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.desan...@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.szil...@gmail.com> > > To: Discussion list for GROMACS users <gmx-us...@gromacs.org> > > Subject: Re: [gmx-users] decreased performance with free energy > > Message-ID: > > < > > cannyew4uszxnnwz56tzbqsjwkt3cu7pf+8hhfxa6nfug0o7...@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.desan...@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-requ...@gromacs.org. -- 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-requ...@gromacs.org.
