On Пятница 18 декабря 2009 23:47:34 David van der Spoel wrote: > Alexey Shvetsov wrote: > > On Пятница 18 декабря 2009 19:29:15 XAvier Periole wrote: > >> Dears, > >> > >> we have been trying to run gmx-4.0.X on new machines with the > >> Intel I7 CPUs. It is a quad core intel on which multi-threading is > >> a "default" feature. This makes the system to behave as a 8 cores > >> machine. > >> > >> We observed some strange behavior of gromacs. Note that is > >> certainly not due to gromacs itself. > >> > >> Running jobs using 4 cores we have observed the following behavior: > >> - the info on the output files (log, xtc, edr ...) is not always printed > >> - gromacs switches cores, eg: cores 1,2,4,5, and then 2,3,5,6 ... and > >> this > >> with no apparent logic. > >> > >> Jobs using 8 cores become extremely slow, more than expected, > >> and if running at all. > >> > >> Running 2 jobs with 4 cores each, one was running with 4 cores, the > >> second was using only 2 cores although mpirun was asked to use 4. > >> > >> This is more disturbing since it was also possible to run two jobs > >> using 4 cores each successfully and have effectively increased > >> efficiency: each job running at 5/6 of the speed of one run on 4 cores > >> and running alone. > >> > >> This was observed with: > >> - Ubuntu-9.10 (karmic) / kernel linux 2.6.31-14-generic (GNOME 2.28.1) > >> - openmpi-1.3.2/1.4.X > >> - gromacs 4.0.5/4.0.7 > >> > >> Anyone has any idea what could be going on on those I7? > >> > >> Thanks, > >> We: Djurre (& XAvier) > > > > Well its usual behavior of systems with HT (Hyper threading) enabled. so > > its better to disable HT on such cpus so any cpu eating application like > > gromacs will run faster on it. > > No, this is not what I have heard from Berk Hess, he said that running 8 > processes on 4 cores gives a speed up of 6-7 times a single core. > > It sounds more like you need to tune the kernel such that jobs stay on > the core they are on. As far as I know Ubuntu is a Desktop OS, maybe you > want a Server OS? > In this case seems cpuaffinity was turned off for mpi apps. check that kernel has cpusets support ale...@xeon /misc/_Work/RecA/pca $ zgrep CPUSET /proc/config.gz CONFIG_CPUSETS=y CONFIG_PROC_PID_CPUSET=y
And check that your openmpi compiled with support of cpusets -- Alexey 'Alexxy' Shvetsov Gentoo Team Ru Gentoo Linux Dev mailto:alexx...@gmail.com mailto:ale...@gentoo.org mailto:ale...@omrb.pnpi.spb.ru
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