Zip compression stuttering

Question

Hello,
I'm writing a program for Zip compressing some files but it's performance is quite odd. It zips the first four files very quickly and then stops for a long time (CPU usage=0%) when closing the 5th entry. Then it zips the next four files and stops again, this time when putting a new entry on the stream. Again, CPU usage=0%. Am I doing something wrong? Here's the code - the getfiles method returns all the files on a directory and is working correctly. Printing the letters a,b,c,d,e is only for debugging purposes.
public static void main(String[] args) throws Exception{
        //get the files
        ArrayList files = getFiles(new File(args[0]));
        int i=0, numFiles=files.size();
        File result = new File("aux.zip"), aux=null;
        byte[] buffer;
        BufferedInputStream in;
        ZipOutputStream out = new ZipOutputStream(new BufferedOutputStream(new FileOutputStream(result)));
        System.out.println("Number of files: "+numFiles);
        // Start the compression
        for (i=0; i<numFiles; i++) {
            aux = (File)files.get(i);
            System.out.println("Working on "+aux);
            in = new BufferedInputStream(new FileInputStream(aux));
            System.out.println("a");
            out.putNextEntry(new ZipEntry(aux.getPath()));
            System.out.println("b");
            int len;
            buffer = new byte[ (int)aux.length() ];
            while ((len = in.read(buffer)) > 0) {
                out.write(buffer, 0, len);
            System.out.println("c");
            out.closeEntry();
            System.out.println("d");
            in.close();
            System.out.println("e");
        out.close();
}Thanx in advance! :)

Answer 1

I tested the code with four small (<3kB) text files and once again, it blocked for a while closing the stream (not the entry) but it didn't create the zip file? Is my code OK?
I never debugged anything using that method, so I'd be thankful for some help. Here's what I got from Ctrl+Break:
Full thread dump Java HotSpot(TM) Client VM (1.5.0_01-b08 mixed mode):
"Low Memory Detector" daemon prio=5 tid=0x009c1ef0 nid=0x218 runnable [0x00000000..0x00000000]
"CompilerThread0" daemon prio=10 tid=0x009c09f8 nid=0x448 waiting on condition [0x00000000..0x0ac5f8bc]
"Signal Dispatcher" daemon prio=10 tid=0x009bfcb8 nid=0x1c8 waiting on condition [0x00000000..0x00000000]
"Finalizer" daemon prio=9 tid=0x009b70f8 nid=0x124 in Object.wait() [0x0abdf000..0x0abdfc64]
     at java.lang.Object.wait(Native Method)
     - waiting on <0x02a80850> (a java.lang.ref.ReferenceQueue$Lock)
     at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:116)
     - locked <0x02a80850> (a java.lang.ref.ReferenceQueue$Lock)
     at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:132)
     at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)
"Reference Handler" daemon prio=10 tid=0x009b5c08 nid=0x3f4 in Object.wait() [0x0ab9f000..0x0ab9fce4]
     at java.lang.Object.wait(Native Method)
     - waiting on <0x02a80760> (a java.lang.ref.Reference$Lock)
     at java.lang.Object.wait(Object.java:474)
     at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)
     - locked <0x02a80760> (a java.lang.ref.Reference$Lock)
"main" prio=5 tid=0x00235ee0 nid=0x4e0 runnable [0x0006f000..0x0006fc38]
     at java.io.FileOutputStream.writeBytes(Native Method)
     at java.io.FileOutputStream.write(FileOutputStream.java:260)
     at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:65)
     at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:123)
     - locked <0x02aa6ed8> (a java.io.BufferedOutputStream)
     at java.io.FilterOutputStream.close(FilterOutputStream.java:140)
     at java.util.zip.DeflaterOutputStream.close(DeflaterOutputStream.java:144)
     at java.util.zip.ZipOutputStream.close(ZipOutputStream.java:310)
     at CryptoWorker.main(CryptoWorker.java:61)
"VM Thread" prio=10 tid=0x009b3208 nid=0x3d8 runnable
"VM Periodic Task Thread" prio=10 tid=0x009c3490 nid=0x2d4 waiting on condition