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Alessandro Pedretti
A new distributed paradigm for parallel computing
UNIVERSITÁ DEGLI STUDI DI MILANOFacoltà di Scienze del Farmaco
Typical scenario in a lab
Internet
Firewall
Servers
PCs
Networkdevices
Ethernet infrastructure100-1000 Mbit/s
Several PCs with heterogeneous hardware / OSs.
Very high computational power “fragmented” on the local network.
Hard possibility to use all computational power to run a single complex calculation.
Parallel computing without cluster paradigm.
Client/server architecture with hot-plug capabilities.
Possibility to perform calculations with different pieces of software without changing the main code.
Expandable by scripting languages.
High-level database interface integrated in the main code and supporting the most common SQL database engines (Access, MySQL, SQLite, SQL Server, etc).
Easy configuration by graphic interface.
High performances and security.
Main features
… to develop WarpEngine:
What we need …
High-level database interface.
Fast customizable Web server.
Script engine.
Graphic environment.
Plug-in expandability
Scripting languages
Molecule editing
Surface mapping
File format conversion
Database engine
Graphic interface
Property calculation
MM / MD calculations
Trajectory analysis
Server scheme
UDP server HTTP server
Client manager
Project manager
Jobmanager
VEGA ZZcore
Databaseengine
IP filterPowerNetplug-in
Main program
To clientsTCP/IP, HTTP,broadcast
Optional encrypted tunnelprovided by WarpGate
Client scheme
UDP client HTTP client
Project manager
Multithreadedworker
VEGA ZZcore
PowerNet plug-in Main program
To the serverTCP/IP, HTTP, broadcast
Graphic interface
Hardware for the test
1 PC configured as client and server:Quad-core
9 PC configured as client:1 six-core7 quad-core1 dual-core1 single-core
37 cores42 Gb ram
> 3 Tb storage
Operating systems:6 Windows 7 Pro x643 Windows 7 Pro1 Windows XP Pro
Network connection:Ethernet 100 Mbs
Communication stress test:delivery of empty jobs to the clients and receive of the result from them.
79.651,78 jobs / min.
Preliminary performance test
Database stress test:extraction (by SQL query), decompression and delivery of molecules to the clients and answer.
41.115,00 molecules / min.
Apache Bench 2.0.41100 requests with concurrency level of 5.
3.205,13 pages / sec.1,560 ms / request
Microsoft IIS 6.01.066,67 pages / sec.
4,688 ms / request
Software & data for the test
APBS – Adaptive Poisson-Boltzmann SolverCalculation of solvation energy.
PLANTS – Protein-Ligand ANT systemStructure-based virtual screening.
Database of drugs in .mdb format174.398 molecules, average MW 353,70.
Human M2 muscarinic receptorPDB ID: 3UON.
Both programsare single-threaded
APBS – Solvation energy calculation.174.398 molecules, two APBS calculation for each molecule (reference and solvated state).
Time required by a single thread calculation: 13 days 5 hours
Time required by WarpEngine: 8 hours 36 minutes
WarpEngine speed: 339,10 jobs / min.
Real case tests
PLANTS – Virtual screening.174.398 molecules, M2 target, search speed 2.
Time required by a single thread calculation: 36 days 22 hours
Time required by WarpEngine: 1 day 0 hour 1 minute
WarpEngine speed: 121,00 jobs / min.
WarpEngine is easy expandable by scripting language, so it’s possible to add some other calculation types:
The future …
Semi-empirical calculations MOPAC
Ab-initio calculations FireFly / PC GAMESS
Other virtual screening methods AutoDock, Vina
Rescore of docking poses VEGA, XScore
Molecular mechanics calculations AMBER, AMMP, NAMD
Other applications …