[gmx-users] mdrun -nc

[Justin A. Lemkul]

Hsin-Lin Chiang wrote:
> 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?

> 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.

> 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.

> 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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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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