[gmx-users] MPIRUN on Ubontu

Linus Östberg bioinf at talavis.eu
Mon Dec 27 19:24:02 CET 2010


In order to use MPI on Ubuntu with the distribution-supplied package,
you need to use a combination of mpirun and mdrun_mpi, e.g.

mpirun -np 2 mdrun_mpi -deffnm md

to run on two cores.

On Mon, Dec 27, 2010 at 7:04 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> גדעון לפידות wrote:
>>
>> Hi all,
>> I have recently installed Ubonto on my computer (i5 processor) and
>> installed gromacs 4.0.7. I have installed openmpi and fftw but when using
>> mpirun command instead of getting parallel processes it simply runs the same
>> job four times simultaneously. How do I make the necessary adjustments.
>
> Properly compile an MPI-enabled mdrun.  Since you've provided no detail on
> how you did the installation, the only thing to suggest is that you've done
> something wrong.  Follow the installation guide:
>
> http://www.gromacs.org/Downloads/Installation_Instructions
>
> Alternatively, use the newest version of Gromacs (4.5.3), which uses
> threading for parallelization instead of requiring external MPI support.
>
> -Justin
>
>> Thanks,
>>  Gideon
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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