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Hi,<br><br>You can simply use plain unix cat, that will be much faster and does not use memory.<br>If you want the time of the frames right, run trjconv with the right option on the catted<br>frames.<br><br>Berk<br><br>> Date: Wed, 13 Oct 2010 08:41:17 +0200<br>> From: spoel@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] why does trjcat take so much memory?<br>> <br>> On 2010-10-13 01.54, chris.neale@utoronto.ca wrote:<br>> > I have 28,000 .xtc files, each having a single frame and each 150K. If I<br>> > run du -hs on the directory containing these .xtcs, I get 4.4 GB.<br>> > Nevertheless, when I run trjcat -f *.xtc -o ../tot.xtc , my memory<br>> > consumption goes over 11 GB and then I run out of available memory.<br>> The program reads the first frame of all files, and since we roughly <br>> have three times compression from xtc to float your figures of 4 vs. 11 <br>> Gb. match perfect.<br>> <br>> Although this is an extreme case, where there is a clear workaround <br>> (more memory) it could be worthwhile looking into an enhancement that <br>> releases the memory again after checking the first frame of all files. <br>> It is anyway impossible to keep 28,000 files open. Please file a <br>> bugzilla as an enhancement.<br>> <br>> Another workaround is to do this in 10 steps or so. Some scripting <br>> required but not too bad.<br>> <br>> ><br>> > Sure, I could find a larger memory system, but why does it take >=3x<br>> > more memory than the individual files took in disk space? Does anybody<br>> > know any commands<br>> ><br>> > This is gromacs 4.0.5 and 4.0.7 and 4.5-beta2.<br>> ><br>> > Thank you,<br>> > Chris.<br>> ><br>> <br>> <br>> -- <br>> David van der Spoel, Ph.D., Professor of Biology<br>> Dept. of Cell & Molec. Biol., Uppsala University.<br>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>> spoel@xray.bmc.uu.se http://folding.bmc.uu.se<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br> </body>
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