[gmx-users] Segmentation Fault (Address not mapped)

[Mark Abraham]

darrellk at ece.ubc.ca wrote:
> Dear GROMACS Gurus,
> I am experiencing a segmentation fault when mdrun executes. My simulation
> has a graphene lattice with an array (layer) of ammonia molecules above
> it. The box is three times the width of the graphene lattice, three
> times the length of the graphene lattice, and three times the height
> between the graphene lattice and the ammonia molecules. I am including
> the mdp file and the error message.

Probably your system is exploding when integration fails with excessive 
forces. You should look at the bottom of stdout, stderr, *and* the .log 
file to diagnose. The error message you give below is merely the 
diagnostic trace from the MPI library, and it not useful for finding out 
what GROMACS thinks the problem might be. Further advice below.

> ***************************************************************************
> .mdp file
> title           =FWS
> ;warnings       =10
> cpp             =cpp
> ;define         =-DPOSRES
> ;constraints    =all-bonds
> integrator      =md
> dt              =0.002 ; ps
> nsteps          =100000
> nstcomm         =1000
> nstxout         =1000
> ;nstvout                =1000
> nstfout         =0
> nstlog          =1000
> nstenergy       =1000
> nstlist         =1000
> ns_type         =grid
> rlist           =2.0
> coulombtype     =PME
> rcoulomb        =2.0
> vdwtype         =cut-off
> rvdw            =5.0
> fourierspacing  =0.12
> fourier_nx      =0
> fourier_ny      =0
> fourier_nz      =0
> pme_order       =4
> ewald_rtol      =1e-5
> optimize_fft    =yes
> 
> ; This section added in to freeze hydrogen atoms at edge of graphene
> lattice to prevent movement of lattice
> ;energygrp_excl = Edge Edge Edge Grph Grph Grph
> freezegrps      = Edge Grph ; Hydrogen atoms in graphene lattice are
> associated with the residue Edge

See comments in 7.3.24 of manual. You need the energy group exclusions.

Mark

> freezedim       = Y Y Y Y Y Y; Freeze hydrogen atoms in all directions
> 
> ;Tcoupl         =berendsen
> ;tau_t          =0.1    0.1
> ;tc-grps                =protein non-protein
> ;ref_t = 300 300
> 
> ;Pcoupl = parrinello-rahman
> ;tau_p = 0.5
> ;compressibility = 4.5e-5
> ;ref_p = 1.0
> 
> ;gen_vel = yes
> ;gen_temp = 300.0
> ;gen_seed = 173529
> ***************************************************************************
> 
> ***************************************************************************
> ERROR IN OUTPUT FILE
> [node16:25758] *** Process received signal ***
> [node16:25758] Signal: Segmentation fault (11)
> [node16:25758] Signal code: Address not mapped (1)
> [node16:25758] Failing at address: 0xfffffffe1233e230
> [node16:25758] [ 0] /lib64/libpthread.so.0 [0x3834a0de80]
> [node16:25758] [ 1] /usr/lib64/libmd_mpi.so.4(pme_calc_pidx+0xd6)
> [0x2ba295dd0606]
> [node16:25758] [ 2] /usr/lib64/libmd_mpi.so.4(do_pme+0x808)
> [0x2ba295dd4058]
> [node16:25758] [ 3] /usr/lib64/libmd_mpi.so.4(force+0x8de)
> [0x2ba295dba5be]
> [node16:25758] [ 4] /usr/lib64/libmd_mpi.so.4(do_force+0x5ef)
> [0x2ba295ddeaff]
> [node16:25758] [ 5] mdrun_mpi(do_md+0xe23) [0x411193]
> [node16:25758] [ 6] mdrun_mpi(mdrunner+0xd40) [0x4142f0]
> [node16:25758] [ 7] mdrun_mpi(main+0x239) [0x4146f9]
> [node16:25758] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4)
> [0x3833e1d8b4]
> [node16:25758] [ 9] mdrun_mpi [0x40429a]
> [node16:25758] *** End of error message ***
> mpirun noticed that job rank 7 with PID 25758 on node node16 exited on
> signal 11 (Segmentation fault).
> 7 processes killed (possibly by Open MPI)
> ***************************************************************************
> 
> Could you please let me know what you think may be causing the fault?
> 
> Much thanks in advance.
> 
> Darrell Koskinen
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