Hi,
I've only found $AMBERHOME/AmberTools/src/configure.rej .
I've checked the files that were supposed to be patched by bugfix.11,
but wasn't able to confirm if they were patched or not due to my lack
of programming knowledge. Any tips here?
One other thing. Why is it that this simulation ran successfully on my
GTX275 computer but has problems with my GTX460?
Thank you
Fabrício
2011/7/27 Scott Brozell <sbrozell.rci.rutgers.edu>:
> Hi,
>
> The patch command should create a reject file: blabla.rej.
> So look for files with a rej extension.
> Also since in bugfix 11 there are only a few files to be patched in
> src/pmemd/src/cuda, you could look at those files to see if the
> patch has been applied:
> http://ambermd.org/bugfixes/11.0/bugfix.11
>
> scott
>
> On Tue, Jul 26, 2011 at 10:07:28AM -0300, Fabrício Bracht wrote:
>> 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 Wed Jul 27 2011 - 09:00:03 PDT
