MapReduce is a popular computing model for parallel data processing on large-scale datasets, which can vary from gigabytes to terabytes and petabytes. Though Hadoop MapReduce normally uses Hadoop Distributed File System (HDFS) local file system, it can be configured to use a remote file system. Then, an interesting question is raised: for a given application, which is the best running platform among the different combinations of scale-up and scale-out Hadoop with remote and local file systems. However, there has been no previous research on how different types of applications (e.g., CPU-intensive, data-intensive) with different characteristics (e.g., input data size) can benefit from the different platforms. Thus, in this paper, we conduct a comprehensive performance measurement of different applications on scale-up and scale-out clusters configured with HDFS and a remote file system (i.e., OFS), respectively. We identify and study how different job characteristics (e.g., input data size, the number of file reads/writes, and the amount of computations) affect the performance of different applications on the different platforms. Based on the measurement results, we also propose a performance prediction model to help users select the best platforms that lead to the minimum latency. Our evaluation using a Facebook workload trace demonstrates the effectiveness of our prediction model. This study is expected to provide a guidance for users to choose the best platform to run different applications with different characteristics in the environment that provides both remote and local storage, such as HPC cluster and cloud environment.