Using LXC and LXD for Bioinformatics - (ii)

Using LXC and LXD for Bioinformatics - (ii)


We have been researching alternative virtualization/containerization stacks to be installed on the servers. The first model we considered was Docker (on top of CoreOS) and thought that was wonderful. CoreOS promised to run a minimal operating system, and then every program could be sheltered within a Docker container. Moreover, Docker/CoreOS promised to get ‘bare metal’ performance.

However, after careful consideration, we decided to reject the model for security reasons. Our current plan is to use virtualization and then one of the virtualized OSs can be used for container experiments. Moreover, the container technology will be anything but Docker, because we want them to run on unprivileged mode.

For virtualization, there are three alternatives - ESXi (owned by VMWare–> EMC –> Dell), Xen and KVM. After going through all discussions on the Type 1 vs Type 2 hypervisors, we realized that they are mostly too simplistic models of currently available programs. For example, KVM is a ‘type 2’ hypervisor (i.e. needs a native operating system to run instead of ‘bare metal’), but it actually performs as good as native operating system. Anyway, here are more details on the three choices.

ESXi - closed source and became too expensive after EMC’s purchase of VMWare.

Xen - open-source and appears very impressive.

KVM - open-source and supposedly less feature-rich than Xen, because Xen has been in development for over a decade.

Initially we were going for Xen. However, a benchmark on MAFFT made us choose KVM. Not that the differences are anywhere beyond third digit, but at least it shows that KVM does not degrade performance.


Guest operating systems

We are currently planning to choose Arch Linux.

A simple, lightweight distribution

You’ve reached the website for Arch Linux, a lightweight and flexible Linux distribution that tries to Keep It Simple.

Currently we have official packages optimized for the i686 and x86-64 architectures. We complement our official package sets with a community- operated package repository that grows in size and quality each and every day.

Our strong community is diverse and helpful, and we pride ourselves on the range of skillsets and uses for Arch that stem from it. Please check out our forums and mailing lists to get your feet wet. Also glance through our wiki if you want to learn more about Arch.


Containerization - LXC/LXD

LXD is in early development. So, mostly we will be working with LXC. A good introduction is here. We plan to install four guest O/Ss and one of them will be used for experimentation with LXC.


Web stack - NGINX, GO framework, Postgres, some kind of CMS

We will discuss this topic, when we reach there.

Written by M. //