Thank you for the insight Mark.
To get it on the record, this is fairly annoying for trjcat (not
trjconv). If anyone else has run into this, then please do post
because a memory efficient cat mechanism will only be coded if there
is sufficient interest.
But again, thanks for your good answer Mark, probably you are correct.
Chris.
----- Original Message -----
From: [email protected]
Date: Wednesday, October 13, 2010 10:55
Subject: [gmx-users] why does trjcat take so much memory?
To: [email protected]
[Hide Quoted Text]
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.
Mark
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