[gmx-users] Vacuum simulation in Gromacs 5

[Szilárd Páll]

On Sun, Jun 14, 2015 at 6:54 PM, Jan Jirsák <janjirsak at gmail.com> wrote:
> Hi,
>
> I did the test and found out that -nt 8 is even slower than -nt 1 !!

FYI: "-nt" is mostly backward compatibility option and for clarity
it's best to use either -ntmpi or -ntomp, depending on what you mean.

> However, I think that simulation hasn't even properly started with 8
> threads and got stuck somewhere in the beginning.
>
> Details:
> I used a short run (1000 steps) for testing. mdrun -nt 1 finished
> after ca 11 hours, whereas not a single checkpoint or run log record
> have been saved for mdrun -nt 8 (and simulation is still running). Not
> even starting energies were displayed - last record in a log file is a
> SETTLE citation.

That's probably a stuck which should not happen and I'd consider that
a bug. Can you share your input files?

> In top I noticed both processes used up to 100% CPU, but considerably
> differed in the use of memory. Relevant lines:
> PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND
> 117710 jan       20   0 5313776 4.642g   9940 R  98.9  3.7  52:47.19
> mdrun
> 117686 jan       20   0  547344  24456   8712 R  92.7  0.0  54:48.92 mdrun

That definitely does not look good.

BTW, in contrast with Mark's opinion I do think top is indicative. If
you wanted to use 8 cores and told mdrun to do so but you get load
only on one core, you can be (almost) certain that something is not
right.

--
Szilárd

> The first listed process (117710) is the single thread simulation (-nt 1).
>
> Thank you for any insight,
> Jan
>
> 2015-06-12 14:35 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:
>> Hi,
>>
>> Top need not be indicative. Run the same with -nt 1 and observe whether the
>> performance changes. And don't run anything else on these cores.
>>
>> Mark
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