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 - 11:34:37 CDT

Hi Ross,

Just to elaborate a bit on the output issue... This job was running on 1
node (4 CPUs) and writing the output on the local disk. This job was the
last step of a multiple step job in which the initial steps were run
with sander.MPI (AMB 10). The sander output of the initial steps looks
absolutely fine and there is no apparent problem neither with my system
nor with simulation itself. The problem appeared only in the last step
that as run with pmemd.
I will look into it ..I'll test to see if I get the same problem on a
different node.

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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