A quick look at the archives shows that several people have had this
problem.
I have observed this problem as well. Might be worth a look, since
incomplete restart files generated during a run are useless.
Dean
On 12/22/11 3:54 PM, "Sasha Perkins" <slperks49.gmail.com> wrote:
>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
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Dec 24 2011 - 13:30:03 PST
