Write "compressed" Array to increase IO performance?

Question

I have an int and float array each of length 220 million (fixed). Now, I want to store/upload those arrays to/from memory and disk. Currently, I am using Java NIO's FileChannel and MappedByteBuffer to solve this. It works fine, but it takes near about 5 seconds (Wall Clock Time) for storing/uploading array to/from memory to disk. Now, I want to make it faster.

Here, I should mention most of those array elements are 0 ( nearly 52 %).

like:

int arr1 [] = { 0 , 0 , 6 , 7 , 1, 0 , 0 ...}

Can anybody help me, is there any nice way to improve speed by not storing or loading those 0's. This can compensated by using Arrays.fill (array , 0).

Answer 1

The following approach requires n / 8 + nz * 4 bytes on disk, where n is the size of the array, and nz the number of non-zero entries. For 52% zero entries, you'd reduce storage size by 52% - 3% = 49%.

You could do:

void write(int[] array) {
    BitSet zeroes = new BitSet();
    for (int i = 0; i < array.length; i++)
        zeroes.set(i, array[i] == 0);
    write(zeroes); // one bit per index
    for (int i = 0; i < array.length; i++)
        if (array[i] != 0)
            write(array[y]);
}

int[] read() {
    BitSet zeroes = readBitSet();
    array = new int[zeroes.length];
    for (int i = 0; i < zeroes.length; i++) {
        if (zeroes.get(i)) {
            // nothing to do (array[i] was initialized to 0)
        } else {
            array[i] = readInt();
        }
    }
}

Edit: That you say this is slightly slower implies that the disk is not the bottleneck. You could tune the above approach by writing the bitset as you construct it, so you don't have to write the bitset to memory before writing it to disk. Also, by writing the bitset word by word interspersed with the actual data we can do only a single pass over the array, reducing cache misses:

void write(int[] array) {
    writeInt(array.length);
    int ni;
    for (int i = 0; i < array.length; i = ni) {
        ni = i + 32;
        int zeroesMap = 0;
        for (j = i + 31; j >= i; j--) {
            zeroesMap <<= 1;
            if (array[j] == 0) {
                zeroesMap |= 1;
            }
        }
        writeInt(zeroesMap);
        for (j = i; j < ni; j++)
            if (array[j] != 0) {
                writeInt(array[j]);
            }
        }
    }
}

int[] read() {
    int[] array = new int[readInt()];
    int ni;
    for (int i = 0; i < array.length; i = ni) {
        ni = i + 32;
        zeroesMap = readInt();
        for (j = i; j < ni; j++) {
            if (zeroesMap & 1 == 1) {
                // nothing to do (array[i] was initialized to 0)
            } else {
                array[j] = readInt();
            }
            zeroesMap >>= 1;
        }
    }
    return array;
}

(The preceeding code assumes array.length is a multiple of 32. If not, write the last slice of the array in whatever way you like)

If that doesn't reduce proceccing time either, compression is not the way to go (I don't think any general purpose compression algorithm will be faster than the above).