Skip navigation.
Home

Blogs

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
wget ftp://ftp.ncbi.nih.gov/refseq/R_norvegicus/mRNA_Prot/rat.1.rna.fna.gz
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.

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.

Syndicate content