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

[Lei Qian]

Thanks Dr. Lemkul,

This explanation makes sense to me.
Thank you!

Because I sent links to Both *gmx-users at gromacs.org <gmx-users at gromacs.org>*
and *gromacs.org_gmx-users at maillist.sys.kth.se
<gromacs.org_gmx-users at maillist.sys.kth.se>*
Please disregard the link I sent to *gromacs.org_gmx-users at maillist.sys.kth.se
<gromacs.org_gmx-users at maillist.sys.kth.se>*

Thank you again for your time and help!




On Wed, Aug 28, 2019 at 11:05 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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