Posted on by Mateusz Lango Posted in Blogs 2015 — 2 Comments ↓

After a fabulous training week in Jülich (which was already covered by many other SoHPC participants e.g. here) I arrived to the European Green Capital – Ljubljana. The city is really beautiful and you really should visit this place. However, my blog post will be about one serious issue we have here.

Every day in the morning we cycle to the university from our dorm thanks to the city bike system and the extensive net of cycle paths. After a few hours of hard work, there is a time for the most important point in our day schedule: a lunch. Lunch in Ljubljana take us usually a whole hour which is a very nice change after working in Poland. In Poznan almost always I have my lunch in the rush, between classes or in the middle of work, by picking something from the university

Taking coffee (and ice creams!) with best rommie ever 😉

canteen. Here, we have a calm walk to the one of local restaurants where we order something from the lunch offers menus which are pretty cheap and tasty (a perfect and rare combination). After having a lunch and a nice conversation in the meantime, we head to one of the coffee houses to take a cup of coffee with milk. Of course, we have a pretty good coffee machine at the university where we can take as much coffee as we want, however, citing one of the famous personage of SoHPC  “in the coffee house they prepare a coffee for you and you can feel as a king at least for a minute“. Once we had a coffee on the top floor of one of the Ljubljana’s skyscrapers, another time we were in the vegan place (great place for a masochists coffee drinkers) and sometimes we pick one of the coffees on the picturesque alleys.

I suppose that you didn’t discover our main problem yet. Well, in Ljubljana there is so many different restaurants (and coffees!) that we usually can’t decide where to go! It’s really terrifying, because the lunch should be the time of relax and instead every single day we are facing a very hard, multi-criteria decision making & optimization problem. I’ve already discovered some heuristics which we follow. If Sam is really hungry we should go to Maxi where he can get a big schnitzel with a plenty of potatoes. We haven’t repeated our mistake and we have never been in the vegan coffee ever again. The only chance that we will eat in “Daisy” is when Leon is coming with us. But besides this simple rules we usually have no clue where to go… And at this point HPC takes the stage! Why? Because we are able to formulate our struggle as a linkage prediction problem.

We can construct a graph with nodes representing the Ljubljana’s restaurants and coffee places, with one additional node for our university/starting position. Later, to each node we can add some additional information to the nodes: the distance from the university, if we were there before (and how many times), if we liked the food there and when we were there for the last time (we usually don’t repeat restaurants in the consecutive days). We can also provide some additional information e.g. “is Sam very hungry?”, “is Leon coming with us?” etc.

The most important problem of the modern world as a graph

The most important problem of the modern world as a graph

Now, the problem is reduced to the prediction of the edges in the graph. For example, if we decide to go to Maxi, and later to the coffee on the street, the algorithm should predict three edges in our graph. One edge from the university to Maxi, one from Maxi to the coffee and one from the coffee to the university. How the computer can predict where we should go? Well, we can provide to the algorithm the information of the restaurants in Ljubljana (with all additional information mentioned before) and the history of our past lunches. Basing on that the program can e.g. extract frequent patterns of our decisions and infer the knowledge about about them. This inferred knowledge is later used to predict edges in our graph in the future.

res2

One possible solution for our problem.

Unfortunately, the computer usually needs to consider all possible edges to determine which of them are the most probable ones. In our simple graph this is not a problem at all, but if we consider much bigger graph, which occurs in more important (???), scientific applications then we are in a serious trouble. Why? For instance, if our graph contains 200 000 nodes, than there is almost 20 000 000 000 possible edges! My SoHPC project aims to solve this problem using huge computational resources offered by HPC. Do you want to know how I will do it? Wait for my next post 😉

 

Posted on by Tomislav Subic Posted in Blogs 2015 — 2 Comments ↓
No photoshop, this is the real sun!

A sunny day in Princes Street Gardens

  “It’s gonna be cold and rainining up there the whole time…”

If I got a pound every time  I heard that in the last months, I could buy a kilt (which are not cheap by the way). While most of my fellow SoHPCers are fleeing the north in order to spend their summer on the sunny Mediterranean beaches, I am doing the opposite. Many will not believe me, but I actually like the weather here. When the only summer you know is +30°, hiding from the sun and sweating in the shade for three months, you kinda try to avoid that. And it’s not so bad as everybody thinks: from the 25 days that I’ve been here, it only rained for 6 days, and by that I mean the real rain, not the 10 minutes light showers that you don’t even need a jacket for. On the other hand, it was cloudy most of the time. The temperatures range from 15° to 23°, perfect if you ask me. Nevertheless, we enjoyed the few sunny  summer hours we had! In Croatia, we don’t really have weather like this; we only have hot summers which turn into cold-ish and windy winters, anything in between is practically nonexistent. I’ll consider this my first Spring/Autumn experience ever!

But let’s go back a few weeks. If you read any of the other blog posts, you probably know that we had a killer training week at the JFZ, which none of us didn’t quite expect to be so awesome. Apart from all the things we learned and the fun we had, I’ll just add that we have all made friends for life. I have made a special connection with my Juelich roommate Anurag, who told me all his life stories and so much more, whom I had to drag out of the bed every morning and with whom I shared late night meals.

It was a mean garlic bread!

Anurag showing off his cooking skills

Another thing no one wants to mention, but I will, is that my teammate Leon (who also happens to be one of the main coordinators) and me, won the go-kart race. It was wild, as you can see on the photo.

Spraying the champagne all over the place! Haters gonna hate.

Winning team of the SoHPC go-kart race. Photo credit goes to Dr. Ivo Kabadshow

Back to our Scottish experience. I always wanted to visit some place outside Europe, so this came as the perfect opportunity! I have yet to meet my Scottish idol, Gordon Ramsay, who, I have to say, gave me a completely wrong impression of Scottish people. I didn’t hear a single swear word, a little disappointed to be honest. The niceness of the people here still amazes me after a couple of weeks, I guess I am used to different mentality at the Balkans (nothing against that of course!).

Think twice before ordering the large one.

Schottish breakfast

Playing that sweet sound.

One of the many bagpipers around Edinburgh

Edinburgh is a compact little city, which really has no main square (or at least we didn’t find it), but there are lots of places spread around the city such as pubs and markets where it gets really crowded over the weekends and after work. Certain parts of the city have a brewery smell. I have not yet decided if it bothers me or not. Another thing we like to enjoy here is the food. From the classics such as fish&chips, haggis or black pudding and to basically anything fried. I’ll just include a picture of the Scottish breakfast which is more of a breakfast, lunch and dinner combined.
A part of the experience is also riding the double-deckers to work  every morning and listening to the sweet music of bagpipes, which always finds a way to you, regardless where you are.

And last, but not least, some words about work and my project. We have all settled in pretty well at the EPCC. Our mentors are really nice and supportive, and we have developed a friendly relationship with them. They are always available for us and do their best to help us out with every problem we might have. I meet often with my mentor Nick, we usually set a task and when I do it, we meet again, talk about the next step and decide what to do next. That can result in a few meetings per day, or a meeting every other day. I have started to do some prototype visualisations of moisture and clouds in the atmosphere, but more on that in my next blog post.

As I come to the end, I realize that this blog post has it all: work stuff, breakfast food, a coordinator spraying champagne, a slick selfie, and an Indian guy cooking.

 

Posted on by Petr Valenta Posted in Blogs 2015 — No Comments ↓

Traditionally, the process of performing numerical simulations consists of three separate steps: First, the input parameters (such as initial or boundary conditions) are specified, then the simulation is executed and finally, in order to determine the result, it is necessary to explore and analyse generated data. For several decades, increasing power of computer clusters and advancement in parallel computing methods allow scientists to perform more and more accurate simulations in various fields of human research.

On the other hand, increasing demands of the simulations need more data to be stored on a disk and analysed. However, the capabilities of computing environment which is responsible for transferring the data and communication have not grown up as rapid as the computational power. Dumping and processing of all the data calculated during the simulation would take too much time, so in practice this usually means that they are stored only at several time-steps or at much coarser resolution than the original data. The rest is just discarded and the significant part of information may be potentially lost.

In situ visualization stands for the technique, where the data are visualized in real-time, as it is being produced by simulation, and without involving storage resources. By using the visualization and simulation together, one can overcome the bottleneck of data transfer. Furthermore, this approach allows to monitor and interact with running simulation, so its parameters can be modified and scientist can immediately see the effect on investigating phenomena.

 

In situ visualization allows to observe results during the simulation runtime.

In situ visualization allows to observe results during the simulation runtime.

Researchers in OGS (National Institute of Oceanography and Experimental Geophysics) use a 3D numerical model OGSTM–BFM to study the nutrient and carbon cycles in the Mediterranean Sea and their sensitivity to climatic changes. The model computes biogeochemical fluxes which transform organic and inorganic components. Recent requirement of increasing the spatial and temporal scales of the simulations encounters aforementioned problems, thus the computation time is longer and it becomes very difficult to analyse produced data.

During the two months stay at CINECA supercomputing centre, I will be involved in a development of the 3D in situ visualization tool, which can be used to check and analyse the OGSTM–BFM model behaviour by consistently evaluating how the biogeochemical processes are influenced by the nutrient and carbon cycles, specifically related to the three main boundary conditions: the Atlantic inflow at Gibraltar Strait, the terrestrial inputs at rivers and the atmospheric deposition. The tool will be also beneficial to control the correctness of the computations during the simulation runtime. The implementation should be designed in such a way that allows portability to other coupled modelling systems used at OGS for many different purposes.

In general, in situ visualization creates an opportunity to explore and analyse much more data than is possible with traditional techniques. Also, as high performance computing moves towards the exascale era, in situ approach is widely predicted to become more and more important as an efficient tool for speed-up of large scale simulations.

 

Posted on by Samanta Makurat Posted in Blogs 2016 — 4 Comments ↓

First month has already passsed. That was really fast. But that is what happens when you have limited time for unlimited activities – which Greece for sure gives you, and which, for sure gives you a project in Molecular Dynamics (MD).

That is how the exemplary MD system looks like. Protein surrounded with water in a box of certain dimensions. You can see red atoms as oxygen, white - hydrogen, blue - nitrogen etc.

That is how the exemplary MD system looks like. Protein surrounded with water in a box of certain dimensions. You can see red atoms as oxygen, white – hydrogen, blue – nitrogen etc.

For those unfamiliar with the topic, MD simulation is a very powerful tool in the theoretical study of biomolecules. The simulation allows you to observe behavior of system in time, providing the description of atomic and molecular interactions which all together govern macroscopic properties of the system. That basically (and a bit oversimplifying) means that you if you have a system containing up to a few millions atoms connected with each other (e.g. protein in water) and want to see how does it change with time, you can run a simulation (usually in nanosecond scale) and can observe macroscopic changes like: conformation changes, protein interactions or folding. Visualisation

Seems easy, right? What I described above is a fun part – when the simulation is already running, HPC computers do the work for you and you don’t have to worry. There is only one condition: “garbage in, garbage out”. This is probably the most principal rule of computational chemistry – if you want a simulation to be reliable, you have to prepare it very carefully.

How do you do that? Well, as it is the first time I have dealt with this methodology and such a big system I had to learn about MD and software used for preparation and simulation first. That included reading a lot and performing a few tutorials: Schroedinger’s Maestro, NAMD, Gromacs. If you are familiar with these, you can start the real work: creating the system. What does it mean? The initial structure of the protein is obtained from structural biology studies and there are usually a few available structures for a protein. Every one of them is a bit different – they might have different ligands, different residues missing. Your aim is to search the literature and find the best one – and if none is perfect – think about how to make it perfect from homology modeling – which is basically taking what you need from different protein structures and mixing it to one.

When you’re ready with the literature it’s time to put some hands on. In my project I will study: human thymidine kinase 1 enzyme (hTK1). That is one of these enzymes that none of the 3 available structures (1w4r, 1xbt and 2orv in pdb) is perfect. As I wrote above, that means that it’s my duty to make it like that with the use of proper tools. What I’ve found out is that hTK1 is the most active in its tetrameric form, and as this might be important for simulation I decided that I want to simulate it as a tetramer. Because 2orv is a dimer I rejected this structure. From the remaining two: 1w4r and 1xbt I created a homology model in Maestro. That was needed because only one of four monomers in 1w4r had a full structure of the active site and 1xbt contained essential metal atoms (Mg, Zn). Still, to make the system work we need proper ligands inside. hTK1 changes its quaternary structure upon ATP binding and that is what we want to observe, but both structures contained only the inhibiting thymidine triphosphate (TTP)

My enzyme is ready for further steps!

My enzyme is ready for further steps!

on the dT binding site. In order to describe both binding sites and changes upon ATP binding we had to find similar protein that would contain substrates/products or different inhibitor bounded in a way that both binding sites are solved. Here, I found similar, although not human thymidine kinase (2orw) that contained inhibitor 4TA built both from both substrate sites – deoxyadenosine and deoxythymidine, connected with 4 phosphate groups. That makes both binding sites properly occupied and the inhibitor easy to change for substrates (just delete one of the phospates) for further simulations if needed. Here, again Maestro helped to overlap the structures and change TTP to 4TA.

Visiting Aris supercomputer with Dimitris and Juan

Visiting Aris supercomputer with Dimitris and Juan

This, along with 3 extremely intensive days in GRNET with the absolute master of MD (and patience) – Dimitris Dellis, where I’ve learnt about HPC infrastructure here and how to prepare remaining steps of simulation and run it on ARIS is what I did for last 3 weeks. Now, that the protein is ready, I have to transfer it from Maestro to Gromacs and start a simulation. That’s a plan for this week. Keep your fingers crossed! I will report how it went, soon.

Posted on by Anna Gradou Posted in Blogs 2016 — 4 Comments ↓

If we make a wordcloud for all the things that we said during the training week in Juelich, the biggest word would be “WHERE” I guess. Was that nerdy enough for an introduction for an HPC summer program?  “Where are you from?” and “Where will you go after the training week?”. Well for me the answer was that I’m from Greece and I’ll go to Edinburgh so everybody was wondering if I can survive the lack of sun and the rain since I am used to double temperature during the summer.

Can you see the clouds?

Portobello Beach

Well, guys it’s not that bad! Enough with the bad advertising of the Scottish capital. It’s not raining everyday and it’s pretty common to enjoy your sunny not extremely cloudy days with a cider at the park or the beach! Yes, Portobello Beach is really nice although there is a reason why it’s not crowded with people. You can enjoy your swimming walk there but only if you have your windbreaker with you.

IMG_0161

View of the city from the Edinburgh Castle

Edinburgh has so many places to discover. Picturesque streets and shops, museums and galleries and so many parks. This city is full of green and beautiful parks and hills. You can simply take the bus and chose a random park that you see on the map and you will feel like you went to the countryside to enjoy  nature. If you enjoy more urban life (ok, I admit that for myself) you can think of anything, then check it online -> Edinburgh people will have a festival for it. During the summer this is the city of festivals! Edinburgh Art Festival, The Royal Edinburgh Military Tattoo, Edinburgh Festival Fringe, Edinburgh International Festival, International Book Festival, International Film Festival, Jazz & Blues Festival, Edinburgh Mela! Street musicians, street bands, bagpipe musicians are everywhere.

DSC_0120

Tomislav being artistic at the Holyrood Park

Street Musicians

Fringe Festival Preview

Ok, I am talking about my weekends so far, I should admit that.. Well, my visits at the EPCC are more often than the ones at the parks! So far, I met really nice people here. Everyone is friendly and willing to help you with anything you need. During the first week, Marta, Tomislav and I attended some HPC and MPI courses, doing exercises about image processing and “playing” with ARCHER, the latest UK National Supercomputing Service. It was a very good opportunity to find out more about ARCHER software and hardware and get access to the supercomputer to submit some jobs. Everyone at the EPCC is keen on teaching summer students new things so we had the chance to attend a demo of Wee ARCHIE,  a suitcase-sized supercomputer. It is designed and built in a way so that students can see the inside parts of it and understand what a supercomputer is. We also found out that we can run our applications on Wee ARCHIE by the end of the summer! So far, I am working on the Smartphone Task Farm application, that visualizes how the master process distributes the tasks and at the end combine the results. The application will be used for outreach events where users can load a page and become a worker node using their smartphone. By the end of August I will maybe have the chance for a real-life testing of the app at one outreach event of EPCC. The view of the beach from the office makes all  this summer work easier!

13823188_10207937539650444_565265864_n

Summer is here!

 

Posted on by Marco Forte Posted in Blogs 2016 — No Comments ↓

Possibly fictitious excerpt from the Python Conference announcement of Virtual Environments.

Snake oil - Python get it?...

Possibly fictitious gentlemen introducing virtual environments

Most honorable Python developers, please raise your hand if you’ve ever gone from the highs of writing Python to the dreary comedowns of library version control.

“Everybody raises hands”

Raise your hand if you’ve ever been stuck all day trying to get version 1.4.2a of library A to work alongside 1.23 of library B in Python 2.7 for project one, all the while you need 1.5c of library A and who knows what for library B to get it to work for Python 3!!

“ People jump up and down, flailing their arms in agreement”

As expected, ladies and gentlemen, this version control malady of Python has afflicted us all at one stage or another. Some consider it the price the gods put on the usage of this holiest of languages.

“ The crowd agrees, discontent develops, the priestly python developer consults his holy PEP https://www.python.org/dev/peps/ to try soothe the crowd, ‘for purity this must be so!’”

I stand here today in defiance, I’m here to tell you that a group of apostatic engineers have given me the solution. In the goodness of my heart I’m gonna share it with you all today. Available for one conference only, at the low low price of free, do you good people desire it!? Are you prepared for revolution!?

“The crowd erupts in anticipation and agreement, people high fiving left and right, up high AND down low. A poor soul, who has been manualy managing library versions for 20 projects, faints in the corner of shock, never believing such a thing possible”

The answer ladies and gentlemen,… The answer is Virtual Environments.

 

As you can tell Virtual Environments are clearly a big deal in Python. As listed on the website.

“A Virtual Environment is a tool to keep the dependencies required by different projects in separate places, by creating virtual Python environments for them. It solves the “Project X depends on version 1.x but, Project Y needs 4.x” dilemma, and keeps your global site-packages directory clean and manageable.”

Ideally you have a main python3 installation, which has all up to date library versions, that is a catch all for simple test projects. Then for each separate project it’s recommended, that you use the VirtualEnv tool to create a virtual environment that has all the library versions you want to use. You can have different virtual envs with different python versions also.

 

Here’s a quick outline of how it’s done. You can install it via PIP (Comes with python):

$ pip install virtualenv

Then for your project

$ cd my_project_folder

$ virtualenv venv

This will create a folder in the current directory that contains all Python executable files, along with a copy of ‘pip’ you can use to install project specific libraries.

To use a specific version of python for your project use

$ virtualenv -p /usr/bin/python2.7 venv

This will create a python2.7 virtual environment

To activate your virtual environment, type

$ source /venv/bin/activate

Now anything you do in python will be as if this environment was your main one.

To deactivate:

$ deactivate

It’s that easy! It might not seem necessary when beginning a project but trust me. Once you start adding a lot of libraries, a problem is going to crop up eventually and you’ll wish you took these simple steps at the beginning.

Something to note, if you are using the Anaconda distribution of Python you can use their implementation of VirtualEnvironments. http://conda.pydata.org/docs/using/envs.html. I’ve been using this and it’s perfect for Scientific Python work. Also if you like automation, you might like this tool which automatically activates the virtual environment when you enter your projects folder, https://github.com/kennethreitz/autoenv.  Also here’s an actual Python Conference talk about Virtual Environments, https://www.youtube.com/watch?v=Xdv7vwIIThY

I mean, people, Snake oil <—> Python, pun of a lifetime. Maybe I’ll do more of these Pythonic public service announcements. Drop me a comment if you have any questions or feedback!

( Image: Link Carol M. Highsmith [Public domain], via Wikimedia Commons)

Posted on by Jiří Blahoš Posted in Blogs 2015 — 1 Comment ↓

I was invited to participate in SummerOfHPC for the last moment, because one of the guys had some complications and had to cancel his participation. I was really surprised and happy to get this unexpected opportunity all of sudden. So, on Saturday 9th of July, I left my home to start this exciting experience that was lying ahead. I crossed the Czech Republic by a train first, and then took a plane from Prague directly to Dublin, the capital of Ireland. After my plane, shook by the strong Irish wind, finally landed at Dublin airport, my journey was finished.

20160713_174406

Tower Building – ICHEC Dublin office location

On Monday, I reached the ICHEC (Irish Centre for High-End Computing) building near the Liffey river. I met some of the people working there, who kindly welcomed me to my new working place, including my project supervisor, Dr. Adam Ralph. He introduced me to the problematics of the project and assigned me some initial tasks. The main aim of my project is visualisation of fluid and waves. Honestly, I can not imagine a better place to work on water simulation code than Ireland, which is surrounded by the ocean, and the ICHEC office itself is located right next to the Grand Canal in Dublin.

Specifically, I will work on visualising the output from a mathematical model, provided by ICHEC. The model is a simple program, written in Fortran, which serially executes given number of steps of a time simulation of wave propagation in fluid. The other task included in my project is to parallelise the code of the model, so it can take an advantage of high performance computer clusters and supercomputers. For this, I will get a chance to lay my fingers (not literally) on Fionn – ICHEC’s supercomputer cluster.

A ship sailing off the Dublin bay - a practical example of shallow water

A ship sailing off the Dublin bay – a typical example of shallow water

The core of the model is shallow water equations. These equations are derived as a simplification of Navier – Stokes equations, which are probably most common equations used for fluid flow modeling. The shallow water equations are used for modeling the fluid flow in situations where the horizontal size of the area is far bigger than the vertical, and the flow in vertical direction is negligible. The examples of such situations could be beach waves, ocean flows, tsunami (even though oceans are definitely not shallow, their depth is still nothing compared to their horizontal size), air flows in atmosphere, and others.

My work on the project has only just begun, and so has my exploration of interesting places in Dublin and whole Ireland. And I believe there are plenty of them, so I look forward to the following weeks and share my new impressions and progress with you.

Posted on by Shaun Lahert Posted in Blogs 2015 — 2 Comments ↓

As Ambra covered most of the technicalities of what we are working on here in Cyprus in her wonderful blog on lattice QCD and supercomputers. I will talk more about our experiences so far in Jülich, Germany where we had our training week and Nicosia, Cyprus where we are currently staying. I thought for a while how best to describe the training week and I honestly don’t think I could do the experience justice. One would think averaging 6 hours sleep a night followed by 10 hour days where we learned about a different aspects of HPC would be a nightmare but it was genuinely an awesome week. Beginning with a Sunday night interrupted by two separate fire alarms in the Forschungszentrum guest house we spent our Monday being introduced to each other and learning about PRACE, the Summer of HPC program and touring the super computing facilities at the Forschungszentrum. Tuesday to Friday was dedicated to sampling different aspects of HPC which included MPI, OpenMP, Visualisation, Go-Karting and CUDA. Ok Go-Karting is not part of HPC but we did go on Thursday and it was pretty awesome. Unfortunately the day  was marred by some controversy whereby a nameless PRACE  employee intentionally threw the qualifiers to gain a faster team mate for the relay race. He won his trophy in the end but one disgruntled intern described it as a ‘trophy of lies’. In the future the people at the Forschungszentrum should definitely look into to including Go-Karting on all their  HPC courses and also a possible lifetime ban for said nameless employee.

Me about to destroy my competitors.

Me about to destroy my competitors on the asphalt.

 

After the aforementioned destruction of my competitors

Post destruction of aforementioned competitors.

 

Other highlights were watching the EURO 2016 games in the local Irish bar (which I learned were in every European city apparently) and the different themed dinner parties held in the garden of the guest house. The guys at Jülich who organised all this really deserve a big shout out for all they did, although I am not sure how much longer I would have lasted on a diet of gummi bears, sparkling water and pork. Our flights out were booked for 2:45 am on Friday Night , which is what we get for leaving it to a travel agent I guess, so the final nights revelries definitely took its toll on our 13 hours of travel to Larnaca Airport. I should thank and apologise to Ambra for putting up with what was probably the worst travel partner imaginable, I will rate sobering up in an airport at 6 am 0/5 stars and would not recommend.

We were picked up in Nicosia by our adviser Giannis on Saturday who kindly brought us to the Cyprus Institute first so we could learn all about our projects and have work for the weekend if we wanted, I had not slept for 30 hours at this point so I was overjoyed at his enthusiasm. Following our ‘brief’ introduction we did some grocery shopping before being brought to our dorms where I proceeded to sleep for 14 hours. The following Sunday was spent touring the city of Nicosia and the surrounding area with our site coordinator Stelios who made an awesome guide albeit a slightly less than awesome driver. I should say now that everyone in Cyprus drives in a similar fashion whereby orange lights seem to be more of a challenge then a warning and red lights are a matter of opinion.

Our first week in the institute was spent primarily acclimatising to the heat, on Monday we decided it would make sense to walk in the morning as it was only 25 minutes away. This was a mistake and upon arrival we felt like we had just trekked across a desert. Entering our shared office we were then greeted by sub-zero temperatures as people in Cyprus know how to use air conditioning. Some of this may be slight hyperbole as my memory of that day is quite foggy. The rest of the week we took the bus and began learning about lattice QCD, in my case I focused on learning how to start with a theory defined on Minkowski Spacetime and bring it to a theory defined on a discrete Euclidean Spacetime (the lattice in lattice QCD).  I will go into more detail about this and what people are interested in calculating on the lattice in my next blog (when I learn myself). Along side learning the theory I did some basic analysis on some lattice data which was previously analysed so I could compare results and ensure I had the right idea. On Friday night we went for a meal and drinks with the lattice crew and some others from the University of Cyprus nearby and we got to know everyone a bit better.

The following week was spent in a similar fashion to the first, learning the theory and doing some more advanced analysis. I am not sure if they know exactly what they want me to do yet but so long as I am learning I am happy. Next week there will be big lattice QCD conference on in Southampton, England and most of the lattice people from the Institute will be attending. Ambra and I are planning a 1 week trip to Ayia Napa  to make the most of the temporary lack of supervision. So I guess that sums up my experiences so far on the Summer of HPC, there are many things I have left out like falling off my bike in the most idiotic way possible on the second day in Julich and of course all the interesting and funny people I have met. But I will leave you now with some pictures I have taken so far in Cyprus.

 

View from the bus stop

View from the bus stop.

 

The walk home

The walk home through the park

 

Duck Pond on the walk home.

Duck Pond in the park.

 

Cypriot Bakery

Cypriot Bakery

 

More baked goods.

More baked goods, Cyprus has load of these bakeries which is awesome for someone who can’t eat gluten.

 

Posted on by Ambra Abdullahi Hassan Posted in Blogs 2015 — 3 Comments ↓

Note: On monday I started working on the PRACE Summer of HPC project called: Mixed precision linear solvers for lattice QCD. Since I think that most people don’t know about the subject I will write this post to tell you more about lattice QCD. You don’t have to have a degree in physics to understand (or to enjoy it) and I promise I will not use math formulas or difficult words.

 

The wonders of the subatomic world: tiny particles and huge computers.

QCD studies how quarks and gluons stuck together to form protons and neutrons in the atoms.

QCD studies how quarks and gluons stuck together to form protons and neutrons in the atoms.

You probably have heard of protons and neutrons before. They are component of the atomic nuclei, we are all made of. However there are some particles that are smaller than neutrons and protons and they are called quarks and gluons.

Quarks and gluons are confined through strong interaction to form neutrons and protons and QCD is the theory that explains how this happens. In a very simplistic way, we could tell that QCD is the theory of how is it possible for our world to exist, starting from the tiniest part of us.

Ok, I have explained what QCD is, but what is lattice QCD? In QCD there are some arduous math expressions called path integrals. Does it sounds troublesome?

Don’t worry because you don’t have to deal personally with path integrals: thank to lattice QCD these path integrals are discretised in such a way that they are reduced to numerical computations. These computations are carried out on supercomputers, and they are incredibly challenging: thousands of scientists in the world are studying new methods to solve lattice QCD problems, and they are even creating special supercomputers for this purpose.

IMG_20160715_124027_0

Some of the formulas you could incur when dealing with lattice QCD (thanks to Jacob, who gave us an introductory lesson on this topic)

To sum up, until now we have the following: we have a theory (QCD) that tries to explain how matter is composed, starting from the tiniest particles. This theory is very complicated, and so we have an approach (lattice QCD) that transforms integrals paths in a very complex numerical problem. Finally, we need supercomputers to solve this very complex numerical problem.

You are probably thinking: Do you really need a supercomputer for computing interactions between tiny particles? The answer is yes: these computations are extremely difficult. How difficult, you may wonder?

First of all, lattice QCD is one of the original computational grand challenges.

“A grand challenge is a fundamental problem in science or engineering, with broad applications, whose solution would be enabled by the application of high performance computing resources that could become available in the near future”

Other grand challenges are speech recognition and computer vision, plasma dynamics for fusion, weather forecasting (if you are interested, check the Wikipedia page )

Moreover lattice QCD is so computationally expensive, that many supercomputers have been designed exclusively to solve this kind of problems. During our training week in Juelich for the PRACE Summer of HPC we had the opportunity to see QPRACE. QPRACE is a supercomputer developed for lattice QCD, and its computational cores are an enhanced version of the PlayStation 3 processor! However, many other famous supercomputers have been designed keeping in mind the challenge posed by lattice QCD: the IBM Blue Gene/L is one of those. Just to give you an idea, IBM Blue Gene/L cost 100 millions of dollars, and it took 5 years to create it. Consider that a single scientist would take 177000 years to perform the computations that Blue Gene can do in one second! Finally, QCD is such an important problem in HPC, that it has been used for years as a benchmark: if you really wanted to test your supercomputer, you had to do that on a QCD problem!

 

QPRACE, the supercomputer designed for lattice QCD. Copyright: FZ Jülich (http://www.fz-juelich.de/ias/jsc/EN/Expertise/Supercomputers/QPACE/QPACE_node.html)

QPRACE, the supercomputer designed for lattice QCD. Copyright: FZ Jülich

This is what I found out during the first days working on the project. I told you about the physical problem, and its importance in HPC. In the following posts I will talk more about the techniques we will use to tackle this important problem and I will keep you updated about my progress.

 

 

Posted on by Anurag Dogra Posted in Blogs 2015 — No Comments ↓

It was a wonderful experience in  SoHPC 2016 first week training in Fz-Juelich super computing center where I attended lectures on MPI, OpenMP, CUDA, and ParaView visualizations. And I added some new friends in my life. It was really interesting for me to meet new people from different parts of Europe  under one roof ,thanks to Summer Of HPC. We enjoyed a lot together. After Friday night fare well party it was time to say ‘sayonara’ means to say goodbye to each other and to pack our bags to fly to our respective project sites.With full of excitement and enthusiasm, I landed in Bologna (my project site) beautiful lively city, with nice people and with one super computing center named – Cineca.

Cineca, my work place having four supercomputers Pico, Galileo, Marconi and Fermi. And me and my colleague Petr got the opportunity to start our work with Pico. We started our work from reading a so called ParaView Catalyst user guide luckily it was only 66 pages book, and not so boring. While reading I got engrossed in it and I finished reading it in two days but did not understand every part of it, then luckily on Tuesday we met Paolo Lazzari who showed us some python codes for ParaView which generates some visualizations and he gave us some tasks to play with that code.Then on Wednesday we met Silvano , VTK expert and he discussed about VTK libraries and basic functions which we have to use in our project.But still I was in dilemma and thinking  how we are going to run examples using ParaView Catalyst. So it was the time to solve the mystery of ParaView Catalyst.

Discussion on Paraview Catalyst

Discussion on ParaView Catalyst Problems

On Thursday Petr and I decided to run some ParaView Catalyst examples. So I decided that I have to run the examples on Pico , the initial problem I saw was the old ParaView version, so I downloaded the new ParaView Source version on Pico and trying to install it but there was some problem with qt version while building it.I tried a lot sorting it, installed older version of qt. But still the same errors. Time was passing by and two days got over. Then after thoughtful discussion with my colleague Petr, I decided to build ParaView without qt. It worked fine. Then I started working with the examples. After loading proper modules I was able to compile and run my examples. But I was more excited to see the Visualization output on ParaView GUI, for that I have to fix the issue of connecting two different nodes – one for simulation and other for visualization. It was as usual ‘The generation gap’ problem, between the nodes  so I downloaded the new ParaView binary installer version and brought them to the same age group. In the end they got connected, but still no visualization. I was trying every possibility which was coming in my mind. It was very important for us to run a catalyst example on Pico. I discussed the problems with Luigi Calori, Silvano and Massimiliano. The problem was the simulation code was running fine on one node but it was not able to communicate with the visualization node. On Thursday Massimiliano also showed us the simulation code which I have to use in my project. One week 4 days got over , still I was not able to see the running visualization, while going home I was sad and I said to myself I have one more day to fix this. I took a deep breathe and just relax.

First InSitu visualization - ParaView Catalyst

My first InSitu visualization – ParaView Catalyst

Friday morning with fresh brain I tried again. I read again some documentations on pvserver and I got a new idea for Pico and discussed with Luigi Calori. We tried it and after doing some changes in some files. It worked, I was so happy at that moment, got motivation to work further. After lunch we met Francesca Delli Ponti, to learn some basics of Blender a new software to render images and to make videos from visualizations. I liked it.

So this was my story of solving the mystery of ParaView Catalyst and I must say “Be patient, be stubborn and stick to problem. Definitely you are gonna solve it”.

My first blender made video “Introduction to Cineca and my colleagues”.Check this out.

Posted on by Marta Cudova Posted in Participants 2016 — 2 Comments ↓

Marta CUDovA. Parallel computing is her destiny. For sure!

Marta Cudova is a 25 years old Czech girl coming from the heart of the South Moravia, a lovely city called Brno. She has just finished her master’s studies in the field of Computer and Embedded Systems at the Brno University of Technology. Her master’s thesis focused on the acceleration of algorithms for clustering tunnels in proteins. Such a computation is performed on huge multidimensional datasets and the clustering process is very computationally intensive. Now, she continues as a PhD student at the same school. She would like to specialize in High Performance Computing and parallelisation of scientific applications. This is also the reason why she decided to attend the Summer of HPC.

Marta's graduation. Debugging duck set the sail.

Marta’s graduation. Debugging duck set the sail.

However, computers are not Marta’s only hobby. Marta loves traveling, music, dancing and sports like badminton, skiing and bouldering. She has taken a great interest in motorbikes and she also owns one – a KTM Duke 390 (which is awesome). Marta usually rides a motorbike with her boyfriend and father (I guess they race and she is the best one! – I have seen her skills on gokarts).

Marta teaching how to skate.

Marta teaching how to skate.

Marta used to work as an in-line skating instructor during summer holidays for the last 6 years. She was mainly teaching small children. But now, everything changed! Marta is going to the wonderful, historical, capital city of Scotland – Edinburgh, where she will not be skating. Instead, she will be working on the problem of parallelisation scientific python applications at EPCC under Dr Neelofer Banglawala. Marta will be working with applications in the field of fluid dynamics computation, especially. That is wonderful! Visiting Great Britain and staying there for some time has always been Marta’s big dream. Thus, she is very very proud and happy to stay in such a lovely country for two whole months. She also hopes she becomes a Python Ninja after finishing the SoHPC (although she is a Python Ninja already in my opinion).

Now, Marta enjoyed a great week in Juelich where she met a lot of interesting people and made a lot of new friends. Marta is a little bit sad because she has to go to Edinburgh and leave such a great group of people. But she’s looking forward to meeting new people and she also hopes she will meet her new friends in future.

Marta's first flight in this pretty nice and very old war airplane.

Marta’s first flight in this pretty nice and very old war airplane.

Posted on by Juan Eiros Zamora Posted in Blogs 2015 — 4 Comments ↓
Entrance to the Biomedical Research Foundation Academy of Athens. From left to right: Dr. Zoe Cournia, Juan Eiros and Samanta Makurat.

Entrance to the Biomedical Research Foundation Academy of Athens. From left to right: Dr. Zoe Cournia, Juan Eiros and Samanta Makurat.

When we got invited to SoHPC, both of us were very excited. Samanta was sitting with friends in a bar when she received an e-mail and celebrated it immediately. Juan had just woken up (cultural differences, am I right?) but he surely was equally excited. As time passed, probably all of us started to be anxious, not only of leaving home for two months, but also of people that one would have to spend time with. Super-smart guys that would look into their laptops all day, not really trying to socialize – isn’t that what you think of computer scientists at first? It got even worse after reading the agenda of SoHPC training week – the thought of 10 hours/day by the computer, doing things far exceeding the skills of a computational chemist was a recipe for disaster.

 

The training week  was serious and exhilarating at the same time.

Gyros. Adding fries inside a kebab is an idea worthy of the Olympian Gods.

Gyros. Adding fries inside a kebab is an idea worthy of the Olympian Gods.

We met lots of interesting characters, and had a wonderful time during the evenings (shout out to Ross Lynch and his awesome Irish pub). All good things come to an end, it was really hard to say goodbye, and from this place we should thank not only SoHPC students, but mostly: the organizers for taking great care of us. Coffee in the mornings was highly sought-after and received with gratitude, and evening activities such as go-karting triggered lifelong rivalries amoungst some of the participants.

Interface of Maestro. Our companion for the next two months. A ligand is shown as sticks bound to a protein, whose molecular surface is coloured according to its electrostatic potential.

Interface of Maestro. A ligand is shown as sticks docked to a protein, whose molecular surface is coloured according to its electrostatic potential.

For almost a week now we’re in our placement destination – the Biomedical Research Foundation of the Academy of Athens (BRFAA). So far so good, although it was not an easy start. Suffocating heat and no AC in our rooms was the first thing to welcome us in Greece. Juan, living alone in a quiet street far from any life in the city, and Samanta – sharing a flat with 8 other people. Enthralling isn’t it?

Bossa nova in Megaro Moussikis. From left to rigt: Juan Eiros, Samanta Makurat, Dr. Zoe Cournia and Dr. Ioannis Liabotis.

Bossa nova in Megaro Moussikis. From left to rigt: Juan Eiros, Samanta Makurat, Dr. Zoe Cournia and Dr. Ioannis Liabotis.

Buses take you anywhere and at night taxis are cheap. Our first day welcomed us with mouth-watering Greek food and friendly people everywhere. To relieve some stress before meeting our supervisor on Monday we enjoyed the EuroCup final with Greek beer in the evening.

 

BRFAA looks as serious as it sounds and is tricky to reach on foot. Not a very encouraging start – we got lost and we were late for meeting with our supervisor – Dr. Zoe Cournia the first day. After a short introduction we started our training week in Greece. Not to bore you with the details: Maestro with Desmond, Glide and LigPrep tutorials were planned just for the first two days. Remaining 3: ChemBioServer, FEP Mapper and NAMD with VMD. Sounds like lots of work? Good. It was. Still, we enjoy sitting in our office: mostly because of air-condition, very good atmosphere, and the lab members. Apart from all these software, Samanta has also learnt to enjoy coffee (Juan was already pro), because Greeks not only know how to work, but also how to enjoy their evenings – like on Thursday, when we went to Brazilian concert together with Zoe and Ioannis from GRNET. But social life here is probably a topic for another blog post. This week we’re finishing our tutorials and next week: hands on real work, and as soon as our calculations are ready to start: GRNET and even more PRACE with Ioannis Liabotis.

Our office. Equiped with the best AC unit in all Athens.

Our office. Equiped with the best AC unit in all Athens.

 

 

Posted on by Marco Forte Posted in Participants 2016 — 1 Comment ↓
Thomas in traditional maesters attire, complete with magical staff

Thomas in traditional maesters attire, complete with magical staff

Thomas of House Wright, was born in the frigid north, outside the capital Winterfell, near enough as makes no matter. An ambitious youth, he had known from an early age that he would take up the pursuit of knowledge. When he reached manhood at age ‘eight and ten’ he gave a sacred vow to become a maester of the Citadel. His intellect was soon recognized and he swiftly rose above his peers and mastered the study of arithmetic, both theoretical and magical. As part of his studies he had a year long excursion to a guild of arcane arts where he developed for the weirwood.net. He successfully forged his lead and silicon links this year.

Events took a turn for the worse for Thomas thanks to the action by the Norths declaration of independence from the union kingdoms of Europos. This left him with an ultimate not to be missed opportunity to further his study in the rest of Europos before full blown secession. The prospect of travelling and meeting other people in his field wholly appealed to him. The impeccable honor of his house compelled him to attempt to diplomatically ease relations between the north and the rest of the 28 Kingdoms. After consulting a weirwood, it was clear to him, the SOHPC program was the ‘program that was promised’.

Thomas traveled south across The Neck to the quiet town of Juelich. A town, appearing peaceful but in truth it’s trees conceal a center of supreme magical power. Here he participated in a week long meeting of maesters as part of SOHPC, much and more was learnt of High performance magic. Thomas will use this experience when he travels across the narrow sea to Irlandos, the most beautiful country in the world, it is known. Here he will work on the visualization of fluid and waves through high performance magical(HPM) means, with a local order of maesters who specialize in HPM. This project will be an opportunity to put his theoretical work into practice and experience it first hand. This will be of particular importance when he will return to the north to castle black and study to become an Arch Maester in theoretical models of concurrency.

End

This post was written in honor of great conversations with real life Thomas about George R.R Martins “A song of Ice and Fire” series. Thomas is an excellent fellow and will no doubt make an excellent SoHPC student, in addition he is very well equipped to start his PhD in September. For some trivia, his favorite Roman emperor is Constantine because of the work he did restoring the empire to greatness, though Thomas casually ignores Constantine’s execution of his own son.

His project – https://summerofhpc.prace-ri.eu/visualisation-of-fluids-and-waves/

The north – UK, Winterfell – London, magic – computers, Citadel – York,
Maester – Undergraduate, studied – mathematics and computer science
weirwood.net – worked on websites, Norths independance – brexit
The neck – brittish channel, castle black – Edinburgh, Arch Maester – PhD

Awkwardly angled photo at Cologne Cathedral to exclude 'intimate' couple on other side of fountain.

Awkwardly angled photo at Cologne cathedral to exclude ‘intimate’ couple on other side of fountain.

Posted on by Thomas Wright Posted in Participants 2016 — No Comments ↓
Marco's grand day out (Cologne)

Marco spreading parallelism in Cologne

Each year aspiring young programmers, engineers, and scientists from throughout the fabled land of Europe set out on a noble quest to tour the furthest reaches of the realm, seeking to master the arcane art of parallelism, and spread the honour of High Performance Computing, in a grand spectacle known only as the Summer of HPC. Most noble among these is Marco Forte, a maths student from Dublin on an incredible journey through Europe, passing first through the deepest forests of Juelich, Germany, and then on to the sunny coasts of Barcelona, Spain where he will dine with the valiant knights whom reside there, and bring parallelism to their Python applications.

In the days before his quest began, Marco did his undergraduate studies in mathematics at University College Dublin, however at the end of his degree he decided to move towards computation, and so apply for the Summer of HPC, followed by a PhD in Trinity College Dublin in signal processing at the end of the summer. His interest in computing had however already began to develop even before he started his degree when taught himself C# using online tutorials.

Like all true knights, his favourite language is Python, the most versatile and intuitive of companions. He also argues that there is a lot to be gained from making it easier to use Python in scientific applications, as whilst it may not be able to compete with lower level languages such as C and Fortran on raw performance, it greatly lowers the barrier of entry, and promises to make HPC accessible to a greater variety of scientists as well as trained programmers. In his project he will be working on developing and example of a parallel application using PyCOMPS, a library for parallelizing Python code. This aims to make it easier to modify existing scientific applications to take advantage of parallelism when they need to scale to larger datasets.

Not only does Marco have fine taste in programming languages, he is a connoisseur of history, holding a keen interest in the Romans. He is a big fan of the History of Rome podcast, and never misses a chance to visit the local Roman sites (including in Cologne where he visited the Roman arch and history museum).

Adventurer profile:
Name: Marco Forte
Project: https://summerofhpc.prace-ri.eu/development-of-sample-application-in-pycompsscompss/
University: Trinity College Dublin
Favourite language: Python
Favourite PEP: PEP311
Favourite Roman emperor: Hadrian

Posted on by Sofia Kypraiou Posted in Blogs 2015, Participants 2016 — No Comments ↓

10294991_10202414056406815_7700303017260128835_oAnna Gradou is a young student from Athens, Greece. She is 23 years old and she is currently finishing her undergraduate studies at the Department of Informatics and Telecommunications of the University of Athens. She is doing her thesis which is related to the CHESS project, an effort towards achieving personalized storytelling for museum visits. She will be working on an extension related to digital applications for personalized information according to a user profile extracted by a the facebook account of the visitor.

During her studies she was interested in system analysis, design and development of user interfaces to improve user experience. Last year she attended a university class of Parallel Systems. She founded it really challenging and she was fascinated by the computational techniques of parallelism . That’s why her Summer of HPC experience will be continued to Edinburgh, working on a distributed application on the project of “Smartphone Task Farm” , at the Edinburgh Parallel Computing Centre (EPCC) at the University of Edinburgh. This can be an opportunity to combine these two fields. She will work on graphics development and visualization using 3D features as well as beta-testing techniques Task Farmques. She is looking forward to this internship and she is sure that she will gain a lot of knowledge.

Anna loves traveling and the mobility programs, like PRACE are a very good opportunity to combine knowledge with traveling. She did her Erasmus in Paris in 2014 and fell in love with the city and its people. Anna is interested in cinema. She has been a member of the Cinema Club of the University of Athens since 2012, and has taken part in short independent movies as a production assistant and video editor.

 

 

Posted on by Johannes Pekkilä Posted in Participants 2016 — No Comments ↓

indexMateusz Lango is an ambitious PhD student from the Institute of Computing Science in Poznan University of Technology in Poland. In the PRACE Summer of HPC programme, he will be investigating how link prediction algorithms can benefit from being solved in parallel on state-of-the-art computers and software.

These algorithms are used to predict the appearance of connections in, say, social networks or scientific literature. In the era of big data, where potentially groundbreaking discoveries could be lost in the stream of mediocrity, Mateusz’s work on link prediction could help researchers to find more relevant articles to their research, which consequently could lead to new discoveries.

After the training week in Germany, Mateusz will be heading to the capital of Slovenia, Ljubjlana, where he will spend a pleasant vacation (i.e. working hard, reading a big proportion of scientific papers and writing programs until his fingers catch fire). The forecast for the weather in Slovenia is very warm, but so are his feelings towards this project.

When Mateusz is not working, he enjoys learning about Mexican culture and watching movies (and he actually uses his computer in Spanish!). In addition, he’s an avid cyclist and recently took up climbing.

Posted on by Ambra Abdullahi Hassan Posted in Participants 2016 — No Comments ↓

Peter Labus is a 29 years old PhD student at the International School of Advanced Studies in Trieste, a harbor city located in the north-east of the wonderful country of Italy.

Peter Labus, one of the partecipant at the PRACE Summer of HPC

Peter Labus, one of the partecipants at the PRACE Summer of HPC

While completing his PhD in Theoretical Physics he is attending a Master’s program in High Performance Computing (Although at times exhausting it is very rewarding, he says).

He is working on Elementary Particle Physics and Gravity and he is using powerful numerical methods to efficiently tackle some of the most challenging problems in this field.

During the PRACE Summer of HPC he wants to focus on the practical aspects of writing optimized parallel codes for supercomputers. He will spend two months at the Julich Supercomputing Center in Germany to work on lattice Quantum Chromo Dynamics. This is a discretized version of the theory of elemental particles that form the nuclei of atoms. Lattice QCD is one of the most computationally expensive areas in High Performance Computing, requiring enormous resources and even specially designed supercomputers (this is not bad for such tiny particles, isn’t it?). If you are not familiar with quantum field theory, you probably just need to know that these kind of simulations are used to study how matter interacts and it provides information on the phase of matter few millisecond after the Big Bang (to know more about Peter’s project, see https://summerofhpc.prace-ri.eu/phine-quarks-and-cude-gluons/).

Peter is excited about starting this experience and looks forward to join Julich Supercomputing Center’s research group (There he will meet researchers using simulations to gain deeper understanding on a wide range of phenomenons) .  We are sure he will do a great job!

But in Peter’s life there is room for other hobbies other than physics and supercomputing: he likes playing the Viola, boxing, rock climbing, yoga, meditation and singing under the shower (mostly opera singing). He does not have time to be bored, I suppose!

Posted on by Anna Gradou Posted in Participants 2016 — No Comments ↓

sofia_kypraiouSophia Kypraiou is a young student from Greece. She is an undergraduate student at the Department of Informatics and Telecommunications of the University of Athens and she will graduate during September. She is currently finishing her thesis on “Temporal Recommendation on Graphs via Long-and Short-term Preference Fusion” under the supervision of the professor Yannis Ioannidis. She would like to continue her studies doing her Master (after she takes a year off traveling and gaining more practical experience concerning her science). She would like to focus her further studies on Data Mining and Analysis, Big Data and Machine Learning.

She is a hard worker who enjoys learning new technologies. During the Prace Summer of HPC program she will be working in Barcelona on a visualization project. She will be doing the visualization data pipeline in PyCOMPs/COMPSs. She is excited to work at the impressive supercomputer center of Spain – MareNostrum and looking forward to gain as much knowledge as she can during these two months. She is excited to have this opportunity to work on parallel applications using the high technology provided by the Supercomputer Center and she plans to take advantage of this internship to gain more knowledge than a university class could provide. Real life advanced programming stuff!

She likes traveling and especially trips to the countryside because she is a real nature lover. In her free time she goes hiking and she plays the piano. She is a Free/Open Source Software supporter. Lately she participated at the Nasa Space Apps Challenge with the project “Climate Watch”. The team made it to the top 25 People’s Choice Semi-Finalist! She always wanted to travel to Spain so PRACE was the best choice to finish her Bachelor studies. She is looking forward to eating paella and improving her Spanish!

Posted on by Shaun Lahert Posted in Participants 2016 — No Comments ↓
Outside the Cyprus Institute

Outside the Cyprus Institute

Shaun Lahert is a recent graduate of Theoretical Physics from Trinity College Dublin. He is spending this summer at the Cyprus Institute on PRACE’s Summer of HPC. Shaun will be working on Lattice QCD, in particular he will be examining the topological susceptibility of the QCD vacuum by direct calculation of low-lying eigenmodes. This work will involve simulations on Europe’s largest supercomputer Piz Daint, based in Switzerland.

Shaun’s interest in High Performance Computing stems from his undergraduate degree where he completed multiple projects of mathematical modeling and computational simulation. As HPC lies at the forefront of these two topics he was thrilled to be accepted to the program to further develop his programming skills. Shaun heard about PRACE through his computational physics professor as well as other students who had participated in the program previously and recommended it. Following the internship Shaun hopes to begin a PhD in computational physics, however he is currently undecided on the topic and will decide after the program is over.

Posted on by Gozde Sarıkaya Posted in Participants 2016 — No Comments ↓

biograpghy photo

Her name is Katerina Galata. She 21 years old and comes from Athens, Greece. She is an undergraduate chemical engineer in the National Technical University of Athens. At the moment, she is doing her diploma in particle simulations in order to study the thermodynamic properties of mixtures, under the supervision of Professor Doros Theodorou.

Her interest in MD simulations led her to apply to the Summer of HPC 2016. She got accepted to the project which takes place in Bratislava, in the Slovac Academy of Sciences, through which she is going to use math and MPI programming through the simulations, and that is the reason why she is really excited about it.

Her project is about calculations of nanotubes by utilizing the helical symmetry properties. The aim is to implement MPI parallelization to enable high accurate calculations for the band structures of nanotubes. Currently a new unique code is developed for fully ab initio calculations of nanotubes that explicitly uses the helical symmetry properties. So there are a lot of things to try out during the project in order to get the best result. She is really looking forward to this project since this is a good chance to help science and industry optimize the materials in which nanotubes are used. This would be a great benefit even for the everyday life, since the quality of products will get better at the same price. She really hopes that the outcome of this project would actually even help some other scientists as far as it concerns their experimental researches.

Besides studying to the university, she is pursuing a diploma in piano. She can speak English, German and French. In the meantime, she is responsible for the site of Chemecon, as a member of their IT team. Chemecon is an organization of chemical engineering students who try to make the students of the university get familiar to the industry and understand what a chemical engineer does on a daily routine. She is also the founder of another volunteering organization of students, which we call CodeG. Through that they try to teach more and more women to code.

The summer of HPC is going to be a great opportunity to learn new things and cooperate with amazing people. So she thanks PRACE for that.

Facebook
Twitter
Follow by Email