On Fri, Sep 7, 2018 at 4:15 PM Benson Muite <benson.mu...@ut.ee> wrote:
> Check if the routines you will use have been ported to use GPUs. Time > and profile a typical run you will perform on your current hardware to > determine the bottlenecks, and then choose hardware that will perform > best on these bottlenecks and is within your budget. > > Note that benchmarking can be quite time consuming - even without > performance optimization. If you have an idea of the simulations you > will run and have profiled your code, and will primarily do these > simulations, then it is probably easiest to go to a computer store where > they have several available workstations, run your benchmark yourself > and choose the best value system. > Not a bad suggestion, but these days people shop online. Even if one would opt for a physical store, benchmarking each candidate doesn't sound feasible (or easily done). You'd need to have multiple systems assembled, OS and benchmarks scripts ready on a bootable drive, and measure performance of each system before buying. > > On 09/06/2018 08:09 PM, Olga Selyutina wrote: > > Thank you, > > > > to use these tests isn’t a problem, but available workstation are too > old, > > so test results won’t be helpful in choosing actual components. I have an > > access to high-performance cluster, but it also couldn’t be the basis > > because of its high cost. If it is hard to give the certain > recommendation, > > I would to know at least how do performance correlate with the number of > > cores/threads and core frequency? What is more important the core > frequency > > or number of cores? What is preferable, Intel or AMD? How should be > > correlated GPU and CPU performance? > > > > In the previous letters in mail-list I found recommendations on purchase > of > > Threadripper 1950X+GeForce GTX-1080Ti, I think that more cheap and > similar > > effective choice is TR 1950X+GeForce GTX-*1080*. Will there be > significant > > differences with 1)TR 19*20*X+GeForce GTX-1080 2) Intel 7900x+GeForce > > GTX-1080? > > > > 2018-09-05 20:53 GMT+07:00 Benson Muite <benson.mu...@ut.ee>: > > > >> Hi Olga, > >> > >> The authors of: > >> > >> https://github.com/bio-phys/MDBenchmark/tree/version-1.3.2 > >> > >> https://zenodo.org/record/1318123 > >> > >> May be helpful. If your data is not confidential, you may consider > running > >> Gromacs remotely on a cloud high performance computing resource, or > >> benchmarking remotely and then purchasing a suitable configuration. > >> > >> Some other information: > >> http://manual.gromacs.org/documentation/current/user-guide/ > >> mdrun-performance.html# > >> http://www.gromacs.org/GPU_acceleration > >> https://extras.csc.fi/chem/courses/gmx2007/Erik_Talks/buildi > >> ng_clusters.pdf > >> http://www.gromacs.org/Documentation/Performance_checklist > >> > >> On 09/05/2018 12:02 PM, Olga Selyutina wrote: > >> > >>> Hello, > >>> > >>> I need help in choice of the workstation for MD simulations using > GROMACS. > >>> It is supposed to study systems consisting from 30-50k atoms, in > >>> particular, lipid bilayer models. Since the last generation of Intel > and > >>> Ryzen CPU has made a big leap in performance, available workstation > can’t > >>> be taken as a basis. Please, help to choose components of the > workstation, > >>> particularly, GPU and CPU with total cost about $2000. What is better, > to > >>> buy two GPUs(sli) or one GPU but more effective? > >>> > >>> > >> -- > >> 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.
