HPC research

NEXTGenIO: the end is just the beginning

Author: Michele Weiland
Posted: 7 Nov 2019 | 14:55

After four years of hard work, the NEXTGenIO project has now come to an end. It has been an extremely enjoyable and successful collaboration with a dedicated group of HPC users, software and tools developers, and hardware providers from across Europe.

Precision persistent programming

Author: Adrian Jackson
Posted: 30 Oct 2019 | 12:48

Targeted Performance

Optane DIMM

Blog post updated 8th November 2019 to add Figure 6 highlighting PMDK vs fsdax performance for a range of node counts.

Following on from the recent blog post on our initial performance experiences when using byte-addressable persistent memory (B-APM) in the form of Intel's Optane DCPMM memory modules for data storage and access within compute nodes, we have been exploring performance and programming such memory beyond simple filesystem functionality.

For our previous performance results we used what is known as a fsdax (Filesystem Direct Access) filesystem, which enables bypassing the operating system (O/S) page cache and associated extra memory copies for I/O operations. We were using an ext4 filesystem on fsdax, although ext2 and xfs filesystems are also supported.

Exploring the binding mechanism of glycomimetics to galectins through simulations

Author: Guest blogger
Posted: 21 Oct 2019 | 11:13

Domenica Capasso was an HPC-Europa visitor to University College London from 12 June to 11 August 2019. In this blog article she describes her work and time in London.

In June this year, I returned to London and I spent two months at the Department of Chemistry at UCL, funded by HPC-Europa and hosted by Professor Francesco Luigi Gervasio. My project concerns the galectins, β-D-galactoside binding proteins with important implications for tumorigenesis, inflammatory response and autoimmune disorders. During my first visit, we created a virtual library of candidate compounds, containing two saccharide residues with a bridging sulphur/selenium atom. These derivatives, targeting galectins, were obtained using structure-based drug design approaches and are synthesised and tested in my Institute in Naples.

Global or local - which is best?

Author: Adrian Jackson
Posted: 9 Oct 2019 | 17:30

Selfish performance

Sharing of resources has challenges for the performance and scaling of large parallel applications. In the NEXTGenIO project we have been focusing specifically on I/O and data management/storage costs, working from the realisation that current filesystems will struggle to efficiently load and store data from millions of processes or tasks all requesting different data sets or bits of information.

Optimizing CPU oversubscribed reductions

Author: Guest blogger
Posted: 6 Sep 2019 | 11:17

Gladys Utrera was an HPC Europa3 visitor to EPCC from 1st of July to the 3rd of August 2019. She has been an HPC Europa visitor before - in this brief blog article she tells us what she did this time.

Hi! My name is Gladys Utrera and I currently work at the Computer Architecture Department of the Universitat Politècnica de Catalunya in Barcelona, Spain. There I combine teaching of parallel computing and operating systems subjects with research on HPC topics and parallel programming models. Thanks to the HPC-Europa3 programme I could spend four weeks at the EPCC in the University of Edinburgh with my host Mark Bull who is a very well-known expert in my research areas. This is my third research visit to EPCC, and the second as an HPC-Europa visitor. 

My research involves executions on large multi-core node clusters. In addition, performance evaluations on machines with different architectures characteristics like ARCHER and Cirrus, enrich my results greatly. 

Benchmarking MPI implementations on ARM

Author: Nick Brown
Posted: 30 Aug 2019 | 11:32

The recent installation of Fulhame, the ARM HPC machine based here in EPCC as part of the Catalyst UK programme, raises plenty of interesting opportunities for exploring the HPC software ecosystem for ARM. One such aspect is the relative performance of different MPI implementations on these machines and this is what I was talking about last week at the MVAPICH User Group (MUG) workshop.

My HPC-Europa visit to Cambridge

Author: Guest blogger
Posted: 29 Jul 2019 | 16:27

Hi! My name is Concetta Cozza. I am a PhD student in Life Science at University ‘Magna Graecia’ of Catanzaro. This summer I visited the research group of Professor Michele Vendruscolo based at the University of Cambridge for three months with the HPC-Europa3 transnational access programme.

PRACE Summer of HPC 2019

Author: Mario Antonioletti
Posted: 29 Jul 2019 | 14:55

PRACE Summer of HPC (SoHPC) offers summer placements at HPC centres across Europe to late-stage undergraduates and/or Masters students. Up to twenty top applicants from across Europe spend two months working on projects related to PRACE technical or industrial work. Here are the three SoHPC visitors who are collaborating on projects with EPCC staff. 

Evaluation of a phase diagram with a novel technique in an HPC-Europa3 funded collaboration

Author: Guest blogger
Posted: 19 Jul 2019 | 09:22

György Hantal was an HPC-Europa3 visitor from 18th March to 17th May 2019.

I am György Hantal (pictured here with Durham castle in the background), a postdoctoral researcher from the University of Vienna. I was an HPC-Europa3 visitor for two months, hosted by Dr. Lívia Bartók-Pártay at the University of Reading's Department of Chemistry and supported by EPCC in Edinburgh.

Preparing programming models for Exascale

Author: Daniel Holmes
Posted: 18 Jun 2019 | 15:03

To make future heterogeneous systems easier to use efficiently, the EPiGRAM-HS project is improving and extending existing programming models with Exascale potential. We are working with the MPI and GASPI programming models primarily, but also applying our changes to HPC applications like Nek5000, OpenIFS and iPIC3D, and AI frameworks like TensorFlow and Caffe. We expect the trend towards specialisation of hardware will continue and therefore large machines will become more and more heterogeneous.