From: Ivan Gregoretti (ivangreg_at_gmail.com)
Date: Fri Mar 07 2014 - 09:08:44 CST
Hi Douglas,
I think that using tee is a great suggestion. I do not expect
buffering of the data that is directed to standard output (the
computer screen).
This does require me to kill the ongoing simulation and start all over
again, now with tee. I'll try it.
Thank you all.
Ivan
Ivan Gregoretti, PhD
Bioinformatics
On Fri, Mar 7, 2014 at 9:55 AM, Douglas Houston
<DouglasR.Houston_at_ed.ac.uk> wrote:
> namd2 file.conf | tee file.log
>
> This might make it easier to monitor exactly what is being written to the
> file.
>
>
>
> Quoting Ivan Gregoretti <ivangreg_at_gmail.com> on Fri, 7 Mar 2014 09:52:43
> -0500:
>
>> 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
>>>
>>
>>
>>
>
>
>
>
> _____________________________________________________
> Dr. Douglas R. Houston
> Lecturer
> Institute of Structural and Molecular Biology
> Room 3.23, Michael Swann Building
> King's Buildings
> University of Edinburgh
> Edinburgh, EH9 3JR, UK
> Tel. 0131 650 7358
> http://tinyurl.com/douglasrhouston
>
> --
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> Scotland, with registration number SC005336.
>
>
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