From: Ivan Gregoretti (ivangreg_at_gmail.com)
Date: Fri Mar 07 2014 - 10:57:31 CST
Hi Salvatore,
I just re-run this simulation using tee and now I have a better
understanding of the problem. It's not that my system is delaying
(buffering) output to file. It's a problem with namd2 itself.
I'll close this tread and open a new thread with a proper title in a
few minutes.
Thank you,
Ivan
Ivan Gregoretti, PhD
Bioinformatics
On Fri, Mar 7, 2014 at 11:43 AM, Cosseddu, Salvatore
<S.M.Cosseddu_at_warwick.ac.uk> wrote:
> Hi Ivan,
>
> That's quite strange. What version of namd are you using? I've never experienced anything like that with namd2.8 and namd2.9.
>
> What do you mean by "buffering the output in memory". Do you see the RAM usage increasing? How often does namd write in the log file? As far as I know, tail just follows the file descriptor and it should not theoretically create a conflict. Sometime checks and update your screen. Your kernel should be aware of what's going on to avoid clashes.
>
> Are you sure you have redirected correctly the output? Is there something written in the log file? With tee you actually duplicate the output, and if the redirection ">" and "tail" don't work, piping to tee will not work either. Before trying it you should check whether your tail is broken, or you are redirecting in the wrong way.
>
> It might also be a problem of memory http://stackoverflow.com/questions/9799451/tail-f-makes-disk-full
> maybe namd is filling the file system. To be honest there are many others possible explanations.
>
> Regards
> Salvatore
>
>
> ________________________________________
> From: Ivan Gregoretti <ivangreg_at_gmail.com>
> Sent: 07 March 2014 14:52
> To: Cosseddu, Salvatore
> Cc: namd-l_at_ks.uiuc.edu list
> Subject: Re: namd-l: Monitoring progress of an ongoing molecular dynamics simulation
>
> Hello Salvatore,
>
> I should have anticipated that response. Indeed, looking at the tail
> of the .log file is what I've been doing but the system is buffering
> the output in memory instead of writing to to the file.
>
> Perhaps this is an anomaly and the simulation crashed even though all
> processors continue working at full speed.
>
> Any thoughts?
>
> Ivan
>
>
>
>
> Ivan Gregoretti, PhD
> Bioinformatics
>
>
>
> On Fri, Mar 7, 2014 at 9:21 AM, Cosseddu, Salvatore
> <S.M.Cosseddu_at_warwick.ac.uk> wrote:
>> Dear Ivan,
>>
>> When you submit a calculation you usually use something like
>>
>> $ namd2 file.conf > file.log
>>
>> You you want to monitor the simulation you can just use
>>
>> $ tail -f file.log
>>
>> or
>>
>> $ less file.log
>>
>> and then press "F". If you want your output to be written more often you can change output frequency parameters such as outputEnergies.
>>
>> Regards
>> Salvatore
>>
>> ________________________________________
>> From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Ivan Gregoretti <ivangreg_at_gmail.com>
>> Sent: 07 March 2014 14:08
>> To: namd-l_at_ks.uiuc.edu list
>> Subject: namd-l: Monitoring progress of an ongoing molecular dynamics simulation
>>
>> Hello everybody,
>>
>> Could you share the way you monitor progress of an ongoing MD
>> simulation? ie What simulation step, roughly?
>>
>> We need to monitor progress using command line tools, not GUI. It
>> would be trivial with unix tools if the output weren't binary.
>>
>> I guess that a solution might involve VMD in text mode but all
>> suggestions are welcome.
>>
>> Thank you,
>>
>> Ivan
>>
>>
>>
>>
>>
>>
>> Ivan Gregoretti, PhD
>> Bioinformatics
>>
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