[gmx-users] Signal 11 crash

[Justin A. Lemkul]

程迪 wrote:
> 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.
> 
> 

Then you can't claim that "nothing is logged" - this is the kind of error that 
Gromacs will report.  Your system is unstable, probably due to insufficient 
energy minimization or equilibration.  See here:

http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

> 
> ------------------------------
> 
> Message: 3
> Date: Tue, 30 Mar 2010 12:43:50 +0200
> From: Sander Pronk <pronk at cbr.su.se <mailto:pronk at cbr.su.se>>
> Subject: Re: [gmx-users] Signal 11 crash
> To: Discussion list for GROMACS users <gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <23481805-5219-49D9-A697-75775B8039F9 at cbr.su.se 
> <mailto: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 <mailto:chengdi at mail.ustc.edu.cn>
>  > Tel.: +86-15321055911
>  >
>  > --
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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