hpc

Matlab on diet

application, hpc
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…
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Lusting after GlusterFS

hpc

GlusterFS is an open source, distributed file system capable of scaling to several petabytes and handling thousands of clients. The HPC team at UCT had some time to play and implement Gluster. The idea behind Gluster is to scale the …

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MrBayes Sumt SegFaults

hpc
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 …
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GPGPUs

GPU, hpc
We attended a GPGPU programming course at the Center for High Performance Computing this week.  The course focused on new developments in OpenCL and included some very interesting presentations.  We had a also had a brief discussion on the new…
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Evolution of the Cape Sedges

application, hpc
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), Mr Bayes .... we use Monte Carlo Markov Chain (MCMC) sampling…
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Power disruptions

hardware, hpc
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…
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Memory issues

hpc, operating system
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…
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Crux tandem mass spectrometry

application, hpc
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…
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