[gmx-users] Segmentation Fault (Address not mapped)
David van der Spoel
spoel at xray.bmc.uu.se
Mon Jul 13 21:31:05 CEST 2009
darrellk at ece.ubc.ca wrote:
> 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.
>
try ngmx
if VMD crashes then probably the gro file does not match the trr file
(more atoms in trr than in gro).
> 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
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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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