Setting Up A Mpi Environment

Question

[Kartik Sunagar]

Dear all,

I would like to set-up a MPI environment to run the HyPhy GA-Branch test on a local computer. Is it possible to set up a MPI environment in a computer with a multi-core processor and if yes, how do I do this? I am not a bioinformatics student and have no clue how to accomplish this. Any help or suggestions will be extremely useful.

Thank you very much, Kartik

Answer 1

[Hranjeev]

I haven't got time to test these steps. Assuming you're on Linux, here's a quickie:

1. Download MPICH2 from http://www.mcs.anl.gov/research/projects/mpich2/
2. Unpack, configure, make and install
3. Add the mpich2 install directory to the .bash_profile
4. To run your program on a dual core: $mpirun -np 2 ./HYPHYMPI BASEPATH=/your abs path to hyphy dir/ GABranch/ModelSelectorBranchLocal.bf

[Kartik Sunagar]

Thank you very much HRanjeev. I will follow your instructions and let you know. Cheers!

Answer 2

[Kartik Sunagar]

After a lot of searching I found that for windows machines at least, MPICH2 seems fairly easy to install and use. However, I did not understand how to configure it and it keeps returning an error: "Error while connecting to host, No connection could be made because the target machine actively refused it". I had disabled the firewall before trying this. I guess I have to setup a connection or host something. If somebody could tell me how to tackle this, I would really appreciate it.

PS: I am mainly looking to do this in Windows. Ubuntu will be my last resort...

Cheers, Kartik

[Hranjeev]

You have to find a way to compile your code and run C:Program FilesMPICH2binmpiexec.exe" -n 5 [?]; This probably can give you some hints http://auriza.site40.net/notes/mpi/mpich2-on-windows-xp/