Accelerating molecular dynamics simple tweaks to instant clusters

INSPIRING CREATIVE AND INNOVATIVE MINDS

Accelerating MD..Simple Tweaks and Instant Clusters

Mohd Shahir ShamsirBioinformatics Research Group (BIRG)

Faculty of Biosciences & BioengineeringUniversiti Teknologi Malaysia



Summary

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


Bioinformatics Research Group (BIRG)Faculty of Biosciences & Bioengineering

Just Google Us…


MD…

• What?• Why?• How?

• COVERED!!


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




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


Simple Tweaks



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


Compilation

• Winner self-compile


Beowulf OpenMPI vs MPICH2 (pre)

• Winner MPICH2


Pre and Self Compiled MPI

• Self OpenMPI = MPICH2


What we found

• Single machine– 66 % improvement

• Parallel environment– 64 % improvement

• Compilation, software chosen affect performance


Instant MD, anyone?



Instant MD cluster

• Lots of under utilised computers in labs• Idle mode after office hours, holidays, etc.


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…)


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!


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


Some Screenshots


Some Screenshots


Some Screenshots


Some Screenshots


Some Screenshots


Some Screeshots


Available at http://birg1.fbb.utm.my/birghpc

or Just Google birghpc

http://birg1.fbb.utm.my/birghpc


Conclusion

• birgHPC– instant cluster conversion– Bioinformatics tools– Auto configurations

• http://birg1.fbb.utm.my/birghpc– ISOs– guide



Acknowledgements

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


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


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

http://etherboot.org/wiki/start

http://etherboot.org/wiki/start


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


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



FAQs

• Multi users?– No, designed for single user– Future release, maybe SGE or PBS

• Installed on hardisk permenantly?– Not tested, technically possible, Google

• Performance– On par with hardisk-installed cluster (tested up to

6 nodes)


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


FAQs

• birgHPC criteria (PCs = compute, server = head)

Education

Accelerating molecular dynamics simple tweaks to instant clusters