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  • abyss-pe error

    For the ABySS, I can run it successfully local.

    However, when I submit a job to sever like this, there is always an error message like this:

    which: no mpirun in (/tmp/156113.1.all.q:/usr/local/bin:/bin:/usr/bin)

    However, I have already installed the MPI.

    Can anyone give me some suggestions?

    Thanks!

    Jingjing

  • #2
    Make 100% sure that mpi is installed and in your PATH. Use a different program than ABySS to test out your mpi and submission process. mpi installation varies with the system thus it is hard to give explicit instructions. But what you could do is as simple as creating batch job that has the one-line 'mpirun', submit it to your queue, and look at the resulting output. If the output complains about the lack of mpirun then you know that it is indeed not installed via the batch queuing system.

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    • #3
      If you installed mpi on your cluster, it's unlikely you installed it in those directories. In most clusters you'd need root level access to do so. So, hopefully you instead installed it on your home directories. This means you'll need to add that directory to your bash profile. If you tried to install it to the usr/local, usr/bin locations you probably had permission problems that caused an error during install that you didn't notice.

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