Containers and HPC
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A short presentation at a CSC internal workshop of the prospects of using container technologies, especially Docker, in the context of High Performance Computing (HPC).
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Containers and HPC
- 1. Containers and HPC Olli-Pekka Lehto (@ople) Services for Research Work Together Days Dec 17th 2015
- 2. Making It Easy to Do Custom HPC Environments Or rather.. Olli-Pekka Lehto (@ople) Services for Research Work Together Days Dec 17th 2015
- 3. What is Docker? • Helps to manage and run applications with complex dependencies quickly and efficiently • Management framework for Linux Containers • Containers: – Instances isolated within a namespace – Kernel shared with host OS – Resources guaranteed using Linux cgroups • Grown into a complete ecosystem – docker-swarm, docker-machine, docker-compose…
- 5. Docker Adoption is Rapid
- 6. Interest in HPC is growing http://www.lanl.gov/projects/apex/_assets/docs/APEX2020_draft_tech_specs_v1.0.pdf http://investors.cray.com/phoenix.zhtml?c=98390&p=irol-newsArticle&ID=2112970
- 7. Why Docker • Fast initialization (10-1000x vs VMs) • Small memory overhead • Efficient disk usage • Bare-metal access to devices • Built-in version control and repository support – Simple sharing of containers • Simple launch mechanism – Can be run within batch job queue system
- 8. Bare-metal HPCCloud HPC CSC-built apps User-built CSC- compatible apps Hosting Windows Non-SLURM batch queue system Ubuntu “I need/want Root” VM image app Web Servers Preservation of SW stack Secure access Complex stack Current Choices for HPC Workloads
- 9. Cloud HPC Container HPC Bare-metal HPC CSC-built apps User-built CSC- compatible apps Hosting Windows Non-SLURM batch queue system Ubuntu “I need/want Root” VM image app Secure access Web Servers Preservation of SW stack Complex stack Containerized app Future Choices for HPC Workloads
- 10. Example Case “My HPC application needs Ubuntu” • Alternative 1: Adapt the application – Takes time and work – May not be possible with ISV codes • Alternative 2: Run it in the cloud – You may get to play cluster admin! – Scheduling is limited in OpenStack (no backfill etc.) – Running a short job has large initialization overhead – Performance penalties • Alternative 3: Run it in a container – No need to touch the application – Nearly as easy to run as a normal job – Very little overhead – Can use the normal batch job scheduler
- 11. Challenges for HPC Use • Security model is problematic – Initially designed for server environments • Only trusted users have shell access to server – Containers launched as root – Access to bare metal & device drivers • Requires an overlay FS & kernel modules – Relatively new Linux OS version needed • Daemon must run on every compute node • Low-level driver compatibility? – GPU, InfiniBand, Lustre
- 12. Shifter • Alternative to Docker daemon – Adapts containers to HPC use • Repacks into a new filesystem (squashfs) – Integrates with batch job queue systems • No need to run a daemon on compute nodes • Developed by NERSC for Cori (Cray XC40) – Pre-release version available – Cray is productizing it • Parallel jobs? Driver issues? https://www.nersc.gov/research-and-development/user-defined-images/ https://bitbucket.org/berkeleylab/shifter
- 13. Next Steps / Ideas • Piloting Shifter in 2016 – Sisu, Taito, Taito-shell • Custom interactive containers in taito-shell • Containerized CSC compute environment? – Customers could run on their own laptops, workstations and/or clusters – Starting point for users’ own customizations – Having our environment in config management would make it easier
- 14. Extras
- 15. EasyBuild + Docker? • Dockerfile can be used to define a container – Simple flat file with a script-like syntax – Specific to Docker • Using EasyBuild with Docker? – Target also VMs or bare-metal with same config – Update portions of the stack easily – Manage dependencies – Leverage the rich set of EasyBuild configs – Which way to do it? • Using EasyBuild in a container or • Building containers with EasyBuild?