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

[darrellk at ece.ubc.ca]

Hi Mark,
I used editconf on my .gro file with zero space between my solvent and
the box and the resulting box had the exact same dimension as the
initial box. I also performed a number of simulation runs with different
mdp parameters hoping this would provide me some indication of the cause
of the fault but to no avail. I looked through the log files, error
files, and output files and could not find any output to help me
identify the source of my error.

Could you please let me know how I can look at my structure at each point
as you indicate below as I do not see any files output that provide me
to do so? I tried to look at the .trr file but when I try to load it
into VMD, it causes an error. I am assuming this error is caused because
the .trr file did not complete correctly due to the segmentation fault.
Please advise.

Thanks.

Darrell

>Date: Tue, 07 Jul 2009 09:19:42 +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: <4A52868E.6010807 at anu.edu.au>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>darrellk at ece.ubc.ca wrote:
>> 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.
>
>Sure, but if there's something malformed with your model physics or
>starting configuration, then large forces can make anything explode.
>
>Look at your structures at each point and see where things start to go
>wrong. Make sure you've used editconf on your starting structure to
>provide the right box dimensions.
>
>Mark
>
>> 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