Re: [AMBER] Failure kReduceSoluteCOM with GPU

From: Fabrício Bracht <bracht.iq.ufrj.br>
Date: Sat, 30 Jul 2011 23:26:25 -0300

Hi Scott. This calculation works fine on amber cpu. I haven't had this
type of problems with the restraint energy. But I'll look into it.

As for Ross' answer. I'm glad to see that the problem reproduces with
you. If you need anything, just let me know.
Thank you again.
Fabrício

2011/7/30 Scott Le Grand <varelse2005.gmail.com>:
> First, try running this on CPU AMBER.  It looks to me like it's broken there
> as well.  This is beause your restraint energy starts off somewhere in the
> proximity of Neptune on the first iteration.  What happens from there is
> dependent on whether you're on a GPU or CPU to some extent but it's separate
> but equally bad.
>
> To see what I mean, set ntpr=1 in your md.in file and compare step 1
> energies on both CPU and GPU.
>
> Also, I got a file from Ross to replicate this but your command line in this
> thread uses different file names than are in the archive.  Could you send me
> your exact command line based on what you sent Ross?
>
> Scott
>
>
>
> 2011/7/29 Fabrício Bracht <bracht.iq.ufrj.br>
>
>> Hi Ross. Just cheking to see if you received my last email with the
>> file attached.
>> Thank you
>> Fabrício
>>
>> 2011/7/27 Ross Walker <ross.rosswalker.co.uk>:
>> > Hi Fabricio,
>> >
>> > If they are identical this means that this may be a new bug, although we
>> may
>> > have already inadvertently fixed it in the development version. Can you
>> send
>> > me your input files please (direct to me is fine) so I can try it here
>> and
>> > see if I can reproduce it.
>> >
>> > All the best
>> > Ross
>> >
>> >> -----Original Message-----
>> >> From: Fabrício Bracht [mailto:bracht.iq.ufrj.br]
>> >> Sent: Wednesday, July 27, 2011 12:05 PM
>> >> To: AMBER Mailing List
>> >> Subject: Re: [AMBER] Failure kReduceSoluteCOM with GPU
>> >>
>> >> Hi Ross. Here is my result to md5sum *.
>> >> md5sum: B40C: Is a directory
>> >> f4ed79de194d836246009d5c29051574  cuda_info.fpp
>> >> a9e4f660fcb5347b1273a8e3f76d3e74  gpu.cpp
>> >> 307e64e078aa5f1f22bd78fd224c9f4b  gpu.h
>> >> 9e6a4f93e46046cda29369feb0dd32e8  gputypes.cpp
>> >> 46f8ccf2bbee063ff35a73945b16a3a2  gputypes.h
>> >> 90ba8d068522a00074707a529469f5ea  kCalculateGBBornRadii.cu
>> >> 97fbbcfb8a3833509d94072ecab05643  kCalculateGBNonbondEnergy1.cu
>> >> 79fb7a5bba2a19ba351a7dd5996d31fc  kCalculateGBNonbondEnergy2.cu
>> >> 67a458e51a76162edbcc907e7135500c  kCalculateLocalForces.cu
>> >> ce308f4fbe9468d5505beb0099d58e76  kCalculatePMENonbondEnergy.cu
>> >> 9b240d418e391a71b590e6dc3bc3b0ff  kCCF.h
>> >> 5561a56bc236291cb87b4770453d67a4  kCLF.h
>> >> 86f220029e3a943a186ebcfd16e2dcd9  kCPNE.h
>> >> 9905ed2e705bccf1ae705279d85d0e57  kForcesUpdate.cu
>> >> edf2d74af7a4d401ccecc7bfa6d036c3  kNeighborList.cu
>> >> fd65d023597024a68565c5a0e5ffd86c  kNTPKernels.h
>> >> 49f952b429618228fca8e23f44223c58  kPGGW.h
>> >> 4aea91b87cbb3cf62b9fddafe607ab48  kPGS.h
>> >> 9c5951cdf94402d2c0396b74498f72f5  kPMEInterpolation.cu
>> >> 46f01611524128ea428c069ef58bd421  kPSSE.h
>> >> ada7d510598c88ed4adb8d32a9dbf73d  kRandom.h
>> >> eefe9bd32e04ba2bbe2eb5611a6464bd  kShake.cu
>> >> b07e184d2840ffae27d8af5415fae04a  kU.h
>> >> 6947e1fae477c0bb9c637062a0ddbfd8  Makefile
>> >> e5a6173273e6812669c21abcd1530226  Makefile.advanced
>> >> They are exactly the same. Now I really don´t know what to do. What do
>> >> you suggest?
>> >> Fabrício Bracht
>> >>
>> >> 2011/7/27 Ross Walker <ross.rosswalker.co.uk>:
>> >> > Hi Fabricio,
>> >> >
>> >> > Please take a look at the following which explains what md5sum's are:
>> >> > http://en.wikipedia.org/wiki/Md5sum
>> >> >
>> >> > In summary it creates an 'almost' unique fingerprint of a file. Thus
>> >> if I
>> >> > run md5sum on the files in my directory and you run md5sum on the
>> >> files in
>> >> > your directory one can compare the fingerprints produced. If they are
>> >> the
>> >> > same then we know the files are identical. The following is the list
>> >> of
>> >> > md5sum's for the files in my cuda directory which represents the
>> >> currently
>> >> > fully up to date released copy of AMBER with all bugfixes applied.
>> >> You
>> >> > should go to your machine and do the following:
>> >> >
>> >> > cd $AMBERHOME/src
>> >> > make clean
>> >> > cd pmemd/src/cuda
>> >> > md5sum *
>> >> >
>> >> > And then see if the fingerprint given (the bunch of letters and
>> >> numbers
>> >> > before each file) matches those I list below for each file. If they
>> >> do then
>> >> > we know your patch was all applied correctly and your system may be
>> >> > highlighting a real bug in the code. Note the GTX275 and GTX460's are
>> >> VERY
>> >> > different chip architectures hence why a subtle bug such as this may
>> >> only
>> >> > manifest itself on one card and not the other.
>> >> >
>> >> > All the best
>> >> > Ross
>> >> >
>> >> > foo.linux-jh9j:~/amber11_as_of_jul_22/src/pmemd/src/cuda> md5sum *
>> >> > md5sum: B40C: Is a directory
>> >> > f4ed79de194d836246009d5c29051574  cuda_info.fpp
>> >> > a9e4f660fcb5347b1273a8e3f76d3e74  gpu.cpp
>> >> > 307e64e078aa5f1f22bd78fd224c9f4b  gpu.h
>> >> > 9e6a4f93e46046cda29369feb0dd32e8  gputypes.cpp
>> >> > 46f8ccf2bbee063ff35a73945b16a3a2  gputypes.h
>> >> > 90ba8d068522a00074707a529469f5ea  kCalculateGBBornRadii.cu
>> >> > 97fbbcfb8a3833509d94072ecab05643  kCalculateGBNonbondEnergy1.cu
>> >> > 79fb7a5bba2a19ba351a7dd5996d31fc  kCalculateGBNonbondEnergy2.cu
>> >> > 67a458e51a76162edbcc907e7135500c  kCalculateLocalForces.cu
>> >> > ce308f4fbe9468d5505beb0099d58e76  kCalculatePMENonbondEnergy.cu
>> >> > 9b240d418e391a71b590e6dc3bc3b0ff  kCCF.h
>> >> > 5561a56bc236291cb87b4770453d67a4  kCLF.h
>> >> > 86f220029e3a943a186ebcfd16e2dcd9  kCPNE.h
>> >> > 9905ed2e705bccf1ae705279d85d0e57  kForcesUpdate.cu
>> >> > edf2d74af7a4d401ccecc7bfa6d036c3  kNeighborList.cu
>> >> > fd65d023597024a68565c5a0e5ffd86c  kNTPKernels.h
>> >> > 49f952b429618228fca8e23f44223c58  kPGGW.h
>> >> > 4aea91b87cbb3cf62b9fddafe607ab48  kPGS.h
>> >> > 9c5951cdf94402d2c0396b74498f72f5  kPMEInterpolation.cu
>> >> > 46f01611524128ea428c069ef58bd421  kPSSE.h
>> >> > ada7d510598c88ed4adb8d32a9dbf73d  kRandom.h
>> >> > eefe9bd32e04ba2bbe2eb5611a6464bd  kShake.cu
>> >> > b07e184d2840ffae27d8af5415fae04a  kU.h
>> >> > 6947e1fae477c0bb9c637062a0ddbfd8  Makefile
>> >> > e5a6173273e6812669c21abcd1530226  Makefile.advanced
>> >> >
>> >> >> -----Original Message-----
>> >> >> From: Fabrício Bracht [mailto:bracht.iq.ufrj.br]
>> >> >> Sent: Wednesday, July 27, 2011 8:53 AM
>> >> >> To: AMBER Mailing List; Scott Brozell
>> >> >> Subject: Re: [AMBER] Failure kReduceSoluteCOM with GPU
>> >> >>
>> >> >> 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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>> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >> >> >
>> >> >>
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Received on Sat Jul 30 2011 - 19:30:03 PDT
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