Dear community, I share the results of scaling- performance test. I used this command and checked the core usage with the help of htop tool (http://hisham.hm/htop/): gmx mdrun -ntmpi 1 -ntomp N -pin on -deffnm <md_job> &
Where N is the number of (logical) cores, and hardware is Intel(R) Core(TM) i7-6700 @3.40 GHz, 16 GB RAM and no GPU. I tested two polymer chains of different size (psu10= 552 atoms; psu36= 1956 atoms), 1ns NPT simulations of the previously-equilibrated system, md settings were Berendsen thermostat and barostat, V-rescale, time step 1fs, rcut-off 1.0 nm, PME for coulombic computation. In this link the figures: https://goo.gl/bVZKcU And the table with the values if problems in opening the figures: PSU10 (552 atoms) N wall-time ns/day 1 1057.166 81.7025 2 631.117 136.908 3 461.265 187.448 4 352.821 244.886 5 440.070 196.393 6 386.782 223.346 7 348.273 248.083 8 389.243 255.187 ------------------ PSU36 (1956 atoms) N wall-time ns/day 1 2259.990 38.231 2 1254.619 68.870 3 875.394 99.267 4 672.042 128.570 5 822.385 105.056 6 712.061 121.338 7 628.172 137.551 8 576.145 149.963 Kind regards, Javi 2017-11-21 13:50 GMT+01:00 Javier E <jluquedisa...@gmail.com>: > Dear users, > > I'm doing a performance analysis following this link > http://manual.gromacs.org/documentation/5.1/user-guide/ > mdrun-performance.html and wanted to ask: > > Is there a "standard" procedure to test performance in gromacs (on single > nodes, one multi-processor CPU)? Following there are some results, the > system is a small polymeric chain of 542 atoms with no water and NPT 100 ps > runs (if more information about md settings are needed please ask): > > Running on 1 node with total 4 cores, 8 logical cores > Hardware detected: > CPU info: > Vendor: GenuineIntel > Brand: Intel(R) Core(TM) i7-6700 CPU @ 3.40GHz > SIMD instructions most likely to fit this hardware: AVX2_256 > SIMD instructions selected at GROMACS compile time: AVX2_256 > > GROMACS version: VERSION 5.1.4 > Precision: single > Memory model: 64 bit > MPI library: thread_mpi > OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32) > GPU support: disabled > OpenCL support: disabled > > > gmx mdrun -ntmpi 1 -ntomp # -v -deffnm out.tpr > > > _______________________________________________________________ > -ntomp | MPI / OpenMP- | Wall time (s)| ns/day | % CPU | > Note?* | > ------------------------------------------------------------ > ------------------------------------------------- > 1 | 1/1 | 1075.764 | 80.315 | > 100.0 | No | > 2 | 1/2 | 619.679 | 139.427 | > 200.0 | Yes | > 3 | 1/3 | 458.721 | 188.350 | > 299.9 | Yes | > 4 | 1/4 | 356.906 | 242.081 | > 399.8 | Yes | > 5 | 1/5 | 433.572 | 199.275 | > 499.0 | Yes | > 6 | 1/6 | 378.951 | 227.998 | > 598.0 | Yes | > 7 | 1/7 | 355.785 | 242.844 | > 693.1 | Yes | > 8 | 1/8 (default) | 328.520 | 262.081 | > 779.0 | No | > ------------------------------------------------------------ > ------------------------------------------------- > > *NOTE: The number of threads is not equal to the number of (logical) cores > and the -pin option is set to auto: will not pin thread to cores. > > > If (MPI-Threads)*(OpenMP-Threads) = number of threads, does mdrun uses > number of cores= number of threads, and this can be seen in the %CPU usage? > > For example, as I installed GROMACS in default, the GMX_OpenMP_MAX_THREAD > is set at 32 threads, but this will never happen with this hardware (4 > cores, 8 logical), is this correct? By now I'm re-running the exact same > tests to have at least one replica, and extending the system size and the > and run time. Any suggestions on how to deep further in this kind of tests > are welcome, > > Best regards > -- > > ________________________________________ > > *Javier Luque Di Salvo* > > Dipartamento di Ingegneria Chimica > > Universitá Degli Studi di Palermo > *Viale delle Scienze, Ed. 6* > *90128 PALERMO (PA)* > *+39.09123867503 <+39%20091%202386%207503>* > -- ________________________________________ *Javier Luque Di Salvo* Dipartamento di Ingegneria Chimica Universitá Degli Studi di Palermo *Viale delle Scienze, Ed. 6* *90128 PALERMO (PA)* *+39.09123867503* -- 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.