Cool, I was thinking as a hack you could run say 10ns on the GPU and
then iwrap with sander on the CPU and then repeat...trivial to script
up...
~Levi
On 6/10/10, Sasha Buzko <obuzko.ucla.edu> wrote:
> 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...
>>> -----------------------------------------------------------
>>>
>>> _______________________________________________
>>> 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
>>
>>
> _______________________________________________
> 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 - 14:30:06 PDT
