[Bioclusters] clue wanted: parallel mrbayes

[Christopher Smith]

There seem to be #if defined(MPI_ENABLED) blocks within the source files,
but the MPI makefile doesn't define this macro (is it supposed to be defined
by mpicc?). You probably need -DMPI_ENABLED in your CFLAGS.

-- Chris



On 29/9/04 07:02, "Chris Dagdigian" <dag@sonsorol.org> wrote:

> 
> 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
> appreciated.
> 
> 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
> 
> 
> Regards,
> Chris
> 
> 
> 
> 
> 
>