[gmx-users] Mutant_md_1ns.log, WT_md_1ns.log + 1 more item

[Justin Lemkul]

On 8/28/19 10:52 AM, Lei Qian (via Google Drive) wrote:
> I've shared some items with you:
>
> Mutant_md_1ns.log
> https://drive.google.com/file/d/1qDoghj6Orc8yJTnLgvuhOERzMUfaH2Dd/view?usp=sharing&ts=5d66951d 
>
>
> WT_md_1ns.log
> https://drive.google.com/file/d/1gSTOnEpIj6UcqnfuNS-TvOosQKJCWJsa/view?usp=sharing&ts=5d66951d 
>
>
> WT_md_10ns.log
> https://drive.google.com/file/d/1UeLAcT4UZ6IpUKWJL7ahNRKmYmFt0Eeg/view?usp=sharing&ts=5d66951d 
>
>
> They're not attachments -- they're stored online. To open these items, 
> just click the links above.
>
> Dear Users,
>
> Sorry for this inconvenience.
> Could I ask a question about Gromacs running time for my Wide Type and 
> mutant protein (only 1 residue mutant)? Thanks!
>
> I attach the three log files here.
> (1) WT protein running for 1ns production step.(wall time: 1hour 40min).
> (2) WT protein running for 10ns production step (wall time: 6days 09h17).
> (3) Mutant protein running for 1ns production step. (wall time: 
> 17hours 30min).
>
> From the log files, I can find each of them ran on one node with 24 
> cores.
> It seems the wall times for (1) and (2) do not have linearly 
> proportional relationship. And (3) running took much longer time than 
> I expected, since mutant protein is only one residue mutant.

Was something else running when you did the 10-ns WT and 1-ns mutant 
runs? Your 1-ns WT run is fast:

                  (ns/day)    (hour/ns)
Performance:       14.348        1.673

But your 10-ns WT and 1-ns mutant are basically the same performance 
(much slower):

(WT)
                  (ns/day)    (hour/ns)
Performance:        1.566       15.329

(Mutant)
                  (ns/day)    (hour/ns)
Performance:        1.371       17.502

So I don't really see a difference between WT and mutant. The difference 
in performance is likely due to the hardware or other processes being 
run at the same time, causing a lag in performance.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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