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About Lev Lafayette

Crocodile Logo

Lev Lafayette has an MBA (Technology Management) from the Chifley Business School, where he was on the Dean's List, a Graduate Certificate in Project Management from the same institution, and an honours degree from Murdoch University in Politics, Philosophy and Sociology which is commented upon by the Vice-Chancellor of the time. Many years later he completed a Graduate Certificate in Adult and Tertiary Education at the same institution.

He is a certified PRINCE2 Practioner, and an Adult and Workplace Trainer. Clearly not satisfied with one masters degree, he's started another, this time a Master of Education at the University of Otago. With a interdisciplinary approach, Lev's interests include the political implementation of universal pragmatics, the relationship between communications technology and society, and comparative economic systems. On again and off again, he plods his way through completing a PhD in Social Theory as well.

Professionally however, Lev is an experienced systems administrator, specialising in the Linux operating system and scientific applications, a project manager, systems engineer, and quality management systems coordinator, specifically for ISO 9001 (Quality assurance) and ISO 270001 (Information Technology Security). He also does a lot of training for researchers and technical staff in Linux, High Performance Computing, mathematical programming, Postgresql, and related subjects, with graduates and post-doctoral researchers from a variety of organisations including: RMIT, La Trobe University, the University of Melbourne, Deakin University, Swinburne University, Victoria University of Technology, Monash University, the Australian Synchrotron, the Department of Environment and Primary Industries, the University of Sydney, Macquarie University, the University of New South Wales, the University of Western Australia, the Australian Institute of Health Innovation, the Westmead Millennium Institute, the Australian Radiation Protection and Nuclear Safety Agency, and the Australian Institution of Marine Science.

Previous employment and clients include several years working as a computer systems trainer and database management for the Parliamentary Labor Party in Victoria. Following this he worked for the Ministry of Foreign Affairs in Timor Leste (East Timor) managing their computer network and providing training and technical expertise to that Ministry in their first year of self-governance. Dr. Ramos-Horta provided the following comments on his work.

Lev works for the Research Platforms group at the University of Melbourne as the Senior High Performance Computing Support and Training Officer, and prior to that Victorian Partnership for Advanced Computing, as a systems administrator for Linux clusters. As per those roles, this site is mostly dedicated to issues concerning High Performance Computing, Scientific Computing and Supercomputing. Lev is involved in Linux Users of Victoria, having spent four years as President, two years as Public Officer, two years as Vice-President, a year as Treasurer and is now in his third year as an ordinary committee member. He is has a coordinating role in the annual Multicore World conference and typically take the role of MC.

The crocodile logo was designed by Victoria Jankowski. It was first used on the cover of Neon-komputadór, the first IT training manual for the Ministry of Foreign Affairs in East Timor which was printed and translated by the United Nations Development Programme. The crocodile represents the Timorese people and is the emblem of their land. The integrated circuit represents their independent connectivity to the wider world.

You can also find a political site that Lev subscribes to, The Isocracy Network, a synthesis of several progressive political orientations, and RPG Review which covers his interests in roleplaying and simulation games, including as editor of the namesake journal. This includes being the author of one very ironic RPG (Papers & Paychecks), a co-author of another (Fox Magic, author a supplement (Rolemaster Companion VI), as well as plot and character development in the computer game Cargo. He has also been a playtester for RuneQuest, Traveller, Basic Role Playing, and Eclipse Phase.

As a secular humanist with an interfaith perspective, he manages and contributes to the Lightbringers website which includes various addresses and essays on philosophy and religoin.

Finally he also has a livejournal account, which will probably be quite boring to anyone who doesn't know him personally.

That's enough of me talking about myself in the third person like Cerebus The Aardvark.

Drupal "Access denied" Message

It happens rarely enough, but on occasion (such as an upgrade to a database system (e.g., MySQL, MariaDB) or system version of a web-scripting language (e.g., PHP), you can end up with one's Drupal site failing to load, displaying only the error message similar to:

PDOException: SQLSTATE[HY000] [1044] Access denied for user 'username'@'localhost' to database 'database' in lock_may_be_available() (line 167 of /website/includes/

A Tale of Two Conferences: ISC and TERATEC 2017

This year the International Supercomputing Conference and TERATEC were held in close proximity, the former in Frankfurt from June 17-21 and the latter in Paris from June 27-28. Whilst the two conferences differ greatly in scope (one international, one national) and language (one Anglophone, the other Francophone), the dominance of Linux as the operating system of
choice at both was overwhelming.

Rattus Norvegicus ESTs with BLAST and Slurm

The following is a short tutorial on using BLAST with Slurm using fasta nucleic acid (fna) FASTA formatted sequence files for Rattus Norvegicus. It assumes that BLAST (Basic Local Alignment Search Tool) is already installed.

First, create a database directory, download the datafile, extract, and load the environment variables for BLAST.

mkdir -r ~/applicationtests/BLAST/dbs
cd ~/applicationtests/BLAST/dbs
gunzip rat.1.rna.fna.gz
module load BLAST/2.2.26-Linux_x86_64

Having extracted the file, there will be a fna formatted sequence file, rat.1.rna.fna. An example header line for a sequence:

>NM_175581.3 Rattus norvegicus cathepsin R (Ctsr), mRNA

Spartan and NEMO: Two HPC-Cloud Hybrid Implementations

High Performance Computing systems offer excellent metrics for speed and efficiency when using bare metal hardware, a high speed interconnect, and parallel applications. This however does not represent a significant portion of scientific computational tasks. In contrast cloud computing has provided management and implementation flexibility at a cost of performance. We therefore suggest two approaches to make HPC resources available in a dynamically reconfigurable hybrid HPC/Cloud architecture. Both can can be achieved with few modifications to existing HPC/Cloud environments.

Teaching High Throughput Computing: An International Comparison of Andragogical Techniques

The importance of High Throughput Computing (HTC), whether through high performance or cloud-enabled, is a critical issue for research institutions as data metrics are increasing at a rate greater than the capacity of user systems [1]. As a result nascent evidence suggests higher research output from institutions that provide access to HTC facilities. However the necessary skills to operate HTC systems is lacking from the very research communities that would benefit from them.

An Overview of SSH

SSH (Secure Shell) is secure means, mainly used on Linux and other UNIX-like systems, to access remote systems, designed as a replacement for a variety of insecure protocols (e.g., telnet, rlogin etc). This presentation will cover the core useage of the protocol, its development (SSH-1 and SSH-2), the architecture (client-server, public key authentication), installation and implementation, and some handy elaborations and enhancements, and real and imagined vulnerabilities.
Plenty of examples will be provided throughout along with the opportunity to test the protocol.

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.

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