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From the numbers are nice department

HPC users have always want to be "close to the metal." A recent report by IBM has tested the popular Docker project against native performance (bare metal) and KVM (Kernel-based Virtual Machine). The tests include Linpack, STREAM memory benchmark, nuttcp for network bandwidth, netperf for network latency, fio and Redis for block I/O speeds, and the SysBench oltp benchmark for testing MySQL. The scripts used for testing are available for download.

The paper entitled An Updated Performance Comparison of Virtual Machines and Linux Containers (PDF) provides some solid numbers that may help in designing future HPC systems. As on might suspect, Docker containers were found to perform similar to native bare metal tests. For instance, Docker matched the bare metal Linpack tests while KVM was slower by more than half. Of course, you can have flexibility and bare metal performance using something like Warewulf.