why are java's BigInteger gcd and modInverse so slow?

I'm trying to use java.math.BigInteger for some exact integer matrix computations in which the scalar values get up to millions of digits. I've noticed that some of the builtin BigInteger operations are unexpectedly very slow-- particularly some cases of gcd, and many more cases of modInverse. It seems I can implement my own versions of these functions that are much faster.

I wrote a program that prints timings for calculating gcd(10^n-3, 10^n) for increasing values of n up to a million or so, using either the builtin gcd or my own simple alternative implementation:

private static java.math.BigInteger myGcd(java.math.BigInteger a, java.math.BigInteger b)
{
    a = a.abs();
    b = b.abs();
    while (true)
    {
        if (b.signum() == 0) return a;
        a = a.mod(b);
        if (a.signum() == 0) return b;
        b = b.mod(a);
    }
} // myGcd

I ran it using java 8 under ubuntu linux, runtime version 1.8.0_111-8u111-b14-2ubuntu0.16.04.2-b14. Timings are roughly similar, relatively, on a macbook with java runtime 1.8.0_92.

Builtin gcd is roughly quadratic:

# numDigits seconds
1 0.000005626
2 0.000008172
4 0.000002852
8 0.000003097
16 0.000019158
32 0.000026365
64 0.000058330
128 0.000488692
256 0.000148674
512 0.007579581
1024 0.001199623
2048 0.001296036
4096 0.021341193
8192 0.024193484
16384 0.093183709
32768 0.233919912
65536 1.165671857
131072 4.169629967
262144 16.280159394
524288 67.685927438
1048576 259.500887989

Mine is roughly linear (for the case described; yes, I know it has to be quadratic in the worst case):

# numDigits seconds
1 0.000002845
2 0.000002667
4 0.000001644
8 0.000001743
16 0.000032751
32 0.000008616
64 0.000014859
128 0.000009440
256 0.000011083
512 0.000014031
1024 0.000021142
2048 0.000036936
4096 0.000071258
8192 0.000145553
16384 0.000243337
32768 0.000475620
65536 0.000956935
131072 0.002290251
262144 0.003492482
524288 0.009635206
1048576 0.022034768

Notice that, for a million digits of the case described, the builtin gcd takes more than 10000 times as long as mine: 259 seconds vs. .0220 seconds.

Is the builtin gcd function doing something other than the euclidean algorithm? Why?

I get similar timings for the builtin modInverse vs. my own implementation using the extended euclidean algorithm (not shown here). The builtin modInverse does poorly in even more cases than the builtin gcd does, e.g. when a is a small number like 2,3,4,... and b is large.

Here are three plots of the above data (two different linear scales and then log scale):

linear scale small linear scale large log scale

Here's the program listing:

/*
  Benchmark builtin java.math.BigInteger.gcd vs. a simple alternative implementation.
  To run:
    javac BigIntegerBenchmarkGcd.java
    java BigIntegerBenchmarkGcd mine > OUT.gcd.mine
    java BigIntegerBenchmarkGcd theirs > OUT.gcd.theirs

    gnuplot
      set title "Timing gcd(a=10^n-3, b=10^n)"
      set ylabel "Seconds"
      set xlabel "Number of digits"
      unset log
      set yrange [0:.5]
      #set terminal png size 512,384 enhanced font "Helvetica,10"
      #set output 'OUT0.gcd.png'
      plot [1:2**20] "OUT.gcd.theirs" with linespoints title "a.gcd(b)", "OUT.gcd.mine" with linespoints title "myGcd(a,b)"
      #set output 'OUT1.gcd.png'
      unset yrange; replot
      #set output 'OUT2.gcd.png'
      set log; replot
*/
class BigIntegerBenchmarkGcd
{
    // Simple alternative implementation of gcd.
    // More than 10000 times faster than the builtin gcd for a=10^1000000-3, b=10^1000000.
    private static java.math.BigInteger myGcd(java.math.BigInteger a, java.math.BigInteger b)
    {
        a = a.abs();
        b = b.abs();
        while (true)
        {
            if (b.signum() == 0) return a;
            a = a.mod(b);
            if (a.signum() == 0) return b;
            b = b.mod(a);
        }
    } // myGcd

    // Make sure myGcd(a,b) gives the same answer as a.gcd(b) for small values.
    private static void myGcdConfidenceTest()
    {
        System.err.print("Running confidence test... ");
        System.err.flush();
        for (int i = -10; i < 10; ++i)
        for (int j = -10; j < 10; ++j)
        {
            java.math.BigInteger a = java.math.BigInteger.valueOf(i);
            java.math.BigInteger b = java.math.BigInteger.valueOf(j);
            java.math.BigInteger theirAnswer = a.gcd(b);
            java.math.BigInteger myAnswer = myGcd(a, b);
            if (!myAnswer.equals(theirAnswer)) {
                throw new AssertionError("they say gcd("+a+","+b+") is "+theirAnswer+", I say it's "+myAnswer);
            }
        }
        System.err.println("passed.");
    }

    public static void main(String args[])
    {
        boolean useMine = false;
        if (args.length==1 && args[0].equals("theirs"))
            useMine = false;
        else if (args.length==1 && args[0].equals("mine"))
            useMine = true;
        else
        {
            System.err.println("Usage: BigIntegerBenchmarkGcd theirs|mine");
            System.exit(1);
        }

        myGcdConfidenceTest();

        System.out.println("# numDigits seconds");
        for (int numDigits = 1; numDigits <= (1<<20); numDigits *= 2)
        {
            java.math.BigInteger b = java.math.BigInteger.TEN.pow(numDigits);
            java.math.BigInteger a = b.subtract(java.math.BigInteger.valueOf(3));

            System.out.print(numDigits+" ");
            System.out.flush();

            long t0nanos = System.nanoTime();
            java.math.BigInteger aInverse = useMine ? myGcd(a, b)
                                                    : a.gcd(b);
            long t1nanos = System.nanoTime();

            double seconds = (t1nanos-t0nanos)/1e9;
            System.out.println(String.format("%.9f", seconds));
        }
    } // main
} // class BigIntegerBenchmarkGcd

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