PS:
Care to know what can you do?
- as noted above try offloading only the nonbondeds (or possibly the hybrid
PME mode -pmefft cpu)
- check if your GPU has application clocks that can be bumped
- if you have the means, consider getting a bit faster GPU; the Quadro
M2000 in your machine is both slightly dated and low-end  similar board as
the GTX 950



--
Szilárd

On Wed, Feb 28, 2018 at 10:26 PM, Szilárd Páll <pall.szil...@gmail.com>
wrote:

> Thanks!
>
> Looking at the log file, as I guessed earlier, you can see the following:
>
> - Given that you have a rather low-end GPU and a fairly fast workstation
> CPU the run is *very* GPU-bound: the CPU spends 16.4 + 54.2 = 70.6% waiting
> for the GPU (see lines 628 and 630)
>
> - this means that the default behavior of offloading both the nonbonded
> and PME tasks to the GPU is not beneficial (try the other parallel modes)
>
> - mdrun is still using 8 cores / 16 threads *for the parts of the run that
> require it* (Bonded forces (2.7%), Integration / Constraints (2.6 % / 4.9
> %) etc.), but as this takes <30% of the runtime, that gives you your
> average of 4.5 utilization (0.3*16 = 4.8). That you "see" 9 threads active
> is just the averaging/sampling effect of from your minitoring tools.
>
> Cheers,
>
> --
> Szilárd
>
> On Wed, Feb 28, 2018 at 10:12 PM, Mahmood Naderan <nt_mahm...@yahoo.com>
> wrote:
>
>> >The list does not accept attachments, so please use a file sharing or
>> content sharing website so >everyone can see your data and has the context.
>>
>> I uploaded here
>>
>> https://pastebin.com/RCkkFXPx
>>
>>
>>
>> Regards,
>> Mahmood
>>
>>
>
-- 
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