Deploying OpenNebula in an HPC environment
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Presentació a càrrec d'Alfred Gil (HPCNow!) duta a terme a l'OpenNebula TechDay celebrat al CSUC el 8 de maig de 2019.
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Deploying OpenNebula in an HPC environment
- 1. Deploying OpenNebula in an HPC environment Alfred Gil Chief Computational Scientist & Cofounder OpenNebula Cloud TechDay Barcelona, May 2019
- 2. • HPCNow! company overview • Motivation • Architecture • Implementation • Conclusions
- 3. Quick introduction to HPCNow! ● Global HPC consulting company ● IT + scientific background ● HPC services and solutions ● User-oriented company ● Hardware agnostic Company overview
- 4. System Administrators and User Support Top500 Supercomputer Users Company overview
- 5. IISW
- 6. Batch scheduler Slurm, LSF, PBS, Torque, SGE Cluster manager sNow!, xCat, Rocks, Bright Monitoring & alerts tools Ganglia, Nagios, Icinga, Grafana, Elastic Search Parallel file system BeeGFS, Lustre, GPFS, HDFS, CEPH Company overview
- 7. User environment User libraries, Modules, EasyBuild, Spack Development tools Compilers: GNU, Intel, PGI, IBM XL compilers; Debuggers and profilers: V-Tune, DDT, GDB Scientific and engineering applications More than 100 references. Contact us to know more. Company overview
- 8. Virtualization OpenNebula, OpenStack, VMware, Xen-Source Containers Singularity, Docker, Docker Swarm, LXD Remote visualization TurboVNC, VirtualGL, Websocket, DCV, X2Go HPC Portal EnginFrame Company overview
- 9. Contributions to HPC Community Company overview
- 10. Public sector Private Companies Company overview
- 12. • HPCNow! company overview • Motivation • Architecture • Implementation • Conclusions
- 13. What is High Performance Computing? Many tasks and/or threads working together to solve different parts of a single larger problem. This is achieved with parallel programming, which usually requires large shared memory systems or low latency and high bandwidth network. Motivation
- 14. HPC users need more than just compute solution ❅ Workflow: Pre-processing and post-processing, workflow frameworks,... ❅ Web services: RStudio, Galaxy, Jupyter notebook, JMS,... ❅ Software managers: Anaconda, EasyBuild, Spack,... ❅ Prebuilt software: Docker, Singularity, VM image (NeuroDebian,..),... Motivation
- 15. Convergence Solution HPC Cluster, Singularity, Docker Swarm, OpenNebula Allows to dynamically re-architect / re-purpose the HPC solution to accommodate different roles / user needs. Motivation
- 16. Dynamic Provisioning Hybrid nodes Vestibulumcongue Vestibulum congue Vestibulum congue Spare Nodes OpenNebula Slurm DockerSwarm Use Resource scontrol update node=X state=RESUME onehost enable X docker node update --availability active X 1 Release Resource scontrol update node=X state=DOWN onehost offline X docker node update --availability drain X 2 Motivation
- 17. • HPCNow! company overview • Motivation • Architecture • Implementation • Conclusions
- 18. mgmnt compute mgmnt hybrid storage Use case Architecture
- 19. mgmnt Management node ● VM’s (xen) ○ slurm01 slurmctld ○ slurmdb01 slurmdbd ○ ceph01 ceph-deploy ○ oneceph01 oned, sunstone, oneflow, onegate ○ login01 ○ ldap01 ● exports /home via NFS Architecture
- 20. Global configuration ● OpenNebula v5.6.0 ● Ceph v13.2.1 mimic ● Datastore ○ standard ceph configuration ■ cephds type Image ■ ceph_system type System ● Nodes with kvm hypervisor ● NIC’s with virtio model Architecture
- 21. • HPCNow! company overview • Motivation • Architecture • Implementation • Conclusions
- 22. Stumbling blocks along the way ● Snapshots ○ datastore for images configured as raw ■ recommended for ceph using RBD ○ images stored as raw, even created as qcow2 ○ snapshot of system disk, and recovering from ceph ■ rbd ls -l -p one ● Bridge destroyed when no virtual NIC linked ○ switch keep_empty_bridge to true in /var/lib/one/remotes/etc/vnm/OpenNebulaNetwork.conf ■ bug preventing to transfer config to hypervisors at /var/tmp/one/etc/vnm/OpenNebulaNetwork.conf ○ create virtual network with PHYDEV unset one-2-103-0 one-2-103-0@0 one-2-104-0 Implementation
- 23. Stumbling blocks along the way ● VM could not communicate with each other ○ switch net.bridge.bridge-nf-call-iptables parameter to 0. ○ tried to do it persistent in /etc/sysctl..d/bridge-nf-call.conf and /usr/lib/sysctl.d/00-system.conf ■ bug prevents for working, when sysctl runs the bridge kernel module is not already loaded. ○ fixed by modifying /usr/lib/systemd/system/libvirtd.service Type=notify EnvironmentFile=-/etc/sysconfig/libvirtd ExecStart=/usr/sbin/libvirtd $LIBVIRTD_ARGS +ExecStartPost=/usr/bin/sleep 30s +ExecStartPost=/usr/sbin/sysctl -w net.bridge.bridge-nf-call-iptables=0 +ExecStartPost=/usr/sbin/sysctl -p ExecReload=/bin/kill -HUP $MAINPID KillMode=process Restart=on-failure Implementation
- 24. Stumbling blocks along the way ● VM creation from Sunstone ended with FAILED status ○ error: Cannot check QEMU binary /usr/bin/qemu-system-x86_64: No such file or directory ■ ln -s /usr/libexec/qemu-kvm /usr/bin/qemu-system-x86_64 Implementation
- 25. • HPCNow! company overview • Motivation • Architecture • Conclusions
- 26. Conclusions ● We architected and implemented a solution deploying nodes with hybrid role. ● This solution allows dynamically re-purpose the cluster to accommodate the user needs. ● OpenNebula has been found to be a really easy tool to install, deploy and manage. ● Useful tips and collaboration in the forum to troubleshoot issues. Conclusions
- 27. info@hpcnow.com www.hpcnow.com Marie Curie, 8 - 08042 Barcelona (Spain) 34 Fernly Rise, 2019 Auckland (New Zealand) Barcelona Auckland