[gmx-users] decreased performance with free energy

[Szilárd Páll]

David,

Yes, it is greatly affected. The standard interaction kernels are very
fast, but the free energy kernels are known to not be as efficient as they
could and the larger the fraction of atoms involved in perturbed
interactions the more this work dominates the runtime.

If you are trying to set up production runs on this specific
hardware/software combination that you ran the tests on? There are a few
things you could try to get a bit better performance, but details may
depend on hardware software.

Expect major improvements in the upcoming release, we are doing some
thorough rework/optimization of the free energy kernels.

Cheers,
--
Szilárd


On Thu, Jul 18, 2019 at 10:24 AM David de Sancho <david.desancho at ehu.eus>
wrote:

> Thanks Szilárd
> I have posted both in the Gist below for the free energy simulation
> https://gist.github.com/daviddesancho/4abdc0d40e2355671ead7f8e40283b57
> May it have to do with the number of particles in the box that are affected
> by the typeA -> typeB change?
>
> David
>
>
> Date: Wed, 17 Jul 2019 17:09:21 +0200
> > From: Szil?rd P?ll <pall.szilard at gmail.com>
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Subject: Re: [gmx-users] decreased performance with free energy
> > Message-ID:
> >         <
> > CANnYEw4usZxnnwZ56tZbqSJwkT3Cu7Pf+8hhFXa6nFUg0o7U_g at mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Hi,
> >
> > Lower performe especially with GPUs is not unexpected, but what you
> report
> > is unusually large. I suggest you post your mdp and log file, perhaps
> there
> > are some things to improve.
> >
> > --
> > Szil?rd
> >
> >
> > On Wed, Jul 17, 2019 at 3:47 PM David de Sancho <david.desancho at ehu.eus>
> > wrote:
> >
> > > Hi all
> > > I have been doing some testing for Hamiltonian replica exchange using
> > > Gromacs 2018.3 on a relatively simple system with 3000 atoms in a cubic
> > > box.
> > > For the modified hamiltonian I have simply modified the water
> > interactions
> > > by generating a typeB atom in the force field ffnonbonded.itp with
> > > different parameters file and then creating a number of tpr files for
> > > different lambda values as defined in the mdp files. The only
> difference
> > > between mdp files for a simple NVT run and for the HREX runs are the
> > > following lines:
> > >
> > > > ; H-REPLEX
> > > > free-energy = yes
> > > > init-lambda-state = 0
> > > > nstdhdl                 = 0
> > > > vdw_lambdas = 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
> > >
> > > I have tested for performance in the same machine and compared the
> > standard
> > > NVT run performance (~175 ns/day in 8 cores) with that for the free
> > energy
> > > tpr file (6.2 ns/day).
> > > Is this performance loss what you would expect or are there any
> immediate
> > > changes you can suggest to improve things? I have found a relatively
> old
> > > post on this on Gromacs developers (
> > https://redmine.gromacs.org/issues/742
> > > ),
> > > but I am not sure whether it is the exact same problem.
> > > Thanks,
> > >
> > > David
> > > --
> > > Gromacs Users mailing list
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.