[gmx-users] trjcat crashes with error 9360 killed when concatenating large number of frames, bug ?

[maria goranovic]

thanks for the help .. will try

On Wed, Jun 15, 2011 at 3:02 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> maria goranovic wrote:
>
>> I am using the command:
>>
>> trjcat -f *gro -o temp.xtc -cat
>> to concatenate about 40,000 frames of 14,000 atoms each. The commands
>> works well for 10,000 frames, but crashes for 40,000 frames after reading
>> all the frames. There is sufficient disk space. Is this a bug of some kind?
>>
>
> Not a bug, but rather clunky code - trjcat consumes a huge amount of
> memory.  If your .gro files are large, then that is the likely limitation.
>  Convert the .gro frames to .xtc with trjconv, then concatenate those
> instead.
>
> -Justin
>
>
>  --
>> Maria G.
>> Technical University of Denmark
>> Copenhagen
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
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-- 
Maria G.
Technical University of Denmark
Copenhagen
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