We thought it would be interesting to mint ourselves some Amazon Cloud servers and put them to the test. The results were quite interesting when compared to our home grown cluster.
First order of business was to create 3 t1.micro
…Staying connected with Eduroam
For those of you who travel as often as we do to conferences or visit research / higher education institutions will find it rather annoying that on arrival your laptop or wireless smart device does not automatically connect to the …
First citation
Today we received our first citation. It's taken about 18 months, which is longer than expected, however we're extremely pleased and are hoping for another two citations by end of July. The paper was co-written by Dr Olivier and Dr…
BISRU and LS-DYNA
We've recently taken on some new users and a new package. Researchers in UCT's Blast Impact and Survivability Unit will be making use of ls-dyna, a strongly coupled multi-physics solver, on ICTS's HPC cluster.
Our first user is a…
New version of Crux availabe
We've upgraded our Crux tandem mass spectrometry analysis software from version 1.35 to 1.36 to take advantage of new functionality.…
Compile / Install / Deploy OpenFOAM 2.0
Big-Bytes decided to write up a quick tutorial on how to install OpenFOAM 2 in the user space. Administrators and users constantly battle with dependencies especially with the latest software releases. This problem begins when a system administrator installs and…
Compiling ABySS
From the ABySS web site: ABySS (Assembly By Short Sequences) is a de novo,
parallel, paired-end sequence assembler that is designed for short
reads. The single-processor version is useful for assembling genomes up
to 100 Mbases in size.…
10 years of computing
Today the combined work effort of our clusters reached 10 years worth of processing time, that is the equivalent of one processor working continuously for 10 years. We only started taking on serious workloads in April this year so while…
Matlab on diet
Over the past week we became aware of an issue with Matlab and its desire to consume as many CPUs as possible. This despite the fact that we were no longer running the parallel library. This thread outlines the problem…
Velvet and BioPerl
We recently ported Velvet, a short sequence assembler, to our cluster. It can be compiled with multi-threading via OMP, however there does not seem to be an elegant way to control its behaviour in a clustered environment other…