Thanks Jason for quick reply
Now it is clear to me.
Thanks once again.
> Hello,
>
> On Wed, Apr 13, 2011 at 12:40 AM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
>>
>> Hello all
>>
>> I am running AMBER ADVANCED TUTORIALS TUTORIAL 3 - SECTION 3.5 Nmode
>> analysis.
>> Here I am confused about number of frames, numberof processor and thread.
>>
>> Input file is:
>>
>> Input file for running entropy calculations using NMode
>> &general
>> endframe=50, keep_files=2,
>> /
>> &nmode
>> nmstartframe=1, nmendframe=50,
>> nminterval=5, nmode_igb=1, nmode_istrng=0.1,
>> /
>>
>>
>> progress.log file is:
>>
>> 50 frames were read in and processed by ptraj for use in calculation.
>> Processing 10 frames with normal mode analysis.
>>
>
> This is to be expected from your input file, but I think you know that
> already.
>
>
>>
>> Starting calculations
>>
>>
>> Starting nmode calculations...
>> master thread is calculating 2 frames
>>
>>
>> I am running it in 5 processor.
>>
>
> This is why. You are analyzing 10 frames total, with 5 processors. Thus,
> each processor is taking 2 frames. In MPI-lingo, what you're actually
> executing, though, is called a "thread". So what you're running here are 5
> threads, not 5 "processors". (Although if you have 5 processors available,
> one would hope that the 5 threads run on 5 processors). There's nothing in
> MPI *against* running more "threads" than you have physical processors (it's
> just inefficient). The master thread is the thread that does all of the
> printout (for all intents and purposes, it's an arbitrarily assigned
> thread). It will also *always* operate on the largest number of frames.
> For instance, if you had 11 frames and 5 processors, the master thread would
> analyze 3 frames while the rest analyzed 2.
>
> Hope this helps clarify things,
>
> Jason
>
>
>> Here total frames processed are 10 then why calculation only for 2 frames.
>>
>> What is mean by "thread" in progress.log?
>>
>> So can anybody sugesst me to clear it.
>>
>> Sangita Kachhap
>> JRF
>> BIC,IMTECH
>> CHANDIGARH
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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> http://lists.ambermd.org/mailman/listinfo/amber
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Wed Apr 13 2011 - 02:00:05 PDT
