Merge #75 - Terminate ArrayBuilder threadpool

(very) surprisingly, a static thread pool executor will prevent the
JVM from ever properly shutting down, because of a circular nature
of the references. Static variables and thread objects are GC roots,
and the thread pool object references its child threads while the
threads themselves reference the threadpool. No amount of GC runs
will make anything unreachable, so the JVM can't finalize and
shut down. To break the cycle, we need to forcibly shutdown the
thread pool, which causes it to kill its threads and allows the GC
to unravel the references.

see also: https://stackoverflow.com/a/10395700

Author: PerilousApricot

src/main/java/edu/vanderbilt/accre/laurelin/Root.java

@@ -110,15 +110,37 @@ static class TTreeDataSourceV2PartitionReader implements InputPartitionReader<Co
         private Map<String, SlimTBranch> slimBranches;
 
         /**
-         * Thread factory for async processing/decompression of baskets
+         * ThreadPool handling the async decompression tasks
          */
-        private static ThreadFactory namedThreadFactory =
-                new ThreadFactoryBuilder().setNameFormat("laurelin-arraybuilder-%d").build();
+        private static ThreadPoolExecutor staticExecutor;
 
         /**
-         * ThreadPool handling the async decompression tasks
+         *  (very) surprisingly, a static thread pool executor will prevent the
+         *  JVM from ever properly shutting down, because of a circular nature
+         *  of the references. Static variables and thread objects are GC roots,
+         *  and the thread pool object references its child threads while the
+         *  threads themselves reference the threadpool. No amount of GC runs
+         *  will make anything unreachable, so the JVM can't finalize and
+         *  shut down. To break the cycle, we need to forcibly shutdown the
+         *  thread pool, which causes it to kill its threads and allows the GC
+         *  to unravel the references.
+         *  <p>
+         *  see also: https://stackoverflow.com/a/10395700
          */
-        private static ThreadPoolExecutor staticExecutor = new ThreadPoolExecutor(1,1,60L, TimeUnit.SECONDS,new LinkedBlockingQueue<Runnable>());
+        static {
+            ThreadFactory factory = new ThreadFactoryBuilder().setNameFormat("laurelin-arraybuilder-%d").build();
+            staticExecutor = new ThreadPoolExecutor(1, 1,
+                                                    5L, TimeUnit.SECONDS,
+                                                    new LinkedBlockingQueue<Runnable>(),
+                                                    factory);
+            staticExecutor.allowCoreThreadTimeOut(true);
+            Runtime.getRuntime().addShutdownHook(new Thread() {
+                @Override
+                public void run() {
+                    TTreeDataSourceV2PartitionReader.staticExecutor.shutdownNow();
+                }
+            });
+        }
 
         /**
          * Holds the async threadpool if enabled, null otherwise