hpc

New toys for spring

hardware, hpc
To celebrate spring we've deployed some more worker nodes and disk space.  Yet another 200 series server with 4 cores and 4GB of RAM, as well as two new 400 series servers.  These last two servers come out of the…
Read More

More CPUs, more applications

hpc
Today we added another node to the 200 series.  This brings our cluster CPU count to 100 cores.  This doesn't include the GPU server as this is only being used for testing purposes.  The latest server only has 4GB or…
Read More

10 years of computing

application, hpc, sagrid
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…
Read More

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…
Read More

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…
Read More

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…
Read More

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 …

Read More

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 …
Read More
Menu