Folding@Home HPC for COVID-19

March 2020, news was spreading of a rapidly evolving pandemic with potentially deadly concequences and societies were struggling to slow the tide. Less than a week before working remotely was made mandatory, in an effort to reduce human contact nationwide, I saw the news Folding@home update on SARS-CoV-2 (10 Mar 2020) the Folding@Home project was rapidly onboarding COVID-19/SARS-COV-2 protein folding projects to aid with early understanding of the virus in hopes of discovering ways to block the virus from interacting with human cells, preventing infection....

July 25, 2023 · 3 min · 639 words

HPC Newsletter | September 2022

Keeping up with High Performance Computing’s ever-expanding horizon, with a chance of clouds. ☁️ ...

September 29, 2022 · 1 min · 197 words

HPC Newsletter | August 2022

Keeping up with High Performance Computing’s ever-expanding horizon, with a chance of clouds. ☁️ ...

August 31, 2022 · 1 min · 184 words

HPC Newsletter | July 2022

Keeping up with High Performance Computing’s ever-expanding horizon, with a chance of clouds. ☁️ ...

July 29, 2022 · 4 min · 709 words

Cray HPC

On the 50th Anniversary of Cray Research Inc.’s founding by Seymour Cray, I thought I’d summarise my brief but intensely interesting experience with the last crop of Cray Supercomputer systems. ...

April 6, 2022 · 3 min · 609 words

Try out Spack on Arm HPC | CP2K

Diverse users running across a diverse set of architectures, it seems Spack was built just for this! I want to share my experiences with Spack, here my focus is on CP2K. My build environment is a Cray XC50 running Thunder X2 Arm CPUs. Spack is a source-based package manager and build system, all builds take place in self-contained environments. Every installed package is defined by a spec, the spec is a string that represents the enabled features, compiler, etc....

June 4, 2021 · 6 min · 1108 words

Robinhood NoSQL - Mixing tables

In Robinhood NoSQL I experimented with porting the Robinhood database from Elasticsearch, it being a commonly-used NoSQL database with specialisation in behaving like a Search Engine. Having ingested the ENTRIES table I now need to augment the records with filepaths from ANNEX_INFO, as I found out previously: ...

September 4, 2018 · 3 min · 435 words

Robinhood NoSQL

Robinhood provides indexing, search and management capabilities to computing centres with massive high-performnace filesystems, namely Lustre. It does this by scanning every file on the filesystem as efficiently as possible to initially populate its MySQL/MariaDB relational database, then it continuously listen for changelogs coming from Lustre to keep its state in-line with reality. ...

August 31, 2018 · 5 min · 898 words

Patching Lustre 2.10 for Linux 4.14

The Lustre community supports recent point-releases of RHEL/CentOS but those patches don’t seem to come back into existing Lustre releases, since those releases don’t officially support later kernels. I installed client 2.10 thinking it had the best chance of working but encountered huge numbers of errors when compiling! ...

July 16, 2018 · 2 min · 243 words