AMBER Archive (2008)

Subject: Re: AMBER: timing info output from pmemd

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Fri Jul 11 2008 - 07:33:31 CDT

In fact, I was trying to test whether I still get the output problem
described before in the previous thread by using mdout_flush_interval to
0 or other value. In parallel, I wanted to see how much slower pmemd is
when mdout_flush_interval is set to 0 for instance. Since the ouptut
problem appears in average only after about 25000 steps, having such a
regular output about the timing (in a similar fashion NAMD does) would
tell me immediately the difference in performance between runs using
different mdout_flush_interval without the need to test that in advance.

If the difference in performance is significant, it would be useless to
run tests of at least 25000 steps to see if the output problem is still
present.

On the other hand, I am thinking of going into compiling a version of
amber 10 for my own use as the compilation we have here produces these
problems and I was thinking that such a regular timing output would be
convenient for fast tests of different compilations (using different
compilers). But of course this can be done by running the benchmarking runs.

To summarize, this output is not really a necessary feature .. I was
just wondering if there is an option to have it.

Vlad

Robert Duke wrote:
> No, and I guess I don't understand why you would want to be able to do
> that. Are you looking for variations in the performance of the
> machine, or what? In pmemd there is what is basically a
> parallelization log (logfile), which is sort of similar to the sander
> profile file in that it offers summary parallel performance info. It
> also has the ability to dump details about how fft's are being
> distributed and details about workload redistribution, including just
> how much time each processor is spending doing what since the last
> workload redistribution. This is intended for working on parallel
> performance problems, and the higher dumping levels may not even be
> documented (the namelist variable is loadbal_verbose in &cntrl,
> default 0, 1 gives a bit additional info, by 3 you are getting a whole
> bunch of detail). This may not be what you want, but it is what I use
> to debug parallel performance problems.
> Regards - Bob Duke
>
> ----- Original Message ----- From: "Vlad Cojocaru"
> <Vlad.Cojocaru_at_eml-r.villa-bosch.de>
> To: "AMBER list" <amber_at_scripps.edu>
> Sent: Friday, July 11, 2008 4:49 AM
> Subject: AMBER: timing info output from pmemd
>
>
>> Dear Bob, amber users,
>>
>> Is there a way to print timing info (time/mdstep) at regular
>> intervals in pmemd (and/or sander) ?
>>
>> Vlad
>>
>> --
>> ----------------------------------------------------------------------------
>>
>> Dr. Vlad Cojocaru
>>
>> EML Research gGmbH
>> Schloss-Wolfsbrunnenweg 33
>> 69118 Heidelberg
>>
>> Tel: ++49-6221-533266
>> Fax: ++49-6221-533298
>>
>> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>>
>> http://projects.villa-bosch.de/mcm/people/cojocaru/
>>
>> ----------------------------------------------------------------------------
>>
>> EML Research gGmbH
>> Amtgericht Mannheim / HRB 337446
>> Managing Partner: Dr. h.c. Klaus Tschira
>> Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
>> http://www.eml-r.org
>> ----------------------------------------------------------------------------
>>
>>
>>
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-- 
----------------------------------------------------------------------------
Dr. Vlad Cojocaru

EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg

Tel: ++49-6221-533266
Fax: ++49-6221-533298

e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de

http://projects.villa-bosch.de/mcm/people/cojocaru/

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Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
http://www.eml-r.org
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