hpc

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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Blast!

application, hpc
Subsequent to the installation of MrBayes we decided to deploy BLAST on the HPC cluster to complement the package on our Grid cluster.  BLAST (Basic Local Alignment Search Tool) is a free bioinformatics package…
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Getting Gromacs

application, hpc, MPI
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…
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New worker nodes added to ICTS HPC

hpc, maui, torque
Over the last week ICTS engineers have been adding 5 new BL460 blades to the cluster.  The OS install took place on Tuesday, applications on Wednesday and our first user is already running jobs on the CPUs. New worker nodes The 400 series…
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