accelerating molecular dynamics simple tweaks to instant clusters
DESCRIPTION
Talk presented in IPharm's CADD 2010.TRANSCRIPT
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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
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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
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INSPIRING CREATIVE AND INNOVATIVE MINDS
Bioinformatics Research Group (BIRG)Faculty of Biosciences & Bioengineering
Just Google Us…
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INSPIRING CREATIVE AND INNOVATIVE MINDS
MD…
• What?• Why?• How?
• COVERED!!
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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
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INSPIRING CREATIVE AND INNOVATIVE MINDS
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INSPIRING CREATIVE AND INNOVATIVE MINDS
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INSPIRING CREATIVE AND INNOVATIVE MINDS
• Microwulf cluster• 26 Gflops, $2500, 11" x 12" x 17", • airline overhead baggage compliant
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INSPIRING CREATIVE AND INNOVATIVE MINDS
Simple Tweaks
INSPIRING CREATIVE AND INNOVATIVE MINDS
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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
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INSPIRING CREATIVE AND INNOVATIVE MINDS
Compilation
• Winner self-compile
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INSPIRING CREATIVE AND INNOVATIVE MINDS
Beowulf OpenMPI vs MPICH2 (pre)
• Winner MPICH2
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INSPIRING CREATIVE AND INNOVATIVE MINDS
Pre and Self Compiled MPI
• Self OpenMPI = MPICH2
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INSPIRING CREATIVE AND INNOVATIVE MINDS
What we found
• Single machine– 66 % improvement
• Parallel environment– 64 % improvement
• Compilation, software chosen affect performance
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INSPIRING CREATIVE AND INNOVATIVE MINDS
Instant MD, anyone?
INSPIRING CREATIVE AND INNOVATIVE MINDS
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INSPIRING CREATIVE AND INNOVATIVE MINDS
Instant MD cluster
• Lots of under utilised computers in labs• Idle mode after office hours, holidays, etc.
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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…)
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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!
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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
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INSPIRING CREATIVE AND INNOVATIVE MINDS
Some Screenshots
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INSPIRING CREATIVE AND INNOVATIVE MINDS
Some Screenshots
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INSPIRING CREATIVE AND INNOVATIVE MINDS
Some Screenshots
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INSPIRING CREATIVE AND INNOVATIVE MINDS
Some Screenshots
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INSPIRING CREATIVE AND INNOVATIVE MINDS
Some Screenshots
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INSPIRING CREATIVE AND INNOVATIVE MINDS
Some Screeshots
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INSPIRING CREATIVE AND INNOVATIVE MINDS
Available at http://birg1.fbb.utm.my/birghpc
or Just Google birghpc
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INSPIRING CREATIVE AND INNOVATIVE MINDS
Conclusion
• birgHPC– instant cluster conversion– Bioinformatics tools– Auto configurations
• http://birg1.fbb.utm.my/birghpc– ISOs– guide
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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
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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
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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
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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
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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
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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)
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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
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INSPIRING CREATIVE AND INNOVATIVE MINDS
FAQs
• birgHPC criteria (PCs = compute, server = head)