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.scripps.edu [mailto:owner-amber.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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Received on Sun Jun 29 2008 - 06:07:48 PDT
