>On 23/12/2010 10:01 PM, Wojtyczka, André wrote: >> Dear Gromacs Enthusiasts. >> >> I am experiencing problems with mdrun_mpi (4.5.3) on a Nehalem cluster. >> >> Problem: >> This runs fine: >> mpiexec -np 72 /../mdrun_mpi -pd -s full031K_mdrun_ions.tpr >> >> This produces a segmentation fault: >> mpiexec -np 128 /../mdrun_mpi -pd -s full031K_mdrun_ions.tpr > >Unless you know you need it, don't use -pd. DD will be faster and is >probably better bug-tested too. > >Mark
Hi Mark thanks for the push into that direction, but I am in the unfortunate situation where I really need -pd because I have long bonds which is the reason why my large system is decomposable just into a little number of domains. > >> So the only difference is the number of cores I am using. >> >> mdrun_mpi was compiled using the intel compiler 11.1.072 with my own fftw3 >> installation. >> >> While configuring and make mdrun / make install-mdrun no errors came >> up. >> >> Is there some issue with threading or mpi? >> >> If someone has a clue please give me a hint. >> >> >> integrator = md >> dt = 0.004 >> nsteps = 25000000 >> nstxout = 0 >> nstvout = 0 >> nstlog = 250000 >> nstenergy = 250000 >> nstxtcout = 12500 >> xtc_grps = protein >> energygrps = protein non-protein >> nstlist = 2 >> ns_type = grid >> rlist = 0.9 >> coulombtype = PME >> rcoulomb = 0.9 >> fourierspacing = 0.12 >> pme_order = 4 >> ewald_rtol = 1e-5 >> rvdw = 0.9 >> pbc = xyz >> periodic_molecules = yes >> tcoupl = nose-hoover >> nsttcouple = 1 >> tc-grps = protein non-protein >> tau_t = 0.1 0.1 >> ref_t = 310 310 >> Pcoupl = no >> gen_vel = yes >> gen_temp = 310 >> gen_seed = 173529 >> constraints = all-bonds >> >> >> >> Error: >> Getting Loaded... >> Reading file full031K_mdrun_ions.tpr, VERSION 4.5.3 (single precision) >> Loaded with Money >> >> >> NOTE: The load imbalance in PME FFT and solve is 48%. >> For optimal PME load balancing >> PME grid_x (144) and grid_y (144) should be divisible by #PME_nodes_x >> (128) >> and PME grid_y (144) and grid_z (144) should be divisible by >> #PME_nodes_y (1) >> >> >> Step 0, time 0 (ps) >> PSIlogger: Child with rank 82 exited on signal 11: Segmentation fault >> PSIlogger: Child with rank 79 exited on signal 11: Segmentation fault >> PSIlogger: Child with rank 2 exited on signal 11: Segmentation fault >> PSIlogger: Child with rank 1 exited on signal 11: Segmentation fault >> PSIlogger: Child with rank 100 exited on signal 11: Segmentation fault >> PSIlogger: Child with rank 97 exited on signal 11: Segmentation fault >> PSIlogger: Child with rank 98 exited on signal 11: Segmentation fault >> PSIlogger: Child with rank 96 exited on signal 6: Aborted >> ... >> >> Ps, for now I don't care about the imbalanced PME load unless it's >> independent from my problem. >> >> Cheers >> André ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
