Introducing LBDream and Literature-based discovery

lbdream

In my last blog post, I described general MapReduce paradigm which allows us to create big data processing systems in a fairly simple way. In this blog post, I will describe more in detail what I’m doing in my project, 

Bratislava: Chapter 2 out of 3

Nanotube by the simulation

How to MPI So… In order to face the segmentation fault, Katerina performed changes in the allocations .. But not only in the makefiles, but into the input files too.. And that defeated the segmenation fault. But now she should

How to Blender: Supercomputer Edition

blender kmeans flooded

Welcome everyone. Today I will walk you step by step through how I use Blender in this project. This post will contain many pictures, as the content is pretty graphic, but they have been slightly modified for simplicity and to keep the focus on

Assingnare Locus

AsignareLocus

Assignare Locus, the computer scientists equivalent of Expecto Patronum. This is the final blog in the trilogy, I am going to summarise the rest of the exciting experience I had in Slovenia along with a full description of the final

Greece. A place to be.

Random View in Greece. Get used to it, because it's that beautiful everywhere here.

Choosing Greece and BRFAA, Zoe Cournia lab, for my PRACE Summer of HPC destination was probably one of the best decisions of my life. To be honest, the project was pretty difficult sometimes and I had a few days of

Introduction to ParaView Catalyst

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

In my previous article you can find a brief introduction to the In Situ Visualization Technique which allows to explore simulation data during the run-time without involving storage resources of a supercomputer. Now it’s time to go a little bit further

Reaching the shore

A celtic cross - a typically shaped cross with a circle, combining christian and celtic culture

It’s the 2nd of September now, and I am back in the Czech Republic again. I left Dublin 2 days ago, after finishing the work on my Summer of HPC project in ICHEC. So, let’s have a look back now

From an edge to the whole picture

Hi there! It’s almost the end of summer holidays and the summer of HPC, and I still haven’t made to tell you everything about what I’m working on. I was done with the CFD exercise so I started with a new one

Better Jota that down, are you sure thats Ricet.

FullBarrier

I feel like the second book in a trilogy is always the best, so fingers crossed this will be the best blog. After the first week in Ljubljana, my supervisor let me loose. This meant all the hard work and

A short tour of lattice QCD

QCD Lagrangian

As my first blog was completely non technical I am now contractually obliged by the powers that be to talk about some technical stuff of what I am actually doing. I decided I would have a go at explaining what lattice

Dare to visualize – Tornado effect

2

Sometimes in life we have to accept dares, challenges or we even have to make self commitments to achieve success. By the way, this is human nature, after reaching one milestone we look to the next, and according to me:

A Matryoshka linear solver

Matrioska multigrid method

As I described in my previous posts, solving a linear system in a lattice QCD applications can be a very long process. We really want to optimize this linear solver, so we can find some answers about matter in our

Two applications for two techniques

Marta_final

Having already introduced you to the technique that will be used for my project in one of my previous posts let me share with you some more things about the application. The application will be used at outreach events and

Sophie’s World, Chapter 2: The project

David Bowie

In case you have cheched out this video, you might be wondering what this project is all about. In case you haven’t, I will wait for you 3:33 minutes to see it and return 🙂 Ok, now a little background

Has the rain stopped yet?

rain

Indeed, as the summer comes to an end I realize I had a lot of rain – both here in Scotland and on my computer screen. My project was to develop a weather visualisation application which will be used at

The secret of Big Data programmers

big-data

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

IMG_20160728_155420

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

20160814_193512 (copy)

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!

bitmoji-20160811021730

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

14375129967_ac4cbc22e2_z

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

screenshotfeaturevis

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

WhatsApp-Image-20160704

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

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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