Clustalw-Mpi From Ubuntu Server 12.04 Runs Slower In Multicpu Mode

Question

[loic.laureote]

Hi,

I have one bioinformatics question, Some of us works on a beowulf cluster dedicated to bioinformatics. So on our cluster we've got some package installed from ubuntu repository. Testing our package we found something strange. By comparing clustalw-mpi performance from 1 cpu to 4 cpu, we realized that something goes wrong.

config : clustalw-mpi 0.13 and openmpi 1.5

On a little dataset we found :

On a quadricore 3 gigahertz :

1 cpu = 51 secondes
4 cpu = 1m49 secondes

When you compile clustalw-mpi by yourself everything goes ok.

It is a normal beaviour, or did I miss something??

[Istvan Albert]

well it is not normal behavior :-) and it appears that the default compilation attempts to run with a configuration that is not suited for your system

Answer 1

[Hamish]

I can't be certain, but it could have something to do with the MPI version of ClustalW being packaged by Debian (see http://packages.debian.org/sid/clustalw-mpi) and thus being built against the Debian version of Open MPI. Checking the repositories for my Ubuntu 12.04 LTS installations I see:

• clustalw-mpi - 0.15-1
• libopenmpi1.3 - 1.4.3-2.1ubuntu3

Which, as expected, corresponds to the Debian packages:

• http://packages.debian.org/sid/clustalw-mpi
• http://packages.debian.org/sid/libopenmpi1.3

FYI it appears that I am see clustalw-mpi 0.15-1 and not clustalw-mpi 0.15-2 due to platform support.

However you appear to have different versions, an older version of clustalw-mpi and a newer version of Open MPI, so may be this mismatch is causing the issues you see. The issue going away when you compile ClustalW MPI yourself, supports this possibility.

By the way, if you are using ClustalW MPI to perform protein multiple sequence alignments, you may want to consider moving to using Clustal Omega instead. Clustal Omega addresses many of the scalability issues seen with ClustalW and generally returns better alignments.