We consider smooth flows preserving a smooth invariant measure, or, equivalently, locally Hamiltonian flows on compact orientable surfaces and show that, when the genus of the surface is two, almost every such locally Hamiltonian flow with two non degenerate isomorphic saddle has singular spectrum. More in general, singularity of the spectrum holds for special flows over a full measure set of interval exchange transformations with a hyperelliptic permutation (of any number of exchanged intervals), under a roof with symmetric logarithmic singularities. The result is proved using a criterion for singularity based on tightness of Birkhoff sums with exponential tails decay. A key ingredient in the proof, which is of independent interest, is a result on translation surfaces well approximated by single cylinders. We show that for almost every translation surface in any connected component of any stratum there exists a full measure set of directions which can be well approximated by a single cylinder of area arbitrarily close to one. The result, in the special case of the stratum H(1,1), yields rigidity sets needed for the singularity result.