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Discovering relationships between materials' microstructures and mechanical properties is a key goal of materials science. Here, we outline a strategy exploiting Bayesian optimization to efficiently search the multidimensional space of microstructures, defined here by the size distribution of precipitates (fixed impurities or inclusions acting as obstacles for dislocation motion) within a simple two-dimensional discrete dislocation dynamics model. The aim is to design a microstructure optimizing a given mechanical property, e.g., maximizing the expected value of shear stress for a given strain. The problem of finding the optimal discretized shape for a distribution involves a norm constraint, and we find that sampling the space of possible solutions should be done in a specific way in order to avoid convergence problems. To this end, we propose a general mathematical approach that can be used to generate trial solutions uniformly at random while enforcing an Euclidean norm constraint. Both equality and inequality constraints are considered. A simple technique can then be used to convert between Euclidean and other Lebesgue $p$-norm (the 1-norm in particular) constrained representations. Considering different dislocation-precipitate interaction potentials, we demonstrate the convergence of the algorithm to the optimal solution and discuss its possible extensions to the more complex and realistic case of three-dimensional dislocation systems where also the optimization of precipitate shapes could be considered.