doing some test runs to optimize the mdrun settings for my hardwarei noticed a couple of things i fail to understand (everything below is gmx-2018on an intel CPU 6 cores, 2 threads each, and GTX 1060)
1) when i start a run as in, e.g.: prompt> gmx mdrun -v -nt 12 -ntmpi 1 -ntomp 12 -deffnm mcz >& er &and then look at cpu usage with the command, prompt> htopthen htop claims that there are not 12 but in fact 14 gmx instances running12 of which use about 100& CPU each, and the remaining two close to 0%such unexpected extra processes i also see with a number of other variations of the gmx mdrun command -is this a problem of htop? 2) at http://manual.gromacs.org/documentation/2018/user-guide/mdrun-performance.htmlit says: gmx mdrun -nt 6 -pin on -pinoffset 0 gmx mdrun -nt 6 -pin on -pinoffset 3 Starts two mdrun processes, each with six total threads.Threads will have their affinities set to particularlogical cores, beginning from the logical corewith rank 0 or 3, respectively. The above would workwell on an Intel CPU with six physical cores andhyper-threading enabled. Use this kind of setup onlyif restricting mdrun to a subset of cores to share anode with other processes. ... if these are logical and not physical cores (is this threads vs hyper-threads??) shouldn't this actually be: mdrun -nt 6 -pin on -pinoffset 0 mdrun -nt 6 -pin on -pinoffset 6 ?? 3) can anybody explain what -pinstride really is/does ?is there ever any good reason for this not being 1 ? cheers,michael =============================== Why be happy when you could be normal? -- 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.
