[gmx-users] Regarding Gromacs 5.0.3 parallel computation

[Téletchéa Stéphane]

Le 10/12/2014 07:22, Bikash Ranjan Sahoo a écrit :
> I tried to do a small simulation in Gromacs 4.5.5 using 30 cores for 200
> ps. The computation time was 4.56 minutes . The command used was "dplace -c
> 0-29 mdrun -v -s md.tpr -c md.gro -nt 30 &".
>
> Next I ran the same system using Gromacs 5.0.3. The command used was
> "dplace -c 0-29 mpirun -np 30 mdrun_mpi -v -s md.tpr -c md.gro". The
> simulation was extremely slow and took 37 minutes to complete only 200 ps
> MD.

Dear Bikash,

You are more or less benchmarking threads versus mpi, right?

Note also that dplace for such rounded number (30) is probably not
optimal either except if your number of processors is in the 
multiplicity of 30 (hexacores?).

Best,

Stéphane

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