High-performance computing (HPC) systems are increasingly shared by a variety of data-and metadata-intensive parallel applications. However, existing parallel file systems employed for HPC storage management are unable to differentiate the I/O requests from concurrent applications and meet their different performance requirements. Previous work, vPFS, provided a solution to this problem by virtualizing a parallel file system and enabling proportional-share bandwidth allocation to the applications; but it cannot handle the increasingly diverse applications in today's HPC environments, including those that have different sizes of I/Os and those that are metadata-intensive. This paper presents vPFS+ which builds upon the virtualization framework provided by vPFS but addresses its limitations in supporting diverse HPC applications. First, a new proportional-share I/O scheduler, SFQ(D)+, is created to allow applications with various I/O sizes and issue rates to share the storage with good application-level fairness and system-level utilization. Second, vPFS+ extends the scheduling to also include metadata I/Os and provides performance isolation to metadata-intensive applications. vPFS+ is prototyped on PVFS2, a widely used open-source parallel file system, and evaluated using a comprehensive set of representative HPC benchmarks and applications (IOR, NPB BTIO, WRF, and multi-md-test). The results confirm that the new SFQ(D)+ scheduler can provide significantly better performance isolation to applications with small, bursty I/Os than the traditional SFQ(D) scheduler (3.35 times better) and the native PVFS2 (8.25 times better) while still making efficient use of the storage. The results also show that vPFS+ can deliver near-perfect proportional sharing (>95% of the target sharing ratio) to metadata-intensive applications.