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ppohBEM is an open-source software package im- plementing the boundary element method. One of its main software tasks is the solution of the dense linear system of equations, for which, ppohBEM relies on another software package called HACApK. To reduce the cost of solving the linear system, HACApK hierarchically compresses the coefficient matrix using adaptive cross approximation. This hierarchical compression greatly reduces the storage and time complexities of the solver and enables the solution of large-scale boundary value problems. To extend the capability of ppohBEM, in this paper, we carefully port the HACApK’s linear solver onto GPU clusters. Though the potential of the GPUs has been widely accepted in high-performance computing, it is still a challenge to utilize the GPUs for a solver, like HACApK’s, that requires fine-grained computation and global communication. First, to utilize the GPUs, we integrate the batched GPU kernel that was recently released in the MAGMA software package. We discuss several techniques to improve the performance of the batched kernel. We then study various techniques to address the inter-GPU communication and study their effects on state-of- the-art GPU clusters. We believe that the techniques studied in this paper are of interest to a wide range of software packages running on GPUs, especially with the increasingly complex node architectures and the growing costs of the communication. We also hope that our efforts to integrate the GPU kernel or to setup the inter-GPU communication will influence the design of the future-generation batched kernels or the communication layer within a software stack.