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

Roland Schulz roland at utk.edu
Wed Oct 13 09:09:04 CEST 2010

On Wed, Oct 13, 2010 at 2:41 AM, David van der Spoel
<spoel at xray.bmc.uu.se>wrote:

> On 2010-10-13 01.54, chris.neale at utoronto.ca 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.

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