Hi Scott. Any idea about my problem?
Thank you
Fabrício
Em 26 de julho de 2011 10:07, Fabrício Bracht <bracht.iq.ufrj.br> escreveu:
> Hi Scott. How do I check if this specific bugfix has been applied
> correctly? Would it be something like md5sum * in
> $AMBERHOME/src/pmemd/src/cuda/ . And what should I look for?
> Thank you
> Fabrício
>
> 2011/7/26 Scott Brozell <sbrozell.rci.rutgers.edu>:
>> Hi,
>>
>> This looks like a problem addressed by bugfix.11.
>> I have not been following your threads closely,
>> but i read that you were having problems with the bugfixes.
>> You might inspect the files listed in bugfix.11 to determine
>> whether the bugfixes were really applied, while you are waiting
>> for someone that as been following your threads closely to reply.
>>
>> scott
>>
>> On Tue, Jul 26, 2011 at 12:44:10AM -0300, Fabrício Bracht wrote:
>>> Since I finally was able to compile amber11 with cuda support on my
>>> for my gtx460, I thought everything was fine, but it seems that now I
>>> have to set a few things in order to get my system running again. Let
>>> me explain more.
>>> I was simulating a protein inside a micele. I had a few tens of
>>> nanoseconds simulated on a gtx275. The system is comprised of water,
>>> organic solvent, surfactant, counterions and my protein (aprox. 60000
>>> atoms). When I tried to start a simulation using my restart files from
>>> the GTX275 on my gtx460 machine, I got the following error.
>>> Error: unspecified launch failure launching kernel kReduceSoluteCOM
>>> cudaFree GpuBuffer::Deallocate failed unspecified launch failure
>>>
>>> I thought it might have something to do with a problem in the restart
>>> file or something like this, so I recreated the inpcrd and prmtop
>>> files for the last configuration and tried to start a new fresh one in
>>> my gtx460 machine. Well, it didn't work out. I got the same error
>>> lines again.
>>> Here is my configuration file.
>>> MD parameters
>>> &cntrl
>>> imin = 0,
>>> irest = 1,
>>> ntx = 7,
>>> ntb = 2, pres0 = 1.0, ntp = 1, taup = 2.0,
>>> cut = 9.0,
>>> ntr = 1,
>>> ntc = 2,
>>> ntf = 2,
>>> tempi = 300.0,
>>> temp0 = 300.0,
>>> ntt = 3,
>>> gamma_ln = 1.0,
>>> nstlim = 5000000, dt = 0.002,
>>> ntpr = 10000, ntwx = 10000, ntwr = 1000
>>> /
>>> Restraints
>>> 5.0
>>> RES 1 317
>>> END
>>> END
>>>
>>> And here is the command line:
>>> pmemd.cuda -O -i md.in -c micel2.3.inpcrd -p micel2.3.prmtop -r
>>> md3.rst -o md3.out -ref micela2.3.inpcrd -inf md3.info -x md3.mdcrd
>>
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>>
>
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Received on Tue Jul 26 2011 - 16:30:03 PDT
