accelerating molecular dynamics simple tweaks to instant clusters
DESCRIPTION
Talk presented in IPharm's CADD 2010.TRANSCRIPT
INSPIRING CREATIVE AND INNOVATIVE MINDS
Accelerating MD..Simple Tweaks and Instant Clusters
Mohd Shahir ShamsirBioinformatics Research Group (BIRG)
Faculty of Biosciences & BioengineeringUniversiti Teknologi Malaysia
INSPIRING CREATIVE AND INNOVATIVE MINDS
INSPIRING CREATIVE AND INNOVATIVE MINDS
Summary
• Introduction to BIRG• MD: What, Why and How• Improving performance• Simple Tweaks…• Instant MD cluster– birgHPC• Short video demo
INSPIRING CREATIVE AND INNOVATIVE MINDS
Bioinformatics Research Group (BIRG)Faculty of Biosciences & Bioengineering
Just Google Us…
INSPIRING CREATIVE AND INNOVATIVE MINDS
MD…
• What?• Why?• How?
• COVERED!!
INSPIRING CREATIVE AND INNOVATIVE MINDS
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
INSPIRING CREATIVE AND INNOVATIVE MINDS
INSPIRING CREATIVE AND INNOVATIVE MINDS
INSPIRING CREATIVE AND INNOVATIVE MINDS
• Microwulf cluster• 26 Gflops, $2500, 11" x 12" x 17", • airline overhead baggage compliant
INSPIRING CREATIVE AND INNOVATIVE MINDS
Simple Tweaks
INSPIRING CREATIVE AND INNOVATIVE MINDS
INSPIRING CREATIVE AND INNOVATIVE MINDS
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
INSPIRING CREATIVE AND INNOVATIVE MINDS
Compilation
• Winner self-compile
INSPIRING CREATIVE AND INNOVATIVE MINDS
Beowulf OpenMPI vs MPICH2 (pre)
• Winner MPICH2
INSPIRING CREATIVE AND INNOVATIVE MINDS
Pre and Self Compiled MPI
• Self OpenMPI = MPICH2
INSPIRING CREATIVE AND INNOVATIVE MINDS
What we found
• Single machine– 66 % improvement
• Parallel environment– 64 % improvement
• Compilation, software chosen affect performance
INSPIRING CREATIVE AND INNOVATIVE MINDS
Instant MD, anyone?
INSPIRING CREATIVE AND INNOVATIVE MINDS
INSPIRING CREATIVE AND INNOVATIVE MINDS
Instant MD cluster
• Lots of under utilised computers in labs• Idle mode after office hours, holidays, etc.
INSPIRING CREATIVE AND INNOVATIVE MINDS
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…)
INSPIRING CREATIVE AND INNOVATIVE MINDS
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!
INSPIRING CREATIVE AND INNOVATIVE MINDS
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
INSPIRING CREATIVE AND INNOVATIVE MINDS
Some Screenshots
INSPIRING CREATIVE AND INNOVATIVE MINDS
Some Screenshots
INSPIRING CREATIVE AND INNOVATIVE MINDS
Some Screenshots
INSPIRING CREATIVE AND INNOVATIVE MINDS
Some Screenshots
INSPIRING CREATIVE AND INNOVATIVE MINDS
Some Screenshots
INSPIRING CREATIVE AND INNOVATIVE MINDS
Some Screeshots
INSPIRING CREATIVE AND INNOVATIVE MINDS
Available at http://birg1.fbb.utm.my/birghpc
or Just Google birghpc
INSPIRING CREATIVE AND INNOVATIVE MINDS
Conclusion
• birgHPC– instant cluster conversion– Bioinformatics tools– Auto configurations
• http://birg1.fbb.utm.my/birghpc– ISOs– guide
INSPIRING CREATIVE AND INNOVATIVE MINDS
Acknowledgements
• Chew Teong Han - Alchemist• Farizuawana – Graphics• Joyce Tan – Testing• Funding from you via LHDN via MOSTI• Michael Creel for Pelican HPC
INSPIRING CREATIVE AND INNOVATIVE MINDS
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
INSPIRING CREATIVE AND INNOVATIVE MINDS
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
INSPIRING CREATIVE AND INNOVATIVE MINDS
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
INSPIRING CREATIVE AND INNOVATIVE MINDS
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
INSPIRING CREATIVE AND INNOVATIVE MINDS
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)
INSPIRING CREATIVE AND INNOVATIVE MINDS
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
INSPIRING CREATIVE AND INNOVATIVE MINDS
FAQs
• birgHPC criteria (PCs = compute, server = head)