Hi, Please try to run the very same simulation that crashes on CPUs only (-nb cpu). If that also crashes, please file a bug report because we surely have a software bug.
If that does not crash, we will have to dig a bit deeper into what could be causing the issue. Log files from the two runs would be useful, could you share them? Cheers, -- Szilárd On Tue, Jan 15, 2013 at 12:10 AM, sebastian < sebastian.wa...@physik.uni-freiburg.de> wrote: > Hey GROMACS users, > > using mdrun (version 4.6-beta3) on a GPU node (1 nvidia K10 with cuda > drivers and runtime 4.2 + 2 times intel 6 core E5 with hyper threading and > SSE4.1) I get allways after a few or few 100 ns the following segfault: > > line 15: 28957 Segmentation fault mdrun -deffnm pdz_trans_NVT_equi_4 -maxh > 95 > > I can restart the system using the cpt file and run the it for the next > few or few 100 ns and when I get the same segfault again. > The same system runs on a different cluster (mdrun version 4.6-beta3 on a > GPU node (1 nvidia M2090 with cuda drivers and runtime 4.2 + 2 times intel > 6 core X5 and SSE4.1) fine for 1μs without any complains. > > My system consists of a 95 residue protein solvated in approx 6000 spc > water molecules. > .mdp parameters: > > ; > title = ttt > cpp = /lib/cpp > include = -I../top > constraints = hbonds > integrator = md > cutoff-scheme = verlet > > dt = 0.002 ; ps ! > nsteps = 500000000 ; total 5 ns > nstcomm = 25 ; frequency for center of mass motion removal > nstcalcenergy = 25 > nstxout = 100000 ; frequency for writting the trajectory > nstvout = 100000 ; frequency for writting the velocity > nstfout = 100000 ; frequency to write forces to output trajectory > nstlog = 1000000 ; frequency to write the log file > nstenergy = 10000 ; frequency to write energies to energy file > nstxtcout = 10000 > > xtc_grps = System > > nstlist = 25 ; Frequency to update the neighbor list > ns_type = grid ; Make a grid in the box and only check atoms in > neighboring grid cells when constructing a new neighbor > rlist = 1.4 ; cut-off distance for the short-range neighbor list > > coulombtype = PME ; Fast Particle-Mesh Ewald electrostatics > rcoulomb = 1.4 ; cut-off distance for the coulomb field > vdwtype = cut-off > rvdw = 1.4 ; cut-off distance for the vdw field > fourierspacing = 0.12 ; The maximum grid spacing for the FFT grid > pme_order = 6 ; Interpolation order for PME > optimize_fft = yes > pbc = xyz > Tcoupl = v-rescale > tc-grps = System > tau_t = 0.1 > ref_t = 300 > > energygrps = Protein Non-Protein > > Pcoupl = no;berendsen > tau_p = 0.1 > compressibility = 4.5e-5 > ref_p = 1.0 > nstpcouple = 5 > refcoord_scaling = all > Pcoupltype = isotropic > gen_vel = no > gen_temp = 300 > gen_seed = -1 > > Since I have no clue on which paramter should be tuned any guess would be > very welcomed. > > Thanks > > Sebastian > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- 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
