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#37437 - 03/26/19 10:17 AM Re: Free version of CHARMM in parallel [Re: pmj]
SNOW001 Offline
Forum Member

Registered: 11/12/18
Posts: 16
Hello,

I run your file with different cores, when include:
{
stream gbsw_2.inp
stream dyna_2.inp (100 steps)
}
the time consumed:
1 core:
$$$$$ JOB ACCOUNTING INFORMATION $$$$$
ELAPSED TIME: 18.00 MINUTES
CPU TIME: 18.01 MINUTES
4 cores:
$$$$$ JOB ACCOUNTING INFORMATION $$$$$
ELAPSED TIME: 9.08 MINUTES
CPU TIME: 8.80 MINUTES


and when include:
{
stream gbsw_2.inp
stream emap.str
stream dyna_2.inp (100 steps)
}
the time consumed:
1 core:
$$$$$ JOB ACCOUNTING INFORMATION $$$$$
ELAPSED TIME: 18.62 MINUTES
CPU TIME: 18.63 MINUTES
4 cores:
$$$$$ JOB ACCOUNTING INFORMATION $$$$$
ELAPSED TIME: 10.50 MINUTES
CPU TIME: 9.91 MINUTES



Edited by SNOW001 (03/26/19 10:20 AM)

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#37438 - 03/27/19 04:20 AM Re: Free version of CHARMM in parallel [Re: SNOW001]
pmj Offline
Forum Member

Registered: 01/15/19
Posts: 46
Thank you so much for testing it. I see now that there is nothing wrong with the compilation I suppose. This the CPU time I get while running the script on 1, 4, 8, 12 and 16 cores. But in the end, I find it really slow on 16 cores for approximately 120 000 atoms (I managed to do around 10 ns/per day). I also tested the EEF1 with the EMAP and it seems not parallelised at all. Perhaps I will look into some other options.

GBSW EMAP NProc 1 4 8 12 16

+ + CPU time/min 23.38 11.16 10.17 12.28 10.2
+ - CPU time/min 21.12 9.40 8.13 11.16 8.17

Once more thank you for your help!
Have a great day

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#37439 - 03/27/19 04:28 AM Re: Free version of CHARMM in parallel [Re: pmj]
lennart Online   content

Forum Member

Registered: 09/25/03
Posts: 4742
Loc: ~ 59N, 15E
Note that for benchmarking parallel jobs it is generally the elapsed time that is important (ie, the time YOU have to wait), not the CPU-time.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#37440 - 03/27/19 04:37 AM Re: Free version of CHARMM in parallel [Re: lennart]
pmj Offline
Forum Member

Registered: 01/15/19
Posts: 46
Dear Prof. Nilsson,

I used the time ./run.sh command for each test. The time in the table is real time.

From what I saw in the CHARMM output files, the elapsed time and the cpu time are more or less the same.

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