Hi Hannes,
Okay - then my next guess is the NVIDIA driver taking ages to load for some reason. That can happen if there is a misbehaving GPU for example. Can you try putting the driver in persistence mode and see if that changes anything. As root:
nvidia-smi -pm 1
Then try again.
All the best
Ross
> On Sep 21, 2016, at 1:01 PM, Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk> wrote:
>
> Hi Ross,
>
> Input is read from local hard disk and binary is on SSD. This is all on
> my workstation and I don't have any issues with these. Serial run looks
> fine but I do see that hostname is always 'Unknown' (also for serial
> and MPI CPU). I see in the code (master_setup.F90) that the HOSTNAME
> environment variable is queried but this doesn't work (inerr==0).
>
> Many thanks,
> Hannes.
>
>
> On Wed, 21 Sep 2016 12:16:40 -0700
> Ross Walker <ross.rosswalker.co.uk> wrote:
>
>> Hi Hannes,
>>
>> That behavior sounds really weird. My initial guess would be file I/O
>> issues meaning the reading of the input files is ridiculously slow.
>> The second might be some kind of crazy long DNS timeout. PMEMD calls
>> hostname so it record the hostname of the machine running the
>> calculation in mdout. If this is timing out for some reason that
>> might be why the setup time is always 240s.
>>
>> Both of those should be independent of GPU though. Can you try the
>> serial CPU code with the exact same input setting and see if you get
>> the same behavior?
>>
>> All the best
>> Ross
>>
>>> On Sep 21, 2016, at 11:06 AM, Hannes Loeffler
>>> <Hannes.Loeffler.stfc.ac.uk> wrote:
>>>
>>> Hi,
>>>
>>> I have a strange issue with the GPU variant of pmemd and seemingly
>>> overlong runtimes. I have benchmarked a 30000 atoms sytems which is
>>> reported to make about 32 ns/day. But the wall clock time just
>>> doesn't match with that. After running with different nstlim I
>>> realized that the setup time is constant at 240 s and top shows me
>>> that the CPU only gets busy after that time (not sure what the GPU
>>> does if it does anything).
>>>
>>> What could be the cause of this behaviour? The card is a Quadro
>>> M4000, pmemd16 compiled with gcc4.9.2/cuda 7.5.17, driver is
>>> currently 370.28 but I have also tried the current long term
>>> version.
>>>
>>> Many thanks,
>>> Hannes.
>>>
>>>
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Received on Wed Sep 21 2016 - 13:30:03 PDT
