AMBER Archive (2009)

Subject: Re: [AMBER] error in output file

From: Vikas Sharma (vs_vikassharma_at_yahoo.co.in)
Date: Thu Apr 23 2009 - 08:55:20 CDT

thanks a lot Ross

 

________________________________
From: Ross Walker <ross_at_rosswalker.co.uk>
To: AMBER Mailing List <amber_at_ambermd.org>
Sent: Thursday, 23 April, 2009 6:58:18 PM
Subject: RE: [AMBER] error in output file

Hi Vikas,

You should use 'tail' or 'less' which is effectively a read only version of
vi. Using vi is find but if you accidentally did <esc>:wq to quit then you
may have inadvertantly written something to the output file which would
break the handle that sander currently has open causing the file to no
longer be written to.

Alternatively your system could just be buffering a LOT of output data. In
the second case you just need to wait until your job finishes and the buffer
should then get flushed to disk. If however, it is the first case then you
are toast and will need to rerun your simulation.

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Vikas Sharma
> Sent: Thursday, April 23, 2009 4:58 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] error in output file
>
> Thanks Carlos..
> So is there any remedy?
>
> actually 2 days ago i used ssh to for logging in to the node..the to
> check the output i used gedit which is not allowed in ssh...so i could
> not see the output..so then i used vi editor
>
>
>
>
> ________________________________
> From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
> To: AMBER Mailing List <amber_at_ambermd.org>
> Sent: Thursday, 23 April, 2009 5:12:02 PM
> Subject: Re: [AMBER] error in output file
>
> sounds like the simulation is running fine but your filesystem is
> buffering the write to the mdout file. often the data doesn't get
> flushed until the file is closed. the mdinfo file is closed at each
> write, so it's got current data.
>
>
>
> On Thu, Apr 23, 2009 at 7:39 AM, Vikas Sharma
> <vs_vikassharma_at_yahoo.co.in> wrote:
> > Dear All
> >
> > i am running production MD..when i checked the output file from
> remote host i could see 170000 steps completed...after 2 days today
> again i checked the output file i could see the same no. of steps being
> completed...then i checked the mdinfo file i could see 545000 steps
> completed..then i logged directly in the node and checked the output
> file,it again showed 170000 steps as completed and the mdinfo file
> showed 545000 steps as completed...when i top i could see the job still
> running.........
> >
> > please suggest a solution..
> >
> >
> >
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