1 Bio Applications Virtualization using Rocks Nadya Williams UCSD

2 VM Rocks frontend Opal toolkit Job Scheduler (SGE) Applications VM configuration key parts all networking all networking all services all services configuration configuration master master working nodes working nodes configuration configuration app deployment app deployment

3 VM reconfiguration Autodock Vina MGL tools: autodock autogrid) Receptor transformation Gromos clustering PDB2PQR OPAL toolkit Updated VM Rocks VM configuration Applications Applications

4 One host as an example: rocsk- 214.sdsc.edu

5 VM creation and deployment process # rocks add cluster fqdn=$FQDN ip=$IP num-computes=0 fe- name=$NAME # rocks create keys key=private.key passphrase=no > public.key # rocks set host power $NAME action=install key=private.key # rocks open host console $NAME key=private.key Install frontend and desired rolls Shutdown VM Copy VM disk to shared area (gfarm) Create a VM with desired applications: original site /opt/vm-scripts/local-vc-deploy bioapp5 1 /vm-images Deploy VM: hosting site # /root/vm/VMreconfig # reboot Start running applications on a new host Reconfiure VM: hosting site Run one time Run one time Run many times Run many times

6 How we can use VM Single frontend VM VM cluster EC2 VM EC2 cluster Clone VM Create VM Deploy and Reconfigure VM

7 Lessons learned Focus on minimizing time to uptime through easy automatic VM setup Simplification, Unification and Automation of the VM creation (tight integration with Rocks environment) Easy automated reconfiguration Easy automated deployment into existing environment Guarantee reproducibility Interoperability Create VM anywhere – deploy anywhere. Works now with Rocks. Get missing features by creating bridges between different Virtualizations Future work Extend to VM cluster deployment Extend to EC2 deployment Convert Xen VM image into KVM

8 Historical Lessons … Inscription on an ancient Jade plate Pang made this treasured vessel. May it be used and treasured by my descendents for years.