Dear amber users/coders,
I am having a similar problem with my GPU. I would like to ask if we
will have this new bug fix today.
thank you so much
peker milas
On Sun, Jan 2, 2011 at 12:17 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Dmitry,
>
> This problem is known, it is caused by the 10 angstrom cutoff with a relatively small box size. If you set your first simulations cutoff to 8 angstroms it should work fine.
>
> A bugfix addressing this problem and some other minor issues will be released on Monday. Stay tuned.
>
> All the best
> Ross
>
>> -----Original Message-----
>> From: Dmitry Mukha [mailto:dvmukha.gmail.com]
>> Sent: Sunday, January 02, 2011 6:12 AM
>> To: AMBER Mailing List
>> Subject: [AMBER] calculations failed on GPU with ntr=1 (with bugfix 11
>> applied)
>>
>> Amber 11 pmemd.cuda fails to get a meaningful results with the following
>> input, but with the second one works fine. All available bugfixes including
>> 11th were applied. The output files are attached to the mail. Surprisingly,
>> all steps were completed, but with NaN bond and huge angle energy values.
>> Also coordinates became infinite.
>>
>> Stage 4 - density equilibration
>> &cntrl
>> imin=0,irest=1,ntx=5,
>> nstlim=25000,dt=0.002,
>> igb=0, ntc=2,ntf=2,ntp=1, taup=1,
>> cut=10.0, ntb=2,
>> ntpr=500, ntwx=500, ntwr=25000,
>> iwrap=1,
>> ioutfm=1, ig=75397747,
>> ntt=3, gamma_ln=2.0, temp0=300.0,
>> * ntr=1*,
>> &end
>> Restraints for PMEMD
>> 2.0
>> RES 1 1
>> END
>> END
>>
>> Stage 4 - density equilibration
>> &cntrl
>> imin=0,irest=1,ntx=5,
>> nstlim=25000,dt=0.002,
>> igb=0, ntc=2,ntf=2,ntp=1, taup=1,
>> cut=10.0, ntb=2,
>> ntpr=500, ntwx=500, ntwr=25000,
>> iwrap=1,
>> ioutfm=1, ig=75397747,
>> ntt=3, gamma_ln=2.0, temp0=300.0,
>> * ntr=0,*
>> &end
>> Restraints for PMEMD
>> 2.0
>> RES 1 1
>> END
>> END
>> *
>> $ uname -a*
>> Linux 2.6.31.5-127.fc12.x86_64 #1 SMP Sat Nov 7 21:11:14 EST 2009 x86_64
>> x86_64 x86_64 GNU/Linux
>> *$ cudafe --version*
>> cudafe: NVIDIA (R) Cuda Language Front End
>> Portions Copyright (c) 2005-2010 NVIDIA Corporation
>> Portions Copyright (c) 1998-2005 Edison Design Group Inc.
>> Based on Edison Design Group C/C++ Front End, version 4.1 (Nov 3 2010
>> 16:25:55)
>> Cuda compilation tools, release 3.2, V0.2.1221
>>
>> --
>> Sincerely,
>> Dmitry Mukha
>> Institute of Bioorganic Chemistry, NAS, Minsk, Belarus
>
>
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Received on Mon Jan 03 2011 - 08:00:05 PST
