[gmx-users] Segmentation fault on HPC

[Tomek Wlodarski]

Hi Mark,

Thanks for replay.
Actually log file ends without any error:

Started mdrun on rank 0 Sun Jan  4 12:30:40 2015
           Step           Time         Lambda
              0        0.00000        0.00000


   Energies (kJ/mol)
          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
    1.00844e+05    2.04719e+05    5.69917e+03    6.63396e+04   -4.67549e+05
        LJ (SR)        LJ (LR)   Coulomb (SR)   Coul. recip. Position Rest.
    1.46339e+06   -3.74511e+04   -9.86464e+06   -1.81675e+06    4.91794e+01
      Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
   -1.03454e+07    8.79250e+05   -9.46610e+06   -9.46610e+06    2.00415e+02
 Pressure (bar)   Constr. rmsd
   -5.12367e+03    5.80732e-06

I found something strange - when I changed nstxout value I was able to run
simulation for more than 90k steps without error (I killed simulation
because I was running out of space on my disc ;))
So my simulation is running OK when I have:
dt                       = 0.002   ; 2 femtosecond time step for integration
nsteps                   = 50000   ; 100 ps

; OUTPUT CONTROL OPTIONS
nstxout                 = 1    ; save coordinates every 2 ps
nstvout              = 5000    ; save velocities every 2 ps
nstenergy            = 5000    ; save energies every 2 ps
nstlog               = 5000

I tired different values of nstxout and simulations always crash...
changing dt to 0.001 also does not help
Interestingly when I reduce nstep to 500 my simulation crashes as
well..even though I have nstxout = 1...
Is this indication that my simulation is not stable or something else is
happening?
Thanks a lot.
Best,

tomek






On Sat, Jan 3, 2015 at 2:45 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> What do the ends of  the .log files say?
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up is a heavy
> favourite.
>
> Mark
>
> On Sat, Jan 3, 2015 at 1:56 PM, Tomek Wlodarski <tomek.wlodarski at gmail.com
> >
> wrote:
>
> > Hi,
> >
> > I am trying to set up simulation on HPC.
> > Energy minimization in vacuum and in water works great (using 4 nodes
> with
> > 96 cores altogether)
> > But when I am trying to run standard md with:
> >
> > aprun -n 96 mdrun_mpi -v -deffnm md >& out
> >
> > I always end up with this error (I tried it also on different gromacs
> > versions: 4.6.5, 5.0, 5.0.4):
> >
> >
> > starting mdrun 'Protein in water'
> > 500000 steps,   1000.0 ps.
> > step 0
> >
> > NOTE: Turning on dynamic load balancing
> >
> > _pmiu_daemon(SIGCHLD): [NID 00383] [c1-0c2s15n3] [Sat Jan  3 12:26:44
> 2015]
> > PE RANK 72 exit signal Segmentation fault
> > _pmiu_daemon(SIGCHLD): [NID 00380] [c1-0c2s15n0] [Sat Jan  3 12:26:44
> 2015]
> > PE RANK 1 exit signal Segmentation fault
> > _pmiu_daemon(SIGCHLD): [NID 00382] [c1-0c2s15n2] [Sat Jan  3 12:26:44
> 2015]
> > PE RANK 48 exit signal Segmentation fault
> > [NID 00380] 2015-01-03 12:26:44 Apid 12376091: initiated application
> > termination
> > Application 12376091 exit codes: 139
> > Application 12376091 exit signals: Killed
> > Application 12376091 resources: utime ~16s, stime ~8s, Rss ~63064,
> inblocks
> > ~363834, outblocks ~1173496
> >
> >
> > Do you have any suggestion what is wrong (why I can run EM not MD?)? I
> > checked different system and gromacs run ok.
> > Thanks.
> > Best,
> >
> > tomek
> > --
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