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A Java sizeof, implemented using the Java instrumentation API. Can either get the memory consumed either only by a single 

object or by a single object and all the references it contains.  Requires a command-line change to add a Java agent to
the command-line; see the Sizeof.java javadoc for details.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3889 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-07-27 18:44:15 +00:00
parent f5566a6593
commit 6c93b13428
3 changed files with 154 additions and 3 deletions
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5
build.xml
View File

@ -141,6 +141,9 @@
<jar jarfile="${dist.dir}/StingUtils.jar">
<fileset dir="${java.classes}" includes="**/utils/**/*.class"/>
<manifest>
<attribute name="Premain-Class" value="org.broadinstitute.sting.utils.instrumentation.Sizeof" />
</manifest>
</jar>
<jar jarfile="${dist.dir}/GenomeAnalysisTK.jar">
@ -152,7 +155,7 @@
<include name="**/oneoffprojects/**/*.class" />
</fileset>
<manifest>
<attribute name="Main-Class" value="org.broadinstitute.sting.gatk.CommandLineGATK"/>
<attribute name="Main-Class" value="org.broadinstitute.sting.gatk.CommandLineGATK" />
</manifest>
</jar>

7
java/src/org/broadinstitute/sting/gatk/datasources/utilities/BAMFileStat.java
View File

@ -23,14 +23,14 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.datasources;
package org.broadinstitute.sting.gatk.datasources.utilities;
import org.broadinstitute.sting.commandline.CommandLineProgram;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.instrumentation.Sizeof;
import java.io.File;
import java.io.PrintStream;
import java.lang.reflect.Field;
import java.util.Map;
import java.util.List;
@ -175,6 +175,9 @@ public class BAMFileStat extends CommandLineProgram {
}
System.out.printf("%nOverall: %d bins, %d chunks, %d linear index entries",numBins,numChunks,numLinearIndexEntries);
if(Sizeof.isEnabled())
System.out.printf(", total index size in bytes: %d",Sizeof.getObjectGraphSize(index));
System.out.println();
reader.close();
}

145
java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java 100644
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@ -0,0 +1,145 @@
/*
* Copyright (c) 2010, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.instrumentation;
import org.broadinstitute.sting.utils.StingException;
import java.lang.instrument.Instrumentation;
import java.lang.reflect.Field;
import java.lang.reflect.Modifier;
import java.lang.reflect.Array;
import java.util.IdentityHashMap;
/**
* A sizeof implementation for Java. Relies on the Java instrumentation API, so
* it must be added as an agent to function properly.
*
* To run, add -javaagent:/Users/mhanna/src/Sting/dist/StingUtils.jar as a command-line
* JVM argument.
*
* @author mhanna
* @version 0.1
*/
public class Sizeof {
/**
* Instrumentation object. Registered by the JVM via the premain() method.
*/
private static Instrumentation instrumentation;
/**
* Called by the JVM before the agent is started.
* @param args Arguments?
* @param inst Instrumentation object, used to perform instrumentation in the JVM.
*/
public static void premain(String args, Instrumentation inst) {
instrumentation = inst;
}
/**
* Is this Sizeof operator enabled? To enable, add the -javaagent directive listed in the class-level javadoc.
* @return True if sizeof() is enabled. If false, any calls to utility methods of this class will throw an exception.
*/
public static boolean isEnabled() {
return instrumentation != null;
}
/**
* Gets the size of the given object. Retrieves the size for only this object; any reference fields in the object will only be
* counted as single pointers.
* @param o The object to sizeof().
* @return Gets the best possible approximation we can get of the size of the object in memory. On Sun JVM, includes some object padding.
*/
public static long getObjectSize(Object o) {
if(!isEnabled())
throw new StingException("Sizeof operator is currently disabled! To enable, review the documentation in Sizeof.java");
return instrumentation.getObjectSize(o);
}
/**
* Gets the size of the given object, including the size of the objects to which this object refers.
* @param o The object to sizeof().
* @return Gets the best possible approximation we can get of the size of the object in memory, including all references within each object.
*/
public static long getObjectGraphSize(Object o) {
if(!isEnabled())
throw new StingException("Sizeof operator is currently disabled! To enable, review the documentation in Sizeof.java");
IdentityHashMap<Object,Object> objectsSeen = new IdentityHashMap<Object,Object>();
return getObjectGraphSize(o,objectsSeen);
}
/**
* The engine for walking the graph of all objects and their children.
* @param o The object to traverse.
* @param objectsSeen A list of all objects already seen.
* @return Gets the best possible approximation we can get of the size of the object in memory, including all references within each object.
*/
private static long getObjectGraphSize(Object o,IdentityHashMap<Object,Object> objectsSeen) {
// Size of a null object itself (as opposed to the reference to the null object) is 0.
if(o == null)
return 0;
// Don't allow repeated traversals of the same object.
if(objectsSeen.containsKey(o))
return 0;
objectsSeen.put(o,o);
// Get the size of the object itself, plus all contained primitives.
long totalSize = instrumentation.getObjectSize(o);
// Get the size of (non-primitive) array elements.
Class<?> classToInspect = o.getClass();
if(classToInspect.isArray()) {
if(!classToInspect.getComponentType().isPrimitive()) {
for(int i = 0; i < Array.getLength(o); i++)
totalSize += getObjectGraphSize(Array.get(o,i),objectsSeen);
}
}
// Walk the descendents of each field of this class. Be sure to avoid synthetic fields like this$0 -- these
// are back references to the parent of the object contained in the inner class.
// Potential BUG: Are there other types of synthetic fields we should be tracking?
while(classToInspect != null) {
for(Field field: classToInspect.getDeclaredFields()) {
if(field.getType().isPrimitive())
continue;
if(Modifier.isStatic(field.getModifiers()))
continue;
if(field.isSynthetic())
continue;
field.setAccessible(true);
Object fieldValue;
try {
fieldValue = field.get(o);
}
catch(IllegalAccessException ex) {
throw new StingException("Unable to access field " + field.getName(),ex);
}
totalSize += getObjectGraphSize(fieldValue,objectsSeen);
}
classToInspect = classToInspect.getSuperclass();
}
return totalSize;
}
}