Modelling & simulation
Posted: 7 Aug 2018 | 10:28
Dr Martin Lepšík came on an HPC-Europa3 visit from 16-29 July and was hosted by Dr Emanuele Paci at the University of Leeds. Martin started his visit by coming to Edinburgh.
My name is Martin Lepšík, and I am a Czech computational structural biologist. After 11 years of fruitful research in quantum mechanics-based drug design (at P. Hobza’s group at IOCB, Prague, CR), I decided to enrich my expertise with enhanced-sampling molecular dynamics of lectin-carbohydrate complexes, important for human health and disease.
Posted: 4 Jul 2018 | 10:22
Arnau Miró was an HPC-Europa visitor from 10th Jan–9th Apr 2018. He was hosted by Dr Charles Moulinec at STFC Daresbury Laboratory.
Hello everyone! My name is Arnau Miró and I am a third-year PhD student from Universitat Politècnica de Catalunya. I’m working in the Aerospace department in collaboration with the Barcelona Supercomputing Center Computer Applications in Science and Engineering department. I visited EPCC under the HPC-Europa3 transnational access programme, although I was mainly hosted by Dr Charles Moulinec at STFC Daresbury Laboratory.
Posted: 12 Apr 2018 | 12:22
Dr Domenica Capasso was our first HPC-Europa3 visitor at EPCC but was hosted remotely at UCL from Nov 2017 to Dec 2017. She relates her experiences and research in this blog article.
I recently spent a month in London funded by the HPC-Europa3 programme and hosted by Prof. Francesco Luigi Gervasio at the Department of Chemistry at UCL. This was an exciting experience for me, primarily for my research work but it also provided me with an opportunity to visit London, a city I had never been to before. I arrived in London with interesting biological results on some potential inhibitors of the galectins class of proteins, which had been synthesized at my Institute in Naples. Galectins (Gal) are β-D-galactoside binding proteins that have important implications for many diseases including tumourigenesis, inflammatory response and autoimmune disorders. The general aim of this work is to rationally design novel inhibitors of galectins that could be used as anti-cancer and anti-inflammatory therapies.
Posted: 11 Apr 2018 | 10:49
Miriam Ruiz Ferrández was a recent HPC-Europa3 visitor to Edinburgh who used EPCC resources while being hosted by Napier University. In this article she relates some of her findings and experiences.
Hi everyone! I am a PhD student at the University of Almería, which is located in the south-east of Spain. I spent three months in Edinburgh funded by the HPC-Europa3 programme working on a project entitled: “A Parallel Multi-Objective Algorithm for Optimizing High-Pressure/Temperature Treatments in the Food Industry”. During this research stay, I was collaborating with Professor Ben Paechter at Edinburgh Napier University and I used computing resources provided by EPCC at the University of Edinburgh.
Posted: 21 Apr 2017 | 11:55
Last Thursday marked the opening of the FEAT project (Future Emerging Art and Technology) exhibition in Dundee’s LifeSpace art research gallery. The FEAT project is a pilot that focuses on the synergy between art and science, and how art can bring benefits to the scientific process. EPCC is involved through the INTERTWinE project.
For the past 12 months the artists Špela and Miha have been working with us on a piece related to supercomputing. They have spent time at a number of European supercomputing centres and additional FEAT workshops, such as the one in Vienna last summer that I attended and discussed in a previous blog article.
Posted: 12 Apr 2017 | 16:14
The Next Generation Sound Synthesis project (NESS) has concluded its five-year journey. With true inter-disciplinary focus, genuine user-engagement and over 75 publications overall, the project has been a great success for the University of Edinburgh, and for EPCC in particular.
Posted: 11 Apr 2017 | 17:59
Shall I compare thee...
Performance comparisons are always tricky to get exactly right. They are needed to ensure that we can demonstrate the performance improvements that optimisations, new hardware, new algorithms, etc... have had on an application or benchmark, but there is a lot of latitude in what can be compared, which makes it easy to get a performance comparison wrong and not properly demonstrate whatever it is you're trying to show.
Posted: 10 Apr 2017 | 16:06
Guest blogger Kara Moraw is an undergraduate Informatics student in Bonn, Germany. Here she writes about her 4-week internship with EPCC, spent working with EPCC's Nick Brown on the ARCHER outreach project.
Posted: 2 Feb 2017 | 11:37
Fluidity for tidal modelling
Figure 1: Mesh for the Sound of Islay tidal simulation. Courtesy Dr Creech.
We were recently involved in a project to optimise the CFD modelling package Fluidity for tidal modelling. This ARCHER eCSE project was primarily carried out by Dr Angus Creech from the Institute of Energy Systems in Edinburgh.
Posted: 29 Nov 2016 | 10:07
TensorFlow is an incredibly powerful new framework for deep learning. The “MNIST For ML Beginners” and “Deep MNIST for Experts” TensorFlow tutorials give an excellent introduction to the framework. This article acts as a follow-on tutorial which addresses the following issues:
- The above tutorials use the MNIST dataset of hand written numbers, which pre-exists in TensorFlow TFRecord format and is loaded automatically. This can be a bit mysterious if you have no experience of data format manipulation in TensorFlow.
- Since the MNIST dataset is fixed, there is little scope for experimentation through adjusting the images and network to get a feel for how to deal with particular aspects of real data.