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...
> -----------------------------------------------------------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> -----------------------------------------------------------------------------------
> This email message is for the sole use of the intended recipient(s) and may
> contain
> confidential information. Any unauthorized review, use, disclosure or
> distribution
> is prohibited. If you are not the intended recipient, please contact the
> sender by
> reply email and destroy all copies of the original message.
> -----------------------------------------------------------------------------------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 10 2010 - 14:30:03 PDT
