Hi Ross,
Sorry for the delay. What you saw have sense. Only one question about
the suggestion. Amber is now running over a Fedora 13 and as I see in
CUDA 4.2, it is available for fedora 14. Could I use that version or
should I need to upgrade my Fedora version?. We are finding the same
problem with a Tesla 2090 in CentOS, with CUDA 4.2
Here there are two outputs only varying the ntpr value (1 and 20,
respectively). These simulations where made with GB, but same case
happens with explicit waters in ntp ensemble. They were made with cuda
4.2 and a CentOS 6.3. As I said, if you use, for ntpr 1000 and 10000, no
differences are observed.
A V E R A G E S O V E R 2000 S T E P S
vs A V E R A G E S O V E R 100 S T E P S
NSTEP = 2000 TIME(PS) = 5.500 TEMP(K) = 300.26 PRESS =
0.0 NSTEP = 2000 TIME(PS) = 5.500 TEMP(K) =
300.61 PRESS = 0.0
Etot = -1292.3285 EKtot = 1849.9964 EPtot =
-3142.3248 Etot = -1292.5560 EKtot = 1852.1738
EPtot = -3144.7298
BOND = 465.9291 ANGLE = 1462.0663 DIHED =
815.1164 BOND = 464.2868 ANGLE = 1460.7239 DIHED
= 817.2981
1-4 NB = 525.3658 1-4 EEL = 7885.1834 VDWAALS =
-1173.7162 1-4 NB = 525.6464 1-4 EEL = 7880.5082
VDWAALS = -1174.9187
EELEC = -483.0180 EGB = -12639.2514 RESTRAINT =
0.0000 EELEC = -486.9575 EGB = -12631.3171
RESTRAINT = 0.0000
------------------------------------------------------------------------------
------------------------------------------------------------------------------
Best regards.
Fer
On Fri, 23 Nov 2012 17:27:29 -0800, Ross Walker wrote:
> Hi Fernando,
>
> It would help to see select excerpts from your output files in order
> to be
> able to understand exactly what you are describing here. Firstly why
> the
> GPU code is deterministic on identical hardware this is not
> necessarily
> true when changing the value of ntpr. The reason for this is that the
> code
> only calculates the energy when it is needed for printing. Normally
> it
> just calculates the gradients. Hence when you change ntpr you change
> the
> amount of work being done and this leads to different rounding
> differences
> that will lead to natural divergence of the MD trajectory. This is
> perfectly fine since you should always be running sufficient length
> runs
> to converge the properties you are interested in.
>
> Thus what you are reporting is probably reasonable but it would need
> a lot
> more info to understand fully.
>
> Another note though. You mention CUDA 4.0. Currently AMBER 12 with
> the
> latest patches, including a number of bug fixes for GPU only supports
> CUDA
> 4.2. This suggests to me that you are running with unlatched code. I
> would
> suggest running configure to apply the latest patches and then
> recompiling
> from scratch with cuda 4.2.
>
> All the best
> Ross
>
>
>
> On 11/23/12 3:14 AM, "Fernando Martín García" <fmgarcia.cbm.uam.es>
> wrote:
>
>> Dear Amber users,
>>
>> I have a doubt about ntpr option and GPU (and maybe CPU). I usually
>> run
>> my simulations with ntpr =1000. But we have been trying with
>> different
>> values (1, 500, 1000 and 10000). The system is running on Amber 12,
>> GPU
>> c2070, cuda 4.0.
>>
>> We observed that not difference in energy values between ntpr = 1000
>> and 10000, but they change with ntpr = 1 and 500 (between them and
>> with
>> the other values). I would like to know if it is caused because the
>> frequency in writing the energies what provoke the changes in them
>> (proportional to the frequency). I think I read something about that
>> while energies are been printed, leap-frog algorithm continues with
>> the
>> calculation of the coordinates, what would change dt.
>>
>> Thanks
>>
>> Fernando
>>--
>> ==============================================
>> Fernando Martín García
>> Molecular Modelling Group - Lab 312.1
>> Molecular Biology Center "Severo Ochoa"
>> C/ NICOLáS CABRERA, 1.
>> UAM University. Cantoblanco, 28049 Madrid. Spain.
>> TEL: (+34) 91-196-4662 FAX: (+34) 91-196-4420
>> Web: http://fertoledo.wordpress.com/
>> ==============================================
>>
>>_______________________________________________
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>>http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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--
==============================================
Fernando Martín García
Molecular Modelling Group - Lab 312.1
Molecular Biology Center "Severo Ochoa"
C/ NICOLáS CABRERA, 1.
UAM University. Cantoblanco, 28049 Madrid. Spain.
TEL: (+34) 91-196-4662 FAX: (+34) 91-196-4420
Web: http://fertoledo.wordpress.com/
==============================================
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Received on Tue Nov 27 2012 - 04:00:02 PST
