This document discusses using existing idle computers to create an instant computing cluster for molecular dynamics (MD) simulations called birgHPC. It describes how birgHPC is a Linux distribution that allows various computers connected via LAN to be automatically configured as a computing cluster with tools for MD, bioinformatics and monitoring. Simple instructions and screenshots are provided on setting up and using birgHPC to perform MD simulations using idle computers with no additional cost.

1. Accelerating MD..Simple Tweaks and Instant ClustersMohd Shahir ShamsirBioinformatics Research Group (BIRG)Faculty of Biosciences & BioengineeringUniversiti Teknologi MalaysiaINSPIRING CREATIVE AND INNOVATIVE MINDS

2. SummaryIntroduction to BIRGMD: What, Why and HowImproving performanceSimple Tweaks…Instant MD cluster– birgHPCShort video demo

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

4. MD…What?Why?How?COVERED!!

5. Performance of MD?Speed, speed, speed…SupercomputerIBM Roadrunner ~368 FlopsNankai Star 3.7 ns/day on 32 nodes (DPPC)HPCx 5.2 ns/day on 64 nodes (DPPC)New platformCell-BE: GROMACS, 15x to Pentium 3.0GHzGPU: NAMD, 4 GPU = 16 CPUs

8. Microwulf cluster26 Gflops, $2500, 11" x 12" x 17", airline overhead baggage compliant

9. Simple TweaksINSPIRING CREATIVE AND INNOVATIVE MINDS

10. Tweaks for MD?Hardware ↑ = performance ↑ = $$$ ↑ORTweak Beowulf = performance ↑ = $$$Pre-compiled vs self-compiledMPI librariesTest beds: 3 nodes GridMACS, 7 nodes Beowulf, 1 reference machine

11. CompilationWinner self-compile

12. Beowulf OpenMPIvs MPICH2 (pre)Winner MPICH2

13. Pre and Self Compiled MPISelf OpenMPI = MPICH2

14. What we foundSingle machine66 % improvement Parallel environment64 % improvement Compilation, software chosen affect performance

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

16. Instant MD clusterLots of under utilised computers in labsIdle mode after office hours, holidays, etc.

17. Instant MD clusterMD, parallel computing = high computing resourcesSolution?SupercomputersDedicated computing clusterProblems?$$$??? (I don’t know this, I don’t know that…)

18. A + B = CWhat is A?Existing computersLAN connected, PXE-boot capable, CDROM/USBWhat is B?Linux Live CDAuto configurationWhat is C?Instant, out-of-the-box computing cluster!

19. birgHPCFree, open-source Linux distributionBased on PelicanHPC & Debian LiveGROMACS, NAMD, mpiBLAST, ClustalW-MPI, PyMol, VMDAuto cluster configMPICH2 & OpenMPIAuto slots detectionsGanglia monitoringSimple interface for job submission

20. Some Screenshots

21. Some Screenshots

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. ConclusionbirgHPCinstant cluster conversionBioinformatics toolsAuto configurationshttp://birg1.fbb.utm.my/birghpcISOsguide

28. AcknowledgementsChew Teong Han - AlchemistFarizuawana – GraphicsJoyce Tan – TestingFunding from you via LHDN via MOSTIMichael Creel for Pelican HPC

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

30. FAQsHow to know compute nodes is upFollow the birgHPC boot sequence -> the birgHPC_setup script will show # nodes detectedCannot netbootTry http://etherboot.org/wiki/startHeterogeneous PCs ok?Ok (Thanks Micheal Creel)If 32 bit + 64 bit, use 32 bit PC as head node

31. FAQsStatus monitoringYes -> web browser -> localhost -> Ganglia MonitoringWhat will displayed on compute node?Just a simple login terminal with some warning not to use the nodes, etcLimitations?RAM, RAM, RAM …Everything is loaded to RAM, hence HDD size = RAM size

32. FAQsHeadnode criteriaPreferably 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/birghpcForum?No, but can always refer PelicanHPC forums

33. FAQsMulti users?No, designed for single userFuture release, maybe SGE or PBSInstalled on hardiskpermenantly?Not tested, technically possible, GooglePerformanceOn par with hardisk-installed cluster (tested up to 6 nodes)

34. FAQsI cannot boot from CDRefer user guide -> convert CD ISO to USB drive image -> boot from USBCan I use birgHPC along with existing DHCPPreferably no, DHCP will distribute IP and birgHPC head will distribute IP, causing confusion of IP addressesAlternative, boot DHCP as head node OR unplug DHCP, use another PC as head node

35. FAQsbirgHPC criteria (PCs = compute, server = head)