You are incorrect. Look at the error message more closely:

    Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 49
        at java.util.ComparableTimSort.pushRun(Unknown Source)
        at java.util.ComparableTimSort.sort(Unknown Source)
        at java.util.Arrays.sort(Unknown Source)
        at Test.main(Test.java:80)

The error occurs inside TimSort, not at

    arrayToSort[sum] = 1;

It's a bug with TimSort going out of bounds (which obviously shouldn't happen ever), not the Test.

The equivalent Python code works fine, though.

    >>> a=[0]*sum(rls)
    >>> sum=-1
    >>> for i in rls:
    ...   sum += i
    ...   a[sum] = 1
    ... 
    >>> a.sort()
    >>> 

Takes a real good while, too.

That's because the array to be sorted is packed and inflated, so as to be the worst possible input for that kind of sort.

Worst-case complexity.

Also, I needed to bump my JVM heap up to 16GB (not 9GB as recommended), just to run it.