I was wondering if you would be able to provide any advice for me on an issue I'm having. I'm working on a server trying to get the MPI version of mrbayes installed so I can use more than 1 processor at a time. To do this, mrbayes must be complied with the -mpi flag set.
I've downloaded the source version from the website, and compiled it following the mpi instructions which are as follows:
autoconf
./configure --enable-mpi=yes
make
Once that is done you should be able to start the program mrbayes(mb) through the following command:
mpirun -np 8 mb
where -np is the number of processors.
However I'm finding that this isn't opening a parallel version of mrbayes, it is instead opening 8 versions of mrbayes on the server at once. I also tried this on my local Ubuntu machine as I thought that it was something that I was doing wrong, however this works fine here and I can get it to work in parallel mode. At first I thought that it wasn't working as the MPICH daemon wasn't running to allow the communication between cores, however I checked and it is. I also checked my complication to ensure that mpi mode was correctly enabled and it also is. I have sudo access to the server so it also isn't an issue of permissions.
I was wondering if anybody came across this problem before and if so if you knew how to solve it?
Thanks, I really appreciate you taking the time to read this. Any advice you may have would be appreciated.
Ok so I didn't really solve it but on talking to a colleague they suggested that I copy the executable from my local machine that worked correctly onto the server to see if that would work. We weren't really expecting it to, but it did. So not a proper solution, but a possibility in case anybody ever runs into the same problem.