[gmx-users] what is "MPI process rank 0 (n0, p18041) caught a SIGSEGV"

[Gerrit Groenhof (RUG)]

Recompile the mopac library with larger arrays. You can set these in the 
SIZES file in the mopac sourcedir
(MAXORB).

Do not forget to recompile also mdrun afterwards,as the library (.a) 
will be statically linked.

Gerrit

Mahnam wrote:

>
> In God We Trust
> Hello GMX users
> I want to do QM/MM by Gromacs and mopac7.I installed Gromacs and 
> mopac7.I am using ffoplsaa. grompp make tpr ,but when I run mdrun it 
> says:
> Back Off! I just backed up a.log to ./#a.log.5#
> Reading file a4.tpr, VERSION 3.3 (single precision)
> QM/MM calculation requested.
> Layer 0
> nr of QM atoms 147
> QMlevel: PM3/STO-3G
>  
>            MAXIMUM NUMBER OF ATOMIC ORBITALS EXCEEDED
>            MAXIMUM ALLOWED = 200
> keywords are: PRECISE GEO-OK CHARGE=0 GRAD MMOK ANALYT PM3
>
> Back Off! I just backed up a.edr to ./#a.edr.5#
> Steepest Descents:
>    Tolerance (Fmax)   =  1.00000e+02
>    Number of steps    =         1000
>  counting the number of NH-C=O groups
> *MPI process rank 0 (n0, p18041) caught a SIGSEGV*.
>
> and here is the end of my md.log file
> Initializing LINear Constraint Solver
>   number of constraints is 6
>   average number of constraints coupled to one constraint is 0.0
> Steepest Descents:
>    Tolerance (Fmax)   =  1.00000e+02
>    Number of steps    =         1000
>    Rel. Constraint Deviation:  Max    between atoms     RMS
>        Before LINCS         0.098311   1707   1710   0.093123
>         After LINCS         0.000003   1684   1687   0.000001
> Going to use C-settle (1267 waters)
> wo = 0.333333, wh =0.333333, wohh = 3, rc = 0.08165, ra = 0.0384897
> rb = 0.0192449, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1
> Grid: 9 x 9 x 6 cells
> Configuring nonbonded kernels...
> Testing AMD 3DNow support... not present.
> Testing ia32 SSE support... present.
>  
> I do not have any idea why this is happening?.May I ask you what does 
> it means?
> Any help will be greatly appreciated
>  
> Karim Mahnam
> Institute of  Biochemistry  and  Biophysics (IBB)
> Tehran University
> P.O.box 13145-1384
> Tehran
> Iran
> http://www.ibb.ut.ac.ir/
>
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