AMBER Archive (2008)

Subject: RE: AMBER: pmemd 10 output

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Jun 27 2008 - 11:40:48 CDT

Hi Vlad,

 

This really does look to me like an issue with your file system - I have
never seen this from PMEMD myself and I can't see how you would end up with
this situation - it looks more to me like you have some kind of
malfunctioning raid device or something.

 

I have seen something similar to this on GPFS parallel file systems where
one of the meta data servers had failed such that you only see 4/5 of the
striped data for example. This can happen both in read and write mode, I.e.
a perfectly good file on disk can be read by the user as being bad because
of the striping issues or alternatively if the error occurs during a write
then the data can get written to disk with chunks missing.

 

How reproducible is the problem? Can you try running it and write to a local
scratch disk on the master node instead of a network drive (if that is what
you were doing) and see if the problem recurs.

 

All the best

Ross

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Vlad Cojocaru
Sent: Friday, June 27, 2008 9:25 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: pmemd 10 output

 

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
 
  

--
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Dr. Vlad Cojocaru
 
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Fax: ++49-6221-533298
 
e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
 
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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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