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Windows Server containers provide superior performance because they are lighter weight. They are not dependent on a virtualization layer or the various layers of abstraction that come with it. Instead, they share the Windows Server OS kernel.
Hyper-V containers are slower, but offer better security because they don't share kernel components with the server's parent OS. Instead, they use Hyper-V virtual machines to host containers within dedicated namespaces. This means a Hyper-V container is likely to be physically larger than a comparable Windows Server container. Similarly, a Hyper-V container typically will not perform as well as a Windows Server container and may even consume more system resources.
So when should you use Windows Server containers vs. Hyper-V containers? A Windows Server container is best for general-purpose workloads, while a Hyper-V container is suitable for high-security environments. Hyper-V containers are most commonly associated with multi-tenant environments such as a public or private cloud. Windows Server containers could be risky in such environments because a tenant could potentially attempt to hack the kernel to gain access to other containers.
Windows users get to try Docker containers
DH2i introduces enterprise software for Windows containers
Azure supports containers, reduces VM costs
Dig Deeper on Storage virtualization
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