Talk presented in IPharm's CADD 2010.

1. Accelerating MD..Simple Tweaks and Instant Clusters Mohd Shahir Shamsir Bioinformatics Research Group (BIRG) Faculty of Biosciences & Bioengineering Universiti Teknologi Malaysia INSPIRING CREATIVE AND INNOVATIVE MINDS

2. Summary Introduction to BIRG MD: What, Why and How Improving performance Simple Tweaks… Instant MD cluster– birgHPC Short video demo

3. Bioinformatics Research Group (BIRG)Faculty of Biosciences & Bioengineering Just Google Us…

4. MD… What? Why? How? COVERED!!

5. Performance of MD? Speed, speed, speed… Supercomputer IBM Roadrunner ~368 Flops Nankai Star 3.7 ns/day on 32 nodes (DPPC) HPCx 5.2 ns/day on 64 nodes (DPPC) New platform Cell-BE: GROMACS, 15x to Pentium 3.0GHz GPU: NAMD, 4 GPU = 16 CPUs

8. Microwulf cluster 26 Gflops, $2500, 11" x 12" x 17", airline overhead baggage compliant

9. Simple Tweaks INSPIRING CREATIVE AND INNOVATIVE MINDS

10. Tweaks for MD? Hardware ↑ = performance ↑ = $$$ ↑ OR Tweak Beowulf = performance ↑ = $$$ Pre-compiled vs self-compiled MPI libraries Test beds: 3 nodes GridMACS, 7 nodes Beowulf, 1 reference machine

11. Compilation Winner self-compile

12. Beowulf OpenMPIvs MPICH2 (pre) Winner MPICH2

13. Pre and Self Compiled MPI Self OpenMPI = MPICH2

14. What we found Single machine 66 % improvement Parallel environment 64 % improvement Compilation, software chosen affect performance

15. Instant MD, anyone? INSPIRING CREATIVE AND INNOVATIVE MINDS

16. Instant MD cluster Lots of under utilised computers in labs Idle mode after office hours, holidays, etc.

17. Instant MD cluster MD, parallel computing = high computing resources Solution? Supercomputers Dedicated computing cluster Problems? $$$ ??? (I don’t know this, I don’t know that…)

18. A + B = C What is A? Existing computers LAN connected, PXE-boot capable, CDROM/USB What is B? Linux Live CD Auto configuration What is C? Instant, out-of-the-box computing cluster!

19. birgHPC Free, open-source Linux distribution Based on PelicanHPC & Debian Live GROMACS, NAMD, mpiBLAST, ClustalW-MPI, PyMol, VMD Auto cluster config MPICH2 & OpenMPI Auto slots detections Ganglia monitoring Simple interface for job submission

20. Some Screenshots

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22. Some Screenshots

23. Some Screenshots

24. Some Screenshots

25. Some Screeshots

26. Available at http://birg1.fbb.utm.my/birghpcor Just Google birghpc

27. Conclusion birgHPC instant cluster conversion Bioinformatics tools Auto configurations http://birg1.fbb.utm.my/birghpc ISOs guide

28. Acknowledgements Chew Teong Han - Alchemist Farizuawana – Graphics Joyce Tan – Testing Funding from you via LHDN via MOSTI Michael Creel for Pelican HPC

29. FAQs Boot sequence Head node -> run birgHPC_setup -> follow instructions -> boot compute node -> script on head node will show # of nodes detected, confirm -> done Headless compute nodes (no monitor) Have to get a monitor -> set boot sequence to netboot -> done

30. FAQs How to know compute nodes is up Follow the birgHPC boot sequence -> the birgHPC_setup script will show # nodes detected Cannot netboot Try http://etherboot.org/wiki/start Heterogeneous PCs ok? Ok (Thanks Micheal Creel) If 32 bit + 64 bit, use 32 bit PC as head node

31. FAQs Status monitoring Yes -> web browser -> localhost -> Ganglia Monitoring What will displayed on compute node? Just a simple login terminal with some warning not to use the nodes, etc Limitations? RAM, RAM, RAM … Everything is loaded to RAM, hence HDD size = RAM size

32. FAQs Headnode criteria Preferably big RAM because of shared folder (/home) 2 Ethernet port if you want internet connection (still work if you got only one eth) Guide? http://birg1.fbb.utm.my/birghpc Forum? No, but can always refer PelicanHPC forums

33. FAQs Multi users? No, designed for single user Future release, maybe SGE or PBS Installed on hardiskpermenantly? Not tested, technically possible, Google Performance On par with hardisk-installed cluster (tested up to 6 nodes)

34. FAQs I cannot boot from CD Refer user guide -> convert CD ISO to USB drive image -> boot from USB Can I use birgHPC along with existing DHCP Preferably no, DHCP will distribute IP and birgHPC head will distribute IP, causing confusion of IP addresses Alternative, boot DHCP as head node OR unplug DHCP, use another PC as head node

35. FAQs birgHPC criteria (PCs = compute, server = head)