-->tail -5000 filename > filename.new
mv filename.new filename sync
This will copy the last 5000 lines from the file to a temporary file.
Now you probably want to restart whatever service it is that created the file to release it's file lock on the file.
/usr also fills up sometimes because of apache. The first thing you should look at is usually the apache logs.
cd to /usr/local/apache
and type "du -sh *" and chances are you'll find that the logs/error_log or logs/access_log is very large.
Feel free to delete them or use the tail trick above.
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