[Bioclusters] clue wanted: parallel mrbayes

Chris Dagdigian bioclusters@bioinformatics.org
Wed, 29 Sep 2004 10:02:57 -0400

Hi folks,

I'm looking for pointers on getting mrbayes to take advantage of 
MPICH-1.2.6 when doing Markov Chain Monte Carlo (MCMC) analysis.

As far as I can tell the 'mb' binary that compiled cleanly against 
mpich-1.2.6 (ch_p4 transport device) using 'mpicc' behaves exactly the 
same as 'mb' compiled without MPI support :)

The mrbayes manuals are not exactly helpful. The basic summary of the 
manual regarding parallel operation goes like this: "You can use Pooch 
to run MCMC analysis tasks on multiple Apple machines and it will 
compile for MPICH". That's about it.

Launching the 'mb' binary with mpirun causes the app to seemingly only 
run on the the node where mpirun was invoked. There is no sign that the 
app is honoring the machines file or doing anything on a remote system.

I'm missing something simple and obvious here. Any tips would be 

Info I'd appreciate if anyone has it:

1. Makefile examples for MB using LAM-MPI or MPICH

2. Does MCMC output in any way let you know that it is running in 
parallel mode? Is there anything unique about the output that would tell 
me the MPI method is being used? What sorts of processes will be started 
on remote machines?

3. mpirun examples for mrbayes or any integration/usage scripts used to 
run the app in a parallel environment.

4. any other debugging, verbose logging or troubleshooting tips


Chris Dagdigian, <dag@sonsorol.org>
BioTeam  - Independent life science IT & informatics consulting
Office: 617-665-6088, Mobile: 617-877-5498, Fax: 425-699-0193
PGP KeyID: 83D4310E iChat/AIM: bioteamdag  Web: http://bioteam.net