import junit.extensions.PA;
+/**
+ * Provides a simple test that memory is released when all windows are closed.
+ * <ul>
+ * <li>generates a reasonably large alignment and loads it</li>
+ * <li>performs various operations on the alignment</li>
+ * <li>closes all windows</li>
+ * <li>requests garbage collection</li>
+ * <li>asserts that the remaining memory footprint (heap usage) is 'not large'
+ * </li>
+ * </ul>
+ * If the test fails, this means that reference(s) to large object(s) have
+ * failed to be garbage collected. In this case:
+ * <ul>
+ * <li>set a breakpoint just before the test assertion in
+ * {@code checkUsedMemory}</li>
+ * <li>if the test fails intermittently, make this breakpoint conditional on
+ * {@code usedMemory > expectedMax}</li>
+ * <li>run the test to this point (and check that it is about to fail i.e.
+ * {@code usedMemory > expectedMax})</li>
+ * <li>use <a href="https://visualvm.github.io/">visualvm</a> to obtain a heap
+ * dump from the suspended process (and kill the test or let it fail)</li>
+ * <li>inspect the heap dump using visualvm for large objects and their
+ * referers</li>
+ * <li>Tips:</li>
+ * <ul>
+ * <li>Perform GC from the Monitor view in visualvm before requesting the heap
+ * dump</li>
+ * <li>View 'Objects' and filter classes to {@code jalview}. Sort columns by
+ * Count, or Size, and look for anything suspicious. For example, if the object
+ * count for {@code Sequence} is non-zero (it shouldn't be), pick any instance,
+ * and follow the chain of {@code references} to find which class(es) still hold
+ * references to sequence objects</li>
+ * <li>If this chain is impracticably long, re-run the test with a smaller
+ * alignment (set width=100, height=10 in {@code generateAlignment()}), to
+ * capture a heap which is qualitatively the same, but much smaller, so easier
+ * to analyse; note this requires an unconditional breakpoint</li>
+ * </ul>
+ * </ul>
+ * <p>
+ * <h2>Fixing memory leaks</h2>
+ * <p>
+ * Experience shows that often a reference is retained (directly or indirectly)
+ * by a Swing (or related) component (for example a {@code MouseListener} or
+ * {@code ActionListener}). There are two possible approaches to fixing:
+ * <ul>
+ * <li>Purist: ensure that all listeners and similar objects are removed when no
+ * longer needed. May be difficult, to achieve and to maintain as code
+ * changes.</li>
+ * <li>Pragmatic: null references to potentially large objects from Jalview
+ * application classes when no longer needed, typically when a panel is closed.
+ * This ensures that even if the JVM keeps a reference to a panel or viewport,
+ * it does not retain a large heap footprint. This is the approach taken in, for
+ * example, {@code AlignmentPanel.closePanel()} and
+ * {@code AnnotationPanel.dispose()}.</li>
+ * <li>Adjust code if necessary; for example an {@code ActionListener} should
+ * act on {@code av.getAlignment()} and not directly on {@code alignment}, as
+ * the latter pattern could leave persistent references to the alignment</li>
+ * </ul>
+ * Add code to 'null unused large object references' until the test passes. For
+ * a final sanity check, capture the heap dump for a passing test, and satisfy
+ * yourself that only 'small' or 'harmless' {@code jalview} object instances
+ * (such as enums or singletons) are left in the heap.
+ */
public class FreeUpMemoryTest
{
private static final int ONE_MB = 1000 * 1000;
@BeforeClass(alwaysRun = true)
public void setUp()
{
- Jalview.main(new String[] { "-nonews", "-props",
- "test/jalview/testProps.jvprops" });
+ Jalview.main(
+ new String[]
+ { "-nonews", "-props", "test/jalview/testProps.jvprops" });
String True = Boolean.TRUE.toString();
Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", True);
Cache.applicationProperties.setProperty("SHOW_QUALITY", True);
Cache.applicationProperties.setProperty("SHOW_IDENTITY", True);
}
- /**
- * A simple test that memory is released when all windows are closed.
- * <ul>
- * <li>generates a reasonably large alignment and loads it</li>
- * <li>performs various operations on the alignment</li>
- * <li>closes all windows</li>
- * <li>requests garbage collection</li>
- * <li>asserts that the remaining memory footprint (heap usage) is 'not large'
- * </li>
- * </ul>
- * If the test fails, this suggests that a reference to some large object
- * (perhaps the alignment data, or some annotation / Tree / PCA data) has
- * failed to be garbage collected. If this is the case, the heap will need to
- * be inspected manually (suggest using jvisualvm) in order to track down
- * where large objects are still referenced. The code (for example
- * AlignmentViewport.dispose()) should then be updated to ensure references to
- * large objects are set to null when they are no longer required.
- *
- * @throws IOException
- */
@Test(groups = "Memory")
public void testFreeMemoryOnClose() throws IOException
{
+ long expectedMin = 37L;
+
File f = generateAlignment();
f.deleteOnExit();
- long expectedMin = 35L;
- long usedMemoryAtStart=getUsedMemory();
- if (usedMemoryAtStart>expectedMin)
- {
- System.err.println("used memory before test is "+usedMemoryAtStart+" > "+expectedMin+"MB .. adjusting minimum.");
- expectedMin = usedMemoryAtStart;
- }
doStuffInJalview(f);
Desktop.instance.closeAll_actionPerformed(null);
long usedMemory = availableMemory - freeMemory;
return usedMemory;
}
+
/**
* Requests garbage collection and then checks whether remaining memory in use
* is less than the expected value (in Megabytes)
* - identify large objects in the heap and their referers
* - fix code as necessary to null the references on close
*/
- System.out.println("Used memory after gc = " + usedMemory + "MB");
+ System.out.println("Used memory after gc = " + usedMemory
+ + "MB (should be <" + expectedMax + ")");
assertTrue(usedMemory < expectedMax, String.format(
"Used memory %d should be less than %d (Recommend running test manually to verify)",
- usedMemory,
- expectedMax));
+ usedMemory, expectedMax));
}
/**
* wait until Tree and PCA have been computed
*/
while (af.viewport.getCurrentTree() == null
- && dialog.getPcaPanel().isWorking())
+ || dialog.getPcaPanel().isWorking())
{
waitFor(10);
}
int width = 100000;
int height = 100;
ag.generate(width, height, 0, 10, 15);
+ ps.close();
return f;
}
}
git://source.jalview.org / jalview.git / commitdiff