[Bioclusters] MrBayes issues in parallel

Matthew King kingdom at wsu.edu
Tue Jan 11 17:24:34 EST 2005

I have implemented parallel MrBayes on our G5 Xserve cluster using 
MPICH with the Bioteam's Inquiry software. we have 12 dual processor 
I am having the following issues

1. when I use the nolocal argument with mpirun MrBayes will run through 
the analyses twice. If I do not use the nolocal argument it runs 
through only once. i use the command
:mpirun -np 4 -nolocal -machinefile 
<pathtomachinefile>/machinefile.freebsd.ppc <pathtoMrbayes>/mb_mpi 
I have it set up so that I am using specific machine files to designate 
which processors to run on. we run only 4 chains so i am only picking 4 
processors. I have not yet implemented it into the SGE yet.

2. When I include the quit command at the end of the MrBayes block I 
get a debugging error WARNING: Memory (2) has not been freed hit any 
key. This error makes it so the program does not quit automatically.

Any ideas would be much appreciated.


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