Center for Computational Sciences, University of Tsukuba
http;//www.ccs.tsukuba.ac.jp/OmniRPC
and CONFLEX-GOmniRPC: A Grid RPC System for Parallel Computing
Support of master-workers programming model for parametric search grid applications.
Grid RPC APIs based on Ninf GridRPC.
Thread-safe RPC design allows programmers to use
Tokyo Inst. of Tech.
OpenMP for easy-to-use parallel programming.
PC
PC
The persistence model of automatic-initializable RPC
PC
PC
Grid test-bed onremote module enables re-use of the connection toNII SuperSINETPCCluster
RPC executables for efficient execution.
and Tsukuba WAN
Support for clusters with private IP address withPC
RemotePC
Univ. ofPC
scaling up to 1000 hosts.
Procdure
PC
TsukubaCalls
The RPC agent in a remote host works as a proxy
PC Cluster
between the client and the cluster internal hosts withPCPC
I/O multiplexing of communications.
PC
Grid Tech.
PC
Seamless programming environment from local
Research Center,
ClientPC Cluster AIST
cluster to grid. It can use "rsh" in a cluster, andGlobus GRAM or "ssh" in a grid for job invocation.
OmniRPC System
Webpage: http://www.omni.hpcc.jp/OmniRPC/CONFLEX-G: Grid-enabled Molecular Conformational Space Search Program
CONFLEX (developed by Prof. Goto, Toyohashi Institute of Technology) Process of CONFLEX-G
is one of the most efficient molecular conformational space searchprograms.
Accurate, automated conformation searching and analysis critical todrug discovery and chemical engineering.
Capability to completely search the conformational
space of a flexible molecule to find every optimal structureof chemically significant conformers.
GaucheGauche +2D drug libraries → 3D structure database∆E=0.9 kcal/mol∆E=0.9kcal/mol
Structure optimization with Molecular Mechanics.
Anti
Exhaustively search conformational space∆E=0.0 kcal/mol
Lowest-Conformer-First Selection Rule of Initial Structure
Highly efficient algorithm in producing several superior trialtructures. (Corner Flip, Edge Flip, Stepwise Rotation)
CONFLEX is parallelized using OmniRPC for a grid environment
with Master/ Workers programming model.
OmniRPC persistent data model (automatic initializable remotemodule facility) allows subsequent RPCs to reuse initialized
dataset. It eliminates worker program initialization at every PRC.
Selection ofinitialstructure

LocalPerturbationGrid Environment

TrialStructures

PC Cluster

Geometry
Optimization
Task Pool
TrialStructures

Conformation
Database

PC Cluster

Comparison&Store

Toyohashi Univ. of Tech.
Toyo Cluster
Dual Athlon 2600+
8 nodes

TrialStructures

PC Cluster

Univ of Tsukuba
Dennis Cluster
Dual P4 Xeon 2.4GHz
14 nodesAlice Cluster
Dual Athlon 1800+
20 nodesTokushima Univ.
Toku Cluster
P3 1.0GHz
8 nodesAIST
UME Cluster
Dual P3 1.4GHz
32 nodesPerformance of CONFLEX-G for Small Peptides
in a Grid Environment.

AlaX16

Toyo (16)AlaX04

Dennis (28)

Clusters ( # of Nodes)

Clusters ( # of Nodes)

Dennis(1)Performance Impact ofOmniRPC Automatic Initializable Module Facility

Alice (36)
Ume (56)
Dennis (28) + Toyo (16)Dennis (28) + Alice (36)Dennis (28) + Ume (56)
Alice (36) + Ume (56)
05

10

15
2025
Speed Up Ratio

30

35

AlaX04 (180 atoms, degree of parallel:45, # of all trial struct.:360)
AlaX16 (180 atoms, degree of parallel:160, # of all trial struct.:480)40

Toyo (16)Dennis (28)
Ume (56)
Without OmniRPC AIM
Dennis (28) + Toyo (16)With OmniRPC AIMDennis (28) + Ume (56)
0

1000

2000

3000

Elapsed Time (s)

4000

5000

6000