[gmx-users] simulation end with Segmentation fault, error message said something about libSystem.B.dylib

[Itamar Kass]

On Thu, Oct 15, 2009 at 1:40 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> Itamar Kass wrote:
>
>> Hi,
>>
>> Lately few of my simulations had ended up with wired output:
>>
>> Writing final coordinates.
>> step 500000, remaining runtime:     0 s         [xn068:94365] *** Process
>> received signal ***
>> [xn068:94365] Signal: Segmentation fault (11)
>> [xn068:94365] Signal code: Address not mapped (1)
>> [xn068:94365] Failing at address: 0x108ee9000
>> [xn068:94365] [ 0] 2   libSystem.B.dylib
>> 0x00000000844e83fa _sigtramp + 26
>> [xn068:94365] [ 1] 3   ???
>> 0x0000000000801b78 0x0 + 8395640
>> [xn068:94365] *** End of error message ***
>>
>>
>> In addition, the output files are not usable. We use apple with 10.5
>> (server version) and gromacs (4.0.5) is compiles using 64bit.
>>
>> Any idea someone?
>>
>
> What was the command line?
>

mpiexec mdrun_mpi -pd -s one_GroEL_noATP_run2_for_MD6.tpr -o
one_GroEL_noATP_run2_from_MD6.trr -c one_GroEL_noATP_run2_from_MD6.gro -e
one_GroEL_noATP_run2
_from_MD6.edr -x one_GroEL_noATP_run2_from_MD6.xtc -g
one_GroEL_noATP_run2_from_MD6.log -v -stepout 5000

I am using -pd 'cause I am using SHAKE.


What's the end of the .log file?


I gave the mdrun output and not the logfile 'cause there is nothing speaciel
there. It write the temp, energy etc. which look OK and then stop:

           Step           Time         Lambda
         499800      999.60000        0.00000

   Energies (kJ/mol)
       G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
    9.05518e+03    3.39568e+03    2.06800e+03   -2.23433e+02    8.39937e+04
        LJ (SR)        LJ (LR)   Coulomb (SR)   Coulomb (LR)       RF excl.
    4.54232e+05   -2.10739e+04   -3.24147e+06   -3.58373e+04   -6.38806e+04
      Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
   -2.80974e+06    4.96949e+05   -2.31279e+06    3.05107e+02   -3.18227e+01

           Step           Time         Lambda
         499900      999.80000        0.00000

   Energies (kJ/mol)
       G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
    9.09295e+03    3.38158e+03    2.12674e+03   -1.83503e+02    8.36385e+04
        LJ (SR)        LJ (LR)   Coulomb (SR)   Coulomb (LR)       RF excl.
    4.54228e+05   -2.10769e+04   -3.24015e+06   -3.55380e+04   -6.38776e+04
      Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
   -2.80836e+06    4.95856e+05   -2.31250e+06    3.04437e+02   -1.27131e+01

           Step           Time         Lambda
         500000     1000.00000        0.00000

Writing checkpoint, step 500000 at Wed Oct 14 17:34:47 2009

   Energies (kJ/mol)
       G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
    8.53869e+03    3.32588e+03    2.03245e+03   -2.36432e+02    8.41339e+04
        LJ (SR)        LJ (LR)   Coulomb (SR)   Coulomb (LR)       RF excl.
    4.57725e+05   -2.10767e+04   -3.24340e+06   -3.52958e+04   -6.38808e+04
      Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
   -2.80813e+06    4.96000e+05   -2.31213e+06    3.04525e+02    9.63155e+01



> What filesystem are you using?


We are using MAC so this is Mac OS Extended (Journaled).


> Did it fill?
>
> Mark
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