Submitted by lev_lafayette on Fri, 06/15/2018 - 22:58
The PDF file format can be efficiently manipulated in Linux and other free software that may not be easy in proprietary operating systems or applications.
Submitted by lev_lafayette on Sun, 06/03/2018 - 12:19
MrTrix is "a set of tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses". It is mostly designed with post-processing visualisation in mind, but for intensive computational tasks it can make use of high-performance computing systems. It is not designed with messing-passing in mind, but it can be useful for job arrays.
Submitted by lev_lafayette on Tue, 04/03/2018 - 05:35
A number of organisations use a customer service metric known as "Net Promoter", first suggested in the Harvard Business Review. Indeed, it is so common that apparently two-thirds of Fortune 500 companies are using the metric. It simply asks a single question: "How likely is it that you would recommend [company X] to a friend or colleague?".
Submitted by lev_lafayette on Tue, 02/27/2018 - 04:25
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]  Access denied for user 'username'@'localhost' to database 'database' in lock_may_be_available() (line 167 of /website/includes/lock.inc).
Submitted by lev_lafayette on Tue, 12/05/2017 - 05:56
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.
Submitted by lev_lafayette on Mon, 11/13/2017 - 02:07
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
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
Submitted by lev_lafayette on Wed, 10/25/2017 - 03:15
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.
Submitted by lev_lafayette on Wed, 10/18/2017 - 03:07
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 . 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.
Submitted by lev_lafayette on Wed, 08/30/2017 - 11:49
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.
Submitted by lev_lafayette on Mon, 07/03/2017 - 14:00
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.