1. Containers in HPC
By Raja

2. Agenda: What is Containerization ? Different container
Containers in HPC
Why Singularity?
Singularity Architecture
Singularity Workflow
Singularity commands
State of Containers in HPC

3. What is Containerization?
Containers in simple word: solution to the problem of how to get software to run reliably when moved from one environment to another.
a container consists of an entire runtime environment: an application, plus all its dependencies, libraries and other binaries, and configuration files needed to run it, bundled into one package

4. Different Container: Docker Rkt: Rocket
Java containers : standalone Java applications like Tomcat
Unikernels
LXD: From Ubuntu
OpenVZ
Windows Server Containers
Hyper-V Containers

5. Traditional Virtualization & Modern Container:
App2
Guest OS
App3
App1
App4
App5
App6
Virtual Machines
App1
Libs/Bins
App2
App3
App4
Containers
Container Engine
Hypervisor
Host OS
Host OS
Kernel
Hardware
Hardware

6. Containers in HPC: Docker
DevOps, micro services, Enterprise applications
Singularity : Lawrence Berkeley National Laboratory
Application portability (single image file, contain all dependencies) Reproducibility, run cross platform, provide support for legacy OS and apps.
Shifter : The National Energy Research Scientific Computing Center (NERSC)
Utilize the large number of Docker apps. Provides a way to run them in HPC after a conversion process. It also strip out all the requirements of root so that they are runnable as user process.
Univa Grid Engine (UGE)
Running Docker containers in HPC, with UGE managing the Docker daemon process

7. Docker in HPC :Problem Statement
Non-authorized users having root access to any of our production networks is considered a security breech
Docker uses a root owned daemon
No native GPU support
No support for MPI… MPI developers estimate this milestone for 2 years from now!
No Proper InfiniBand driver
Doesn’t support production distributions (yet)… RHEL7 not even completely supported!
Complexities with existing scheduling paradigms
Root owned container daemons are outside the reach of the resource manager
MPI/parallel job runs become increasingly complex

8. Why Singularity ?
The Singularity is run by the user, loads the Singularity container and executes applications as the user.
Shell environment is passed to the contained applications
Singularity supports X11, MPI and resource managers natively.
If you want to be root inside of the container, you must first be root outside of the container

9. Singularity Architecture:

10. Singularity Workflow:

11. Singularity General commands
CONTAINER MANAGEMENT COMMANDS (requires root):
help - Show additional help for a command
bootstrap - Bootstrap a new Singularity image from scratch
selftest - Run some self tests to make sure Singularity is installed and operating properly
copy - Copy files from your host into the container
create - Create a new container image
CONTAINER USAGE COMMANDS:
expand - Grow the container image
exec - Execute a command within container
Export - Export the contents of a container via a tar pipe
run - Launch a runscript within container
Shell - Run a Bourne shell within container
Import - Import/add container contents via a tar pipe
test - Execute any test code defined within container
Mount - Mount a Singularity container image
CONTAINER USAGE OPTIONS:
CONTAINER REGISTRY COMMANDS:
see singularity <command> help
Pull - pull a Singularity Hub container to $PWD

12. State of Containers in HPC:
What works well:
New applications architected with containers in mind
Sequential or multi-threaded
Simple IO and networking dependencies
What can work but with challenges:
Distributed memory apps (like MPI) run on single host
GPU integration (issues are socket affinity, for instance)
What doesn't really work (yet):
Cross-host distributed memory apps
Choices
Re-architect your software
Look towards HPC-specific container technology (Shifter, Singularity)
Wait for mainstream container innovation (like Docker)
Focus adoption on new software

13. Demo on next session 