Ross,
Thanks for the prompt reply. Unfortunately, still after killing the job in
mid cycle, the whole file is still not being written. Additionally, I tried
running this same input file with sander and the complete file IS written
at all the cycles I ask it to write the rst file. The issue seems to be
only present with pmemd. Could there be other reasons as to why the
complete file isn't being written in any of the other cycles besides the
last one? Or if it is a buffering issue, are there any ways to manually
force the complete file to be written?
Thanks in advance,
Sasha Perkins
Graduate Student, Penn State University
On Thu, Dec 22, 2011 at 12:10 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Sasha,
>
> I suspect this is a buffering issue with the file system. Have you tried
> killing a job mid cycle and seeing if the restart file then gets the rest
> of
> the information written to it?
>
> What is happening is that your operating system is buffering the
> information
> being written to the restart file. As far as pmemd is concerned everything
> got written correctly and indeed if it were to close and reopen the restart
> file it would be able to read all the information. Also if your job
> crashes,
> since it is the operating system that is buffering it so the remaining
> restart file information should get flushed. Your best option is to try
> killing a job 'kill -9 PID' and see what happens to the restart file that
> is
> written.
>
> If it is still not writing it then we can take a look and see what else
> might be causing it.
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: Sasha Perkins [mailto:slperks49.gmail.com]
> > Sent: Thursday, December 22, 2011 8:48 AM
> > To: amber.ambermd.org
> > Subject: [AMBER] Restart file for pmemd not showing all information
> >
> > Hello,
> >
> > This is one of my steps in my simulation. I noticed, however, that each
> > time the restart file is written during my run, there are about 80
> > atoms
> > (my system has a total of 9600 atoms) who's information is not written
> > in
> > the restart file, as well as the box information is missing. However,
> > at
> > the end of the run, all information is written for the last cycle.
> > Prior
> > runs with the same input file but using sander showed all information
> > in
> > the restart files every time the file was written.
> >
> > Below is my input file which I am running using pmemd in amber 11.
> > &cntrl
> > imin = 0, irest=1, ntx=5,
> > ntb=2, ntp=1, taup=1.0,
> > pres0=0.98,
> > cut = 20.0,
> > ntc=2, ntf=2,
> > temp0=298.0,
> > ntt=3, gamma_ln=5,
> > nstlim= 400000, dt =0.002,
> > ntpr=100, ntwx= 100, ntwr = 1000
> > &end
> >
> > Any helpful information regarding how to fix this, or if this is
> > normal,
> > would be greatly appreciated since I need all information to be written
> > in
> > the restart files in case my runs unexpectedly get terminated before
> > the
> > maximum number of cycles is reached.
> >
> > Thank you,
> >
> > Sasha Perkins
> > Graduate Student, Penn State University
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Thu Dec 22 2011 - 14:00:03 PST
