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DeiC HPC Interactive HPC Supercomputing UCloud

Interactive HPC reaches 5000 users

On Saturday, December 3rd, DeiC Interactive HPC reached 5000 users.

This means that in the past three months, DeiC Interactive HPC has had 1000 new users.

We’re very proud of the platform’s succes. Since the National HPC services began in November 2020, it has been evident that DeiC Interactive HPC via the platform UCloud has diversified the use of HPC across different fields of research by lowering the threshold for non-experts.

The fast growth of users also reflects that DeiC Interactive HPC has proven extremely useful for teaching and is now increasingly used by universities outside of the consortium of universities running the service.

This story was originally posted on and can be read in full via escience.sdu.dk

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HPC Interactive HPC Research Supercomputing UCloud

UCloud as a complementary HPC tool within theoretical particle physics

Though supercomputers form the key basis of his research, UCloud has been a valuable, complementary tool for Tobias and his colleagues and will most likely continue to be so in future work as well.

Post.doc. Tobias Tsang works within the broader research field of theoretical particle physics. As part of the Centre for Cosmology and Particle Physics Phenomenology (CP3-Origins) at University of Southern Denmark, his research more specifically concerns quantum field theory and quantum chromodynamics (QCD), i.a. how fundamental particles, protons and neutrons, interact with each other:

My research aims to provide high precision predictions based solely on the theory of the Standard Model – the best-known understanding of the interaction of fundamental (i.e. not containing ‘smaller constituents’) particles. This is done via very large-scale numerical simulations using the most powerful supercomputers around the world.

Post.doc. Tobias Tsang, Centre for Cosmology and Particle Physics Phenomenology (CP3-Origins) at University of Southern Denmark

Experience and achievements

More traditional mathematical methods that can be written down with pen and paper do not apply for research on quantum chromodynamics. As such, Tobias’ research relies on a method called ‘Monte Carlo’ which is applied to compute statistical field theories of simple particle systems. Though this type of research is done using very large supercomputers, Tobias has recurrently applied UCloud for exploratory studies of smaller volumes of data:

When doing large scale simulations, we sometimes do it on something called ‘10,000 cores in parallel’, and clearly this is not something we can easily do on a resource like UCloud. But for the small exploratory studies, UCloud is a nice resource in the sense that it is available; you don’t have to sit here on a hot day and burn your laptop to death – you can send it to UCloud and run it there. I think this is kind of the point where I have used UCloud the most; for small exploratory studies and some of the projects that don’t need a huge amount of computer time but still a significant portion.

Post.doc. Tobias Tsang

Though UCloud has served as a supplemental rather than a key tool in Tobias’ work together with the CP3-Origins research centre, he describes it as a nice complement to other HPC resources:

“I don’t think UCloud will ever be the only resource we use. But this is also the design of it; UCloud is not meant to be a huge machine, it is meant to be an available resource that is easy to use and that gives you a playground to set up things really from scratch where you can test things out and run smaller jobs and analyses. In that sense, it is quite complementary to a lot of the things we normally work with. For exploratory studies and for code testing, UCloud will definitely remain very useful.”

Post.doc. Tobias Tsang

At one specific project done at SDU as a collaboration between CP3 and IMADA (Institute of Mathematics and Data Science) a few years back, the vast majority of samples were generated on UCloud, and a significant amount of data production and measurements were also carried out on there [1]. UCloud needs, however, to be considered a part of a whole, according to Tobias:

“It is not that one particular machine made it possible; we would otherwise have found another machine to run it on. But UCloud provided us with a nice set up where we could just use local resources without having to go through big grant applications to get computer time.”

Post.doc. Tobias Tsang

Pros and cons

In terms of time optimization, UCloud has also been a game changer for Tobias:

One of the nice things about UCloud compared to other machines is the wall clock time: quite often, for larger clusters, depending on the cluster though, you are very much restricted by the queue policies. So, there are some clusters where you have a maximum run time of 4 hours, and if you happen to run a small job that is longer than this, then you can’t – you have to always tailor your job to fit exactly and to make the maximum use of it. On UCloud you have a 200-hour wall clock. This is very helpful as for a lot of these things that have to run sequentially, you might not need a huge resource, you just need to have a long enough time span to actually do it.

Post.doc. Tobias Tsang

Though UCloud slowed the work process down a bit in the beginning as everything had to be installed and set up, this downside was quickly resolved and overshadowed by the benefits: 

“Once you get used to it, you can kind of equalize the work process to what you would have on a cluster where everything is just readily installed.”

Post.doc. Tobias Tsang

Despite pros and cons, Tobias describes UCloud as a flexible system:

The fact that UCloud is really just a virtual machine has both positive and negative sides. The positive side is that you are really free to do whatever you want to do; you can install everything and you don’t have any restrictions that you would have on larger clusters where you can’t easily install software, or you can’t install it into the parts where you want to install it. On larger clusters, you are typically limited by the compilers that are already there. So, from that point of view, UCloud, at least to me, seems like a more flexible system. The downside is that you have to install everything; you can’t just quickly run something, you kind of have to constantly install everything from scratch.

Post.doc. Tobias Tsang

Last but not least, Tobias stresses the interaction with the UCloud front office as a major benefit that has helped the research group significantly, especially compared to other clusters with a much longer response time:

One of the nice things with UCloud as a general system is that every time something didn’t work, we got a really quick email back. Any questions we raised were answered quickly, so it was never something that kept us stuck for weeks or months – typically things were resolved in a very timely time scale. And things that we actively suggested as nice features or things that we thought were missing on UCloud were likewise addressed.

Post.doc. Tobias Tsang

[1]  Della Morte, Jaeger, Sannino, Tsang and Ziegler, “One Flavour QCD as an analogue computer for SUSY”, PoS LATTICE2021 (2022) 225, https://doi.org/10.22323/1.396.0225

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Interactive HPC Research UCloud

National Health Data Science Sandbox for Training and Research

UCloud is not just an ideal platform for the individual researcher who wants interactive access to HPC resources or an easy way to collaborate with national or international partners. It is also highly suitable for teaching. Jennifer Bartell and Samuele Soraggi, who are both working on the project National Health Data Science Sandbox for Training and Research, share their experiences with using UCloud.

National “sandbox” platform

The growing amounts of data in all research fields offer researchers new opportunities and possibilities for scientific breakthrough. In the case of health science, the use of large amounts of data has great potential to improve our health care – it can e.g. expand our ability to understand and diagnose diseases. One of the constraints of using health data is that many datasets (e.g. person-specific health records or genomics data) are sensitive from a patient privacy perspective and governed by strict access and usage guidelines. This can be a major challenge in particular for students or researchers who are just learning best practices in handling health data while also developing data science skills.

Go to SDU eScience for full story

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DeiC HPC Interactive HPC Supercomputing UCloud UCloud status Uncategorized

DeiC Interactive HPC reaches 4.000 users on UCloud

We’re approaching the end of the second year with DeiC Interactive HPC – and there are now 4000 users on UCloud!

During the first year with DeiC Interactive HPC, UCloud reached more than 2000 users. We’re glad that the interest in the platform has continued to grow throughout the second year.

Go to SDU eScience for full story

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HPC Interactive HPC Teaching UCloud

Teaching Humanities in UCloud

UCloud has been a game changer for Assistant Professor of Cognitive Science and Humanities Computing (Aarhus University), Ross Deans Kristensen-McLachlan, teaching within the crossroads of cultural studies and data science.

In short, the benefits of UCloud within teaching narrows down to a much more trouble-free teaching process free of unnecessary technical issues, allowing teachers as well as students to focus on the substance of their work.

Benefits when teaching in UCloud

One of the major benefits is the computational resources available in terms of having more computing power, allowing students to focus on state-of-the-art work.

Assistant Professor Ross Deans Kristensen-McLachlan

Ross has been teaching two elective Cultural Data Science bachelor courses as well as a master’s level course on Natural Language Processing (NLP) for students of Cognitive Science. A clear before and after characterises the two elective courses, formerly run on a local server: as more than 25 students typically had to have access to the server, it naturally required a lot of energy and time. As a result, actual time to do state-of-the-art work was typically limited but with UCloud this kind of downtime has been reduced significantly. Barriers that could potentially make students new to computational methods loose interest in the field have therefore also been reduced.

Another major benefit, according to Ross, is that UCloud allows all students to work from the same starting point and reduces possible imbalances between students with brand new computers and students with older computer models:

One thing about UCloud, that I actually think is quite important, is that it kind of democratises access to resources.

Assistant Professor Ross Deans Kristensen-McLachlan

In terms of teaching, several palpable benefits allow teachers and students alike to concentrate on the substantial content of the respective courses. Some challenges do, however, arise in class, though these are typically rather insignificant such as some minor issues when integrating with GitHub.

UCloud and the humanities

When teaching the elective courses on Cultural Data Science, Ross has encountered humanities students with no background within computational methods whatsoever. This, however, turned out to be an advantage as the students were typically open and able to adapt quickly:

Because UCloud has eliminated a lot of former technical obstacles and barriers, students can focus on learning good programming practices and the results of their research. It allows us to focus on the task at hand. The students don’t have to know how the backend works; they don’t have to be computer scientists – they are humanities students and should be able to think about humanities objects (texts, visuals etc.) using computational methods.

Assistant Professor Ross Deans Kristensen-McLachlan

As such, UCloud is “a means to an end”, Ross emphasises. Though computational background knowledge is of course far from irrelevant, the objective for the Cultural Data Science courses has been to educate the students to think critically when working with computational methods:

We are not just looking at data science methods and applying them uncritically. We try to use the students’ main expertise and encourage them to apply their subject knowledge to think critically about their results when working with computational methods. Determining the notion ‘genre’ from a classification model eg. urges the students to think critically about the notion itself – is it even something we can determine from text alone?

Assistant Professor Ross Deans Kristensen-McLachlan

Overall, the students following Ross’ courses have been extremely positive about UCloud, even though some were sceptics to begin with. Two kinds of feedback characterised the reception of UCloud from the students in general: one group fully integrated with UCloud from the start, others came to accept it as a necessary (useful) tool.

Collaborate teaching resources

Among teachers from the department of Linguistics, Cognitive Science, and Semiotics at Aarhus University, UCloud has furthermore improved the internal coherence across the department for the benefit of both students and teachers. As most teachers have moved all their material on to UCloud, students now avoid using one set of tools for one course and one set of tools for another course.

Besides the many teaching-related benefits to be gained from UCloud, Ross further emphasises the ongoing dialogue between users of UCloud and the team who maintain it:

They are very responsive to suggestions. Over the past year it’s (UCloud) become even more fully featured in terms of what you can do with it, and I don’t see that stopping any time soon.

Assistant Professor Ross Deans Kristensen-McLachlan

One potential improvement of UCloud, Ross suggests, could be the implementation of some sort of outreach program in order to get even more people to gain from the benefits:

UCloud gets rid of all the annoying things. As far as I can see there are only benefits – the minor issues are vastly outnumbered by the benefits.

Assistant Professor Ross Deans Kristensen-McLachlan
Categories
HPC Interactive HPC Supercomputing UCloud

New UCloud release

Since we discontinued our support for mounting your local folders onto UCloud using WebDAV, have we been in search of a way to allow the users of UCloud to work with their files locally without having to re-upload them to UCloud after every change. We are happy to announce that we now have a new solution that gives the possibility to synchronize your local files with your UCloud file storage.

Go to SDU eScience for more information on the release

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DeiC HPC Supercomputing UCloud

Call for applications for National HPC resources

As a researcher or Ph.d. Student at a Danish university you can now apply for resources on the national HPC centers, including the Danish part of EuroHPC LUMI.

The second call for applications for regular access to resources on the national HPC centers is now open. This includes applications for the Danish part of EuroHPC LUMI. The call is open for applications from all research areas.

As part of the use of the national e-infrastructures DeiC issues calls for applications on the use of the national resources. The projects are granted resources after application and on basis of assessment of research quality and technical feasibility.

The applications are evaluated by the appointed e-ressource committe and the grants are approved by the DeiC board.

Deadline for applications are 4th of October 2022 midnight, and the resources will be available for use from 1. January 2023.

For more information visit DeiC

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DeiC Event Supercomputing UCloud Workshop

DeiC Interactive HPC Back Office workshop

On May 10th, the SDU eScience Center was visited by colleagues from Aarhus University and Aalborg University for a Back Office workshop in the DeiC Interactive HPC consortium. The DeiC Interactive HPC Back Office collaborates on the development and operation of the facility. 

The overall topic of the workshop was “Developing UCloud apps” and discussion points included development tools, development workflow, deployment of apps on UCloud, to name a few. 

“The main focus of the workshop was to share our knowledge and experience in developing applications for UCloud with other members of the consortium. During the lessons we took a specific use case to demonstrate all the steps of the app development workflow, doing a live coding session with all the participants

Emiliano Molinaro, team leader for the user support team at the SDU eScience Center.

This is an excerpt. Click here for the full story.