[gmx-users] Computational load of Constraints/COM pull force

[Kenny Goossens]

Hi Mark


Here are two (intended as) equivalent runs:

https://uploadfiles.io/wtlu1

<https://uploadfiles.io/wtlu1>https://ufile.io/gmf03


For the disparity of 20ns/day to 90ns/day, the runs were actually subsequent umbrella sampling frames with the same input commands:<https://uploadfiles.io/wtlu1>


<https://uploadfiles.io/wtlu1>https://ufile.io/zfae3

<https://uploadfiles.io/wtlu1><https://ufile.io/zfae3>https://ufile.io/sjq4o


<https://uploadfiles.io/wtlu1>Kind regards,<https://ufile.io/zfae3>


<https://uploadfiles.io/wtlu1>Kenneth<https://ufile.io/zfae3>

<https://uploadfiles.io/wtlu1>

________________________________
Van: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> namens Mark Abraham <mark.j.abraham at gmail.com>
Verzonden: vrijdag 28 september 2018 15:08
Aan: gmx-users at gromacs.org
CC: gromacs.org_gmx-users at maillist.sys.kth.se
Onderwerp: Re: [gmx-users] Computational load of Constraints/COM pull force

Hi,

Are you able to upload the log files from two intended-as-equivalent runs
to a file-sharing service and share the link? We can comment better with
that data.

Mark

On Fri, Sep 28, 2018 at 2:46 PM Kenny Goossens <goossens_kenny at hotmail.com>
wrote:

> Dear all,
>
>
> I am performing umbrella sampling simulations on gromacs 2018.3, and
> because I need to sample every frame for a long time, I am trying to
> optimize the settings I'm using to get the maximum performance from my
> cluster. However, whenever I try running benchmarks, I notice that the
> relative amount of computing time that it takes to calculate constraints
> and COM pull force vary wildly (within a range of 2-30%). As you can
> imagine, this has a dramatic impact on the performance, as my performance
> for identical runs can fluctuate between 20-90 ns per day. I'm not sure if
> this is a general problem, or if this is caused by something I'm doing
> wrong. Is anyone able to help me out with this? Thank you!
>
>
> Kind regards,
>
>
> Kenneth
>
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