October 2019

Online LAMMPS training for ARCHER

Author: Julien Sindt
Posted: 31 Oct 2019 | 15:56

In October I ran an online training course teaching current and potential ARCHER users how to run LAMMPS. LAMMPS is a widely-used open-source molecular dynamics (MD) software developed at the National Sandia Laboratories, and is optimised to run well on HPC facilities. It consistently ranks in the top 10 most used programs on ARCHER. Although the course was run on ARCHER and with ARCHER users in mind, I tried to teach users how to use LAMMPS on any platform.

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.

Fun and Games in Historic Melrose

Author: Lorna Smith
Posted: 23 Oct 2019 | 14:48

Set in the heart of the Scottish Borders and home to Melrose Abbey and Melrose RFC, a visit to Melrose is always a pleasure. Organised by St Mary's School, Bang Goes the Borders (21st September 2019) is a science festival aimed at families. Entirely free, the festival has loads of workshops and drop in sessions.  The ARCHER team and Wee Archie​ were sat alongside workshops and activities around lego robots, apple juice making, plaque busting, bees, birds, and much, much more.

Mining digital historical textual data

Author: Rosa Filgueira
Posted: 23 Oct 2019 | 10:43

Over the last three decades the collections of libraries, archives and museums have been transformed by large-scale digitisation. The volume and quality of available digitised text now makes searching and linking these data feasible, where previous attempts were restricted due to limited data availability, quality, and lack of shared infrastructures. One example of this is the extensive digital collection offered by the National Library of Scotland (NLS) (see Figure 1) [1], which can be accessed online and also downloaded for further digital humanities research.

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.

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