<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Signal 11 on Linux is a segmentation fault: either you've hit a bug in mdrun, or there was some faulty input causing it to crash. <div>You'll need to look at your md.log to see what happened.<div><br></div><div>Sander</div><div><br><div><div>On Mar 30, 2010, at 12:11 , 程迪 wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi, gmx-users<br><br>I just encountered a singal 11 problem. I ran gromacs 4.0.7 on 64bit ubuntu. 4 core Xeon<br><br>imb F 2% step 22400, will finish Wed Mar 31 00:41:41 2010<br>imb F 3% step 22500, will finish Wed Mar 31 00:41:49 2010<br>
imb F 2% step 22600, will finish Wed Mar 31 00:41:57 2010<br>imb F 3% step 22700, will finish Wed Mar 31 00:41:42 2010<br>imb F 2% step 22800, will finish Wed Mar 31 00:41:50 2010<br>imb F 2% step 22900, will finish Wed Mar 31 00:41:58 2010<br>
imb F 3% step 23000, will finish Wed Mar 31 00:41:43 2010<br>imb F 3% step 23100, will finish Wed Mar 31 00:41:51 2010<br>imb F 3% step 23200, will finish Wed Mar 31 00:41:59 2010<br>rank 3 in job 1 chengdi-desktop_38817 caused collective abort of all ranks<br>
exit status of rank 3: killed by signal 11 <br>rank 2 in job 1 chengdi-desktop_38817 caused collective abort of all ranks<br> exit status of rank 2: killed by signal 11 <br>rank 1 in job 1 chengdi-desktop_38817 caused collective abort of all ranks<br>
exit status of rank 1: killed by signal 11 <br><br clear="all">What's wrong? <br><br>My .mdp file is as follows:<br>title = fws <br>cpp = /usr/bin/cpp <br>;constraints = all-bonds<br>
constraint_algorithm= LINCS<br>integrator = md<br>dt = 0.001 ; ps !<br>nsteps = 500000 ; total 500 ps.<br>nstcomm = 1<br>nstxout = 500<br>nstvout = 0<br>
nstfout = 0<br>nstlist = 10 <br>ns_type = grid<br>rlist = 1.0<br>coulombtype = PME<br>rcoulomb = 1.0<br>vdwtype = cut-off<br>rvdw = 1.4<br>
fourierspacing = 0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 6<br>ewald_rtol = 1e-5<br>optimize_fft = yes<br>; Berendsen temperature coupling is on in three groups<br>
Tcoupl = berendsen<br>tc_grps = System<br>tau_t = 0.1<br>ref_t = 300<br>; Pressure coupling is on<br>Pcoupl = parrinello-rahman <br>pcoupltype = isotropic<br>
tau_p = 1.0<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>; Generate velocites is on at 300 K.<br>gen_vel = yes<br>gen_temp = 300.0<br>gen_seed = 173529<br>
; pbc<br>pbc = xyz<br>;pull code<br>pull = constraint<br>pull_geometry = direction<br>pull_dim = N N Y<br>pull_start = yes<br>pull_nstxout = 500<br>pull_nstfout = 100<br>pull_ngroups = 1<br>
pull_group0 = DPPC<br>pull_group1 = MOL<br>pull_vec1 = 0.0 0.0 -1.0<br>pull_rate1 = 0.01<br><br>Any comments is appreciable.<br><br>Di Cheng<br><br>University of Science and Technology of China<br>Hefei, Anhui Province 230026<br>
P. R. China<br>E-mail: <a href="mailto:chengdi@mail.ustc.edu.cn">chengdi@mail.ustc.edu.cn</a><br>Tel.: +86-15321055911<br><br>
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