Transcript ANALISI DELLE PROPRIETA’ INTERATTIVE DI LIGANDI ATTIVI …

UNIVERSITÁ DEGLI STUDI DI MILANO
Facoltà di Scienze del Farmaco
A new distributed paradigm for
parallel computing
Alessandro Pedretti
Typical scenario in a lab
Internet
Servers
PCs
Firewall
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.
Network
devices
Ethernet
infrastructure
100-1000 Mbit/s
Main features
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.
What we need …
… to develop WarpEngine:
High-level database interface.
Fast customizable Web server.
Property calculation
Script engine.
Graphic environment.
Molecule editing
MM / MD calculations
Surface mapping
Trajectory analysis
File format conversion
Database engine
Graphic interface
Plug-in expandability
Scripting languages
Server scheme
Project
manager
UDP server
PowerNet
plug-in
Job
manager
Database
engine
Client
manager
VEGA ZZ
core
HTTP server
IP filter
TCP/IP, HTTP,
broadcast
Main program
Optional encrypted tunnel
provided by WarpGate
To clients
Client scheme
PowerNet plug-in
Main program
Project
manager
Multithreaded
worker
UDP client
HTTP client
TCP/IP, HTTP, broadcast
VEGA ZZ
core
To the server
Graphic interface
Hardware for the test
1 PC configured as client and server:
Quad-core
9 PC configured as client:
1 six-core
7 quad-core
1 dual-core
1 single-core
Operating systems:
6 Windows 7 Pro x64
3 Windows 7 Pro
1 Windows XP Pro
Network connection:
Ethernet 100 Mbs
37 cores
42 Gb ram
> 3 Tb storage
Preliminary performance test
Apache Bench 2.0.41
100 requests with concurrency level of 5.
3.205,13 pages / sec.
Microsoft IIS 6.0
1.066,67 pages / sec.
4,688 ms / request
1,560 ms / request
Communication stress test:
delivery of empty jobs to the clients and receive of
the result from them.
79.651,78 jobs / min.
Database stress test:
extraction (by SQL query), decompression and
delivery of molecules to the clients and answer.
41.115,00 molecules / min.
Software & data for the test
APBS – Adaptive Poisson-Boltzmann Solver
Calculation of solvation energy.
PLANTS – Protein-Ligand ANT system
Structure-based virtual screening.
Database of drugs in .mdb format
174.398 molecules, average MW 353,70.
Human M2 muscarinic receptor
PDB ID: 3UON.
Both programs
are single-threaded
Real case tests
APBS – Solvation energy calculation.
174.398 molecules, two APBS calculation for each molecule (reference and
solvated state).
Time required by a single thread calculation:
Time required by WarpEngine:
WarpEngine speed:
13 days 5 hours
8 hours 36 minutes
339,10 jobs / min.
PLANTS – Virtual screening.
174.398 molecules, M2 target, search speed 2.
Time required by a single thread calculation:
Time required by WarpEngine:
WarpEngine speed:
36 days 22 hours
1 day 0 hour 1 minute
121,00 jobs / min.
The future …
WarpEngine is easy expandable by scripting language, so it’s possible
to add some other calculation types:
Semi-empirical calculations
Ab-initio calculations
Other virtual screening methods
Rescore of docking poses
Molecular mechanics calculations
Other applications …
 MOPAC
 FireFly / PC GAMESS
 AutoDock, Vina
 VEGA, XScore
 AMBER, AMMP, NAMD