Hi Hannes,
Okay, well I am fresh out of ideas other than to say:
"Have you tried turning it off and on again?"
All the best
Ross
> On Sep 21, 2016, at 1:17 PM, Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk> wrote:
>
> Hi Ross,
>
> the tool reports that it has set the GPU to persistent mode but the
> wall clock time is still as bad as it was.
>
> Cheers,
> Hannes.
>
>
> On Wed, 21 Sep 2016 13:08:11 -0700
> Ross Walker <ross.rosswalker.co.uk> wrote:
>
>> 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 - 15:30:02 PDT
