a large part of which was performed using IT4I supercomputers. I would like to thank IT4Innovations for the long-term provision of computational resources!
Štěpán Sklenák and zeolite research
RNDr. Štěpán Sklenák, PhD, DSc. has been a senior researcher at the J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences in Prague since 2004. After obtaining his PhD in 1995, he spent almost ten years at the Technion-Israel Institute of Technology, Yale University, University of California, and Michigan State University. In 2023, he received the Doctor of Chemical Sciences (DSc.) degree from the Czech Academy of Sciences.
His current research focuses on quantum chemical calculations of zeolites to model their structure, reactivity, catalytic activity, and properties.
In 2020, he received the most prestigious Czech scientific award - the Czech Head Invention Award, together with Dr Jiří Dědeček and Dr Edyta Tábor for the creation and description of the structure and reactivity of new, unique types of transition metal cation reaction centres in zeolite matrix and their application in the oxidation of methane to methanol.Do you remember when and how you first encountered a supercomputer?
I only started using supercomputers at IT4I in Ostrava. However, in 1999, I saw the decommissioned CRAY supercomputer on display at a conference in Boulder, CO, USA. It was apparently (it's been 25 years) at this institution, along with an exhibition about Cray's founder, Mr. Seymour Cray.
Which supercomputers at IT4Innovations have you used?
Anselm, Salomon, Karolina, and LUMI.
Which IT4Innovations supercomputer are you currently using for your research, and how important is it for your work?
I am currently using Karolina and Lumi to calculate realistic zeolite models. Using a supercomputer compared to a workstation (i.e., a server) will allow for calculations of zeolites with larger unit cells and use more complex computational models and more computationally intensive computational procedures. Calculations with realistic computational models will enable the estimation of realistic values of reaction energy and rates of chemical reactions catalysed by zeolites, adsorption energy of molecules on zeolites, NM, and vibrational spectra of zeolites and adsorbed molecules on zeolites.
Can you reflect on an achievement you are particularly proud of?
The Award of the Czech Head PROJEKT institute, namely the Invention Award, together with Dr Jiří Dědeček and Dr Edyta Tábor.
It is important to emphasise that the idea of splitting molecular oxygen (i.e., O2) arose in my computational modelling work and was only subsequently confirmed by experiments.
Jiří Klimeš and molecular crystals
Jiří Klimeš works at the Faculty of Mathematics and Physics of Charles University, where he leads a small research group at the Department of Chemical Physics and Optics. They are involved in developing accurate computational methods for calculating the properties of materials and their application. Currently, they are mainly working on molecular crystals, such as some drugs or crystals of simpler molecules, such as water or carbon dioxide.
Do you remember when and how you first encountered a supercomputer?
I gained my first experience with computing on remote computers during my studies when I used MetaCentrum services. This allows users to use systems of various institutions in the Czech Republic. At that time, these systems comprised servers with dozens of processors. The first supercomputer I worked on was HECToR in the UK. It had over ten thousand processors, and in 2007, it was the seventeenth most powerful supercomputer in the world. Back then, we were studying the behaviour of water on the surface of salt and needed to do a lot of computationally intensive calculations. Access to a supercomputer made our work very efficient and allowed us to understand the basic principles governing the behaviour of water and salt.
Which supercomputers at IT4Innovations have you used?
I've been performing computations using IT4Innovations (IT4I) supercomputers nearly since their inception, with my very first application for computational resources being submitted in 2015 when the Salomon supercomputer was launched. It was the first opportunity to apply for computational resources after returning from abroad. I was happy to take advantage of it, as a large part of our research needs to perform computationally intensive calculations. Without the existence of IT4I, the situation would have been much more difficult for me upon my return. Since then, we have been using everything available at IT4I.
Which IT4Innovations supercomputer are you currently using for your research, and how important is it for your work?
Our calculations can be divided into two types, with one being very high memory-intensive and the other being less demanding but again more numerous. With both types, we are mainly trying to understand the accuracy of the simulations and describe the strength of the bonds between molecules. The memory-intensive calculations are primarily performed on Karolina, using up to dozens of its individual servers simultaneously. This allows us to use over 10 TB of computational memory, which is about 1,000 times more than in classical computers. We also extensively use Barbora, as we have optimised one of our computer programs for its processors.
Can you reflect on an achievement you are particularly proud of?
I might mention a paper my postdoc and I published last year in which we analysed one type of error in our calculations. When we calculate the bonds between molecules, we often neglect electrons that are close to the atomic nuclei, or we simplify their description. This allows us to speed up our calculations by an order of magnitude, but it causes some errors in the calculated values. In our calculations, we either had to accept these errors or use a more accurate and computationally intensive description of these electrons. In our paper, we looked at how the error arises and developed a way to reduce it substantially. Although this is a very "technical" topic, I consider it essential as it will hopefully improve the reliability of the data published in the literature.
Martin Friák and development of new materials
Martin Friák works as a group leader at the Institute of Physics of Materials of the Czech Academy of Sciences in Brno. He studied solid-state physics at Masaryk University, both as a Master's and PhD student. Immediately after completing his PhD studies, he left for abroad and worked at two institutes of the Max Planck Society in Germany for 11 years. Since 2013 he has been based again in Brno. He is a theoretical physicist dedicated to computational materials science and the theory-guided design of novel materials. He teaches at Masaryk University and Brno University of Technology. For the past few years, the team has been performing computations using not only classical (super)computers but also quantum computers.
Do you remember when and how you first encountered a supercomputer?
The first time I had the amazing opportunity to be directly in the data room of a supercomputer was several years ago, thanks to IT4Innovations - as a participant in the regular autumn Users' Conference of IT4Innovations. It was great to experience what we usually only know from Hollywood "blockbusters" (in recent years it was, for example, the unforgettable movie The Martian, featuring a somewhat exaggerated scene directly from the supercomputer data room).
Which supercomputers at IT4Innovations have you used?
It is primarily Karolina and Barbora, which help us immensely in our work. However, as we have been loyal and satisfied users of IT4Innovations for many years, we also used Anselm and Salomon when these systems were still in operation.
Which IT4Innovations supercomputer are you currently using for your research, and how important is it for your work?
Within one of the projects supported by the Grant Agency of the Czech Republic, we are studying nanoparticles for medical applications (treatment of cancer by hyperthermia), specifically using Barbara. Karolina is helping us with simulations of quantum computers running in collaboration with the Massachusetts Institute of Technology (MIT) in the USA.
Can you reflect on an achievement you are particularly proud of?
For my research, I have been awarded a total of CZK 30 million for the period 2024-2029 as part of the Academic Award called Praemium Academiae, the highest award given by the Czech Academy of Sciences. I can't wait to see the development of hybrid computational materials science (combining classical and quantum computers with artificial intelligence tools) and its application in the design of novel materials.
Jakub Šístek and mathematical algorithms for HPC
Jakub Šístek focuses on mathematical algorithms for high-performance computing (HPC), such as parallel solvers for numerical linear algebra, scalable domain decomposition methods, and applications to problems of structural mechanics and computational fluid dynamics. He is also interested in vortex identification and visualization in fluid flows. He is currently the head of the Department of Constructive Methods of Mathematical Analysis at the Institute of Mathematics of the Czech Academy of Sciences and an assistant professor at the Department of Applied Mathematics of the Faculty of Information Technology of the Czech Technical University in Prague. Previously, he worked at universities in Denver, Cambridge, and Manchester. He received his Ph.D. in Mathematical and Physical Engineering from the Faculty of Mechanical Engineering of the Czech Technical University in 2008. He received the Ivo Babuška Prize (2009) and the Otto Wichterle Premium (2013).
Do you remember when and how you first encountered a supercomputer?
I first remotely touched a supercomputer in 2005 during my stay at the Edinburgh Parallel Computing Centre (EPCC) within the HPC Europa project. The name of the computer was HPCx, and it was an IBM eServer p5 machine. However, it was located in Daresbury Laboratory, so I cannot say I saw it. The second supercomputer I used was Frost, an IBM BlueGene machine from NCAR in Boulder during my stay in Denver in 2007. The first supercomputer I have actually seen with my own eyes was the Pleiades, a supercomputer at the NASA Ames Research Center, the fourth fastest supercomputer in 2009.
Which supercomputers at IT4Innovations have you used?
I have used the IT4I supercomputers rather continuously since the beginning of the centre. My first successful project application was during the first open call, and I benchmarked our codes and ran some of our simulations on Anselm. I have done a lot of large-scale computations on Salomon, and together with my colleagues, we are currently heavily using Karolina for our research. We have recently added support for GPUs into our main software, the BDDCML solver library, and apart from running on the accelerated nodes of Karolina, we are looking forward to running our computations on LUMI in a few months.
Which IT4Innovations supercomputer are you currently using for your research, and how important is it for your work?
Together with my colleagues, we regularly run large-scale simulations on thousands of CPUs. Consequently, we are happy users of Karolina as the main resource we rely on. Our main research revolves around the development of new scalable methods for computational mechanics of fluids and solids. These methods are based on domain decomposition techniques, mathematical algorithms tailored to parallel processing. Many of our runs are large-scale tests of the scalability of these methods, while the second class of demanding problems is time-dependent simulations of incompressible flows. The datasets generated by these simulations are used to evaluate new methods for vortex identification, which is another research direction within our team.
Can you reflect on an achievement you are particularly proud of?
As a PhD student and postdoc, I had the wonderful opportunity to get exciting experiences from universities in Denver, Cambridge, and Manchester. During these stays, I have been building on the topic I started in my PhD thesis while extending it towards mathematics, mechanical engineering, and high-performance computing. I am happy to say that most of these collaborations are still active. For example, we have recently published a paper on a scalable method for engineering simulations without the need for tedious generating of computational meshes. We have worked on the paper with collaborators from the University of Cambridge for eight years, and we demonstrate the efficiency of the method through parallel computations performed on Salomon and Karolina supercomputers. The paper is available as open access at https://doi.org/10.1016/j.cad.2024.103730.
Martin Zelený and quantum mechanical calculations of magnetic alloys with shape memory
Dr Martin Zelený works at the Institute of Materials Science and Engineering (Faculty of Mechanical Engineering, Brno University of Technology) as the Head of the Department of Structural and Phase Analysis. His research focuses on quantum-mechanical calculations and simulations of thermodynamic stability and mechanical and magnetic properties of progressive materials. Specifically, he is interested in magnetic alloys with shape memory, which exhibit spontaneous macroscopic deformation when placed in a magnetic field. He also investigates high-entropy materials, which can exhibit unique properties by assembling many chemical elements.
Do you remember the very first time you were introduced to a supercomputer?
My first encounter with a supercomputer was during the preparation of my thesis at the Faculty of Chemistry (BUT in Brno), where we had a small computer cluster. Still, the actual big supercomputer I used for my thesis was under the administration of MetaCentrum.
My first excursion to the supercomputer room was during my PhD studies when I visited the Forschungzentrum Jülich, where I visited the Jugene computer.
Which supercomputers at IT4Innovations have you used?
I have progressively used all supercomputers except NVIDIA DGX-2 in my work.
Which IT4Innovations supercomputer are you currently using for your research, and how important is it for your work?
Now, I am using Karolina and LUMI, without which quantum mechanical calculations are impossible. For these calculations, we use the VASP (Vienna Ab initio Simulation Package) program, which allows calculations of the electronic structure, interatomic interactions, and total energy of the studied materials and their crystal structure optimisation. The data thus obtained are then used to predict the macroscopic properties of these materials.
Can you tell us about an achievement that you are particularly proud of?
I consider my most significant achievement to be the study of magnetic alloys with shape memory - in particular, Ni2MnGa alloy, where, together with my colleagues from the Czech Academy of Sciences and the Finnish LUT (University of Lappeenranta), I have described the effect of doping on the stability of the low-temperature phase of martensite. I have also found the necessity of using corrections to improve the accuracy of quantum mechanical calculations for this alloy. This research started during my postdoctoral stay in Finland at Aalto University. It continued during my stay at the Faculty of Mechanical Engineering at Brno University of Technology, where it was supported by a GACR project. Another very important contribution to my professional development was a postdoctoral stay at the University of Vienna, where the VASP program was developed, and I learned how to use it directly from its authors.