[gmx-users] tpi segmentation fault

Sander Pronk pronk at cbr.su.se
Mon Aug 16 13:39:42 CEST 2010

Hi Javier,

I've just committed a fix to the git 4.5 tree. Thanks for reporting this. 


On 13 Aug 2010, at 18:35 , Javier Cerezo wrote:

> 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
> -- 
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> Universidad de Murcia
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