[gmx-users] calculation time

[Mark Abraham]

On 19/10/2011 5:25 PM, ahmet y?ld?r?m wrote:
> Thanks for your reply
> I dont understand "step number is at least as large as nstlist". can 
> you some explain?

The first output you cite was written at step 100, of the 15M you asked 
for. nstlist is in your .mdp file. All this stuff really doesn't matter 
at all.

> Furthermore, if the file system doesnt write the buffer to the 
> destination screen/file, then does that mean there is a problem? for 
> example
> if it shows as the following:
> 15000000 steps,  30000.0 ps.

Not really. There's just some latency between the program writing the 
output and you being able to read it. If the program is allowed to exit 
normally, then all the buffers will be flushed eventually. Details vary 
from case to case and depend on your hardware and OS.

Mark

>
> 2011/10/19 Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>>
>
>     On 19/10/2011 5:04 PM, ahmet y?ld?r?m wrote:
>>     For example;
>>
>>     grompp -f run.mdp -p topol.top -c pr.gro -n index.ndx -o run.tpr
>>     mdrun -v -deffnm run
>>
>>     ...
>>     15000000 steps,  30000.0 ps.
>>     step 100, will finish Sun Nov 27 19:11:00 2011
>>
>>     Sometimes it shows as the following:
>>     15000000 steps,  30000.0 ps.
>>     That is, there is not "will finish Sun Nov 27 19:11:00 2011"
>>     sentence
>
>     It only writes it when certain conditions are true (e.g. step
>     number is at least as large as nstlist), and it only appears when
>     the file system decides to write the buffer to the destination
>     screen/file.
>
>     Mark
>
>
>>
>>
>>     2011/10/19 Emanuel Birru <Emanuel.Birru at monash.edu
>>     <mailto:Emanuel.Birru at monash.edu>>
>>
>>         You can get them in the log file. (At the bottom)
>>
>>         Cheers,
>>
>>
>>
>>
>>
>>
>>
>>         =========================================================
>>         Emanuel Birru
>>         PhD Candidate
>>
>>         Faculty of Pharmacy and Pharmaceutical Sciences
>>         Monash University (Parkville Campus)
>>         381 Royal Parade, Parkville
>>         Victoria 3052, Australia
>>
>>         Tel: Int + 61 3 9903 9187 <tel:%2B%2061%203%209903%209187>
>>         E-mail: emanuel.birru at monash.edu
>>         <mailto:emanuel.birru at monash.edu>
>>         www.pharm.monash.edu.au <http://www.pharm.monash.edu.au>
>>
>>         -----Original Message-----
>>         From: gmx-users-bounces at gromacs.org
>>         <mailto:gmx-users-bounces at gromacs.org>
>>         [mailto:gmx-users-bounces at gromacs.org
>>         <mailto:gmx-users-bounces at gromacs.org>] On Behalf Of Mark Abraham
>>         Sent: Wednesday, 19 October 2011 3:08 PM
>>         To: Discussion list for GROMACS users
>>         Subject: Re: [gmx-users] calculation time
>>
>>         On 19/10/2011 5:26 AM, ahmet y?ld?r?m wrote:
>>         > Dear users,
>>         >
>>         > Sometimes, in the end ( in production simulation), Gromacs
>>         doesn't
>>         > show calculation/finish time on screen, why? How can we
>>         show it?
>>
>>         I don't know what you mean.
>>
>>         Mark
>>         --
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>>
>>
>>
>>     -- 
>>     Ahmet YILDIRIM
>>
>>
>
>
>     --
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>
>
>
> -- 
> Ahmet YILDIRIM
>
>

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