Re: NAMD How to calculate ns/day

From: Shikha Sharma (shksharma398_at_gmail.com)
Date: Wed Dec 07 2016 - 23:01:44 CST

Good morning,

I am installing NAMD on ubuntu facing difficulty in the step "*Set up
build directory and compile"*

*./config Linux-x86_64-g++ --charm-arch net-linux-x86_64 T*his command is
showing error that ./config is not present

please suggest how i can correct this error

On Thu, Dec 8, 2016 at 4:29 AM, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>
wrote:

> Hi!
>
> Probably if you increase the number of steps, the difference will
> decrease. NAMD has some startup cost (parsing all the files etc...). What
> was the absolute wall time? If it was less than about 100 s I would not
> trust the results.
>
> Best,
> Ajasja
>
> On 7 December 2016 at 23:02, Jan Fredin <jfredin_at_sgi.com> wrote:
>
>> Hi,
>>
>> I am running the ApoA1 benchmark using 10,000 time steps and
>> outputtiming=100 with all the other input from the standard benchmark
>> apoa1.namd file. I’m running on a single node of Xeon Haswell with P100
>> GPUs. I am interested in the ns/day and thought 10,000 time steps would be
>> enough to have the WallClock time be usable in the ns/day calculation. I
>> found that taking the reciprocal of the average of the 6 Benchmark time
>> lines day/ns gave 26.3 ns/day but the straight calculation of ns simulated
>> (0.01 ns) and WallClock time (XX sec / 86400 sec/day) gave only 14.3
>> ns/day.
>>
>>
>>
>> What work contributing to the WallClock time is not being included in the
>> Benchmark time lines?
>>
>> Under what circumstances do the 2 methods of calculating ns/day converge
>> to the same value?
>>
>>
>>
>> Thanks,
>>
>> Jan
>>
>> --
>> Dr. Jan Fredin
>> SGI, Sr. Applications Engineer - Lead
>> Austin, TX
>> 651-683-7708 <(651)%20683-7708>
>> jfredin_at_sgi.com
>>
>>
>>
>
>

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