Travel Grant Recipients Reflections on “Introduction to HPC for Life Scientists” Course

Following the successful course on Introduction to High Performance Computing for Life Scientists that took place in Barcelona on the 7 and 8 of March 2023, the recipients of a travel grant to attend the course shared their views about their experience.

Alejandro García

Universidad de Oviedo

The course “Introduction to HPC for life scientists” held in Barcelona introduced me progressively to the world of supercomputing. Two types of blocks were combined, the theory blocks: where I learned useful commands for the management of jobs in clusters and I could know how is the hardware of such powerful technologies as MareNostrum 4; and on the other hand, the practice blocks: where I could put into practice these learned commands, empirically study the usefulness of parallelization through small exercises and carry out a simulation using MareNostrum 4. Due to my limited knowledge in the supercomputing part I was a bit lost in some parts of the last day, but I did not feel a total loss of the main idea of the lectures. I would recommend this course to anyone in the scientific or technological field and even to anyone with an interest in supercomputing since the difculty of knowledge is well regulated in most of the conference. The duration of the blocks was adequate at all times, and the treatment received every day was excellent. As the only point of improvement would be interesting a block mostly practical dedicated to basic commands of unix useful for the management and edition of files (grep, awk, sed, …) since given the regulated difculty of the congress and the work environment (the clusters) could be very useful to teach the attendees some commands that they can use in their day to day working in clusters or in the terminal in general. However, I think it has been a very complete congress and I am very grateful to have been part of it. It only remains for me to thank all the organizers for the good treatment received and the exceptional organization of the course, it has been a pleasure.

Cosmin Alexandru Dicu

University of Salamanca

A conference entitled “Introduction to HPC for Life Scientist”, organised by PerMedCOE and BioExcel, was held in Barcelona on 7 and 8 March. It was a conference that dealt with both theoretical and practical content. It started with the most basic theory: how to connect to MareNostrum, types of architectures in supercomputers and how to manage through its module system. It continued escalating in difficulty with explanations on code parallelisation and GPU simulations, until it reached the practical sessions with GROMACS and PhysiCell. The former is widely used in the simulation of biomolecules and other complex systems, while the latter is used for the simulation of biological cells and tissues. These programmes were designed to achieve a highly optimised simulation environment, which, despite the approximations made, allow valid conclusions to be obtained in reasonable computational time. In my humble opinion, this conference is suitable for any science student: physics, chemistry, biology who wants to dedicate themselves to the field of computational science. I think that the talks were entertaining, and the speakers, who were experts in the field, made the talks, despite their clear focus on an audience specialised in science, very enjoyable. It is also noteworthy that the programs used in this congress are freely available, with a lot of documentation on the net, allowing me to do my own research and continue learning.

Egor Marin

University of Groningen

I’m a PhD student at the University of Groningen. On the 7th and 8th of March I attended the course “Introduction to HPC for Life Scientists”. My background is rather unusual among the participants: I have a lot of experience in protein crystallography and, more recently, cryo-EM, and therefore a good background in Linux-based systems. However, I have almost never run large scale simulations or made intensive use of HPC clusters, especially with high GPU loads. Therefore, the content of the course was very useful for me: It gradually moved from the general architecture of HPC systems to more detailed examples of their applications, such as running GROMACS simulations or using clusters for more general-purpose pipelines using tools such as PyCOMPSs. I found both the talks and the workshops to be very informative, in particular how easy it was to carry out the tutorials provided. The GROMACS tutorial was the most memorable and impressive to me. It included many details about the inner workings of this very complicated software package, as well as impressive examples of orders of magnitude performance improvements. Impressively, the cluster queue was able to adapt to the load of all students simultaneously without noticeable delay. Furthermore, the course was organised in a simple but efcient manner: both lunch and cofee breaks, as well as the on-site internet connection, were simple but reliable. Last but not least, I really enjoyed the discussions after the lectures, especially those concerning my future career choices, as well as the inner workings of PyCOMPSs with one of the core developers (!). All in all, I would highly recommend the school to anyone who is curious about HPC computing, what it can do for you, and how to do it efectively. I hope to attend more of the PerMedCOE events in the future!

Gokce Senger

European Oncology Institute

In March, I attended Introduction to HPC for Life Scientists course in Barcelona, during which I had the opportunity to learn more about high-performance computing and to have hands-on practice of its applications in life sciences like cell microenvironment simulations.

I found the course well-structured in the sense that people with different levels of experiences with HPC/linux could benefit from it. We had a two-day course covering introductory lessons on motivation of using high performance computing, HPC hardware and
parallel computing followed by very useful practical sessions where we had the opportunity to use the HPC infrastructure at the Barcelona Supercomputing Center. In addition to the scientific part of the course, I really liked the Women in science session. It was a nice break to take some time and think about all the challenges that women have been encountering in science. It was also nice to hear personal experiences from people which, I believe, made us realise that we share similar problems and the only way to cope with them is to talk, share and move together.

I am glad that I had the opportunity to attend this training from which I benefit greatly. After the course, I have a better understanding on efficient usage of HPC and parallel programming which I was struggling with more. Now, I feel more confident to apply what I have learned during the training to my research. I would suggest this course to everyone that is new in high performance computing and eager to learn more about it.

José Antonio Quiñonero

Universidad de Murcia

I’m a student in Master Studies in Theoretical Chemistry and Computational Modelling. The past march 7-8th, I had the opportunity to participate in a course on PerMedCoE/BioExcel: Introduction to HPC for Life Scientists 2023 in Barcelona. The course was designed for life science researchers and it provided a great introduction to the field of HPC.

HPC is an important area of research and it is used in many different fields and many important challenges in science, such as protein folding, drug discovery, and tumor evolution, all depend on simulations, models and analyses, and more.

The course was organized by PerMedCoE and it consisted of different lectures and practical sessions. I found the lectures very interesting, as they gave me a lot of insights into the HPC industry. In addition, the practical sessions were very useful, as
they allowed me to get hands-on experience with different HPC tools and technologies. The course was very well organized, the staff was very helpful, and the lectures were really interesting. It provided a great overview of the basics of HPC.

The course was also a great opportunity to meet people from all over the world and make new friends. This experience has allowed me to get in touch with different people from the HPC industry and get to know more about this technology.

Overall, I am very happy with the experience lived in this course, it was a very beneficial experience. I would recommend it to anyone looking to improve their knowledge in this field, interested in HPC or science in general. I would also like to thank the
organizers for their help and support.

Raúl Saavedra

Universidade de Vigo

The conference held on March 7th and 8th, organized by PerMedCOE and BioExcel, entitled Introduction to HPC for Life Scientists contained both theoretical and practical lessons related to parallelization of calculations/simulations, as this is the key to supercomputing. The course is introductory, explaining practically everything from scratch, including basic computer knowledge up to more complex supercomputing theories. From my perspective, I can say that I learned a lot from the course, especially understanding what types of calculations can be parallelized and how to do it. The program is suitable for any life science student or even related fields (e.g. chemistry, physics, engineering), as although simulations related to health and biology are discussed, these same concepts can be applied in a diverse number of fields in the exact sciences. The balance between theoretical lessons, practical sessions, and coffee breaks was very good, making the talks enjoyable without overwhelming the audience. All the participants were very friendly, and fortunately, I had the opportunity to talk with them during breaks, and they were always available and enthusiastic about resolving any doubts. I recommend the conference to anyone interested in simulations in life or health sciences or anyone interested in calculations on supercomputers and their parallelization.”

Valentin Gradisteanu

Universitat de Valencia

The interdisciplinarity is in the air! PerMedCoE/BioExcel: Introduction to HPC for Life Scientists represented for me a great opportunity to complement my academic formation and it did not disappoint by any means. I have been able to meet people with different problems but the same solution: use computer power to have an impact on people’s quality of life.

The rise of personal computers makes it look like there is no limit to what one can do with it, just imagine having around 20.000 computers at your disposal. Nonetheless, it still is a resource and it comes at a price, economical and environmentally speaking, so it is a must to think how you can get the most out of it. A great part of the course was purely practical and, as far my research in computational chemistry goes, I am sure that the information will allow me to reduce the misuse of computational resources and take my results to another level. The professors were clear and they were keen to answer all the questions and doubts such that the interpersonal communication was key to the better understanding of the problems.

And if the computer makes you hungry, we had a lot of break time in which food and drinks to share among the participants, organizers and professors. The environment was idoneous to share knowledge and collaborate with fellows of a wide variety of backgrounds.

Munishikha Kalia

King’s College London

I attended the workshop “Introduction to HPC for life scientists” organized at the Barcelona Supercomputing Center. The workshop was very well structured and organized. During the workshop the basics architecture of the HPC was explained very well. The workshop gave a very nice overview of the HPC usage, and it was well catered for the audience with different levels of experience. The presenters explained the concepts very well and addressed our questions/issues very nicely, they were very approachable and helpful. 

My main motivations of attending the workshop were to attend the Gromacs session. This session was extremely helpful for my ongoing research projects. I was able to learn/understand the key concepts of Gromacs simulation package and was able to learn ways to optimize my current simulations better, especially using GPUs. 

I was profoundly impacted by the women in science session, it was a great bonus in addition to the scientific aspect of the workshop. It was really nice to know the background, history and impact of women in computing and HPC. The social event was a great opportunity to network and meet other people working with HPC. 

Overall, this workshop was very good, and I thoroughly enjoyed it. I would recommend this workshop for anyone interested in HPC.