[gmx-users] Re: mdrun -nc

[Hsin-Lin Chiang]

> >/  Hi,
> />/
> />/  I tried gromacs 4.5.4 in these days and last version I used is 4.0.5.
> />/  I found when I add --enable-threads in installation.
> />/  I can use mdrun -nc 12 to run 12 CPUs together within one machine.
> /
> I assume you mean -nt?
>
Sorry, -nc is a typo of -nt.
> >/  It also amazing me when I type "top" to check the job, only one process
> />/  in computer and the CPU utility is 1200%!!
> /
> Sounds about right.  I see the same on my dual-core workstation.  One process, 2
> threads, and just less than 200% CPU usage.
>
> >/  But I tried to execute it on two machines, then the second machines
> />/  didn't work.
> />/
> /
> You can't execute threads over multiple machines.  For that you need MPI, not
> threading (they are mutually exclusive).  You haven't provided much detail on
> what you actually did in this case and "didn't work" doesn't exactly provide any
> relevant diagnostic information.
If I submit job by the way, mdrun -nt 24, on two machines with 12 threads for each.
The first machine has one process with 1200%, and the second machine has no process working.
> >/  I don't need mdrun_mpi any more because mdrun -nc is faster the mdrun_mpi.
> />/  That make me confused.
> />/  Am I right to use mdrun -nc to run parallel job in this way?
> /
> For a single, multi-core workstation, mdrun -nt is correct.
Thank you for you answer, then I can feel easy in mind to use this argument, -nt.
And also thanks for Phillips's reply.
I understand it now.

Hsin-Lin
> >/  Does the result is the same as which is employed by mdrun_mpi?
> /
> A variety of factors influence whether or not the results are the same.
>
> http://www.gromacs.org/Documentation/Terminology/Reproducibility
>
> >/  (Exactly I never use mdrun_mpi more than one machine since the ethernet
> />/  between machines is very slow here.)
> />/
> />/  If mdrun -nc is available.
> />/  Do we have another commend support CPUs more than one in the same machine.
> />/
> /
> That's what threading is doing, assuming you're invoking the command correctly.
>    As stated above, the option is -nt, not -nc.  mdrun doesn't check for whether
> or not command line arguments are actually valid, so if you're using -nc you're
> not actually doing threading, but the 1200% usage suggests you probably are.
>
> -Justin

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