[gmx-users] Signal 11 crash

[程迪]

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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