Setting Up A Mpi Environment
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10.4 years ago

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

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10.4 years ago
Hranjeev ★ 1.5k

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

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10.4 years ago

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

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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/

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