MPI

Parallel poison solution

application, MPI
Having installed Gromacs last week we decided to run some tests to see how well it performed on our cluster.  We downloaded a tutorial which analysed solutions of funnel web spider venom in water.  Given the bounding block size of…
Read More

6 million monkeys

application, MPI
In order to test the parallel version of MrBayes we ran several simulations of the primates.nex tutorial provided with the installation.  This compares the evolutionary species change and divergence between various primates. Primates Running the parallel version produced predictable results.  "Distributing"…
Read More

Introducing Mr Bayes

application, MPI
One of our students requested that we install MrBayes, software for the estimation of phylogeny on a genetic level.  This is a fairly popular package which has been ported to numerous platforms so we thought we'd have a crack…
Read More

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…
Read More

A stressful day

hardware, hpc, MPI, operating system
Patched kernels on HPC servers to 2.6.18-238.1.1.el5; All went fine except for the head node which has an issue with latest kernel (dies at boot with a kernel panic) so booting it into older version 2.6.18-194.1.1.el5 until we can sort…
Read More

Testing the new cluster with MPI

hpc, MPI
Two new servers have been added to the cluster bringing the core count to 20. Below is a set of simple tests carried out with a C program compiled with mpicc which runs a large number of floating point computations…
Read More

OpenMPI

hpc, MPI, programming
Installed openmpi 1.4-4 as well as the MPI development suite on the test cluter. Configured host based authentication to obviate the ssh password authentication. Compiled a test case program.  Seeing a 50% speed improvement when splitting the workload over 3…
Read More

Maths jobs submitted to HPC cluster

application, hpc, MPI
Our first user has started submitting jobs to the cluster.  The software being used is auto07p for continuation and bifurcation problems in ordinary differential equations.  Auto07 can be compiled with OMP to make it multi-cpu aware.  Currently each job makes…
Read More
Menu