[gmx-users] trjcad segmentation fault

Sukit Leekumjorn leekumjo at vt.edu
Fri Apr 22 09:25:22 CEST 2005


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.

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


David van der Spoel wrote:

>On Fri, 2005-04-22 at 01:14 -0400, Sukit Leekumjorn wrote:
>>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.
>>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 
>>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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