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 - 17:00:04 PDT
