[gmx-users] tpi segmentation fault

Berk Hess gmx3 at hotmail.com
Mon Aug 16 11:49:21 CEST 2010


I don't understand why 4.0.7 gives a segv.

But 4.5-beta probably gives a segv because of a parallel problem.
Could you try 4.5-beta with the mdrun option -nt 1
and report back?



> Date: Fri, 13 Aug 2010 18:35:55 +0200
> From: jcb1 at um.es
> To: gmx-users at gromacs.org
> Subject: [gmx-users] tpi segmentation fault
> Hi all.
> I am trying to perform a tpi (test particle insertion) calculation on a 
> trajectory generated with mpi_mdrun (gromacs 4.0.7, run in a Beowulf 
> cluster of Intel(R) Core(TM)2 Quad CPU    Q6600  @ 2.40GHz). I am using 
> tpi integrator in the mdp file and the following command:
>   $  grompp -f tpi.mdp -c 32hoa_128dmpcwrun.gro -n index_tpi.ndx -p 
> topol_tpi.top
>   $  mdrun -rerun 32hoa_128dmpcwrun.trr -g tpi.log
> I tried different versions of gromcas and for 4.0.X I got a segmentation 
> fault getting the message:
>          trn version: GMX_trn_file (single precision)
>          Reading frame       0 time    0.000   Segmentation fault
> using a compiled version with "config --prefix 
> /home/cerezo/Programs/gromacs4.07" + "make" + "make install". However, 
> it works when I used a precompiled version (got with apt-get, I have 
> kubuntu). So I guess that it may be due to a mistake during the 
> compilation. In addition, other integrators (i.e. md, steep) work 
> correctly with the version I've compiled. My system is and Intel(R) 
> Core(TM)2 Quad CPU    Q8400  @ 2.66GHz. Is there any trick I could try 
> in the compilation?
> I also tried gromacs-4.5-betaX and it works but sometimes (apparently 
> randomly) the calculation gets stops (as if it had entered in an 
> infinite loop) after reading the last frame.
> Thanks for your attention!
> Javier
> -- 
> Estudiante de Doctorado
> ---------------------
> Dpto. Química-Física
> Universidad de Murcia
> 30100 MURCIA (España)
> Tlf.(+34)868887434
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