Re: [gmx-users] Periodic boundary conditions during the simulation

Boundaries of the box used for visualisation are totally arbitrary, it makes not difference when the various simulations are being performed. Most efficient to simply process it at the end to get the visual representation you want Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and

Re: [gmx-users] COMPEL question: Channel filter outside membrane, how to orient compartment boundaries

Hi Erik, I am not sure that the CompEl code as it is can deal with the setup you are describing (but I may be wrong). Below are a few thoughts and things you might want to try. > Am 24.04.2020 um 00:05 schrieb Erik Henze : > > Hi, > I am attempting to study permeation events in an ion channel

Re: [gmx-users] GROMACS performance issues on POWER9/V100 node

Using a single thread per GPU as the linked log files show is not sufficient for GROMACS (and any modern machine should have more than that anyway), but I imply from your mail that this only meant to debug performance instability? Your performance variations with Power9 may be related that you

[gmx-users] 回复: 回复: 回复: Problem with Potential Mean Force calculation

Dear Justin, Please refer to my figures on RG, https://www.researchgate.net/post/GROMACS_2020_pull_code_produces_strange_Po tential_Mean_Force_PMF_result The 1st plot of my question shows the pull force of the Steered MD of 500 ps, and I have visualized that the guest was gradually moved away

Re: [gmx-users] GROMACS performance issues on POWER9/V100 node

I cannot force the pinning via GROMACS so I will look at what can be done with hwloc. On the POWER9 the hardware appears to be detected correctly (only Intel gives note): Running on 1 node with total 128 cores, 128 logical cores, 1 compatible GPU But during the build it fails the

Re: [gmx-users] Artifact in pull-pbc-ref-prev-step-com

Hi Magnus, I see, many thanks for the insights. On Thu, Apr 23, 2020 at 2:45 AM Magnus Lundborg < magnus.lundb...@scilifelab.se> wrote: > Hi Alex, > > pull-group1-pbcatom lets you specify the exact atom used as the PBC > reference. Both 0 and -1 are special cases. For small molecules 0 is >

Re: [gmx-users] GROMACS performance issues on POWER9/V100 node

On Fri, Apr 24, 2020 at 5:55 AM Alex wrote: > Hi Kevin, > > We've been having issues with Power9/V100 very similar to what Jon > described and basically settled on what I believe is sub-par > performance. We tested it on systems with ~30-50K particles and threads > simply cannot be pinned.

Re: [gmx-users] GROMACS performance issues on POWER9/V100 node

> The following lines are found in md.log for the POWER9/V100 run: > > Overriding thread affinity set outside gmx mdrun > Pinning threads with an auto-selected logical core stride of 128 > NOTE: Thread affinity was not set. > > The full md.log is available here: >

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 192, Issue 89

Hi, I use gromacs-2019.4. Sent from my iPhone > On 25 Apr 2020, at 6:54 am, gromacs.org_gmx-users-requ...@maillist.sys.kth.se > wrote: > > Send gromacs.org_gmx-users mailing list submissions to >gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World

Re: [gmx-users] GROMACS performance issues on POWER9/V100 node

Hi, Affinity settings on the Talos II with Ubuntu 18.04 kernel 5.0 works fine. I get threads pinned where they should be (hwloc confirmed) and consistent results. I also get reasonable thread placement even without pinning (i.e. the kernel scatters first until #threads <= #hwthreads). I see only

Re: [gmx-users] GROMACS performance issues on POWER9/V100 node

Hi Szilárd, My comment was as follows: 1. We have been unable to pin threads (mdrun overrides -pin on) with or without stride set to 4. 2. We basically accepted that power9/V100 performance (in ns/day) on identical systems is much worse than that we get from an Intel-based machine. Both