[gmx-users] Re: Significant slowdown in 4.6? (4.6.3)

[Jonathan Saboury]

Figured out the problem. For some reason one thread is being taken up 90%
by the system. If I run it with 6 threads it runs fast. Never experienced
this on linux though, very curious.

Sorry if i wasted your time.

-Jonathan Saboury


On Fri, Sep 20, 2013 at 7:58 AM, Jonathan Saboury <jsabou1 at gmail.com> wrote:

> I have a Intel i7-2630QM CPU @ 2.00GHz on my laptop with 4.6.3 installed
> and a desktop with an i3-3220 with 4.5.5 installed.
>
> I am trying the same energy minimization on each of these machines. My
> desktop takes a few seconds, my laptop takes hours. This doesn't make much
> sense bc benchmarks indicated that my laptop should be faster.
>
> Only conclusion I can come up with is that it is the difference in
> versions. Any other explanations?
>
> Here are the files I am using: http://www.sendspace.com/file/a1cdch
>
> List of commands used are found in: commands.txt
>
> I use the last command "mdrun -v -deffnm em" on each machine, and the
> files were built with 4.6.3 (my laptop).
>
> If you need any more information please let me know.
>
> Thank you!
>
> -Jonathan
>