hpc

Deep sequencing of human papillomavirus

hpc
HPV seq HPV infection is causally linked to cervical and other genital cancers.   The human papillomavirus (HPV) research group at IIDMM, UCT are using next-generation sequencing (NGS) to explore the diversity of this virus in HIV infected individuals. NGS is a powerful…
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Musings on Torque/PBS and OpenMPI

hpc, maui, torque
We've spent most of this week working on mpiBlast, and have bumped our heads against a few problems.  Fortunately we have a very patient user in computational biology who's assisted in running test jobs.  It's been a learning experience so…
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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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