On Wed, Oct 13, 2010 at 2:41 AM, David van der Spoel <[email protected]>wrote:
> On 2010-10-13 01.54, [email protected] wrote: > >> 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. >> > The program reads the first frame of all files, and since we roughly have > three times compression from xtc to float your figures of 4 vs. 11 Gb. match > perfect. > Each first frame is read twice. Thus I think it is 2x the memory. > > Although this is an extreme case, where there is a clear workaround (more > memory) it could be worthwhile looking into an enhancement that releases the > memory again after checking the first frame of all files. It is anyway > impossible to keep 28,000 files open. Please file a bugzilla as an > enhancement. > Yes and it should be easy because the frame isn't reused. Thus freeing it shouldn't have any side effect. Roland
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