Skip navigation.
Home

Blogs

One Million Jobs for Spartan

Whilst it is a loose metric, our little cluster, "Spartan", at the University of Melbourne ran its 1 millionth job today after almost exactly a year since launch.

The researcher in question is doing their PhD in biochemistry. The project is a childhood asthma study:

"The nasopharynx is a source of microbes associated with acute respiratory illness. Respiratory infection and/ or the asymptomatic colonisation with certain microbes during childhood predispose individuals to the development of asthma.

Using data generated from 16S rRNA sequencing and metagenomic sequencing of nasopharyn samples, we aim to identify which specific microbes and interactions are important in the development of asthma."

Moments like this is why I do HPC.

Congratulations to the rest of the team and to the user community.

Duolingo Plus is Extremely Broken

After using Duolingo for over a year and accumulating almost 100,000 points I thought it would do the right thing and pay for the Plus service. It was exactly the right time as I would be travelling overseas and the ability to do lessons offline and have them sync later seemed ideal.

For the first few days it seemed to be operating fine; I had downloaded the German tree and was working my way through it. Then I downloaded the French tree, and several problems started to emerge.

Heredocs with Gaussian and Slurm

Gaussian is a well-known computational chemistry package, and sometimes subject to debate over its license (e.g., the terms state researchers who develop competing software packages are not permitted to use the software, compare performance etc). Whilst I have some strong opinions about such a license, this will be elaborated at another time. The purpose here is to illustrate the use of heredocs with Slurm.

The Why and How of HPC-Cloud Hybrids with OpenStack

High performance computing and cloud computing have traditionally been seen as separate solutions to separate problems, dealing with issues of performance and flexibility respectively. In a diverse research environment however, both sets of compute requirements can occur. In addition to the administrative benefits in combining both requirements into a single unified system, opportunities are provided for incremental expansion.

'Advanced Computing': A International Journal of Plagiarism

Advanced Computing : An International Journal was a publication that I considering writing for. However it is almost certainly a predatory open-access journal, that seeks a "publication charge", without even performing the minimal standards of editorial checking.

I can just tolerate the fact that the most recent issue has numerous spelling and grammatical errors as the I believe that English is not the first language of the authors. It should have been caught by the editors, but we'll let that slide for a far greater crime - that of widespread plagiarism.

The fact that the editors clearly didn't even check for this is in inexcusable oversight.

I opened this correspondence to the editors in the hope that others will find it prior to submitting or even considering submission to the journal in question. I also hope the editors take the opportunity to dramatically improve their editorial standards.

Multicore World 2017: A Review

Multicore World is a small conference held annually in New Zealand hosted by Open Parallel. What it lacks in numbers however it makes up in quality of the presenters. The 2017 conference included a typically impressive array of speakers dealing with some of the most difficult issues facing computational science, and included several important announcements in the fields of supercomputing, the Internet of Things, and manufacting issues.

Nyriad: An Agile Startup Done Right

I have recently spent a few days in the company of Nyriad, a New Zealand IT company specialisng in GPU software. I wish to make a point of a few observations of the company because they are an example of both a startup company that uses agile project management, two terms much maligned and subject to justified cynicism, and does it right. Because I have seen so many colleagues burned by companies and organisations which profess such values and do not do it right, I hope the following observations will be useful for future organisations.

HPC/Cloud Hybrids for Efficient Resource Allocation and Throughput

HPC systems running massively parallel jobs need a fairly static software operating environment running on bare metal hardware, a high speed interconnect to reach their full potential, and offer linear performance scaling for cleverly designed applications. Cloud computing, on the other hand, offers flexible virtual environments and can be used for pleasingly parallel workloads.

Multicore World 2017

The 6th Multicore World will be held on Monday 20th to Wednesday 22nd of February 2017 at Shed 6 on the Wellington (NZ) waterfront. Nicolás Erdödy (Open Parallel) has once again done an amazing job at finding some the significant speakers in the world in parallel programming and multicore systems to attend. Although a short - and not an enormous conference - the technical quality is always extremely high, dealing with some of the most fundamental problems and recent experiences in these fields.

OpenStack and the OpenStack Barcelona Summit

Presentation to Linux Users of Victoria, 7th February, 2017

An overview of cloud computing platforms in general, and OpenStack in particular, is provided introduces this presentation. Cloud computing is one of the most significant changes to IT infrastructure and employment in the past decade, with major corporate services (Amazon, Microsoft) gaining particular significance in the late 2000s. In mid-2010, Rackspace Hosting and NASA jointly launched an open-source cloud-software initiative known as OpenStack, with initial code coming from NASA's Nebula project and Rackspace's Cloud Files project, and soon gained prominence as the largest open-source cloud platform. Although a cross-platform service, it was quickly available on various Linux distributions including Debian, Ubuntu, SuSE (2011), and Red Hat (2012).

OpenStack is governed by the OpenStack Foundation, a non-profit corporate entity established in September 2012. Correlating with the release cycle of the product, OpenStack Summits are held every six months for developers, users and managers. The most recent Summit was held in Barcelona in late October 2016, with over 5000 attendees, almost 1000 organisations and companies, and 500 sessions, spread out over three days, plus one day of "Upstream University" prior to the main schedule, plus one day after the main schedule for contributor working parties. The presentation will cover the major announcements of the conference as well as a brief overview of the major streams, as well the direction of OpenStack as the November Sydney Summit approaches.

Syndicate content