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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Received on Tue Jul 26 2011 - 06:30:04 PDT
