Hi, Sander Pronk<br><br>I checked the md.log file. nothing is logged when the program crash.<br><br>I just used the single precision version of Gromacs. It output some atom cannot be settled when crash happend.<br><br><br>
<br>------------------------------<br>
<br>
Message: 3<br>
Date: Tue, 30 Mar 2010 12:43:50 +0200<br>
From: Sander Pronk <<a href="mailto:pronk@cbr.su.se">pronk@cbr.su.se</a>><br>
Subject: Re: [gmx-users] Signal 11 crash<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:23481805-5219-49D9-A697-75775B8039F9@cbr.su.se">23481805-5219-49D9-A697-75775B8039F9@cbr.su.se</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
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.<br>
You'll need to look at your md.log to see what happened.<br>
<br>
Sander<br>
<br>
On Mar 30, 2010, at 12:11 , 程迪 wrote:<br>
<br>
> 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>
> 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>
> --