Hi, gmx-users I just encountered a singal 11 problem. I ran gromacs 4.0.7 on 64bit ubuntu. 4 core Xeon
imb F 2% step 22400, will finish Wed Mar 31 00:41:41 2010 imb F 3% step 22500, will finish Wed Mar 31 00:41:49 2010 imb F 2% step 22600, will finish Wed Mar 31 00:41:57 2010 imb F 3% step 22700, will finish Wed Mar 31 00:41:42 2010 imb F 2% step 22800, will finish Wed Mar 31 00:41:50 2010 imb F 2% step 22900, will finish Wed Mar 31 00:41:58 2010 imb F 3% step 23000, will finish Wed Mar 31 00:41:43 2010 imb F 3% step 23100, will finish Wed Mar 31 00:41:51 2010 imb F 3% step 23200, will finish Wed Mar 31 00:41:59 2010 rank 3 in job 1 chengdi-desktop_38817 caused collective abort of all ranks exit status of rank 3: killed by signal 11 rank 2 in job 1 chengdi-desktop_38817 caused collective abort of all ranks exit status of rank 2: killed by signal 11 rank 1 in job 1 chengdi-desktop_38817 caused collective abort of all ranks exit status of rank 1: killed by signal 11 What's wrong? My .mdp file is as follows: title = fws cpp = /usr/bin/cpp ;constraints = all-bonds constraint_algorithm= LINCS integrator = md dt = 0.001 ; ps ! nsteps = 500000 ; total 500 ps. nstcomm = 1 nstxout = 500 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in three groups Tcoupl = berendsen tc_grps = System tau_t = 0.1 ref_t = 300 ; Pressure coupling is on Pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 ; pbc pbc = xyz ;pull code pull = constraint pull_geometry = direction pull_dim = N N Y pull_start = yes pull_nstxout = 500 pull_nstfout = 100 pull_ngroups = 1 pull_group0 = DPPC pull_group1 = MOL pull_vec1 = 0.0 0.0 -1.0 pull_rate1 = 0.01 Any comments is appreciable. Di Cheng University of Science and Technology of China Hefei, Anhui Province 230026 P. R. China E-mail: [email protected] Tel.: +86-15321055911
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