[gmx-users] Signal: Segmentation faul

[shikha agarwal]

hi,
HAPPY NEW YEAR

I am experiencing a segmentation fault during mdrun in equlibration step .
error

Wrote pdb files with previous and current coordinates
[shikha-desktop:01719] *** Process received signal ***
[shikha-desktop:01719] Signal: Segmentation fault (11)
[shikha-desktop:01719] Signal code: Address not mapped (1)
[shikha-desktop:01719] Failing at address: 0x8d22a70
[shikha-desktop:01719] [ 0] [0xb87410]
[shikha-desktop:01719] [ 1] mdrun(do_nonbonded+0x769) [0x82a9789]
[shikha-desktop:01719] *** End of error message ***
Segmentation fault





bottom lines of my .log file after energy minimization is this



 Step           Time         Lambda
          11357    11357.00000        0.00000

           Step           Time         Lambda
          11358    11358.00000        0.00000

           Step           Time         Lambda
          11359    11359.00000        0.00000

           Step           Time         Lambda
          11360    11360.00000        0.00000

           Step           Time         Lambda
          11361    11361.00000        0.00000


Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

Steepest Descents converged to machine precision in 11362 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -5.4871900e+06
Maximum force     =  3.9830833e+03 on atom 4511
Norm of force     =  1.9521437e+01

    M E G A - F L O P S   A C C O U N T I N G

   RF=Reaction-Field  FE=Free Energy  SCFE=Soft-Core/Free Energy
   T=Tabulated        W3=SPC/TIP3p    W4=TIP4p (single or pairs)
   NF=No Forces

 Computing:                               M-Number         M-Flops  % Flops
-----------------------------------------------------------------------------
 LJ                                   10523.695513      347281.952     0.4
 Coul(T)                               6405.625131      269036.256     0.3
 Coul(T) [W3]                           226.446553       28305.819     0.0
 Coul(T) + LJ                          4637.739866      255075.693     0.3
 Coul(T) + LJ [W3]                     1706.661036      235519.223     0.3
 Coul(T) + LJ [W3-W3]                141595.844211    54089612.489    69.1
 Outer nonbonded loop                 18947.604080      189476.041     0.2
 1,4 nonbonded interactions             105.189396        9467.046     0.0
 Calc Weights                         11755.000218      423180.008     0.5
 Spread Q Bspline                    250773.337984      501546.676     0.6
 Gather F Bspline                    250773.337984     1504640.028     1.9
 3D-FFT                             1217431.505524     9739452.044    12.4
 Solve PME                            14842.953216      949949.006     1.2
 NS-Pairs                            418574.562328     8790065.809    11.2
 Reset In Box                          1338.886718        4016.660     0.0
 Shift-X                               3916.765450       23500.593     0.0
 CG-CoM                                3918.333406       11755.000     0.0
 Bonds                                  114.131290        6733.746     0.0
 Angles                                 142.695358       23972.820     0.0
 Propers                                102.167104       23396.267     0.0
 Impropers                               28.984462        6028.768     0.0
 RB-Dihedrals                             2.885948         712.829     0.0
 Pos. Restr.                             38.199044        1909.952     0.0
 Virial                                3918.844696       70539.205     0.1
 Settle                                2534.725856      818716.451     1.0
-----------------------------------------------------------------------------
 Total                                                78323890.379   100.0
-----------------------------------------------------------------------------


     R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

 Computing:         Nodes     Number     G-Cycles    Seconds     %
-----------------------------------------------------------------------
 Neighbor search        1      11362    30337.457     6067.7    18.8
 Force                  1      11362    35859.263     7172.1    22.3
 PME mesh               1      11362    12486.060     2497.3     7.8
 Constraints            1      22723     1294.000      258.8     0.8
 Rest                   1               81096.730    16219.8    50.3
-----------------------------------------------------------------------
 Total                  1              161073.511    32215.7   100.0
-----------------------------------------------------------------------
-----------------------------------------------------------------------
 PME spread/gather      1      22724     7169.616     1434.0     4.5
 PME 3D-FFT             1      22724     3654.067      730.8     2.3
 PME solve              1      11362     1662.017      332.4     1.0
-----------------------------------------------------------------------

               NODE (s)   Real (s)      (%)
       Time:   2137.029  32215.651      6.6
                       35:37
               (Mnbf/s)   (GFlops)   (steps/hour)
Performance:    609.130  78323.890        19140.2
Finished mdrun on node 0 Sat Jan  1 02:54:31 2011


hepl me !


regards :
shikha
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