AMBER Archive (2009)

Subject: Re: [AMBER] error in output file

From: Vikas Sharma (vs_vikassharma_at_yahoo.co.in)
Date: Thu Apr 23 2009 - 08:33:49 CDT

Thanks Hemant..
So will i get the complete output file afgter the simulation is complete?
if not hw can i get tjhe complete output file.?

________________________________
From: Hemant Kumar <hemant_at_physics.iisc.ernet.in>
To: AMBER Mailing List <amber_at_ambermd.org>
Sent: Thursday, 23 April, 2009 5:50:25 PM
Subject: Re: [AMBER] error in output file

hi vikas,
same problem I have faced. simulation is running fine no need to
worry,only thing is you will not have updated out file.this generally
happens when you close out without saving(:q only).I suggest you to open
output file with write permission in future(like cat or something else)

With regrads,
Hemant Kumar
CCMT,Department of Physics
IISC,Bangalore

On Thu, 23 Apr 2009, Vikas Sharma wrote:

> 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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