[gmx-users] Segmentation fault error

[Seyed Mojtaba Rezaei Sani]

Hi Mark,

Thanks for your response. I use a rather old version of GROMACS, 4.5.4.
Please find the md.log file in the following link:
https://www.dropbox.com/s/bbmqln6oqjyus0b/md.log?dl=0
I also have to mention that due to reaching the machine precision I could
not
minimized the energy of the system well.

On Fri, Dec 12, 2014 at 7:08 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
>
> Hi,
>
> This is a generic MPI error message. Nobody can tell from it what caused
> it. You need to look at the whole stdout and the mdrun .log file for
> diagnostics. You should also report your Gromacs version. Probably you are
> just http://www.gromacs.org/Documentation/Terminology/Blowing_Up, but
> there
> is a known problem with 5.0.3 which we will fix ASAP.
>
> Mark
>
> On Fri, Dec 12, 2014 at 3:55 AM, Seyed Mojtaba Rezaei Sani <
> s.m.rezaeisani at gmail.com> wrote:
> >
> > *Dear all,*
> > *I am trying to simulate a system of drug carrier consisting of HSPC/CHOL
> > in the form of a vesicle. The code works well for the system when the
> CHOL
> > molecules are not inserted. As I include CHOL molecules I face this
> error:*
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > *starting mdrun 'Chol/HSPC  VESICLE'900000 steps,  27000.0 ps.step
> > 0[compute-0-3:30916] *** Process received signal ***[compute-0-3:30916]
> > Signal: Segmentation fault (11)[compute-0-3:30916] Signal code: Address
> not
> > mapped (1)[compute-0-3:30916] Failing at address:
> > 0x9a200b0[compute-0-3:30916] [ 0] /lib64/libpthread.so.0
> > [0x316940eb10][compute-0-3:30916] [ 1]
> /opt/bio/gromacs/lib/libgmx_mpi.so.6
> > [0x2b291ac0ee2c][compute-0-3:30916] *** End of error message
> >
> >
> ***--------------------------------------------------------------------------mpirun
> > noticed that process rank 10 with PID 30916 on node compute-0-3.local
> > exited on signal 11 (Segmentation
> >
> >
> fault).--------------------------------------------------------------------------*
> >
> > *Here is the mdp file:*
> >
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> >
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> >
> > *title                    = Martiniintegrator               =
> > mddt                       = 0.03  nsteps                   =
> > 900000nstcomm                  = 100comm-grps                =
> > nstxout                  = 1000nstvout                  =
> > 1000nstfout                  = 1000nstlog                   = 1000  ;
> > Output frequency for energies to log file nstenergy                = 100
> > ; Output frequency for energies to energy filenstxtcout                =
> > 1000  ; Output frequency for .xtc filextc_precision            =
> > 100xtc-grps                 = energygrps               = HSPC CHOL
> > Wnstlist                  = 10ns_type                  =
> > gridpbc                      = xyzrlist                    =
> > 1.4coulombtype              = Shift  ;Reaction_field (for use with
> > Verlet-pairlist) ;PME (especially with polarizable
> > water)rcoulomb_switch          = 0.0rcoulomb                 =
> > 1.2epsilon_r                = 15   ; 2.5 (with polarizable
> > water)vdw_type                 = Shift  ;cutoff (for use with
> > Verlet-pairlist)   rvdw_switch              = 0.9rvdw
>  =
> > 1.2  ;1.1 (for use with Verlet-pairlist);cutoff-scheme            =
> > verlet;coulomb-modifier         = Potential-shift;vdw-modifier
> > = Potential-shift;epsilon_rf               = 0   ; epsilon_rf = 0 really
> > means epsilon_rf = infinity;verlet-buffer-drift      =
> > 0.005tcoupl                   = v-rescale tc-grps                  = HSPC
> > CHOL Wtau_t                    = 1.0  1.0 1.0 ref_t                    =
> > 323 323 323Pcoupl                   = berendsen  ; parrinello-rahman ;
> > parrinello-rahmanPcoupltype               = isotropic  ;
> > semiisotropictau_p                    = 3.0        ; 12.0 12.0
> > ;parrinello-rahman is more stable with larger tau-p, DdJ,
> > 20130422compressibility          = 3e-4       ;
> > 3e-4ref_p                    = 1.0        ; 1.0 1.0gen_vel
> > = yesgen_temp                 = 320gen_seed                 =
> > 473529constraints              = none constraint_algorithm     =
> > Lincscontinuation             = nolincs_order              =
> > 4lincs_warnangle          = 30*
> >
> >
> > *I appreciate any help in advance.*
> >
> > --
> > Seyed Mojtaba Rezaei Sani
> >
> > Institute for Research in Fundamental Sciences (IPM)
> > School of Nano-Science
> > Shahid Farbin Alley
> > Shahid Lavasani st
> > P.O. Box 19395-5531
> > Tehran, Iran
> > Tel: +98 21 2310  (3069)
> > --
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-- 
Seyed Mojtaba Rezaei Sani

Institute for Research in Fundamental Sciences (IPM)
School of Nano-Science
Shahid Farbin Alley
Shahid Lavasani st
P.O. Box 19395-5531
Tehran, Iran
Tel: +98 21 2310  (3069)