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 Wide Web, visit >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to >gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at >gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > > 1. Re: GROMACS performance issues on POWER9/V100 node (Szil?rd P?ll) > 2. Re: GROMACS performance issues on POWER9/V100 node (Szil?rd P?ll) > 3. Re: GROMACS performance issues on POWER9/V100 node (Szil?rd P?ll) > > > -- > > Message: 1 > Date: Fri, 24 Apr 2020 22:31:11 +0200 > From: Szil?rd P?ll > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] GROMACS performance issues on POWER9/V100 >node > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > >> 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. > > > What does that mean, how did you verify that? > The Linux kernel can in general set affinities on ppc64el, whether that's > requested by mdrun or some other tool, so if you have observed that the > affinity mask is not respected (or it does not change), that more likely OS > / setup issue, I'd think. > > What is different compared to x86 is that the hardware thread layout is > different on Power9 (with default Linux kernel configs) and hardware > threads are exposed as consecutive "CPUs" by the OS rather than strided by > #cores. > > I could try to sum up some details on how to sett affinities (with mdrun or > external tools), if that is of interest. However, it really should be > something that's possible to do even using the job scheduler (+ along > reasonable system configuration). > > >> As far as Gromacs is concerned, our brand-new >> Power9 nodes operate as if they were based on Intel CPUs (two threads >> per core) > > > Unless the hardware thread layout has been changed, that's perhaps not the > case, see above. > > >> and zero advantage of IBM parallelization is being taken. >> > > You mean the SMT4? > > >> Other users of the same nodes reported similar issues with other >> software, which to me suggests that our sysadmins don't really know how >> to set these nodes up. >> >> At this point, if someone could figure out a clear set of build >> instructions in combination with slurm/mdrun inputs, it would be very >> much appreciated. >> > > Have you checked public documentation on ORNL's sites? GROMACS has been > used successfully on Summit. What about IBM support? > > -- > Szil?rd > > >> >> Alex >> >>> On 4/23/2020 9:37 PM, Kevin Boyd wrote: >>> I'm not entirely sure how thread-pinning plays with slurm allocations on >>> partial nodes. I always reserve the entire node when I use thread >> pinning, >>> and run a bunch of simulations by pinning to different cores manually, >>> rather than relying on slurm to divvy up resources for multiple jobs. >>> >>> Looking at both logs now, a few more points >>> >>> * Your benchmarks are short enough that little things like cores spinning >>> up frequencies can matter. I suggest running longer (increase nsteps in >> the >>> mdp or at the command line), and throwing away your initial benchmark >> data >>> (see -resetstep and -resethway) to avoid artifacts >>> * Your benchmark system is quite small for such a powerful GPU. I might >>> expect better performance running multiple simulations per-GPU if the >>> workflows being run can rely on replicates, and a larger system would >>> probably scale better to the V100. >>> * The P100/intel system appears to have pinned cores properly, it's >>> unclear whether it had a real impact on these benchmarks >>> * It looks like the CPU-based computations were the primary contributors >> to >>> the observed difference in performance. That should decrease or go away >>> with increased core counts and shifting the update phase to the GPU. It >> may >>> be (I have no prior experience to indicate either way) that the intel >> cores >>> are simply better on a 1-1 basis than the Power cores. If you have 4-8 >>> cores per simulation (try -ntomp 4 and increasing the allocation of your >>> slurm job), the individual core performance shouldn't matter too >>> much, you're just certainly bottlenecked on one CPU
[gmx-users] Triclinic box is too skewed
Hi all,
I apply a deform at the xy direction of the box, the rate is 0.01 nm/ps but
I met this error :
Warning: Triclinic box is too skewed.
Box (3x3):
Box[0]={ 1.06717e+01, 0.0e+00, 0.0e+00}
Box[1]={ 5.34312e+00, 1.06717e+01, 0.0e+00}
Box[2]={ 0.0e+00, 0.0e+00, 1.06717e+01}
Can not fix pbc.
Any suggestions about this? Thanks
Regards
--
*Jun ZHOU*
Postgraduate Student ,
Room 117, Building 36
Department of Civil Engineering,
Monash University,
Victoria 3800, Australia.
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[gmx-users] Ways to calculate shear viscosity
Hi all, I have sent this before but no one answers. I want to simulate a couvette flow using gromacs by applying a deform velocity at xz direction. For a pure water box, it works well though there are warnings "the box is too skewed". When I put a surfactant micelle in the middle, that warning still occurs and also terminates the simulation. Does anyone have any suggestions about this? Also, I read some paper they said they apply *the Lees–Edwards sliding brick boundary conditions *to get a shear flow (10.1039/c7cp08349a), and when I search the mailing list, Berk Hess also says he has a patch for this. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2016-October/009325.html. Can anyone show me how to do this? Thanks. -- *Jun ZHOU* Postgraduate Student , Room 117, Building 36 Department of Civil Engineering, Monash University, Victoria 3800, Australia. -- 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.
[gmx-users] Triclinic box is too skewed
Hi all, I want to simulate a liquid system with surfactant micelle in the middle, then I apply a velocity at xy direction. However, I always meet the error "triclinic box is too skewed" and the simulation will stop even using a very small shear rate. Have you met this simulation before, any suggestions will be appreciated. Thanks Regards, -- *Jun ZHOU* Postgraduate Student , Room 117, Building 36 Department of Civil Engineering, Monash University, Victoria 3800, Australia. -- 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.
[gmx-users] Viscosity of non-newtonian fluid
Hi all, Can I use GROMACS to simulate the viscosity of non-newtonian fluid, namely, small polymer in water solution. Since the system is not a homogenous system, I am not sure periodic perturbation method will be feasible for it. Regards, -- *Jun ZHOU* Postgraduate Student , Room 117, Building 36 Department of Civil Engineering, Monash University, Victoria 3800, Australia. -- 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.
[gmx-users] Problems with Non-equilibrium MD
Hi all, I am using non-equilibrium MD to calculate the viscosity of the liquid by applying a shear on xy direction. My problem is that when I observe the trajectory of the simulation, I find only the box deformed and particles did not change correspondingly, as shown in the attached image ( https://drive.google.com/file/d/11GJntUJU7-phc-Bz-hWBICvQWFIGUJDI/view?usp=sharing ). Another question is that when I try to increase the deform rate, there is a warning: triclinic box is to skewed ... cannot fix pbc. And the simulation will stop after 1000 steps. How to prevent this? I also attached my mdp file, can anyone give me some suggestions? Thanks. Regards, -- *Jun ZHOU* Postgraduate Student , Room 117, Building 36 Department of Civil Engineering, Monash University, Victoria 3800, Australia. -- 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.
[gmx-users] Fwd: Problems with Non-equilibrium MD
Hi all, I am using non-equilibrium MD to calculate the viscosity of the liquid by applying a shear on xy direction. My problem is that when I observe the trajectory of the simulation, I find only the box deformed and particles did not change correspondingly, as shown in the attached image. I also attached my mdp file, can anyone give me some suggestions? Thanks. Regards -- *Jun ZHOU* Postgraduate Student , Room 117, Building 36 Department of Civil Engineering, Monash University, Victoria 3800, Australia. -- 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.
[gmx-users] How to use gmx h2order when using four point water model
Hi all, I want to obtain the water dipole orientation at the interface using gmx h2order. It works well when I I use 3 point water model, like SPC/E. The manual says that the order of water should be O H H, but for 4 point water model, there is a vitual atom, and this command cannot output the correct results. Is there any solutions for this poblem? Thanks, Jun -- 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.
