Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FreeUpMemoryTest	106	62	17	0.00%	Show methods

Class FreeUpMemoryTest

Class FreeUpMemoryTest	Line # 106	Total Statements 62	Complexity 17	TOTAL Coverage 0.00%
setUp() : void   setUp() : void	118118	7.07	1.01	0.0 0.00%
testFreeMemoryOnClose() : void   testFreeMemoryOnClose() : void	132132	6.06	2.02	0.0 0.00%
getUsedMemory() : int   getUsedMemory() : int	152152	4.04	1.01	0.0 0.00%
checkUsedMemory(int) : void   checkUsedMemory(int) : void	167167	14.014	5.05	0.0 0.00%
doStuffInJalview(File) : void   doStuffInJalview(File) : void	213213	21.021	5.05	0.0 0.00%
waitFor(int) : void   waitFor(int) : void	281281	2.02	2.02	0.0 0.00%
generateAlignment() : File   generateAlignment() : File	301301	8.08	1.01	0.0 0.00%

 

Contributing tests

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1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
7		* Jalview is free software: you can redistribute it and/or
8		* modify it under the terms of the GNU General Public License
9		* as published by the Free Software Foundation, either version 3
10		* of the License, or (at your option) any later version.
11		*
12		* Jalview is distributed in the hope that it will be useful, but
13		* WITHOUT ANY WARRANTY; without even the implied warranty
14		* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15		* PURPOSE. See the GNU General Public License for more details.
16		*
17		* You should have received a copy of the GNU General Public License
18		* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19		* The Jalview Authors are detailed in the 'AUTHORS' file.
20		*/
21		package jalview.gui;
22
23		import static org.testng.Assert.assertNotNull;
24		import static org.testng.Assert.assertTrue;
25
26		import java.awt.event.MouseEvent;
27		import java.io.File;
28		import java.io.IOException;
29		import java.io.PrintStream;
30
31		import org.testng.annotations.BeforeClass;
32		import org.testng.annotations.Test;
33
34		import jalview.analysis.AlignmentGenerator;
35		import jalview.bin.Cache;
36		import jalview.bin.Jalview;
37		import jalview.datamodel.AlignmentI;
38		import jalview.datamodel.SequenceGroup;
39		import jalview.io.DataSourceType;
40		import jalview.io.FileLoader;
41		import junit.extensions.PA;
42
43		/**
44		* Provides a simple test that memory is released when all windows are closed.
45		* <ul>
46		* <li>generates a reasonably large alignment and loads it</li>
47		* <li>performs various operations on the alignment</li>
48		* <li>closes all windows</li>
49		* <li>requests garbage collection</li>
50		* <li>asserts that the remaining memory footprint (heap usage) is 'not large'
51		* </li>
52		* </ul>
53		* If the test fails, this means that reference(s) to large object(s) have
54		* failed to be garbage collected. In this case:
55		* <ul>
56		* <li>set a breakpoint just before the test assertion in
57		* {@code checkUsedMemory}</li>
58		* <li>if the test fails intermittently, make this breakpoint conditional on
59		* {@code usedMemory > expectedMax}</li>
60		* <li>run the test to this point (and check that it is about to fail i.e.
61		* {@code usedMemory > expectedMax})</li>
62		* <li>use <a href="https://visualvm.github.io/">visualvm</a> to obtain a heap
63		* dump from the suspended process (and kill the test or let it fail)</li>
64		* <li>inspect the heap dump using visualvm for large objects and their
65		* referers</li>
66		* <li>Tips:</li>
67		* <ul>
68		* <li>Perform GC from the Monitor view in visualvm before requesting the heap
69		* dump - test failure might be simply a delay to GC</li>
70		* <li>View 'Objects' and filter classes to {@code jalview}. Sort columns by
71		* Count, or Size, and look for anything suspicious. For example, if the object
72		* count for {@code Sequence} is non-zero (it shouldn't be), pick any instance,
73		* and follow the chain of {@code references} to find which class(es) still hold
74		* references to sequence objects</li>
75		* <li>If this chain is impracticably long, re-run the test with a smaller
76		* alignment (set width=100, height=10 in {@code generateAlignment()}), to
77		* capture a heap which is qualitatively the same, but much smaller, so easier
78		* to analyse; note this requires an unconditional breakpoint</li>
79		* </ul>
80		* </ul>
81		* <p>
82		* <h2>Fixing memory leaks</h2>
83		* <p>
84		* Experience shows that often a reference is retained (directly or indirectly)
85		* by a Swing (or related) component (for example a {@code MouseListener} or
86		* {@code ActionListener}). There are two possible approaches to fixing:
87		* <ul>
88		* <li>Purist: ensure that all listeners and similar objects are removed when no
89		* longer needed. May be difficult, to achieve and to maintain as code
90		* changes.</li>
91		* <li>Pragmatic: null references to potentially large objects from Jalview
92		* application classes when no longer needed, typically when a panel is closed.
93		* This ensures that even if the JVM keeps a reference to a panel or viewport,
94		* it does not retain a large heap footprint. This is the approach taken in, for
95		* example, {@code AlignmentPanel.closePanel()} and
96		* {@code AnnotationPanel.dispose()}.</li>
97		* <li>Adjust code if necessary; for example an {@code ActionListener} should
98		* act on {@code av.getAlignment()} and not directly on {@code alignment}, as
99		* the latter pattern could leave persistent references to the alignment</li>
100		* </ul>
101		* Add code to 'null unused large object references' until the test passes. For
102		* a final sanity check, capture the heap dump for a passing test, and satisfy
103		* yourself that only 'small' or 'harmless' {@code jalview} object instances
104		* (such as enums or singletons) are left in the heap.
105		*/
		0% Uncovered Elements: 83 (83) Complexity: 17 Complexity Density: 0.27
106		public class FreeUpMemoryTest
107		{
108		private static final int ONE_MB = 1000 * 1000;
109
110		/*
111		* maximum retained heap usage (in MB) for a passing test
112		*/
113		private static int MAX_RESIDUAL_HEAP = 45;
114
115		/**
116		* Configure (read-only) Jalview property settings for test
117		*/
		0% Uncovered Elements: 7 (7) Complexity: 1 Complexity Density: 0.14
118	0	@BeforeClass(alwaysRun = true)...
119		public void setUp()
120		{
121	0	Jalview.main(
122		new String[]
123		{ "--nonews", "--props", "test/jalview/testProps.jvprops" });
124	0	String True = Boolean.TRUE.toString();
125	0	Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", True);
126	0	Cache.applicationProperties.setProperty("SHOW_QUALITY", True);
127	0	Cache.applicationProperties.setProperty("SHOW_CONSERVATION", True);
128	0	Cache.applicationProperties.setProperty("SHOW_OCCUPANCY", True);
129	0	Cache.applicationProperties.setProperty("SHOW_IDENTITY", True);
130		}
131
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33 4-
132	0	@Test(groups = "Memory")...
133		public void testFreeMemoryOnClose() throws IOException
134		{
135	0	File f = generateAlignment();
136	0	f.deleteOnExit();
137
138	0	doStuffInJalview(f);
139
140	0	if (Desktop.instance != null)
141	0	Desktop.instance.closeAll_actionPerformed(null);
142
143	0	checkUsedMemory(MAX_RESIDUAL_HEAP);
144		}
145
146		/**
147		* Returns the current total used memory (available memory - free memory),
148		* rounded down to the nearest MB
149		*
150		* @return
151		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
152	0	private static int getUsedMemory()...
153		{
154	0	long availableMemory = Runtime.getRuntime().totalMemory();
155	0	long freeMemory = Runtime.getRuntime().freeMemory();
156	0	long usedMemory = availableMemory - freeMemory;
157
158	0	return (int) (usedMemory / ONE_MB);
159		}
160
161		/**
162		* Requests garbage collection and then checks whether remaining memory in use
163		* is less than the expected value (in Megabytes)
164		*
165		* @param expectedMax
166		*/
		0% Uncovered Elements: 20 (20) Complexity: 5 Complexity Density: 0.36
167	0	protected void checkUsedMemory(int expectedMax)...
168		{
169		/*
170		* request garbage collection and wait for it to run (up to 3 times);
171		* NB there is no guarantee when, or whether, it will do so
172		*/
173	0	long usedMemory = 0L;
174	0	Long minUsedMemory = null;
175	0	int gcCount = 0;
176	0	while (gcCount < 3)
177		{
178	0	gcCount++;
179	0	System.gc();
180	0	waitFor(1500);
181	0	usedMemory = getUsedMemory();
182	0	if (minUsedMemory == null || usedMemory < minUsedMemory)
183		{
184	0	minUsedMemory = usedMemory;
185		}
186	0	if (usedMemory < expectedMax)
187		{
188	0	break;
189		}
190		}
191
192		/*
193		* if this assertion fails (reproducibly!)
194		* - set a breakpoint here, conditional on (usedMemory > expectedMax)
195		* - run VisualVM to inspect the heap usage, and run GC from VisualVM to check
196		* it is not simply delayed garbage collection causing the test failure
197		* - take a heap dump and identify large objects in the heap and their referers
198		* - fix code as necessary to null the references on close
199		*/
200	0	System.out.println("(Minimum) Used memory after " + gcCount
201		+ " call(s) to gc() = " + minUsedMemory + "MB (should be <="
202		+ expectedMax + ")");
203	0	assertTrue(usedMemory <= expectedMax, String.format(
204		"Used memory %d should be less than %d (Recommend running test manually to verify)",
205		usedMemory, expectedMax));
206		}
207
208		/**
209		* Loads an alignment from file and exercises various operations in Jalview
210		*
211		* @param f
212		*/
		0% Uncovered Elements: 27 (27) Complexity: 5 Complexity Density: 0.24
213	0	protected void doStuffInJalview(File f)...
214		{
215		/*
216		* load alignment, wait for consensus and other threads to complete
217		*/
218	0	AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(f.getPath(),
219		DataSourceType.FILE);
220	0	while (af.getViewport().isCalcInProgress())
221		{
222	0	waitFor(200);
223		}
224
225		/*
226		* open an Overview window
227		*/
228	0	af.overviewMenuItem_actionPerformed(null);
229	0	assertNotNull(af.alignPanel.overviewPanel);
230
231		/*
232		* exercise the pop-up menu in the Overview Panel (JAL-2864)
233		*/
234	0	Object[] args = new Object[] {
235		new MouseEvent(af, 0, 0, 0, 0, 0, 1, true) };
236	0	PA.invokeMethod(af.alignPanel.overviewPanel,
237		"showPopupMenu(java.awt.event.MouseEvent)", args);
238
239		/*
240		* set a selection group - potential memory leak if it retains
241		* a reference to the alignment
242		*/
243	0	SequenceGroup sg = new SequenceGroup();
244	0	sg.setStartRes(0);
245	0	sg.setEndRes(100);
246	0	AlignmentI al = af.viewport.getAlignment();
247	0	for (int i = 0; i < al.getHeight(); i++)
248		{
249	0	sg.addSequence(al.getSequenceAt(i), false);
250		}
251	0	af.viewport.setSelectionGroup(sg);
252
253		/*
254		* compute Tree and PCA (on all sequences, 100 columns)
255		*/
256	0	af.openTreePcaDialog();
257	0	CalculationChooser dialog = af.alignPanel.getCalculationDialog();
258	0	dialog.openPcaPanel("BLOSUM62", dialog.getSimilarityParameters(true));
259	0	dialog.openTreePanel("BLOSUM62", dialog.getSimilarityParameters(false));
260
261		/*
262		* wait until Tree and PCA have been computed
263		*/
264	0	while (af.viewport.getCurrentTree() == null
265		|| dialog.getPcaPanel().isWorking())
266		{
267	0	waitFor(10);
268		}
269
270		/*
271		* give Swing time to add the PCA panel (?!?)
272		*/
273	0	waitFor(100);
274		}
275
276		/**
277		* Wait for waitMs miliseconds
278		*
279		* @param waitMs
280		*/
		0% Uncovered Elements: 2 (2) Complexity: 2 Complexity Density: 1
281	0	protected void waitFor(int waitMs)...
282		{
283	0	try
284		{
285	0	Thread.sleep(waitMs);
286		} catch (InterruptedException e)
287		{
288		}
289		}
290
291		/**
292		* Generates an alignment and saves it in a temporary file, to be loaded by
293		* Jalview. We use a peptide alignment (so Conservation and Quality are
294		* calculated), which is wide enough to ensure Consensus, Conservation and
295		* Occupancy have a significant memory footprint (if not removed from the
296		* heap).
297		*
298		* @return
299		* @throws IOException
300		*/
		0% Uncovered Elements: 8 (8) Complexity: 1 Complexity Density: 0.12
301	0	private File generateAlignment() throws IOException...
302		{
303	0	File f = File.createTempFile("MemoryTest", "fa");
304	0	PrintStream ps = new PrintStream(f);
305	0	AlignmentGenerator ag = new AlignmentGenerator(false, ps);
306	0	int width = 100000;
307	0	int height = 100;
308	0	ag.generate(width, height, 0, 10, 15);
309	0	ps.close();
310	0	return f;
311		}
312		}