[gmx-users] why does trjcat take so much memory?

Mark Abraham mark.abraham at anu.edu.au
Wed Oct 13 02:55:38 CEST 2010

----- Original Message -----
From: chris.neale at utoronto.ca
Date: Wednesday, October 13, 2010 10:55
Subject: [gmx-users] why does trjcat take so much memory?
To: gmx-users at gromacs.org

> I have 28,000 .xtc files, each having a single frame and each 
> 150K. If I run du -hs on the directory containing these .xtcs, I 
> get 4.4 GB. Nevertheless, when I run trjcat -f *.xtc -o 
> ../tot.xtc , my memory consumption goes over 11 GB and then I 
> run out of available memory.
> Sure, I could find a larger memory system, but why does it take 
> >=3x more memory than the individual files took in disk space? 

I'd guess that the increased space reflects trjconv converting the compressed .xtc format back to normal precision, and then back to compressed. To cope with all its possibilities, trjconv probably needs to either keep the loaded frames in memory, or use a two-pass algorithm. It does the former.


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