AMBER Archive (2008)

Subject: Re: AMBER: pmemd 10 output

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Fri Jun 27 2008 - 11:24:58 CDT

Hi Ross,

Yes, at some point the ---- lines are truncated, the "check COM
velocity" phrase overflows the data lines. VOLUME starts not be printed
and towards 100000 steps I get lines where "check COM" appears after
NSTEP ... and so on .. the output gets really messy.

As for the input, I am well aware of the performance loss by running NVE
this way. However this was a test run in which I wanted to follow the
pressure of the system. Unfortunately ntp=0 does not allow that.

Best
vlad

Ross Walker wrote:
> Hi Vlad,
>
> I assume you mean the truncated --- lines, missing data and the missing
> carriage returns. This looks to me like a file system issue where your
> machine is actually not writing to disk properly. If this is over a NFS
> mount then I would run some serious stress tests on the system to make sure
> things are working properly.
>
> Also you may want to note that your input file is probably not optimum for
> performance. You have:
>
> ntp=1, taup=9999999, pres0=1.0, comp=44.6,
>
>
> Which is effectively the same as running constant volume, with ntb=1.
> However, computationally it still runs NPT which involves much more
> communication. This generally effects parallel scaling, more than low
> processor count performance.
>
> Generally the performance goes as:
>
> NVE > NVT > NPT
>
> And for thermostats:
>
> NTT=0 > NTT=1 >> NTT=3
>
> Hence you are running an NVT calculation but paying the performance penalty
> for a NPT calculation.
>
> All the best
> Ross
>
>
>> -----Original Message-----
>> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
>> Of Vlad Cojocaru
>> Sent: Friday, June 27, 2008 8:49 AM
>> To: AMBER list
>> Subject: AMBER: pmemd 10 output
>>
>> Dear Amber users,
>>
>> The pmemd of AMBER 10 produces some really strange looking output (see
>> attached, the three dot lines between NSTEP=250 and NSTEP=56500 are
>> there to indicate that I truncated the output). What is actually strange
>> is that the output looks fine till NSTEP=57500. Only after that, the
>> output is messed up.
>>
>> I haven't noticed this with any previous version of pmemd. Also not with
>> sander.MPI from amber 10.
>>
>> Thanks
>> vlad
>>
>>
>> --
>> --------------------------------------------------------------------------
>> --
>> Dr. Vlad Cojocaru
>>
>> EML Research gGmbH
>> Schloss-Wolfsbrunnenweg 33
>> 69118 Heidelberg
>>
>> Tel: ++49-6221-533266
>> Fax: ++49-6221-533298
>>
>> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>>
>> http://projects.villa-bosch.de/mcm/people/cojocaru/
>>
>> --------------------------------------------------------------------------
>> --
>> EML Research gGmbH
>> Amtgericht Mannheim / HRB 337446
>> Managing Partner: Dr. h.c. Klaus Tschira
>> Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
>> http://www.eml-r.org
>> --------------------------------------------------------------------------
>> --
>>
>>
>
>
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-- 
----------------------------------------------------------------------------
Dr. Vlad Cojocaru

EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg

Tel: ++49-6221-533266
Fax: ++49-6221-533298

e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de

http://projects.villa-bosch.de/mcm/people/cojocaru/

----------------------------------------------------------------------------
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
http://www.eml-r.org
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