Re: [gmx-users] problems with intel I7 (2.67 GHz)
[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 listgmx-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
Re: [gmx-users] problems with intel I7 (2.67 GHz)
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 signature.asc Description: This is a digitally signed message part. -- gmx-users mailing listgmx-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
Re: [gmx-users] problems with intel I7 (2.67 GHz)
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? -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-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
Re: [gmx-users] problems with intel I7 (2.67 GHz)
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. -- Alexey 'Alexxy' Shvetsov Gentoo Team Ru Gentoo Linux Dev mailto:alexx...@gmail.com mailto:ale...@gentoo.org mailto:ale...@omrb.pnpi.spb.ru signature.asc Description: This is a digitally signed message part. -- gmx-users mailing listgmx-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
[gmx-users] problems with intel I7 (2.67 GHz)
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) -- gmx-users mailing listgmx-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
