[Bioclusters] Need some help with MrBayes and mpi

Chris Dagdigian dag at sonsorol.org
Thu Apr 7 18:07:45 EDT 2005

First off find out if your users really need the MPI version of MrBayes 
-- some people ask for it just because it sounds cool yet they have no 
idea why or how they are going to benefit.

 From reading the documentation (I'm not a phylogeny expert) it appears 
that only the MCMC analysis stage can take advantage of MPI. If your 
users are not invoking MCMC in their MrBayes scripts then using MPI is 

Among the people I know of using MrBayes on clusters probably half are 
using cluster scheduling software like Grid Engine to simply run 
multiple instances of standalone non-MPI MrBayes across cluster nodes. 
The other 50% have found the MPI enabled version more useful for their 
particular workloads.

It is unclear from your email if you compiled MrBayes yourself using the 
mpicc tools that are customized to your specific mpich-1.2.6 
installation. If you just dropped someone else's prebuilt MrBayes-MPI 
binary on one of your systems it is highly unlikely that it will work at 


Shaila Parashar wrote:

> Hi
> I am not sure whether this is the right mailing list to address this 
> issue. Actually, I am a unix sytem admin, who has been requested to 
> install MrBayes on our cluster.
> We have 4 SUN machines running Solaris 9.  We have mpich-1.2.6 running 
> and is being used extensively. We are not using passwordless ssh , but 
> instead are using  rsh. Students have not faced any problems in using 
> mpich.
> Now I have installed the mpi version of MrBayes on one of the machines 
> and then ran a program called sample.nex
> It gave me the following error
> p1_9962:  p4_error: interrupt SIGSEGV: 11
> I have not been able to find the reason and solution for that error.
> Any suggestions/ideas would be greatly appreciated. A lot of our 
> research work depends on getting this to work correctly.
> If this is not the right mailing list, can any of you please direct me 
> to the right mailing list to address this issue.
> Thanks in advance
> Shaila

Chris Dagdigian, <dag at sonsorol.org>
BioTeam  - Independent life science IT & informatics consulting
Office: 617-665-6088, Mobile: 617-877-5498, Fax: 425-699-0193
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