I am sorry i just noticed something in NTT=1, NTB=2 without ig=-1
case. In first 500 ps run i got a smaller trajectory file (1/4 of
other two 500 ps s). additionally the .out file is 80 times bigger
than other two. one more thing to say, looks like the first 500 ps
stopped unexpectedly but consecutive run started using last updated
coordinates. In other words consecutive runs didn't stop totally and
they continued to produce something...finally below is the actual
error which was on stdout,
Error: unspecified launch failure launching kernel kClearForces
cudaFree GpuBuffer::Deallocate failed unspecified launch failure
best
peker
2011/1/29 peker milas <pekermilas.gmail.com>:
> Hi Ross and Marek,
>
> As a quick update, i run three 1.5 ns simulations with my system. One
> for NTT=3, NTB=1 case with ig=-1, one for NTT=1, NTB=2 with ig=-1 ,
> and another one for NTT=1, NTB=2 without ig=-1. None of them produced
> NaN s. I will continue with other 2 cases. I will let you know about
> the results...
>
> best
> peker
>
> 2011/1/28 Marek Maly <marek.maly.ujep.cz>:
>> Hi Ross,
>> I will also do these tests (just short MDs cca 50 000 steps might be
>> enough I think) soon,
>> and I will let here know the results.
>>
>> Best,
>>
>> Marek
>>
>>
>>
>> Dne Fri, 28 Jan 2011 03:26:48 +0100 Ross Walker <ross.rosswalker.co.uk>
>> napsal/-a:
>>
>>> Hi All,
>>>
>>> I am hoping to be able to get some clarity for this thread so that we can
>>> start to look at what might actually be going on here. Right now there
>>> are a
>>> lot of theories but no real concrete examples to back things up.
>>> Specifically I would appreciate it if someone who sees this NAN problem
>>> could take their simulation and run the following:
>>>
>>> 1) NTT=3, NTB=2 - This one we already know the problem exists.
>>>
>>> 2) NTT=3, NTB=1 - This is NVT and will rule out the barostat if the
>>> problem
>>> still exists.
>>>
>>> 3) NTT=1, NTB=2 - This is NPT but NOT using the random number stream. If
>>> this crashes it means the problem is likely in the barostat rather than
>>> the
>>> random number stream.
>>>
>>> 4) NTT=1, NTB=1 - This is NVT not using the random number stream. If this
>>> crashes then both my theories are wrong.
>>>
>>> 5) NTT=0, NTB=1 - This is NVE, if this crashes then we are in a whole
>>> world
>>> of pain...
>>>
>>> I want to find out specifically which simulation modes show problems and
>>> which do not. I am 'hoping / assuming' that the problem is restricted to
>>> either NPT calculations or Langevin simulations or possibly NPT with
>>> Langevin. However, I need someone to carefully try these options and
>>> document the issue. Everyone's help is greatly appreciated.
>>>
>>> All the best
>>> Ross
>>>
>>> /\
>>> \/
>>> |\oss Walker
>>>
>>> ---------------------------------------------------------
>>> | Assistant Research Professor |
>>> | San Diego Supercomputer Center |
>>> | Adjunct Assistant Professor |
>>> | Dept. of Chemistry and Biochemistry |
>>> | University of California San Diego |
>>> | NVIDIA Fellow |
>>> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
>>> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
>>> ---------------------------------------------------------
>>>
>>> Note: Electronic Mail is not secure, has no guarantee of delivery, may
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>>>
>>>
>>>
>>>
>>>
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>>
>>
>> --
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Received on Sat Jan 29 2011 - 15:30:03 PST
