20 + 10Mb * ( 20 + 4 + 4 ) ~= 280Mb 
(1)     (2)        (3)   (4)   (5)

Introduction

In many scientific developments, we have to deal with grid or matrices of two or more dimensions. A simple and practical approach for storing such objects is multidimensional arrays (array of array of array of array ...). We will demonstrate that this can induce a huge overhead in memory consumption using basic Java arrays (new type[][][]...). Time access are not discussed here but are also lightly increased due to non contiguous memory storage...

This study has previously been done, but results are a little different http://www.javamex.com/tutorials/memory/array_memory_usage.shtml

In memory usage computation, this page is also interesting to read: http://www.javamex.com/tutorials/memory/object_memory_usage.shtml

Finally we propose a data object for storing multidimensional arrays efficiently.

Conventions and notations

• 1 byte = 1 octet = 8 bits
• Mb = Mo
• a wordis architecture dependent (32bits or 64bits, respectively 4o or 8o)

Java array structure

C/C++ array structure

Environment

> java -version
java version "1.6.0_25"
Java(TM) SE Runtime Environment (build 1.6.0_25-b06)
Java HotSpot(TM) 64-Bit Server VM (build 20.0-b11, mixed mode)
>cat /proc/version
Linux version 2.6.38.8-35.fc15.x86_64 (mockbuild@x86-09.phx2.fedoraproject.org) 
(gcc version 4.6.0 20110530 (Red Hat 4.6.0-9) (GCC) ) #1 SMP Wed Jul 6 13:58:54 
UTC 2011
>cat /proc/cpuinfo | grep "model name"
model name    : Intel(R) Core(TM)2 Duo CPU     T7500  @ 2.20GHz

Memory usage

theoretical analysis

case 1: large x small array

case 2: small x large array

results analysis

As we can see there is a huge constant difference (240Mb) between the two approaches and a threshold phenomenon for odd/even values of X.

• The constant difference is due to java array headers storing the memory location, object size and the number of objects (and may be some other values...). This header is not imposed by the JVM specification and may vary depending on the concrete JVM implementation.
• The threshold phenomenon is due to classical invalid link : word alignment(Illegal character in path at index 8: word alignment)

Sharing arrays between Java and C++ using JNI

FAQ: Sharing raw data with native code

You may find yourself in a situation where you need to access a large buffer of raw data from code written in Java and C/C++. Common examples include manipulation of bitmaps or sound samples. There are two basic approaches.

You can store the data in a byteMulti Dimensional Java Arrays. This allows very fast access from code written in Java. On the native side, however, you're not guaranteed to be able to access the data without having to copy it. In some implementations, GetByteArrayElements and GetPrimitiveArrayCritical will return actual pointers to the raw data in the managed heap, but in others it will allocate a buffer on the native heap and copy the data over.

The alternative is to store the data in a direct byte buffer. These can be created with java.nio.ByteBuffer.allocateDirect, or the JNI NewDirectByteBuffer function. Unlike regular byte buffers, the storage is not allocated on the managed heap, and can always be accessed directly from native code (get the address with GetDirectBufferAddress). Depending on how direct byte buffer access is implemented in the VM, accessing the data from code written in Java can be very slow.

The choice of which to use depends on two factors:

Will most of the data accesses happen from code written in Java or in C/C++? If the data is eventually being passed to a system API, what form must it be in? (For example, if the data is eventually passed to a function that takes a byteMulti Dimensional Java Arrays, doing processing in a direct ByteBuffer might be unwise.)

If there's no clear winner, use a direct byte buffer. Support for them is built directly into JNI, and access to them from code written in Java can be made faster with VM improvements.

This article study the overhead of java multidimensional arrays for uniform grids (i.e. rows, columns and any other dimension have the same size along the grid).

Source code

public static void main(String[] args) throws InterruptedException {
       System.out.println("Free: " + Runtime.getRuntime().freeMemory() / 1024 / 1024);
       System.out.println("Max: " + Runtime.getRuntime().maxMemory() / 1024 / 1024);
       System.out.println("Total: " + Runtime.getRuntime().totalMemory() / 1024 / 1024);
       System.out.println("Used: " + (Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory()) / 1024 / 1024);
       int sizeArray = 1024*1024;
       int dim = 1;
       // allocate array
       float[][] pos = new float[sizeArray][dim];
       System.out.println("dim="+dim);
       System.out.println("Free: " + Runtime.getRuntime().freeMemory() / 1024 / 1024);
       System.out.println("Max: " + Runtime.getRuntime().maxMemory() / 1024 / 1024);
       System.out.println("Total: " + Runtime.getRuntime().totalMemory() / 1024 / 1024);
       System.out.println("Used: " + (Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory()) / 1024 / 1024);
    }