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We introduce a class of specially structured linear programming (LP) problems, which has favorable modeling capability for important application problems in different areas such as optimal transport, discrete tomography and economics. To solve these generally large-scale LP problems efficiently, we design an implementable inexact entropic proximal point algorithm (iEPPA) combined with an easy-to-implement dual block coordinate descent method as a subsolver. Unlike existing entropy-type proximal point algorithms, our iEPPA employs a more practically checkable stopping condition for solving the associated subproblems while achieving provable convergence. Moreover, when solving the capacity constrained multi-marginal optimal transport (CMOT) problem (a special case of our LP problem), our iEPPA is able to bypass the underlying numerical instability issues that often appear in the popular entropic regularization approach, since our algorithm does not require the proximal parameter to be very small in order to obtain an accurate approximate solution. Numerous numerical experiments show that our iEPPA is efficient and robust for solving large-scale CMOT problems. The experiments on the discrete tomography problem also highlight the potential modeling power of our model.