Chris, depending on your system size and th interconnect this might be OK.
Thus you need to give us more information. E.g.: how many atoms, how many ns/day, what interconnect, PME?. Also the messages at the end of the md.log might tell you some advices to improve performance. Roland On Tue, Mar 3, 2009 at 10:48 PM, <chris.ne...@utoronto.ca> wrote: > Thanks Mark, > > your information is always useful. In this case, the page that you > reference appears to be empty. All I see is "There is currently no text in > this page, you can search for this page title in other pages or edit this > page." > > Thanks also for your consideration of the massive scaling issue. > > Chris. > > chris.neale at utoronto.ca wrote: > >> Hello, >> >> I am currently testing a large system on a power6 cluster. I have compiled >> gromacs 4.0.4 successfully, and it appears to be working fine for <64 >> "cores" (sic, see later). First, I notice that it runs at approximately 1/2 >> the speed that it obtains on some older opterons, which is unfortunate but >> acceptable. Second, I run into some strange issues when I have a greater >> number of cores. Since there are 32 cores per node with simultaneous >> multithreading this yields 64 tasks inside one box, and I realize that these >> problems could be MPI related. >> >> Some background: >> This test system is stable for > 100ns on an opteron so I am quite >> confident that I do not have a problem with my topology or starting >> structure. >> >> Compilation was successful with -O2 only when I modified the ./configure >> file as follows, otherwise I got a stray ')' and a linking error: >> [cneale at tcs-f11n05]$ diff configure.000 configure >> 5052a5053 >> >>> ac_cv_f77_libs="-L/scratch/cneale/exe/fftw-3.1.2_aix/exec/lib -lxlf90 >>> -L/usr/lpp/xlf/lib -lxlopt -lxlf -lxlomp_ser -lpthreads -lm -lc" >>> >> > Rather than modify configure, I suggest you use a customized command > line, such as the one described here > http://wiki.gromacs.org/index.php/GROMACS_on_BlueGene. The output > config.log will have a record of what you did, too. > > Sorry I can't help with the massive scaling issue. > > Mark > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.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 thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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