speaker: xin zuo heterogeneous computing laboratory (hcl) school of computer science and informatics...

Speaker: Speaker: Xin ZuoXin Zuo

Heterogeneous Computing Laboratory (HCL)Heterogeneous Computing Laboratory (HCL)

School of Computer Science and InformaticsSchool of Computer Science and Informatics

University College DublinUniversity College Dublin

IrelandIreland

International Parallel and Distributed Processing Symposium 2007

HCL Group HCL Group http://hcl.ucd.ie Fourth High-Performance Grid Computing Workshop Fourth High-Performance Grid Computing Workshop – IPDPS 2007

Experiments with a Software Component Experiments with a Software Component

Enabling NetSolve with Direct Communications Enabling NetSolve with Direct Communications

IIn a Non-Intrusive and Incremental Wayn a Non-Intrusive and Incremental Way

Authors: Authors: Xin Zuo, Alexey LastovetskyXin Zuo, Alexey Lastovetsky

Fourth High-Performance Grid Computing Workshop


Outlines

An overview of approach

Enabling NetSolve with direct communication

Design and Implementation of software component

Application and Experiments

Conclusions and further work


Overview of Approach

• About High performance Grid programmingAbout High performance Grid programming

- It has reached a certain level of maturity, examples: NetSolve and Ninf

- Need further development in terms of functionality and quality.

- Particularly, addition of a new feature to a Grid programming system.

- Traditionally, achieved by changing the code of the system.

- It has two serious disadvantages:

1. May introduce bugs which cause system run instable or even crash.

2. To replace the old version, can have very high organizational overhead

and sometimes be simply unrealistic on the Grid.


• The Features of The Features of ApproachApproach:

Non-intrusivenessNon-intrusiveness: : The original system does not change and the new features are provided by a supplementary software component working on the top of the system.

IncrementIncrement: : The supplementary software component does not have to be installed on all computers to enable applications with the new features.

• To demonstrate the feasibility of approachTo demonstrate the feasibility of approach

- We choose NetSolve

- One particular feature: Direct Communication between remote tasks

- Real world Application and Experiments


Overview of Approach


• NetSolve is positioned as a programming system for high performance distributed computing on global networks based on GridRPC.

- http://icl.cs.utk.edu/netsolve/

- NetSolve (GridSolve), is a client-server system that enables users to solve complex scientific problems remotely

• Unnecessary bridge communications: In NetSolve, output data of remote tasks are typically sent back to the client upon completion of each remote task even if the data are only needed as input for some other remote tasks.


• Enabling direct communication



• Consists of three parts

- Client API & Argument Parser: Provide a uniform interface for the client to make remote procedure calls. Despite the modification on the remote side, the wrapper API allows the calls to be made in the same manner. The only difference is in the arguments that can be not only variables storing real data but also handlers.

- Server Connector: responsible for interacting with clients and other Server Connectors to enable direct communications.

- Job Name Service (JNS): responsible for registration of procedure upon its invocation during RPC call. Other procedures may send requests to the JNS to search for registered procedure. JNS is set up on the client side automatically.




• Using software component in NetSolve

- Client programmers: They need to install our wrapper API and Job Name Service on the client side, then compile the client program with the wrapper library. The principle is quite easy: the programmer just replaces the input/output arguments with handlers as the input/output data. Example:

errno=netsl("A", inputA, outputA); errno=netsl("B", outputA, inputB, outputB);

The extended API codes are as follows:

errno=mynetsl("A", inputA, hdlA); errno=mynetsl("B", hdlA, inputB, outputB);



- Procedure developers: The procedure programmers should do nothing to enable direct communications. They develop their own procedures as usual.

- Server administrator: need to install Server Connector on server-side. No re-installation and re-compilation of either NetSolve itself or registered NetSolve procedures are needed.

User Guidance and Software Component on site: http://hcl.ucd.ie


• Architecture of the supplementary software component enabling direct communications in NetSolve

HCL Group http://hcl.ucd.ie Fourth High-Performance Grid Computing WorkshopHCL Group http://hcl.ucd.ie Fourth High-Performance Grid Computing Workshop – IPDPS 2007



• Three typical scientific NetSolve:

- protein tertiary structure prediction

- image processing using sequential algorithms

- matrix chain product.

These three applications have different communication structures.

• Experiment environment: Experiments are conducted using six NetSolve servers, interconnected via a 100 Mbit Ethernet network with a switch enabling parallel communications In School of Computer Science and Informatics, University College Dublin.




Genetic Crossover in Protein Tertiary Structure Prediction System

- It is mainly performed by the protein energy minimization.

- Parallel Simulated Annealing using Genetic Crossover is a minimization engine. NetSolve is a basic tool to use it.



(a) bridge communication (b) direct communication

- Bridge communications exist and they can be eliminated by using our software component.

- By doing so, Genetic Crossovers are executed between servers directly.



Bridge communication time (in seconds); D – Direct communication time (in seconds).

- Experimental results shows that the average communication speedup due to elimination of bridge communications is around 43%.

Protein Size (kb)

Trail 1 Trail 2 Trail 3 Average

SpeedupB D B D B D B D

100050 30 51 30 53 31 52 30

45%

2000106 62 108 63 108 62 107 62

42%

3000175 98 170 100 178 105 174 101

42%



Image processing using sequential algorithms

- Image processing implements a wide range of operations such as smoothing, sharpening, noise reduction, etc.

- Our research aims to optimize communications of data transaction for sequential multimedia operations. In this paper, Linear Combination Filtering is the example.

- NetSolve is a basic tool and functions are taken from Image Processing Library.



(a) (b) (c) (d) (e) (f)

(a) Input image;

(b) Laplacian of (a);

(c) Spatially invariant high-pass filtering [sum of (a) and (b)];

(d) Mask image [Sobel gradient of (a) smoothed by a 5x5 box filter];

(e) Product of (b) and (d);

(f) Space-variant enhancement [sum of (a) and (e)].



- Bridge communications exist. Use our software component to eliminate un-necessary communications between the client and the servers; we select two servers to perform linear combination filtering functions in parallel.

- By doing so, 6 bridges are removed among 11 communications.

Figure. Enabling direct communications between NetSolve servers while performing linear

combination filtering.





Picture Size (kb)


Speedup

B D B D B

D B D

1000 60 29 60 29 61 29 60 29 51%

2000 125 61 122 62 125 63 124 62 50%

3000 195 97 209 98 203 98 200 98 51%



Matrix chain product problem in general scientific computations

- Given N matrices A1, A2, …, An of size N x N, the matrix chain product problem is to compute A1 x A2 x … x An. It is an important computational kernel that is used in computing the characteristic polynomial, determinant, rank, etc.

- One popular solution: Standard binary tree method. Example: n = 8.



(a) bridge communication (b) direct communication

- By using our software component, bridge communications can be removed between NetSolve servers. Figures above depict how it works.

- Communication links are reduced from 14 to 8. Only the result matrix A12345678 is returned to the client.





Matrix Size


SpeedupB D B D B D B D

1000102 66 101 67 103 67 102 67

38%

2000210 132 220 136 212 138 214 135

36%

3000335 220 315 226 310 216 320 221

31%



- Speedup for the three applications increases linearly with the increase of the number of computing servers with direct communication enabled from 0 to six.

Other Experiments

‘o’ – the matrix chain product;

‘.’ – Genetic crossover;

‘*’ – Image processing using sequential algorithms.



- Speedups for the matrix chain product in both homogeneous network and heterogeneous network. It shows that much higher speedup can be achieved in heterogeneous communication networks.

‘*’ – homogeneous network;

‘o’ – heterogeneous network.

Conclusions and Further work

Conclusions:

- we have presented the implementation of a software component enabling direct communications in NetSolve in a non-intrusive and incremental way. We have also presented the results of experiments with three typical real-world applications having different communication structures.

- The experimental results have shown that the performance of NetSolve applications can be significantly and easily improved by using our software component.

Further work:

- Future work is about to test this software component in a larger Grid environment such as Grid Ireland or Grid 5000 in France.


The END

http://www.cs.ucd.ie

http://hcl.ucd.ie

Thank you!


speaker: xin zuo heterogeneous computing laboratory (hcl) school of computer science and informatics...

Documents

experiments hcl group

work hcl group http

grid programming system

direct communication

overview of approach

original system

new features

direct communications