[gmx-users] Signal: Segmentation faul
Amit Choubey
kgp.amit at gmail.com
Mon Jan 3 07:54:04 CET 2011
Your log file does indicate that the steepest descent converged. I dont know
why you have the error messages. Why not go ahead with MD ?
Amit
On Sun, Jan 2, 2011 at 10:35 PM, shikha agarwal <shikhaiiitabi at gmail.com>wrote:
> 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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