nathandunn
commented
9 years ago @cmdcolin It looks like it opens 1-3 files per track loaded and doesn't seem to increase (most of the time) and will eventually release the file handles.
Loading the bam track (Forager RNA-Seq reads), I see that it loads around 14 . . . goes up to 20 or so and then plateaus.
With 3 BAM files I got it to around 80-100 . . and it kind of maxed out (moving back and forth and changing groups).
That being said, in the code there is this line . . can't but help to fix:
// TODO: move up so not recalculating each time
String pathTranslated = request.getPathTranslated();
String rootPath = pathTranslated.substring(0, pathTranslated.length() - request.getPathInfo().length());
String configPath = rootPath + "/config/config.properties";
File propertyFile = new File(configPath);
String filename = null;
cmdcolin
If a bunch of tracks are opened at once, then many duplicate file handles are opened for config.properties, basically until it hits the system limit.
Normal operation: around 250 file handles open
After opening up about 10 bam tracks and scrolling around: over 800 file handles open, all duplicates of config.properties
It will just increase until the "too many open files error" or the garbage collector picks up the objects