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

[darrellk at ece.ubc.ca]

Hi Mark,
I added the energy group exclusions as indicated in your previous
response but am still experiencing the same problem. I looked at the
.log files and see that in one log file it tells me that my box is
exploding. However, I do not have many molecules in my simulation and
therefore do not think that it is possible that my box is exploding from
pressure.

Maybe if I re-state my simulation it will help you in providing me
direction on what might be causing the problem. My simulation consists
of a graphene lattice with a layer of ammonia molecules above it. The
box is very large and there is lots of empty space in the box. So I am a
little confused as to how the box could be exploding.

Thanks again in advance for your help.

Darrell Koskinen

>Date: Fri, 03 Jul 2009 11:41:45 +1000
>From: Mark Abraham <Mark.Abraham at anu.edu.au>
>Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <4A4D61D9.6080700 at anu.edu.au>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>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