We reexamine geometric engineering in the simplest possible case of abelian gauge group U(1), comparing Nekrasov's deformed partition function on the surface side and refined Donaldson-Thomas theory on the threefold side, as well as the underlying vector spaces. We discuss purity phenomena on both sides of the duality. We discuss how this gives some information on the Kontsevich-Soibelman Cohomological Hall Algebra of the conifold quiver