The optical fiber multiple-input multiple-output (MIMO) channel with intensity modulation and direct detection (IM/DD) per spatial path is treated. The spatial dimensions represent the multiple modes employed for transmission and the cross-talk between them originates in the multiplexers and demultiplexers, which are polarization dependent and thus timevarying. The upper bounds from free-space IM/DD MIMO channels are adapted to the fiber case, and the constellation constrained capacity is constructively estimated using the Blahut-Arimoto algorithm. An autoencoder is then proposed to optimize a practical MIMO transmission in terms of pre-coder and detector assuming channel distribution knowledge at the transmitter. The pre-coders are shown to be robust to changes in the channel.