Hi Joshi,
Can you send me the output of the following commands on your machine please:
1) nvidia-smi
2) cat /proc/cpuinfo
Thanks,
All the best
Ross
> On Mar 31, 2015, at 9:13 PM, Himanshu Joshi <himanshuphy87.gmail.com> wrote:
>
> Ok Ross,
> I am using the latest version with all the recent updates.
> Here is the detail.
> GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
> | Version 14.0.1
> |
> | 06/20/2014
>
> Thanks for the helpful suggestion.
>
> On Wed, Apr 1, 2015 at 9:09 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
>
>> Ok - this matches behavior I have seen on other kepler based systems
>> (notably K80s) when running multiple GPUs. My current theory is that one of
>> the more recent updates must have broken things. I'll investigate some more
>> when I get time. In the meantime I suggest just running single GPU runs.
>>
>> All the best
>> Ross
>>
>>> On Mar 31, 2015, at 8:32 PM, Himanshu Joshi <himanshuphy87.gmail.com>
>> wrote:
>>>
>>> Hello Ross,
>>> I ran the with pmemd.cuda and found it printing correctly.
>>> So the problem lies somwhere in pmemd.cuda.MPI.
>>>
>>> Thanks for the help.
>>>
>>> On Tue, Mar 31, 2015 at 11:36 PM, Ross Walker <ross.rosswalker.co.uk>
>> wrote:
>>>
>>>> Hi Joshi,
>>>>
>>>> If you run with just pmemd.cuda instead of cuda.MPI do you see different
>>>> behavior?
>>>>
>>>> All the best
>>>> Ross
>>>>
>>>>> On Mar 31, 2015, at 10:58 AM, Himanshu Joshi <himanshuphy87.gmail.com>
>>>> wrote:
>>>>>
>>>>> Dear Friends,
>>>>> I am running pmemd.cuda.MPI (AMBER14) in Tesla K40s gpu cards for an
>>>>> explicit water DNA system with SPFP precision model. After running few
>>>>> steps sucessfully, I am getting **** for temperature and energy values
>> as
>>>>> typed below followed by the md input file.
>>>>>
>>>>>
>>>>> NSTEP = 45000 TIME(PS) = 54230.000 TEMP(K) = 300.15 PRESS =
>>>>> 0.0
>>>>> Etot = -1102980.4479 EKtot = 216143.9219 EPtot =
>>>>> -1319124.3698
>>>>> BOND = 8297.0959 ANGLE = 17306.9385 DIHED =
>>>>> 22929.3885
>>>>> 1-4 NB = 8627.8031 1-4 EEL = -71177.7576 VDWAALS =
>>>>> 134764.0741
>>>>> EELEC = -1439871.9123 EHBOND = 0.0000 RESTRAINT =
>>>>> 0.0000
>>>>>
>>>>
>> ------------------------------------------------------------------------------
>>>>>
>>>>> check COM velocity, temp: NaN NaN(Removed)
>>>>>
>>>>> NSTEP = 50000 TIME(PS) = 54240.000 TEMP(K) = NaN PRESS =
>>>>> 0.0
>>>>> Etot = NaN EKtot = NaN EPtot =
>>>>> **************
>>>>> BOND = 0.0000 ANGLE = 4770613.6638 DIHED =
>>>>> 0.0000
>>>>> 1-4 NB = ************** 1-4 EEL = ************** VDWAALS =
>>>>> **************
>>>>> EELEC = ************** EHBOND = 0.0000 RESTRAINT =
>>>>> 0.0000
>>>>>
>>>>
>> ------------------------------------------------------------------------------
>>>>> Here is my md input file
>>>>>
>>>>> Production run with constant volume
>>>>> &cntrl
>>>>> ntx=6, irest=1,
>>>>> nmropt=0,
>>>>> ntrx=1, ntxo = 2,
>>>>> ntpr=5000, ntwx=5000, ntwr=10000,
>>>>> ntwv=0,
>>>>> ntf=2, ntb=1,
>>>>> cut=9.0, nsnb=10,
>>>>> nstlim=1000000, nscm=10000,
>>>>> t=0.0, dt=0.002,
>>>>> ntt=1, tautp=0.5
>>>>> ntp=0, pres0=1.0, taup=0.5, comp=44.6
>>>>> tempi=300.0, temp0=300.0,
>>>>> ipol=0, ntc=2, ioutfm = 1
>>>>> /
>>>>> &ewald
>>>>> /
>>>>>
>>>>> Though, I am running another NPT run using Langevin dynamics using
>>>>> anisotropic pressure coupling and MC barostate with same pmemd.cuda.MPI
>>>> and
>>>>> it is running fine.
>>>>>
>>>>> Is it something known problem or I am missing something, please
>> comment.
>>>>> Thanks in advance for your valuable time.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> *With Regards,HIMANSHU JOSHI Graduate Scholar, Center for Condense
>> Matter
>>>>> TheoryDepartment of Physics IISc.,Bangalore India 560012*
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
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>>>
>>>
>>> --
>>>
>>>
>>>
>>> *With Regards,HIMANSHU JOSHI Graduate Scholar, Center for Condense Matter
>>> TheoryDepartment of Physics IISc.,Bangalore India 560012*
>>> _______________________________________________
>>> AMBER mailing list
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>>> http://lists.ambermd.org/mailman/listinfo/amber
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>
>
> *With Regards,HIMANSHU JOSHI Graduate Scholar, Center for Condense Matter
> TheoryDepartment of Physics IISc.,Bangalore India 560012*
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Received on Wed Apr 01 2015 - 00:00:03 PDT
