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

[Kenny Goossens]

Hi,


For completed runs, I refer to umbrella2.log/umbrella3.log. The ligand in these frames are only separated by 0.1 nm, so I don't seehow this could meaningfully impact the computational cost.

Regarding the DD issues, these happen almost always after I parallellize the simulation over more than one node. I should mention that I am simulating an enzyme in a lipid bilayer, so this is most likely the cause. the load balancing issues are also present regardless of the performance.


Kind regards,


Kenneth

________________________________
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 16:30
Aan: gmx-users at gromacs.org
Onderwerp: Re: [gmx-users] Computational load of Constraints/COM pull force

Hi,

That looks like the shape/size of the simulation box has changed such that
the domain decomposition load balancing is having a differently hard time.
Do you have some runs that completed normally? The performance report from
the bottom of the log file is missing from the files you shared.

Mark

On Fri, Sep 28, 2018 at 3:50 PM Kenny Goossens <goossens_kenny at hotmail.com>
wrote:

> Hi Mark
>
>
> Here are two (intended as) equivalent runs:
>
> https://uploadfiles.io/wtlu1
[https://uploadfiles.io/assets/img/welcome/1.gif]<https://uploadfiles.io/wtlu1>

Uploadfiles.io - test4.log<https://uploadfiles.io/wtlu1>
uploadfiles.io
Upload files, for free, securely, anonymously, without limits. @UploadFilesFree


>
> <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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