AMBER Archive (2008)

Subject: Re: AMBER: pmemd 10 output

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Thu Jul 10 2008 - 05:19:08 CDT

Dear Amber users,

Coming back to the pmemd 10 output problem I reported in the thread
below, I did test different nodes (writing locally as well as via the
network), with iwrap=1 and iwrap=0 and the problem is very reproducible.
I get it everytime I run pmemd10 but not sander.MPI 10 or amber9.
Attached is a sample of the output. This is very strange.

If anybody is able to explain this, I'd be very grateful for some
suggestions (could be a compilation issue). If there was a file system
issue, why it doesnt happen with any other executable ?

Best wishes
vlad

-----------------input script --------------------
# NVE production run
 &cntrl
  imin=0, ntx=5, irest=1, ntrx=1, ntxo=1,
  ioutfm=1, ntave=100000, iwrap=0,
  ntpr=250, ntwx=1000, ntwv=25000, ntwe=25000,
  ntf=1, ntb=2,
  dielc=1.0, scnb=2.0, scee=1.2, cut=10.0,
  nsnb=100, igb=0,
  ntr=0,
  nstlim=1000000,
  t=0.0, dt=0.001,
  ntt=3, gamma_ln=0.0, tempi=300.0, temp0=300.0,
  vlimit=15,
  ntp=1, taup=9999999, pres0=1.0, comp=44.6,
  ntc=2, tol=0.00000001,
 /
 

Ross Walker wrote:
>
> 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> [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/
>
>
>
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>
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>
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>
> 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
> ----------------------------------------------------------------------------
> 

-- 
----------------------------------------------------------------------------
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/

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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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