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…
MrBayes Sumt SegFaults
We noticed that while MrBayes jobs have been running OK, the sumt process SegFaults. Not a huge crisis as this can be finished up in post-processing. However our user had already solved this issue on his desktop by applying a …
Evolution of the Cape Sedges
Jack Viljoen, a masters student in the Botany department is working on the evolution of Cape Sedges.
For reconstructing the evolutionary trees of groups like the Cypereae and Schoeneae (Fig. 1),
.... we use Monte Carlo Markov Chain (MCMC) sampling…
.... we use Monte Carlo Markov Chain (MCMC) sampling…Power disruptions
Power to the Rondebosch area dropped again this morning, once for 2 minutes and then a brief brownout just after 11:30. We are assured that this is not "load shedding" by Eskom, although this is of little relief to anyone…
Memory issues
We're currently investigating a memory issue with some of the worker nodes. Memory is not being freed up after jobs complete.
UPDATE - 4 July:
Turns out it's not a memory error. The problem is the way that net-snmp monitors…
Crux tandem mass spectrometry
We recently installed Crux on our cluster for researchers in the IIDMM department at UCT. Unfortunately it's not MPI aware and only runs on single cores. Additionaly the binary we downloaded did not run on the cluster due to a…
Getting Gromacs
Gromacs is used to perform molecular dynamics simulations. It's a popular tool and we decided to install it on our cluster based on the needs of two researchers, one at UCT and the other in Kenya. Gromacs is designed to…