[gmx-users] trjcad segmentation fault

[David van der Spoel]

On Fri, 2005-04-22 at 03:25 -0400, Sukit Leekumjorn wrote:
> David,
> 
> Originally, both trr files are approximately 220 Mb. I did gmxdump the 
> first file (md2 about 1Gb) but the second file (md3)  I could not 
> gmxdump.  The error show is again Segmentation fault.
try gmxcheck instead.



If you get the error then your file md3 is corrupt.

> 
> Below is what I used to create md3.tpr before run parallel.
> 
> tpbconv_d -s md2.tpr -f md2.trr -e md2.edr -n deshuf.ndx -o md3.tpr 
> -extend 10000
> 
> What could be the problem?
> 
> Thanks for your advice
> 
> Sukit
>  
> 
> David van der Spoel wrote:
> 
> >On Fri, 2005-04-22 at 01:14 -0400, Sukit Leekumjorn wrote:
> >  
> >
> >>Hello,
> >>
> >>Has anyone came across this problem in combining 2 .trr files using 
> >>"trjcad" (see below). The combined file was created but could not be use 
> >>to calculate any property using this .trr.
> >>
> >>    
> >>
> >first run gmxcheck on both trr files
> >then check the sizes, and see whether you may have a 2Gb file problem.
> >
> >  
> >
> >>Thanks for your advice in advance.
> >>
> >>Sukit
> >>
> >>Summary of files and start times used:
> >>
> >>          File                Start time
> >>-----------------------------------------
> >>                  md2.trr        0.000 ps
> >>                  md3.trr    10000.000 ps
> >>
> >>Reading frame       0 time    0.000  
> >>lasttime -12345
> >>
> >>Continue writing frames from md2.trr t=0 ps, frame=0     
> >>Last frame       1000 time 10000.000   ->  frame    990 time 9900.000 
> >>ps    
> >>Reading frame       0 time 10000.000  
> >>lasttime 9990
> >>
> >>Continue writing frames from md3.trr t=10000 ps, frame=1000     
> >>Segmentation fault 30 time 10300.001    ->  frame   1030 time 10300.001 ps 
> >>
> >>_______________________________________________
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> >>    
> >>
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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