hi. can i get a link to the redmine issue? I decided to install 4.6.7 instead of 5.0.1 because of this.
On Mon, Sep 22, 2014 at 5:52 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > On Mon, Sep 22, 2014 at 11:02 AM, Machtens, Jan-Philipp < > j.macht...@fz-juelich.de> wrote: > > > Thanks for the reply! > > However, the differences between GPU runs and CPU-only runs for > > Gromacs 5.x that I observe are statistically significant (10-100 ns for > > each test sim) (and reproducible). > > In contrast, with Gromacs 4.6.x I do not have significant differences > that > > I can apparently attribute to the use of GPUs. > > > > OK. I would expect to observe a *total* energy that was constant across 4.6 > and 5 and CPU-only vs with-GPUs. Please open an issue at > http://redmine.gromacs.org/ and describe as much detail as you can. A > tarball with .tpr, grompp-input, and whole .log files would let us analyze > and reproduce your observations and work out what is going on. Thanks! > > Is there any other reason for the deviation with GPU and GROMAC 5.x ? > > > Not by design :-) All the relevant changes that I can think of either > removed code paths for old hardware, or tweaked performance (in various > kinds of ways). There were a bunch of fixes introduced into 4.6.6 and 5.0 > that could be relevant, but we need the gory details to know. > > Mark > > Best, > > JP > > ________________________________________ > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mark > > Abraham [mark.j.abra...@gmail.com] > > Sent: Monday, September 22, 2014 10:25 AM > > To: Discussion list for GROMACS users > > Subject: Re: [gmx-users] Different energies of GPU and CPU-only runs with > > Gromacs 5.x > > > > On Mon, Sep 22, 2014 at 9:44 AM, Machtens, Jan-Philipp < > > j.macht...@fz-juelich.de> wrote: > > > > > Dear all, > > > if I compare GPU-accelerated and CPU-only runs, I get significantly > > > different results/energies with > > > Gromacs 5.x. In contrast, with Gromacs 4.x everything is fine, i.e. no > > > difference between CPU-only runs and with GPU. > > > > > > In short, with Gromacs 5.x using GPUs, I have lower total energy, > higher > > > short-range LJ, higher short-range Coulomb and > > > lower reciprocal Coulomb values. > > > > > > This is a normal consequence of different PME load balancing between CPU > > and GPU. You can use the UNIX diff tool to observe that mdrun is making > > different decisions. > > > > This also leads to altered density and box dimensions, etc.... > > > > > > > MD trajectories are generally not reproducible even if the PME load is > > balanced the same way. Do replicates show the same kind of variation? > > > > Mark > > > > The simulations were run on a single node with either 2x GeForce GTX 780 > Ti > > > or with 1x GTX 770. > > > Compilers tested: gcc 4.8 and icc 14 > > > Cuda Versions: 6.0 or 6.5 > > > ForceField: Amber99sb-ildn > > > > > > The topol.tpr was identical for each simulation. Verlet cut-off scheme > > was > > > used. > > > The mdp file can be accessed here: > > > https://www.dropbox.com/s/kjkglu2p8p11ajn/parameter.mdp?dl=0 > > > Regression tests of the various compilations were always passed. > > > > > > Does someone has the some problems or has a clue what might cause the > > > problems I have with Gromacs5.x when using GPUs ? > > > Many thanks! > > > Best, > > > Jan-Philipp Machtens > > > Postdoctoral Research Fellow > > > Institute of Complex Systems - Cellular Biophysics (ICS-4) > > > Forschungszentrum Jülich, Germany > > > > > > > > > > > > > > > ------------------------------------------------------------------------------------------------ > > > > > > > > > ------------------------------------------------------------------------------------------------ > > > Forschungszentrum Juelich GmbH > > > 52425 Juelich > > > Sitz der Gesellschaft: Juelich > > > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. 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