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 <[email protected] <mailto:[email protected]>>
Subject: Re: [gmx-users] Signal 11 crash
To: Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>>
Message-ID: <[email protected]
<mailto:[email protected]>>
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: [email protected] <mailto:[email protected]>
> 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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