Hi. My name is Sean, I’m 22 years old and I’m currently in Bologna for the training week of the Summer of HPC programme run by PRACE. I’ve just finished my undergraduate degree in Theoretical Physics at Trinity College Dublin. About a week after this programme is over, I will be starting my masters in Artificial Intelligence in Edinburgh.
I got my first experience in High Performance Computing during my final year project and thought Summer of HPC would be a great opportunity to learn more about this exciting area. One thing I’ve realised from the training week is that, even if it’s just a parallel “Hello World” programme to make sure everything works, the novelty of running jobs on a supercomputer that’s too big to fit in one room won’t wear off for a long time.
My main hobby for a number of years has been playing hurling, an Irish sport which would probably take multiple blog posts to explain in any sort of detail. I am also interested in music and often play the guitar to wind down when things get a bit busy. Other than that, I spend a large proportion of my spare time drinking coffee. It’s started to get worryingly expensive, but at least it means I can stay awake long enough to write this.
Once the training week is over, I’ll be going to Luxembourg for the rest of the summer. I will spend the next seven weeks working on performance analysis tools for some well-known deep learning frameworks on HPC systems. I’m really looking forward to working on an interesting project in a country that you don’t get many opportunities to visit.
Episode 1: Meeting amazing people, admiring nature and eating pizzas.
Ciao, Hello, Salut, Hallo, Hola, γεια σας, Merhaba, Zdravo, Szia!* My name is Thizirie. I am from Algeria and I am studying in the baguette, fromage (cheese) and wine country, at Sorbonne University. I have just finished the fourth and penultimate year in Applied Mathematics and Computer Science there and I am so passionate about what I am going to do after graduating: Artificial Intelligence.
This brings us to today’s post! Why am I in an HPC summer school if I want to do work on AI projects later? Well, it is simple. Both are incredibly awesome and large fields but also, HPC has a lot to do with the time optimization in Machine Learning and AI.
Now, you can easily guess which project I am going to do this summer, but let us pretend that you don’t know and I will keep the title secret till the next post!
Amazing people
This week I have met 23 over 24 of the other participants and I must say that, despite all the excitement I am feeling about beginning my project in my future center, I wish we had more time to spend together. It really seems like one of the first selection criteria was kindness. Everyone is so joyful and the more you talk to them, the more you enjoy your stay. The increase is exponential, believe me.
Here are most of the incredible people I was talking about! Don’t forget to check their blog posts too, all their projects are very interesting! – CINECA
Nature
I will just leave you with this picture to encourage you to come and visit Bologna.
Bologna, somewhere in Casalecchio di Reno. The first picture I took here!
The training week
Yes, I know, you thought we never work since we chat a lot and go out? No! We are lucky enough to be hosted by CINECA where we are meeting many talented people who teach us so many interesting HPC programming sides like MPI and OpenMP. Tomorrow we are learning about GPU programming so I am very excited about this day!
Me fangirling in front of the supercomputers rooms of CINECA. Meet Marconi!
It is now time to go to bed and be ready for tomorrow’s class and city center’s tour! Next time you will read about my project!
Ciao!
*Hello in some of 2019 Prace’s participants languages.
Hi Summer-of-HPC-website-reader, I’m Benjamin from Regensburg in Germany. I started studying physics in 2013, and I really loved it (and still love it). But somehow during my master I realized, that even more than the pure physics, the programming and optimization of simulations fascinated me. So, I ended up for my master thesis with a pure HPC topic!
During that time, I first heard about PRACE and this event. I was immediately excited, and applied, even though I haven’t expected to be selected. But it finally happened and I’m so happy to be part of this story.
After our training week in Bologna, which also is such a great event by itself, I’ll be the rest of the summer in Edinburgh with two great fellow students, where I’m going to work on a task-based library.
But there is also a life outside the world of bits and bytes, which I mostly fill with playing in a Band (a time-consuming hobby), some sport (Tennis) and other social activities (which does not mean HPC isn’t a great social activity, this event is an excellent proof on this).
So, I hope this post is just the first of many interesting ones! Stay tuned!
Before the fancy parts of the project, Let me tell you about my story…
I was just a simple Electronics and Communication Engineering student at İzmir Institute of Technology. Until I met with some ancient words:
Fortune favors the bold.
-Latin Proverb
I started to ask myself “Why shouldn’t we / I?”, Then we just started to help the village children that were in need. Also, we started the green campus project to protect the environment.
“Small things can change the world!”
One day, I just asked that “Why shouldn’t I take the courses that I like from the Computer Science Department?” and my life has completely changed after I met with Deep Learning and High-Performance Computing.
This is a simulation example of my grad. project about autonomous drones with a monocular camera to detect specific objects in a given route (left). In order to avoid obstacles in the route, the depth is estimated from monocular images (right) with special deep neural networks and the depth information in the specified box area given as inputs for a deep reinforcement learning network. Without the power of the HPC, the calculation time of the steps would be so long. (Special thanks to my project partners Erman and Burak. The simulation environment made in the Unity with the help of my friend Çağdaş).
Even microseconds are enough to save or lose a life, so that is why High-Performance Computing is important for me.
Obliviously, the last question was “Why shouldn’t I apply for SoHPC?” and, the fortune favored me. BOOM! I was at Bologna, CINECA. A dream came true!
In the first days of CINECA journey, Besides learning new things while using the supercomputer, And eating fancy Italian food,
Delicious Pizza and Pasta of Bologna
The best part of the SoHPC is meeting with cool people and, Having new awesome friendships around the world.
Very first selfie of the groupMe, Jordy, Thizirie and Davide on the Bologna streets.
What you see is the only tip of the Iceberg.
Of course, tedious problems may happenin life, but never forget to:
“Get up, stand up and, don’t give up the fight!”
-Bob Marley
That’s all folks! Hope to see you in the next post! Don’t forget to check all of my friends’ posts, I believe you will enjoy them.
Hi everyone! My name is Pablo Lluch and I was born and raised in the hot and sunny south of Spain. However, I go to university in Edinburgh, UK where I’m doing my bachelors in Artificial Intelligence and Software Engineering. I recently came back from studying my third year abroad in Toronto, Canada where I developed a big interest in computer vision thanks to a very eye-opening course I took, which led me to apply to the summer of HPC. My main interest at the moment is applying Machine Learning to computer vision tasks like object classification or detection, super-resolution and creating interfaces for better human-computer interaction.
Picture of me at my garden before leaving for summer of HPC
I’m going to be based in Ostrava, Czech Republic this summer, where I’ll have mentoring and access to a supercomputer provided by IT4Innovations, a supercomputer centre part of the VSB-Technical University of Ostrava. The project I’ll be doing consists of creating a deep neural network able to perform real-time object detection on the HPC side, and then optimise it and deploy it to an edge device.
Marconi supercomputer at Cineca
I’m writing this post from Bologna, Italy, during the training week. Here, we had the chance to get a glance at the supercomputers located at Cineca supercomputer centre and got lectured about a few HPC-relevant topics like parallel computing, OpenMP or GPU Programming. So that’s all for this post, HPC folks, stay tuned for future blogs if you want to follow my journey at the Czech Republic this summer!
My
name is Andreas, I am 22 years old and I am from Cyprus. I am studying
Mechanical engineering at Nottingham University in a 4-year course (MEng) and I
have currently finished my third year of studies. During my high school years
and up until last year I didn’t enjoy programming and I considered it somewhat
boring. The main reason for this lies behind the fact that I would find no joy
in solving equations numerically because the beautiful and clever mathematical
complexity of an analytical solution is lost behind a rather simplistic
representation of the equation. This has changed about a year ago when my fluid
mechanics professor described how the famous Navier-Stokes equation is highly
non-linear and an analytical solution is said to be impossible. While digging
for solutions I understood that programming and good numerical representation
of equations is a rather complex task and that gained my interest. With the
beginning of my last academic year I made a module choice on software and
mechatronics allowing me to work with C programming language but also learning
a lot about the computer architecture. My group yearlong project was about
constructing a pocketQube Satellite (small satellite) where the tasks of the
satellite were controlled through a raspberry Pi which allowed me to work with
the Linux system and also learn a lot about the Python language which was used
for the creation of the software of the project. Even though I still lack the
skills and experience on programming I decided to further challenge myself by
applying and at last accepting a position for PRACE Summer of HPC 2019. I am
sure that it will be an amazing experience with a lot to learn and up until now
I have met very kind and helping people who care about providing this
experience.
Introduction :: Who am I? Hello World, I am Li Juan Chan. I am currently a fourth year mechanical engineering student from the University of Manchester. You might be wondering how a mechanical engineering student ended up in a HPC research programme. The reason is simple. I do not want to be a typical mechanical engineer!!! I want to develop strong programming skills so that I can run some cool engineering simulations. Have you seen the cool, colourful airflow animation around an airplane? Yes, that is one of the application that mechanical engineers do with supercomputer. In fact, my project in Bologna is similar to this with the title of “In Situ/Web Visualisation of CFD Data using OpenFOAM”. There will be no airplane but I promise you it will be colourful.
My experience in Bologna As soon as I landed on Bologna, the airline that I took sent me a message telling me that my luggage will not arrive. What an unfortunate beginning of this exciting program. The second surprise was a staff working in the Bologna Airport drives a Lamborghini around the airbase!!! The third surprise was PRACE was so generous to rent us such an amazing hotel. On the first day, I met a lot of participants of this program. I also found out that most of them have strong programming background. I was nervous at first as I did not want to fall behind. As you know my background is mechanical engineering and so I do not have a lot of programming experience. However, I guess this makes it a good reason why I should work harder than most of them. In the first week of training, I learned MPI and OpenMP which I have to admit they are hard for me. However, I am still confident that I will master them if I do not give up.
Preview of Next Chapter Before I know, the training is almost finished. Next week, I will be moving into a beautiful house in the city centre of Bologna. Furthermore, I will also start working on my project (in the progress of producing colourful animation). Want to know more about the house and the project? Stay tuned!!!
This is me with the mighty MARCONI Supercomputer
This is the Lamborghini in the airfield that I mentioned
Hi! I am Jordy Ajanohoun, Computer Science and Applied Mathematics Engineering Student.
Welcome to my blog !
I am a 22 years oldfrench student in the lastyearover 5 of my Master of Engineering program at Sorbonne University (Paris, France). In September 2019 I will start a double degree in Montreal, Canada, at ETS school where I will study Computer Graphics (3D graphics, animations, visualization etc) using HPC (High Performance Computing) too and making a related dissertation.
Me in front of the entrance of the Cineca centre during the training week
To wake up every day with this same desire to create, to build. So impressed and passionate by computer science from computer architecture to web development passerby HPC without forgetting video game programming. Excited when discovering a new technology or programming language, imagining all possible combinations with. This is who I am.
This is an example of what I have done by curiosity in order to know more about making video games. It is available on GitHub.
This is a gameplay records of a game I made 5 months ago, using Unreal 4.21 combining C++ & Blueprint.
I am curious, it is why I am supplementing my schooling with MOOCs about different topics like web programming. I madethis static personal portfolio website one year ago for instance.
Why the PRACE Summer of HPC (SoHPC) ?
I think it is clear now that I am completely crazy about science, computer programming, and I.T.! Furthermore I feel comfortable with HPC and tools like OpenMP, MPI and vectorization because I have had a very good course about the topic. Thus, PRACE Summer of HPC was definitely THE place to be for me !
In my opinion, HPC is a milestone for scientists and industrialists not only because it is useful but also because it has become necessary in fields such as: neural networks, cryptography and databases to search or sort out information. Here is one example of cool stuff we can really do with HPC! I have done it with Thizirie Ould Amer, a classmate of mine also taking part in the SoHPC 2019.
Parallel computing on a path-tracing sequential algorithm that performs a photo-realistic rendering with global illumination of a 3D image.
This program is an amazing and wonderful occasion to acquire new knowledge and go further in HPC. I am so proud and honored to have been selected among applicants from the whole Europe ! I really like interacting with people, to discuss with other participants as well as mentors and specialists from different backgrounds. For me, it is the most rewarding aspect of the SoHPC. They all are awesome ! Traveling is also playing an important part in my happiness here in Bologna. The opportunity to go on top with HPC centers across Europe, see HPC computers, discover other cultures and so much more. What else could I ask for? This training week is already unforgettable.
Produce. Relate. Acquire. Challenge.
Explore. This is also what PRACE stands for !
What’s next ?
After this training week, I will be in charge of the project 1915, Distributed Memory Radix Sort, in Dublin, Ireland. You can learn more about that here but above all, my blog is definitely YOUR place to be for that and much more!
Follow me in this incredible and exciting adventure ! I want to share it with you.
Feel free either to comment or to contact me for any kind of questions about me or SoHPC. If you have some advise for me I am here too!
Irén is a chemistry student from Budapest. She has just finished her masters at Eötvös Loránd University, and would like to continue her studies at the Hevesy György PhD School of Chemistry. Her field is theoretical chemistry and she wrote her thesis at the Laboratory of Molecular Structure and Dynamics. She was performing molecular spectroscopy computations there (simulating the rotational-vibrational motion of the molecules) to study some exotic quantum phenomena. These simulations took quite a long time, even on a supercomputer. This made the importance of clever code design and parallelization very clear, so she would like to improve these skills. She will stay with quantum chemistry of her PhD studies; she will compute reaction rate coefficients and investigate the behaviour of molecules in laser fields.
At the CINECA supercomputing center, Bologna
Irén applied for the PRACE Summer of HPC program because it is a good opportunity to discover a new field of science and to meet people from other countries who are also interested in high performance computing. In fact, this is her first professional stay abroad (there were only holidays before). She is having a good time in the training week at CINECA, Bologna. The lectures about parallel programming (MPI, OpenMP) are interesting. She thinks these skills will be useful in the future in every scientific and engineering profession. During the training week, participants practice the freshly learned things using the supercomputers at CINECA, which is a good way to gain a deeper understanding. The city of Bologna also offers an experience in cuisine; one can enjoy the variety of pastas made with sweet tomatoes and try the original pizzas.
Science has an important place in Irén’s life (and daily routine), but after a day of coding she finds it really nice to return to the Bolyai College (a place for talented students of natural sciences and informatics). She likes to chat with her friends, play board games (Dominion usually) or watch a movie. Bolyai College is a very good place to live at, because of the scientific community and the supportive atmosphere made by the people. Irén also likes hiking in the mountains and spends as much time in the nature as possible. During her stay in Bratislava, she is planning to make a trip to the High Tatra Mountains with her boyfriend. She has been there a few times already, but found it amazing so she will go back again.
Hi all! I’m Allison, and I have the great pleasure of being one of the participants in the 2019 Summer of HPC Program. I am Canadian born, Australian raised, and I have just finished studying in Spain. My professional background is in analytics and research, and my recently completed Masters in Big Data Solutions led me to the PRACE summer program.
Following this exciting orientation week in Bologna, I will be heading to Amsterdam. There, I will spend eight weeks working on a Data Architecture project with the e-Ecology team at SURFsara. The goal is to improve how ornithologists query and analyse bird migration radar data. My expertise is more in analytics and Data Science (rather than Data Engineering), so this summer is going to be an exciting new challenge! I can’t wait to begin 🙂
Hello! My name is Perry, hailing from Glasgow, Scotland. I’ve just completed my first degree, an MInf in Informatics, at The University of Edinburgh. For my summer of HPC, I will be working at the BSC, Barcelona.
I’m curious about the roles that computers can play in aiding people to take more direct control of their lives and communities, and am wary of the risks which they enable. My research interests are in machine learning and systems programming, and I am a dilettante of computer security.
In my spare time, I enjoy cooking, and exploring the cuisines of different places. I recently perfected my Hollandaise sauce, and I look forward to seeing what flavours my host city will inspire in me. I also enjoy many different types of music and movies, both old and new, and am constantly reading a wide range of books, both fiction and non fiction. (For years I’ve been maintaining lists of music, films and books to check out. The lists continue grow at a rate faster than I can consume.)
My graduation ceremony at Edinburgh University (woo!), so I arrived a day late to the training week in Bologna, and a delayed flight meant that in my first day I was a sleep-deprived gremlin. A good night’s sleep, and tactical consumption of coffee has seen me back to my usual self.
My graduation photo!
I’m part of a cohort of 25, and we are collected together in the city of Bologna, Italy, for a week of training. The previous cohort had their training week in Edinburgh, and though I like the city, I am grateful for the change of scenery.
This week, we are based in the CINECA, a top research supercomputing centre in Italy. Here, we have the opportunity to use one of the clusters, and familiarise ourselves with some of the HPC tool-chains. So far we have built examples which try to accelerate simple applications such as numerical approximations and manipulations of data objects too large to fit on a single node. Thus far, we have used MPI, and OpenMP, two parallel programming paradigms, with CUDA, and HPC data visualisation upcoming.
To perform the computations, we have been submitting jobs using the Slurm system. This seems to be a standard, as I used it on the GPU teaching cluster at The University of Edinburgh, a collection of 200 GPUs used by students taking courses in deep learning.
We were given a tour of the place. These machines consume a lot of power, and nearly half of that goes towards keeping them from overheating. Running them in a hot country only adds to that power bill…
YT in front of the racks
Our guide gave us a brief technical overview of the black obelisks in the room ahead of us. Once we entered, all of their words were lost to us. An unending roar, regular enough to be almost relaxing, though near the point of being painfully loud. You can see a short video clip of the experience here.
At the end of the week, I’ll be heading to Barcelona, where I’ll be working at the Supercomputing centre there – BSC.
I’ve often heard that nowadays “computation is free”, and that the biggest overheads in modern workloads come from the costs of moving and accessing data. Consequently I will be researching the effects of different memory technologies on workload run time. For example, we might have a type of memory which has much faster read times, but very slow write times. If we leverage this, and place data which we use frequently, and change rarely, we should see improvements.
Dimitrios Voulgaris, a fellow student will be joining me in Barcelona. I have met Dimitrios, and look forward to getting to know him better in the coming weeks.
I will say more about my project as I learn more about it, and hope to present my findings in an interesting way. During the placement, I seek to gain more experience in profiling applications, and using the Valgrind toolsuite, which I believe researchers at my host centre have made valuable extensions to. I am looking forward to meeting the variety of talented individuals that live and work in Barcelona.
Thank you to PRACE for organising the program, and to my peers for being a welcoming multi-disciplinary group. Best of luck to you all!
Hi all! My name is David Izquierdo and I am 21 years old. I am from Sabiñánigo, a little town in the north of Spain, and I will be soon finishing my bachelor’s degree in Aerospace Engineering in the University Carlos III of Madrid.
Since I was a kid, I really enjoyed watching Formula One races. As time went
by, I became more and more interested in motorsports and decided to pursue a
career in F1 by studying Aerospace Engineering. To be honest, at the moment in
which I made that decision I was not even close to aware of how things would
evolve.
During my university studies, I discovered that engineering was indeed the field to which I would like to professionally dedicate my life. In particular, the courses that I took in Fluid Mechanics and Aerodynamics made it clear to me that understanding the behaviour of fluids and looking for new, better ways of solving the Navier-Stokes equations (the equations that describe a viscous fluid’s motion) were some of the challenges that more appealed to me, without forgetting that my final aim is always to apply the knowledge I acquire to the design of race cars -that is why I got involved in the Formula Student team of my university, Formula UC3M-.
Circuit de Barcelona-Catalunya. Formula Student Spain competition, 2019.
HPC (High Performance Computing) became important in my life since, in order
to look for better solutions to those equations that I was mentioning above, it
is important to have access to a significant amount of computational power and
to understand the basics of how a computer runs. When one of the professors of
the CFD Research Group in the Carlos III university told me about the PRACE Summer
of HPC programme (¡gracias Manolo!), I immediately went to the website to check
the proposed projects, and then found out that one of them was about the CFD (Computational
Fluid Dynamics) study of a Formula Student car. It was just tailored for me;
the perfect opportunity to connect the two fields that I like the most and to develop
a project about it.
Luckily for me, I was accepted for the project, so I will be spending the
next two months working on it in the IT4Innovations supercomputing centre in Ostrava,
Czech Republic. Throughout this period, I will make the best of my efforts not
only to develop the project itself, but to explain in this blog things like why
aerodynamics is so important in our daily life, or how this project in
particular, and HPC in general, can help to transform our society. I will try
to make it understandable for all the people, well-versed or not in engineering
or science topics.
Finally, I would like to say that, less than one week after the beginning of
the PRACE Summer of HPC and even before having started the project, the
experience has already been worthy, thanks to all the wonderful people that I
have met during these first days. Good luck to everyone with your projects!
Hello from Bologna! My name is Beckie Lait, I am 21 years old and I have just started my PRACE Summer of HPC journey! I have been looking forward to this opportuity for so long and I am so pleased that it is now upon me.
I come from a small village in England but have just finished my third year out of four, of my Theoretical Physics Integrated Masters degree at the University of Manchester. This means I will be starting the Masters part of the course when I return to University in September. I hope to learn a lot from this incredible experience with PRACE and use it to help me to progress next year.
This is the CINECA centre in Bologna, Italy, where myself and the other 2019 PRACE Summer of HPC students completed our training week.
I am so excited to start the following part of my journey next week after completing the training sessions this week in CINECA, Bologna. On Saturday, I will be travelling to Athens, Greece where I will join the Biomedical Research Foundation in a project regarding High Performance Computing, HPC.
My future dream would be to reduce and to contribute to the elimination of animal testing. After becoming vegetarian at the age of 14 and then vegan at 18, animal rights are extremely important to me and I am ecstatic to be working on a project in Greece that will be able to direct me down this career path of finding reliable and accurate alternatives!
This is a photo of one of the delicious vegan meals I have had since arriving in Bologna.
Make sure to keep an eye out for my future blogs so that I can take you on my journey with me!
Hey everyone, I’m Kara, studying Computer Science in Bonn, Germany. While at university I mostly lean towards courses on IT Security topics, I am excited to work in HPC this summer. Starting next week, I will be in Amsterdam figuring out how to add encryption to PCOCC, the private cloud tool they have running on their supercomputer.
When I’m not studying, I am normally checking on the beautiful balcony/mini-garden my boyfriend and I have (there’s always so much to do!) or fumbling with a telegram bot for planning board game nights a friend and I started programming. I love playing board games (you might have noticed since we have a bot for it) and Pen and Paper, also reading and playing music.
I hope you’ll enjoy following my posts over the next two months! For now, I’ll stop writing and get breakfast – today we are learning all about MPI and since I have never worked with that, I’m expecting quite a demanding day.
Late-stage undergraduate and Master’s students are invited to apply for the PRACE Summer of HPC 2019 programme, to be held in July & August 2019. Consisting of a training week and two months on placement at top HPC centres around Europe, the programme offers participants the opportunity to learn and share more about PRACE and HPC, and includes accommodation, a stipend and travel to their HPC centre. Applications open 18 January 2019.
Current Application Deadline: 25 February 2019
About the PRACE Summer of HPC Programme
PRACE Summer of HPC is a PRACE outreach and training programme that offers summer placements at top HPC centres across Europe to late-stage undergraduates and/or master students. Up to twenty five top applicants from across Europe will be selected to participate. Participants will spend two months working on projects related to PRACE technical or industrial work and produce a report and a visualisation or video of their results.
PRACE SoHPC 2017 participants and trainers during the training week in Ostrava, Czech Republic. The photo was taken during the trip to Dolní oblast Vítkovice, Hlubina a Landek, an old steel factory in Ostrava.
The programme will run from 1 July to 31 August 2019. It will begin with a kick-off training week at CINECA Supercomputing Centre in Bologna (Italy) – to be attended by all participants.
Flights, accommodation and a stipend will be provided to all successful applicants. Two prizes will be awarded to the participants who produce the best project and best embody the outreach spirit of the programme.
Conor O’Mara and Sukhminder Singh are award winners for 2018
Participating in the PRACE Summer of HPC Programme
Applications are welcome from all disciplines. Previous experience in HPC is not required as training will be provided. Some coding knowledge is a prerequisite, but the most important attribute is a desire to learn, and share experiences with HPC. A visual flair and an interest in blogging, video blogging or social media are desirable.
Project Descriptions
Project descriptions with more detailed prerequisites and more information on applying are available on the PRACE Summer of HPC website www.summerofhpc.prace-ri.eu.
Summer of HPC is a PRACE programme that offers summer placements at HPC centers across Europe. Up to 25 top applicants from across Europe will be selected to participate. Participants will spend two months working on projects related to PRACE scientific or industrial work and ideally produce a visualisation or video of their results. The programme will run from July 1st to August 31th 2019. At the end of the programme, two best participants will be awarded for their contribution – there are awards for Best Performance and for HPC Ambassador.
Flights, accommodation & a stipend will be provided to all successful applicants; all you need to bring is your interest in computing and some enthusiasm!
PARTICIPATING IN PRACE SUMMER OF HPC
Applications are welcome from all disciplines. Previous experience in HPC is not required. Some coding knowledge is a prerequisite but the most important attribute is a desire to learn, and share, more about HPC. A strong visual flair and an interest in blogging, video blogging or social media are desirable. Applications are open from 18 January 2019 to 25 February 2019.
Eligibility for the programme
The following eligibility apply:
Applicant must be studying at a European Institution at the time of application.
Be late stage undergraduate student and/or masters student.
Be over the age of 18.
Attached latest CV.
Have the minimum prerequisites outlined by projects.
Be able to pass the Code Test.
Student selects at least 2 projects of their choice.
Recommendation returned before the deadline.
Final year students will be accepted as long as they are registered with a European institution at the time of application.
About PRACE The Partnership for Advanced Computing in Europe (PRACE) is an international non-profit association with its seat in Brussels. The PRACE Research Infrastructure provides a persistent world-class high performance computing service for scientists and researchers from academia and industry in Europe. The computer systems and their operations accessible through PRACE are provided by 5 PRACE members (BSC representing Spain, CINECA representing Italy, CSCS representing Switzerland, GCS representing Germany and GENCI representing France). The Implementation Phase of PRACE receives funding from the EU’s Horizon 2020 Research and Innovation Programme (2014-2020) under grant agreement 730913. For more information, see www.prace-ri.eu.
Do you want more information? Do you want to subscribe to our mailing lists? Please visit the PRACE website: http://www.prace-ri.eu
Ecologists studying animal movement require integrating multiple kinds of data coming from different sources. In particular, at SURFsara we are helping ornithologists to work with a new stream of radar data.
Where the researchers are used to working with relational databases, we will explore the suitability of replacing these by static storage along with an accompanying working environment and practices that would form a virtual lab. Ideally, querying this static database still feels natural (i.e.: you describe which data you want and not how to access it) and ecologists can still apply their existing IT knowledge.
Interns will be free to explore existing tools and work with the radar datasets (see section 9) that ecologists are gathering, guided mainly by our Scalable Data Analytics team to deliver a few characteristic workflows and a guide with best practices. Typical constraints in these fields include ensuring that workflows remain easily scalable with the increase of data volumes.
Virtual lab for bird migration, focusing on (please see section 9): • one of the Distributed Databases • and one of the Data Processing Centers (specifically tailored to the chosen Database of the previous bullet)
Week 1: learning the problem, our initial ideas to tackle the problem and the tools and methodologies
Week 2-3: work on a first approach, coarsely implementing a simple first workflow
Week 4-6: evolve the basic concept into a scalable set-up, implementing a couple of (possibly) more complex workflows
Week 7-8: write a guide with best practices for setting up and working in the developed environment
Final Product Description: We expect as a deliverable:
A set of representative scientific workflows
A guide of best practices for storing and working with the data stream, using the previous workflows as examples to generalise upon
Adapting the Project: Increasing the Difficulty: Distributing computing outside of the dedicated environment and integrating extra data streams can be used as difficulty increases.
Adapting the Project: Decreasing the Difficulty: Limiting functionality and scalability requirements can be used as difficulty decreases.
Resources: We host our own environment for working on this assignment. The interns are free to use their laptops with any hardware and software they see fit to develop their ideas. Technologies we are thinking about include (but are not limited to): Apache Parquet, Apache Spark, Jupyter, R Studio, R, Python. The tools are readily available to download and install in most common operating systems. The interns are free to choose and explore alternatives once they deepen into the matter.
Deployment as a service in the form of Docker containers managed by Kubernetes will also be addressed, but it is not the focus of the assignment.
SURFsara will arrange any internal rights to data and the platform.
One of the grand challenges of HPC is providing programming tools that enable the programmer to write parallel codes capable of scaling to hundreds of thousands, or even millions, of cores. Task-based programming models are seen as one possible solution to this. In this approach, problems are split up into lots of separate tasks and then run when a set of dependencies (such as other tasks finish running) are met. This idea is of great interest to HPC in general because it supports applications with irregular and complex communication patterns, along with allowing programmers of more traditional codes to break apart the synchronous nature of their communication which is often a major limiting factor when it comes to performance and scaling.
However, there is a problem! All current task-based models are based on specific assumptions that limit their utility. For instance, a large number of task-based models express dependencies via variables, which is fine in a single memory space but when we go across to multiple nodes (which you are forced to do to run large problems) then this suddenly isn’t directly applicable and solutions for solving it can make the application more complex and/or have a significant performance impact.
To this end, we developed the Event Driven Asynchronous Tasks (EDAT) model, where the programmer is explicitly aware of the distributed nature of their code but still splits their code up into tasks and drives the interaction between these via events. This can provide significant performance benefits for real-world applications running at large scale (up to 32768 cores.)
Up until this point we have just used the Message Passing Interface, MPI, under the hood as the transport layer for EDAT. However, GASNet, a technology designed to handle the communication for runtimes like EDAT, is potentially a much better fit and also operates much more closely to the hardware level. Therefore a key question, and what this project will be looking to answer, is the performance and scaling benefit that a GASNet transport layer for EDAT will provide to the existing benchmarks that we have used. One example of this is that GASNet should be able to issue hardware interrupts which EDAT can then pick up, rather than requiring a polling thread. This addition of GASNet will be transparent to the end user, but has the potential to be a game changer for the EDAT library and further illustrate the important benefits of this approach.
An illustration of how EDAT works, where the programmer has two processes. Process 0 schedules one task (task 1) and process 1 schedules two tasks (task 2 and 3.) Task 1 has no dependencies, so runs immediately whereas tasks 2 and 3 depend on events and won’t run until these arrive. Task 1 fires an event to process 1 and this matches the dependency of task 2, task 1 then fires another event to process 1 and at the same time task 2 fires an event to itself. These two events match the dependencies of task 3 and this then runs on a core
Learning Outcomes: This project involves tackling one of the grand challenges of HPC – how to most effectively write highly scalable parallel codes. You will be running on state of the art Cray supercomputers, working with and learning about task-based models. You will also gain exposure to runtime technologies lower down the stack that supports parallel programming APIs. Lastly, you will gain experience in running codes on large scale parallel machines as well as aspects including threading and distributed memory programming too.
Student Prerequisites (compulsory): Strong programming background and willingness to learn. Ideally, the student should know how to use C/C++ .
Student Prerequisites (desirable): Experience with C/C++.
Task 2: (2 weeks) –Gain experience with the existing code base. Agree on the exact scope of work and start preliminary implementation and experimentation towards this. Submit a work plan.
Task 3: (3 weeks) – Main development phase of the project where the GASNet transport layer is finalized and benchmarking begun to compare performance against the existing MPI approach. Given time performance tuning will be performed.
Task 4: (2 weeks) – Final tidy up of code and benchmarking experiments. Produce a video demonstration of the work that has been done. Submit final report
Final Product Description:
The development of a transport layer using GASNet for handling the EDAT communications. This will likely be one or more code files
Benchmarking results that compare the performance of the GASNet transport layer with that of the existing MPI layer for a number of benchmarks that we have already developed. This will then most likely form the basis for a paper exploring the performance in the context of writing task-based codes in this manner.
Adapting the Project: Increasing the Difficulty: Whilst the main aim of this project will be to develop a GASNet transport layer and perform benchmark comparisons, there will be the opportunity for more advanced students to then address optimisation aspects of this (including next-generation GASNet-EX) and/or even implement additional transport mechanisms (such as Cray’s DMAPP) for performance comparison.
Adapting the Project: Decreasing the Difficulty: The code is structured such that the specific transport layer inherits from a parent, generic, class. As such this should be entirely pluggable and the only modifications needed are writing a new child class. There is already an MPI implementation and this comprises of a number of distinct pieces of functionality. Hence if the student is struggling we can focus on one or two specific items and still use the existing MPI transport layer for the other parts.
Resources: No major resources needed. The student will need to bring their own laptop running Linux. We will provide time on ARCHER, a Cray XC30, which we host & manage, for this project.
There is an increasing demand for processing confidential data, such as the genetic makeup of humans, personal data, and data that, if leaked or modified, could have serious legal consequences. Normally, supercomputers and clusters are shared by many users, which makes it difficult to meet strict security requirements. Furthermore, network restrictions hinder the flexibility and the open character that make clusters popular.
PCOCC (Private Cloud On a Compute Cluster) is a promising technology that enables creating private HPC-clusters on existing clusters, by automating the setup of KVM virtual machines, connected with an overlay network. These guest private clusters can be tailored to the security requirements per project, whilst maintaining the flexibility and openness of the host cluster.
A security weakness in the current PCOCC software is that disk images that are used for storing persistent cluster data are not encrypted. Because the disk images reside on the host cluster file systems, confidential data could be read by users with enough privileges on the system. Having encrypted volumes will greatly increase the usability of PCOCC for all applications where high levels of security are required.
The underlying virtualisation technology, KVM, does support encrypted volumes, so adding the possibility of using encrypted volumes will involve a modification in the PCOCC software. Luckily, PCOCC is written in Python, Open-source and allows modification.
During the SoHPC, you will make steps towards adding encrypted volumes to the PCOCC software. If successful, you will test the usability and performance of PCOCC clusters with encrypted disk images. To complete this task, you will need to be at least familiar with Python programming and have a keen interest in cluster computing, and virtualization technologies.
Learning Outcomes: In this internship, you will learn about implementing a new feature in an existing, real-world application, in a structured way. Furthermore, you will get a broad experience in how to compute clusters work, and you will become familiar with various aspects of virtualization.
Student Prerequisites (compulsory):
Linux on a user level
Python programming
Virtualisation techniques
Some system maintenance
Unix/Linux networking
Student Prerequisites (desirable): Linux cluster usage and maintenance
Week 1: setting up, getting familiar with the new location
Week 2-3: Literature study; workplan (deliverable)
Week 4-6: implementation; documentation
Week 7: benchmarking; evaluation
Week 8: final project report
Final Product Description: The final result of this project, if successful, will be the added possibility of using encrypted volumes to virtual clusters.
Adapting the Project: Increasing the Difficulty: The difficulty can be increased by further testing.
Adapting the Project: Decreasing the Difficulty:
If the goal of the project is too difficult, another approach is further automating the deployment of private clusters, with various options for security and/or features.
Resources: The student will need access to a cluster with Intel Skylake and Intel Knights Landing systems (provided by us), standard computing resources (laptop) as well as an account on the Cartesius supercomputer (provided by us).
The advent of technological advances in the field of computer-aided drug design has streamlined the drug design process, making it more cost- and time-efficient. One of the most important tasks in the lead optimization phase of the drug design process is to predict, among a series of lead candidates, which ones will bind more strongly to the therapeutic target. In this direction, relative binding free energy methodologies have been developed, which rely on physics-based molecular simulations and rigorous statistical mechanics to calculate the differences in the free energy of binding between a parent candidate drug and analogues. For example, Free Energy Perturbation (FEP) calculations coupled with Molecular Dynamics (MD) simulations calculate the free energy difference between an initial (reference) and an analog (target) molecule to an average of a function of their energy difference evaluated by sampling for the initial state. In this project, free energy perturbation calculations will be performed with NAMD or GROMACS in order to test the methodology for accurate calculation of relative binding free energies between ligands in a test of >200 ligands, which requires HPC resources.
The application of free energy perturbation calculations is a promising strategy for candidate drug optimisation, as it can accurately predict among a series of lead candidates, which ones will bind more strongly to the therapeutic target
Learning Outcomes: Learn how to set up and perform free energy perturbation calculations coupled with Molecular Dynamics simulations. Develop own tools and scripts to automate the process. Understand the ligand-protein binding.
Student Prerequisites (compulsory): Natural science student (Chemistry, Physics, Engineer) that have familiarity with or want to learn how to perform computer simulations.
Student Prerequisites (desirable): Basic programming and Linux OS skills would be desirable.
Week 1. Perform GROMACS or NAMD Tutorial. Familiarize
with Linux OS.
Week 2. Setup the protein system. Read the literature on free energy perturbation calculations.
Week 3. Submit the Work Plan. Familiarize with HPC resources on ARIS, creating and running batch scripts. Submit the MD jobs.
Week 4. Familiarize with analyses tools and perform test calculations on the trajectories.
Week 5. Produce free energy perturbation calculations (FEP).
Week 6. Analyze the trajectories
Week 7. Rationalize the results and gain insights into lead optimization.
Week 8. Write the final report.
Final Product Description: The accuracy of free energy perturbation calculations in a test set from the literature. Assessment of usage in an HPC environment for high-throughput applications.
Adapting the Project: Increasing the Difficulty: The project can be made more difficult if we decide to code to automate the process of FEP.
Adapting the Project: Decreasing the Difficulty: The project can be made less difficult by choosing easier analyses.
Resources: The student will need to have access to ARIS supercomputer facility, the necessary software and analysis tools to run and analyse the trajectories. Local resources for analyses will be provided (office space and desktop).
Organisation: Greek Research and Technology Network S.A.
High-Performance Computing has lately enabled multimillion atom simulations in nanoscale systems. In this project, we will simulate KRAS, a protein, which is mutated in 70% of human cancers in contact with a model cell membrane. The goal of this project is to gain an atomistic and quantitative understanding of the binding conformational landscape of the wild type and G12D mutant K-Ras with the membrane. The outcomes of this project are expected to uncover new target binding sites for drug design. To test the mechanism of KRAS overactivation, enhanced sampling MetaDynamics Molecular Dynamics simulations will be used here to examine the dynamics and conformations of the mutant PI3Ka protein as they occur in microsecond simulations. The dynamics and structural evolution of this oncogenic protein, as described by our simulations, might reveal possible binding pockets, which will be then exploited in order to design small molecules that will target only the oncogenic mutant protein. Both atomistic, as well as coarse-grained simulations, will be used in order to sample the conformational changes of the protein.
Proteins attach to the cell membrane and generate signals that activate cellular pathways. The process by which proteins bind to the membrane is largely unknown, and it is expected that the protein-membrane interface can serve as a new target for drug design. In this image PI3Kα protein is shown attached to a model cell membrane
Learning Outcomes: Learn how to set up and perform enhanced MD simulations. Analyze enhanced MD simulations with standard tools. Develop own tools and scripts for MD simulation analysis. Understand the protein function and dynamics.
Student Prerequisites (compulsory): Natural science student (Chemistry, Physics, Engineer) that have familiarity with or want to learn how to perform computer simulations.
Student Prerequisites (desirable): Basic programming and Linux OS skills would be desirable.
Week 1. Perform GROMACS and PLUMED Tutorial. Familiarize with Linux OS.
Week 2. Setup the protein system. Read the literature on KRAS.
Week 3. Submit the Work Plan. Familiarize with HPC resources on ARIS, creating and running batch scripts. Submit the MD jobs.
Week 4. Familiarize with analyses tools and perform test calculations on the trajectories.
Week 5. Produce enhanced sampling MD trajectories.
Week 6. Analyze the trajectories
Week 7. Rationalize the results and gain insights into the mechanism of KRAS mutant function.
Week 8. Write the final report.
Final Product Description: Mechanism of KRAS attachment to a model cell membrane.
Adapting the Project: Increasing the Difficulty: TheThe project can be made more difficult depending on the analyses that will be performed
Adapting the Project: Decreasing the Difficulty: The project can be made less difficult by choosing easier analyses
Resources: The student will need to have access to ARIS supercomputer facility, the necessary software and analysis tools to run and analyse the trajectories. Local resources for analyses will be provided (office space and desktop).
Organisation: Greek Research and Technology Network S.A.
