On Thu, Dec 13, 2018 at 10:12 PM <pbusc...@q.com> wrote: > Szilard, > > I get an "unknown command " gpustasks in : > > 'mdrun -ntmpi N -npme 1 -nb gpu -pme gpu -gpustasks TASKSTRING >
TASKSTRIGS is a placeholder. It is the manual mapping of tasks to GPU hardware. > > where > typically N = 4, 6, 8 are worth a try (but N <= #cores) and the > > TASKSTRING should have N digits with either N-1 zeros and the last 1 > > or N-2 zeros and the last two 1, i.e.. Would you please complete the i.e... > What's best depends on your hardware, so this is manual tuning territory and it is hard to provide a recipe; what you can try is e.g. assuming 16-cores/32-threads and two GPUs: gmx mdrun -ntmpi 8 -npme 1 -ntomp 4 -nb gpu -pme gpu -gputasks 00000011 gmx mdrun -ntmpi 8 -npme 1 -ntomp 4 -nb gpu -pme gpu -gputasks 00000111 As note before, don't expect this to be more than ~1.5x faster than using one GPU. Thanks again, > Paul > > > > -----Original Message----- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of paul > buscemi > Sent: Tuesday, December 11, 2018 5:56 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] using dual CPU's > > Szilard, > > Thank you vey much for the information and I apologize how the text > appeared - internet demons at work. > > The computer described in the log files is a basic test rig which we use > to iron out models. The workhorse is a many core AMD with now one and > hopefully soon to be two 2080ti’s, It will have to handle several 100k > particles and at the moment do not think the simulation could be divided. > These are essentially of a multi component ligand adsorption from solution > onto a substrate including evaporation of the solvent. > > I saw from a 2015 paper form your group “ Best bang for your buck: GPU > nodes for GROMACS biomolecular simulations “ that I should expect maybe a > 50% improvement for 90k atoms ( with 2x GTX 970 ) What bothered me in my > initial attempts was that my simulations became slower by adding the second > GPU - it was frustrating to say the least > > I’ll give your suggestions a good workout, and report on the results when > I hack it out.. > > Bes > Paul > > > On Dec 11, 2018, at 12:14 PM, Szilárd Páll <pall.szil...@gmail.com> > wrote: > > > > Without having read all details (partly due to the hard to read log > > files), what I can certainly recommend is: unless you really need to, > > avoid running single simulations with only a few 10s of thousands of > > atoms across multiple GPUs. You'll be _much_ better off using your > > limited resources by running a few independent runs concurrently. If > > you really need to get maximum single-run throughput, please check > > previous discussions on the list on my recommendations. > > > > Briefly, what you can try for 2 GPUs is (do compare against the > > single-GPU runs to see if it's worth it): > > mdrun -ntmpi N -npme 1 -nb gpu -pme gpu -gpustasks TASKSTRING where > > typically N = 4, 6, 8 are worth a try (but N <= #cores) and the > > TASKSTRING should have N digits with either N-1 zeros and the last 1 > > or N-2 zeros and the last two 1, i.e.. > > > > I suggest to share files using a cloud storage service like google > > drive, dropbox, etc. or a dedicated text sharing service like > > paste.ee, pastebin.com, or termbin.com -- especially the latter is > > very handy for those who don't want to leave the command line just to > > upload a/several files for sharing (i.e. try "echo "foobar" | nc > > termbin.com 9999) > > > > -- > > Szilárd > > On Tue, Dec 11, 2018 at 2:44 AM paul buscemi <pbusc...@q.com> wrote: > >> > >> > >> > >>> On Dec 10, 2018, at 7:33 PM, paul buscemi <pbusc...@q.com> wrote: > >>> > >>> > >>> Mark, attached are the tail ends of three log files for the same > >>> system but run on an AMD 8 Core/16 Thread 2700x, 16G ram In > >>> summary: > >>> for ntpmi:ntomp of 1:16 , 2:8, and auto selection (4:4) are 12.0, 8.8 > , and 6.0 ns/day. > >>> Clearly, I do not have a handle on using 2 GPU's > >>> > >>> Thank you again, and I'll keep probing the web for more understanding. > >>> I’ve propbably sent too much of the log, let me know if this is the > >>> case > >> Better way to share files - where is that friend ? > >>> > >>> Paul > >> -- > >> 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. > > -- > 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. -- 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.
