HPC

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....

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

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

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

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. ...

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....

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: ...

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. ...

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! ...