On Wed, 2007-11-28 at 14:49 +0100, David van der Spoel wrote: > Hadas Leonov wrote: > > Great, thanks! > > > > It does solve the ia32 compilation problems, but not the lam-mpi > > compilation problems - I still get undefined symbols for a few lam > > variables. > > > > So still using open-mpi, Gromacs works a little better now, for d.villin > > benchmark, the performance are: > > 1 CPU: 13214 ps/day (compared to 3592 ps/day before, and 18000ps/day on > > OSX 10.4) > > 4 CPUs: 38000ps/day (compared to 13714 ps/day before, 41143ps/day on > > OSX 10.4, and 48000ps/day in the gmx published benchmark). > > > > I still didn't get to make a long simulation and see if it crashes. > > > > anymore ideas? is it still something that has to be fixed in the new > > version? > > it's weird that 10.4 would be so much faster. There is a small speed > benefit from using the memory management routines in LAM though, but it > shouldn't be this big. Will the final 3.3.3 version be fixed to compile with lam as well (on Leopard)?
I have tried performing position restraints (2-3 hours), and it still crashed with the following error: --- [tmdec2:86116] *** Process received signal *** [tmdec2:86116] Signal: Segmentation fault (11) [tmdec2:86116] Signal code: Address not mapped (1) [tmdec2:86116] Failing at address: 0xcf9d849c [ 1] [0xbfffd808, 0xcf9d849c] (-P-) [ 2] (spread_on_grid + 0x1fa) [0xbfffd8b8, 0x0004cc53] [ 3] (do_pme + 0x56e) [0xbfffda18, 0x0004d1cc] [ 4] (force + 0x7d9) [0xbfffdc68, 0x0002e90a] [ 5] (do_force + 0x8a4) [0xbfffdd58, 0x0005d16e] [ 6] (do_md + 0x164f) [0xbfffe968, 0x000160ee] [ 7] (mdrunner + 0xb04) [0xbfffeae8, 0x0001453e] [ 8] (main + 0x463) [0xbfffeb78, 0x000186e9] [ 9] (start + 0x36) [0xbfffeb98, 0x00001bee] [10] [0x00000000, 0x0000000e] (FP-) [tmdec2:86116] *** End of error message *** mpirun noticed that job rank 0 with PID 86116 on node tmdec2.ls.huji.ac.il exited on signal 11 (Segmentat ion fault). 1 process killed (possibly by Open MPI) --- Help? Thanks, Hadas > > > > > Thanks again, > > Hadas. > > > > > > On Wed, 2007-11-28 at 10:43 +0100, David van der Spoel wrote: > >> Hadas Leonov wrote: > >>> When is version 3.3.3 due ? > >>> > >> Soon. > >> > >> But meanwhile I put a beta version at the ftp site. > >> > >> ftp://ftp.gromacs.org/pub/gromacs/gromacs_3.3.3_pre1.tar.gz > >> > >> Please use with care, for testing purposes only. > >> > > _______________________________________________ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php