Reading large file in Java -- Java heap space

Question

I'm reading a large tsv file (~40G) and trying to prune it by reading line by line and print only certain lines to a new file. However, I keep getting the following exception:

java.lang.OutOfMemoryError: Java heap space
    at java.util.Arrays.copyOf(Arrays.java:2894)
    at java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:117)
    at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:532)
    at java.lang.StringBuffer.append(StringBuffer.java:323)
    at java.io.BufferedReader.readLine(BufferedReader.java:362)
    at java.io.BufferedReader.readLine(BufferedReader.java:379)

Below is the main part of the code. I specified the buffer size to be 8192 just in case. Doesn't Java clear the buffer once the buffer size limit is reached? I don't see what may cause the large memory usage here. I tried to increase the heap size but it didn't make any difference (machine with 4GB RAM). I also tried flushing the output file every X lines but it didn't help either. I'm thinking maybe I need to make calls to the GC but it doesn't sound right.

Any thoughts? Thanks a lot. BTW - I know I should call trim() only once, store it, and then use it.

Set<String> set = new HashSet<String>();
set.add("A-B");
...
...
static public void main(String[] args) throws Exception
{
   BufferedReader reader = new BufferedReader(new InputStreamReader(new FileInputStream(inputFile),"UTF-8"), 8192);
   PrintStream output = new PrintStream(outputFile, "UTF-8");

   String line = reader.readLine();
   while(line!=null){
        String[] fields = line.split("\t");
        if( set.contains(fields[0].trim()+"-"+fields[1].trim()) )
            output.println((fields[0].trim()+"-"+fields[1].trim()));

        line = reader.readLine();
   }

output.close();

}

Answer 1

Most likely, what's going on is that the file does not have line terminators, and so the reader just keeps growing it's StringBuffer unbounded until it runs out of memory.

The solution would be to read a fixed number of bytes at a time, using the 'read' method of the reader, and then look for new lines (or other parsing tokens) within the smaller buffer(s).