[gmx-users] Segmentation fault error
Mark Abraham
mark.j.abraham at gmail.com
Fri Dec 12 12:09:58 CET 2014
Yes, seems like blowing up, but I would run it on another machine to be
sure.
Mark
On Fri, Dec 12, 2014 at 9:03 AM, Seyed Mojtaba Rezaei Sani <
s.m.rezaeisani at gmail.com> wrote:
>
> 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:*
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > *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)
> --
> Gromacs Users mailing list
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