[gmx-users] Signal 11 crash

[程迪]

Hi, Sander Pronk

I checked the md.log file. nothing is logged when the program crash.

I just used the single precision version of Gromacs. It output some atom
cannot be settled when crash happend.



------------------------------

Message: 3
Date: Tue, 30 Mar 2010 12:43:50 +0200
From: Sander Pronk <pronk at cbr.su.se>
Subject: Re: [gmx-users] Signal 11 crash
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <23481805-5219-49D9-A697-75775B8039F9 at cbr.su.se>
Content-Type: text/plain; charset="utf-8"

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.
You'll need to look at your md.log to see what happened.

Sander

On Mar 30, 2010, at 12:11 , 程迪 wrote:

> 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: chengdi at mail.ustc.edu.cn
> Tel.: +86-15321055911
>
> --
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