[Alexey Shvetsov, 18.12.2009]: >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
The problem of Gromacs stalling on i7 when using multiple CPUs is a MPI problem. It is most likely caused by a shared memory bug in Open MPI that was fixed in the latest release (1.4.1). Switching to openmpi-1.4.1 solves the problem. Best regards, -martti- -- Post-doctoral research fellow Moleculaire Dynamica | University of Groningen Nijenborgh 4, 9747AG Groningen, the Netherlands tel. +(31) 50 363 4339 | fax. +(31) 50 363 4398 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
