[Bioclusters] Need some help with MrBayes and mpi

Shaila Parashar shaila at engr.colostate.edu
Thu Apr 7 18:31:29 EDT 2005


I have forwarded your email to our users to find out if they really need 
Regarding he installation of mrbayes and mpich - I did both of them from 
The reason we considered mpi was that we have a server with 24 
processors and 96 GB of RAM.  The processors themselves have a speed of 
750 MHz. So, when the user ran a job, it was running on one processor 
and was not as fast as we had expected. So it was suggested to use mpi 
so that a number of processors could be used simultaneously. Also we are 
using the Grid engine. In fact we will be submitting the job to grid 
engine which will in turn use the mpich parallel environment and run it 
on mpi.

Any other ideas/suggestions would be greatly appreciated


Chris Dagdigian wrote:

> 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 
> pointless.
> 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 all.
> -Chris
> 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

Shaila Parashar			e-mail:shaila at engr.colostate.edu
UNIX System Administrator	tel:- (970)-491-6555
Engineering Network Services
Colorado State University
Fort Collins, CO 80523-1301
" Smile is a curve that sets things straight. " 

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