[gmx-users] Re: gmx-users Digest, Vol 49, Issue 11

[Ramadas Sunil Pophale]

Ramadas Sunil Pophale wrote:
> Dear gromacs users,
>
> After configuring and installing gromacs, I tested it using 'make
tests'.
> Got the following errors.
>
> *** glibc detected *** realloc(): invalid next size: 0x08255310 ***
> sh: line 1:  7535 Aborted       (core dumped) mdrun >mdrun.out 2>&1
> FAILED. Check files in rb1
> 1 out of 16 simple tests FAILED
>
> I checked the simple/rb1 directory for the .out files. I could not quite
> see the problem described in those. Seems like it's related to 'allowing
a
> memory location that has already been freed to be used again'.
>
> Among the files I checked (checkptr.out, grompp.out, mdrun.out), the
> closest thing to a warning seemed to be
>
> gcq#288: "I Feel a Great Disturbance in the Force" (The Emperor Strikes
> Back) in grompp.out :-)
>
> is there anything in the script file (gmxtest.pl), I need to fix?
>
>
-----------------------------------------------------------------------------
>
> FAILED. Check files in dec+water
> FAILED. Check files in nacl
> FAILED. Check files in tip4p
> 3 out of 14 complex tests FAILED
>
> As for the errors with complex tests, I had 3 of those. I checked the
> checkpot.out files. Only in one case (dec+water) were the LJ numbers
close
> to zero (thus justifying the 'error due to numerical accuracy in adding
up
> many interactions' on wiki). In other 2 cases, the deviations in LJ and
coloumb
> energies were not small.
>
> for example
>
> LJ (SR)          step  50:       14440.2,  step  50:      13501.5
> Coulomb (SR)     step  50:      -90740.2,  step  50:     -84154.3
>
> Not sure if I can simply ignore these. Any suggestions?

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How did you compile? What platform are you running on?

-----------------------------------------------------------------------

Hi David,

I used RedHat-linux 4.0 with intel mkl library for fftw.
The compilation went smoothly. Gromacs was installed in a non-standard
location as I am not the root.

Regards,

Ramdas.