Hello Ross,
I posted my answers between the lines.
Quoting Ross Walker <ross.rosswalker.co.uk>:
> Hi Bongkeun,
>
> Unfortunately it is going to be hard to figure out what is going on here
> without doing some more digging. The error you see is somewhat misleading
> since it is effectively what happens if your system blows up. Some atom gets
> a huge force on it etc etc. There are a number of things that can cause this
> including everything from a bug in the code, issues with force field
> parameters and even flakey hardware. Can you check a few things for me.
>
> 1) Verify you definitely have bugfix.12 applied. Your output file should
> say:
>
> |--------------------- INFORMATION ----------------------
> | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
> | Version 2.1
> | 12/20/2010
>
Yes, it is from bugfix.12
> 2) Verify that you can reproduce this error if you start this calculation
> again on the same hardware. Does it always occur at the same point.
>
No, I got this error randomly.
> 3) Confirm exactly what hardware you are using. If this is NOT a C20XX
> series board then the chance of it being flakey hardware are much higher.
>
It's from C1070 family
> 4) Finally try setting NTPR=1 and rerunning the calculation to see if it
> crashes at the same place. That way we will be able to see exactly what
> happened before the error was triggered.
>
I cannot see any error when using NTPR=1. This error came about once
in 100ns randomly. I assume than heating on GPU may occur this error,
so I separated runs in every 10ns and allowed 5 min idling to cool
down GPUs. Each run spends about 10 hours.
Thanks.
Bongkeun Kim
> Thanks,
>
> All the best
> Ross
>
>> -----Original Message-----
>> From: Bongkeun Kim [mailto:bkim.chem.ucsb.edu]
>> Sent: Monday, February 14, 2011 11:12 AM
>> To: amber
>> Subject: [AMBER] max pairlist cutoff error on octahedral box
>>
>> Hello,
>>
>> I got the following error message when I run on AMBER 11 GPU.
>> -------------------------------------------------------------
>> NSTEP = 420000 TIME(PS) = 155540.000 TEMP(K) = 312.04 PRESS
>> = -187.3
>> Etot = -18757.4114 EKtot = 4575.5386 EPtot =
>> -23332.9500
>> BOND = 58.8446 ANGLE = 136.7403 DIHED =
>> 166.0070
>> 1-4 NB = 56.7262 1-4 EEL = -31.1536 VDWAALS =
>> 3080.9761
>> EELEC = -26801.0907 EHBOND = 0.0000 RESTRAINT =
>> 0.0000
>> EKCMT = 2199.9567 VIRIAL = 2501.7076 VOLUME =
>> 74625.8314
>> Density =
>> 0.9841
>>
>>
> ----------------------------------------------------------------------------
> --
>>
>> | ERROR: max pairlist cutoff must be less than unit cell max sphere
> radius!
>> -----------------------------------------------------------------
>>
>> This error occurred randomly and once I used the last rst file I can
>> continue running. I already applied bugfix 12 and I used cutoff=8
>> Please let me know how to avoid this error.
>> Thank you.
>> Bongkeun Kim
>>
>>
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Mon Feb 14 2011 - 14:00:06 PST
