According to the ncdump header you posted, there is only one time step in the file. It is possible that this is causing the crash, and MCIP should check for this condition somehow and exit with a more appropriate error message. Regardless, no useful MCIP output could be created from a single time step of WRF output. You will need to obtain additional WRF output files.
Here is a link to running the CMAQv5.3.1 tutorial (Benchmark) case, along with a link to download the dataset. This may not include step-by-step instructions for running MCIP, but I believe it includes both WRF and MCIP output, so you could run MCIP and see if you can reproduce the provided data.