[gmx-users] MD simulations on a remote workstation

Mark Abraham mark.j.abraham at gmail.com
Thu Apr 3 01:06:24 CEST 2014


On Apr 2, 2014 10:26 PM, "Amjad Farooq" <amjad at farooqlab.net> wrote:
>
> I have nothing to compare to!

You would have, if you were parallelizing over both machines (which would
usually be a waste of time). You didn't tell us you were only doing I/O
transfer.

> Well, I could run the same simulaton directly
> on the workstation itself. May be I should do that. But, realistically, I
> will have to run the test simulation for at least a month (with everything
> else being equal) to get any meaningful comparison.

Of performance? Two minutes, more like it.

> Anyway, I am wondering whether it would be worth the effort to upgrade my
> 1-Gb ethernet card to 10-Gb? If I am gonna get a mere 10% improvement in
> speed then that is rubbish. But, if that is gonna translate into 100%
> improvement (halve the production run time), then it is worth upgrading.

mdrun reports the time spent in i/o at the end of the log file. You can
measure that faster than type email!

Mark

> That remains to be seen.
>
> Amjad
>
>
>
> On Wed, Apr 2, 2014 at 2:44 PM, Dr. Vitaly Chaban <vvchaban at gmail.com
>wrote:
>
> > I believe the answer pretty much depends on how large speedup you get
> > with your present setup. Would you provide this info?
> >
> >
> >
> > Dr. Vitaly V. Chaban
> >
> >
> > On Wed, Apr 2, 2014 at 7:14 PM, Amjad Farooq <amjad at farooqlab.net>
wrote:
> > > Hi everyone,
> > >
> > > I am running Gromacs 5.0-beta on a remote workstation (next door)
from my
> > > PC. The two machines are networked via 1-Gigabit PCI-E ethernet cards
(on
> > > each machine) and a CAT-6 ethernet cable.
> > >
> > > My question is:
> > > Would my MD simulations benefit in terms of speed if I were to use
> > > 10-Gigabit PCI-E ethernet cards (they are damn expensive)? Is it
worth my
> > > dime and time? How much would I gain in terms of speed? Halve the run
> > time?
> > > Or even better?
> > >
> > > Thank you for any suggestions that you may have.
> > >
> > > Amjad Farooq
> > > --
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