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 - 00:00:02 PDT
