The secret of Big Data programmers

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In my last blog post, I described the problem of linkage prediction in large-scale graphs. I also mentioned that this is a big data processing problem. Today I will present you one of the biggest secrets of big data programmers:

Researching the center of Europe

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After the amazing training week in Juelich Supercomputing Centre where we had a brief introduction to OpenMP, MPI, ParaView, CUDA and some Team Building, it was time to start with the real business. I got into a plane headed to the heart of

What’s in a virtual screening dataset?

In my previous blogpost, I explained the main objectives of my project. During these weeks, I have focused towards the data analysis side of HPC rather than working on optimizing a program that runs on a super computer. I have been working to

Shallow waters – the waves start to spread

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I started the work on my project by exploring the provided simulation code. This is always a great adventure by its own, studying a code someone else has written before you. To those who never tried it, you definitely should.

Why is high performance computing so good for image analysis?

Matches from my castle features detector. Work in progress...

My Summer of HPC project  was officially titled “Development of  a sample application in PyCOMPSs”. As you can probably tell it’s a pretty vague title, and I was given a lot of freedom to come up with my own project,

This is happening!

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According to a plan, last week I’ve finally started my first proper simulation. That means, that upcoming one will finally be more chilled (hopefully). I transferred the files from Maestro to Gromacs, solvated, added ions, minimized, equilibrated (see tutorial, but

Bringing visualisation to the web with Python and Bokeh

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These days the world seems to run on data; from Google, to the NSA/GCHQ, to CERN, everyone seems to want more data, and be willing to go to great lengths to get it. However, once we have all of this

Finding the fireball

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A legend says that there was once a warm sunny day in Scotland. I have started my quest to find out if the myth was true, but I was not the only one. A group of scientists from the UK

Python, MPI, CFD and ARCHER – what is a bigger challenge?

Fast prototyping

Hi Guys! In this blog post, I would like to introduce you my project “Parallelising Scientific Python Applications” which I’m working on at EPCC under Dr. Neelofer Banglawala. Wait! Sit down, don’t worry and get a cup of excellent British tea.

From a Desolate Düren Platform to Spark in Slovakia

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Its been one hell of a first couple of weeks here despite the worrying last leg of the trip to Juelich. Everything was smooth sailing until Düren train where the train to Juelich was leaving from an apparently non-existent platform

The need for speed

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Imagine for a second the following: You are given access to one of the fastest supercomputers on Earth, if not the Universe! You are given a desk in an institute in the middle of pretty much nowhere, you are granted

Sophie’s World, Chapter 1

Sagrada Familia

Time flies. We are already in the middle of the PRACE Summer Of HPC Computing programme and it seems like yesterday when we first arrived for the training week in Germany. So here is a quick recap of our full

If not task farming then what?

SPMD

When I decided to apply for the EPCC project of the Summer of HPC I knew that my project will be related to some outreach events and it will have educational purposes too.  It has to display how parallelism works

Bratislava: Chapter 1 out of 3

Point Zero

Point Zero Once upon a time there was a little girl. Her name was Katerina. Katerina was a great warrior. Until one day she came across with a great challenge:  PRACE Summer of HPC. ‘I have to try it’, she

Recipes for HPC success in Dublin

Scrambled eggs

This year, with my undergraduate degree (in Mathematics and Computer Science at the University of York in the UK) drawing to a close, I decided to deviate from my normal summer schedule of maths books and computer games to take

Familiarizing with Edinburgh

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A bit of history at the beginning. Once upon a time in the town of Edinburgh, Scotland – it was a cloudy summer day, not very cold but also not very warm. Just a typical Scottish day (if you know

Two L’s and two J’s

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Juelich, Germany: I’d like to begin with a little description of the introduction week in Germany, Juelich. Arriving on the Sunday, I was greeted by my roommate and a fabulous cup of English Tea with milk. As the famous saying

Selecting the true magical bullets

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In the early 20th century, Paul Ehrlich laid the intelectual foundation of modern drug-design research through his inspirational concept of ‘magical bullets’. These ‘bullets’ are small chemical compounds with the ability to bind to biological targets, such as proteins or nucleic acids,

Linear solvers are behind lattice QCD

Here it is how it looks likes the matrix representing a linear system in theoretical physics. Fascinating, isn't it?  ( The matrix and the image are taken by http://www.cise.ufl.edu/research/sparse/matrices/)

In my first post I told you about the wonders of lattice QCD, and I explained why we need supercomputing to actually solve problems involving very small particles. I told you about huge machines that can do in one second

Ljubljana’s real problem

The most important problem of the modern world as a graph

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,

Scotland for the summer, seriously?

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  “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

In Situ Visualization Technique

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

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

How to prepare MD simulation? Halfway in Athens.

My enzyme is ready for further steps!

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

Summer in the North

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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

Python Public Service Announcement: Virtual environments

Snake oil - Python get it?...

Possibly fictitious excerpt from the Python Conference announcement of 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”

Timeline

Programme & Application open date announced - 04 January 2016
Call for Applications - 11 January 2016
Call for Applications closes - 19 February 2016
Reference receipt deadline - 21 February 2016
Selection Panel Meeting 18-19 April 2016
Student Offers - 25 April 2016
Student acceptance deadline - 02 May 2016
Training Week - 30 June 2016 - 04 July 2016
Week 3 Plan submitted - 21 July 2016
Final Report submitted - 25 August 2016
Presentations - 29 August 2016
Awards Ceremony - planned for October 2016

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