As far as I know, there is one way currently known to -- in principle -- compute the Mertens function $M(x) = \sum_{n\leq x} \mu(n)$ in time essentially $O\left(x^{1/2}\right)$, namely, a modification of the Lagarias-Odlyzko method.
Mertens' function in time $O(\sqrt x)$
Computing the Mertens function
The Lagarias-Odlyzko method's main variant is designed to compute $\pi(x)$ in time essentially $O(x^{1/2})$. In the last few years, it has been implemented and optimized:
https://arxiv.org/abs/1203.5712
https://arxiv.org/abs/1410.7008
http://www.ams.org/journals/mcom/2017-86-308/S0025-5718-2017-03038-6/home.html
Has the analogue for computing $M(x)$ ever been implemented? If not, why not? Are there significant ways in which this variant of Lagarias-Odlyzko would be much slower or harder to implement than the version for $\pi(x)$?
(One guess is that evaluating residues of $1/\zeta(s)$ may be hard. I know that this is a difficulty when one tries to obtain explicit forms of analytic results on $M(x)$, but I do not know whether the issue is at all relevant to Lagarias-Odlyzko and similar computational methods.)