Ahh excellent! Those mistakes are sometimes hard to track down...
Thanks so much!
~Levi
On Fri, Jun 25, 2010 at 4:53 PM, Scott Le Grand <SLeGrand.nvidia.com> wrote:
> Found the problem and fixed it. In gpu.cpp, in the routine
> gpu_neighborlist_setup, there are three instances of:
>
> If (gpu->sim.ntp > 0)
>
> Change all of them to:
>
> if ((gpu->sim.solventMolecules > 0) || (gpu->sim.soluteAtoms > 0))
>
> Dumb mistake on my part...
>
>
> -----Original Message-----
> From: Sasha Buzko [mailto:obuzko.ucla.edu]
> Sent: Thursday, June 10, 2010 14:01
> To: AMBER Mailing List
> Subject: Re: [AMBER] pmemd.cuda segmentation fault with iwrap=1 on NVT/NVE
>
> Not yet.
> Scott Le Grand is looking into it and should post once he finds the cause.
>
> Sasha
>
>
> Levi Pierce wrote:
> > Was this issue resolved? I am experiencing the same thing with a
> > simple deca-alanine system. I ran with iwrap=0 for 50ns and the water
> > coordinates eventually get so large the restart file and
> > md trajectory file get corrupted. I am running the vanilla Amber11
> > pmemd.cuda version on a GTX480. I can send along any files that might
> > be helpful...
> >
> > Thanks,
> > ~Levi
> >
> > On 5/28/10, Scott Le Grand <SLeGrand.nvidia.com> wrote:
> >
> >> Can you email me an example that shows the iwrap behavior?
> >>
> >> That's likely an easy fix...
> >>
> >>
> >> -----Original Message-----
> >> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf
> >> Of Sasha Buzko
> >> Sent: Friday, May 28, 2010 09:40
> >> To: AMBER Mailing List
> >> Subject: [AMBER] pmemd.cuda segmentation fault with iwrap=1 on NVT/NVE
> >>
> >> Hi all,
> >> I've compiled pmemd.cuda on a 64-bit CentOS 5.3 for use with a GTX280.
> >> The tests came out pretty good - one failure (proteosome, low memory),
> >> and 5 more generated errors. I'm giving the deviceQuery output below.
> >>
> >> I'm testing pmemd.cuda with a pre-equilibrated explicit solvent system
> >> (about 60 000 atoms). The NPT version ran perfectly fine with no errors.
> >> However, runs at NVT or NVE parameters lead to an immediate segmentation
> >> fault whenever iwrap=1. There are no error messages, just instant
> >> failure. At the same time, both sander and regular pmemd run normally
> >> with the input files below. I had to remove the iwrap=1 line for
> >> pmemd.cuda to run.
> >> Ideally, I'd like to keep iwrap enabled for long runs, so I wonder if
> >> it's a known issue and whether it can be fixed.
> >>
> >> Here are the input files for each run of pmemd.cuda
> >>
> >> The NPT input parameters (works ok):
> >> imin = 0, irest = 1, ntx = 7,
> >> ntb = 2, pres0 = 1.0, ntp = 1,
> >> taup = 2.0, iwrap = 1,
> >> cut = 10, ntr = 0,
> >> ntc = 2, ntf = 2,
> >> temp0 = 300.0,
> >> ntt = 3, gamma_ln = 2.0,
> >> nstlim = 20000, dt = 0.001,
> >> ntpr = 1000, ntwx = 1000, ntwr = 1000
> >>
> >> The NVT input parameters (segmentation fault):
> >> imin = 0, irest = 1, ntx = 7,
> >> ntb = 1,
> >> iwrap = 1,
> >> cut = 10, ntr = 0,
> >> ntc = 2, ntf = 2,
> >> temp0 = 300.0,
> >> ntt = 3, gamma_ln = 2.0,
> >> nstlim = 20000, dt = 0.001,
> >> ntpr = 1000, ntwx = 1000, ntwr = 1000
> >>
> >> The NVE input parameters (segmentation fault):
> >>
> >> imin = 0, irest = 1, ntx = 7,
> >> ntb = 1, ntp = 0,
> >> iwrap = 1,
> >> cut = 10, ntr = 0,
> >> ntc = 2, ntf = 2,
> >> temp0 = 300.0,
> >> ntt = 0,
> >> nstlim = 20000, dt = 0.001,
> >> ntpr = 1000, ntwx = 1000, ntwe = 1000, ntwr = 1000
> >>
> >> Any suggestions would be appreciated.
> >>
> >> Thanks in advance
> >>
> >>
> >> Sasha
> >>
> >>
> >>
> >>
> >> [sasha.redwood release]$ ./deviceQuery
> >> ./deviceQuery Starting...
> >>
> >> CUDA Device Query (Runtime API) version (CUDART static linking)
> >>
> >> There is 1 device supporting CUDA
> >>
> >> Device 0: "GeForce GTX 280"
> >> CUDA Driver Version: 3.0
> >> CUDA Runtime Version: 3.0
> >> CUDA Capability Major revision number: 1
> >> CUDA Capability Minor revision number: 3
> >> Total amount of global memory: 1073020928 bytes
> >> Number of multiprocessors: 30
> >> Number of cores: 240
> >> Total amount of constant memory: 65536 bytes
> >> Total amount of shared memory per block: 16384 bytes
> >> Total number of registers available per block: 16384
> >> Warp size: 32
> >> Maximum number of threads per block: 512
> >> Maximum sizes of each dimension of a block: 512 x 512 x 64
> >> Maximum sizes of each dimension of a grid: 65535 x 65535 x 1
> >> Maximum memory pitch: 2147483647 bytes
> >> Texture alignment: 256 bytes
> >> Clock rate: 1.30 GHz
> >> Concurrent copy and execution: Yes
> >> Run time limit on kernels: Yes
> >> Integrated: No
> >> Support host page-locked memory mapping: Yes
> >> Compute mode: Default (multiple host
> >> threads can use this device simultaneously)
> >>
> >> deviceQuery, CUDA Driver = CUDART, CUDA Driver Version = 4243455, CUDA
> >> Runtime Version = 3.0, NumDevs = 1, Device = GeForce GTX 280
> >>
> >>
> >> PASSED
> >>
> >> Press <Enter> to Quit...
> >> -----------------------------------------------------------
> >>
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Received on Fri Jun 25 2010 - 19:30:03 PDT
