Taiwan UniGrid

Taiwan UniGridTaiwan UniGrid

Yeh-Ching ChungDepartment of Computer Science

National Tsing Hua UniversityHsin-Chu, 300, Taiwan

OutlineOutline

• Introduction• Portal• Broker and Scheduler• Resource Information Service• Storage Service• Applications• Conclusion

Introduction (1)Introduction (1)• The purpose of grid computing is to

integrate various resources within a large network environment.

• The purpose of the UniGrid project is to build a platform for academic research using grid-related technologies in Taiwan.

Introduction (2)Introduction (2)

• 9 institutes join to develop the system– 國網中心– 清華大學資工系– 中研院資科所– 東華大學資工系– 東海大學資科系– 中華大學資工系– 靜宜大學資管系– 興國管理學院電子商務學系– 台灣大學大氣科學系

Introduction (3)Introduction (3)

• All institutes that participate in the UniGrid project contribute some resources.

• These resources can be used in collaboration for large scale applications.

Introduction (4)Introduction (4)• System Architecture

OutlineOutline


PortalPortal

• The UniGrid portal provides an interface for UniGrid users to use the resources available in the UniGrid system.

• Functionalities of the portal– System status monitoring– Single sign-on– User workflow management– Project information

System Status Monitoring (1)System Status Monitoring (1)

• UniGrid users can examine the status of system resources through the portal.

• The portal gathers the current system information from the information service and present these information to the users.

System Status Monitoring (2)System Status Monitoring (2)

• Screenshot of the system status monitoring web page

Single Sign-On (1)Single Sign-On (1)

• Single sign-on is a mechanism whereby a single authentication can permit a user to access all resources where he has access permission, without the need to enter multiple passwords.– All user account information are kept in a

database at the portal site.– When a user requests a service, his verification

data is passed to that service.– The request will be granted only if the identity

is verified by the verification web service

Single Sign-On (2)Single Sign-On (2)• User identity verification through single sign-

on service

User Workflow Management (1)


• A UniGrid user can design and save his own workflows at the UniGrid portal.

• A user can select any workflow he designed and execute the workflow through the UniGrid portal.

• A user can also monitor the status of his workflow through the UniGrid portal.



• Structure of a workflow

sequentialexecution

parallelexecution

Workflow



• The workflows of each user is stored in the portal storage in XML format.

• <flow name="testflow" numstages="3"><stage name="stage1" numjobs="1">

<job id="0"><sortkey>1</sortkey> <runtype>mpi</runtype><workdir>/home/test/</workdir><filename>mm_mpi</filename><runrp>true</runrp> <datafile/> <argu>256</argu><otherurl/> <cpuno>4</cpuno>

</job></stage>…</flow>



• Screenshot of the workflow editing web page



• When an user submits a workflow, the portal will pass the selected workflow information to the broker.

• Upon receiving an execution request, the resource broker will find the required resource for that workflow and schedule its execution.



UniGrid User

UniGrid PortalWorkflow Database

BrokerJob Status Database

WorkflowXML

Job Status

Scheduler Scheduler



• Users can examine the execution status of his workflow through the portal’s workflow monitoring system.

• All workflow execution information are stored in a database at the machine with resource broker installed on it.

• The portal queries the database and obtain the current status of a particular workflow.

• The status information is processed and presented in the form of web pages.



• Screenshot of the workflow monitoring web page



• Screenshot of the UniGrid workflow management web page

OutlineOutline


Broker & Scheduler (1)Broker & Scheduler (1)

• The broker provides a uniform interface to access available resources in the UniGrid system.

• The broker uses the resource information service to obtain the current status of the resources in the system.

• After these information are gathered, the broker will allocate the resources that meets the requirements of the current job.

• The jobs are then passed to the corresponding local schedulers to be executed locally.


• Broker workflow


• Each participating organization has a local scheduler (Condor) installed to schedule the jobs assigned to that organization.

• Condor– A scheduler for large collections of distributively o

wned computing resources– Developed by the researchers at University of Wisc

onsin– Specialized for compute-intensive jobs – Uses the “ClassAd” mechanism to match job req

uirements to machine status and schedule the jobs according to the matching results

Related Research (1)Related Research (1)• Tools have been developed to

simulate different load sharing and scheduling policies on computing grid and analyze their performance

• Queuing methods– Independent clusters – Multiple queues

• Forwarding to no-need-to-wait site • Forwarding to shortest-queue site • Forwarding to least-load site, load=

clusterinprocessorsofNumber

mparallelisiJobruntimeiJobi

____

)).().((

Related Research (2)Related Research (2)

• Queuing methods (cont’d.)– Single queue

• Multi-pool centralized queue • Single-pool centralized queue

– One big cluster – Two-level scheduling

• Empty queue only • Shortest queue first• Least load first

– Two-level local queues• Forwarding to shortest-queue site


• Scheduling policies– Non-FCFS

• Multi-pool centralized queue• Single-pool centralized queue

– FCFS• Two-level scheduling

• The performance of Non-FCFS is three times better than FCFS


• Implementation Approaches– Multi-Pool Centralized Queue

• Global queue scheduling in the broker, no local queuing system

• Global queue scheduling in the broker, making sure available processors through local queuing system

– Single-Pool Centralized Queue• Global queue scheduling in the broker, no

local queuing system


– Two-Level Scheduling (Empty-Queue-Only Multi-Pool Grid)• Global queue in the broker, local queues in the l

ocal queuing systems


• Simulation resultsLoad sharing methods Average waiti

ng time(sec.)Standard deviation

Average waiting

ratio

Standard deviation

Independent clusters 2772.63 10797.80 21.46 148.07

Local queue based methods

Forwarding to no-need-to-wait site

111.08 1658.17 0.51 8.76

Forwarding to shortest-queue site 91.80 1560.22 0.41 15.59

Forwarding to least-load site 86.28 1477.90 0.30 9.32

Centralized queue based methods

Multi-pool centralized queue 127.64 1487.69 1.03 20.53

Single-pool centralized queue(slowdown ratio: 6)

2184.36 17251.00 23.84 273.75


200.71 2845.86 1.88 37.81


117.57 1749.76 0.90 19.42


61.71 946.55 0.47 13.88

Single-pool centralized queue(no slowdown)

50.36 774.95 0.37 11.00


• Simulation results (cont’d.)

One big cluster 50.36 774.95 0.37 11.00

Two-level scheduling

Empty-queue-only multi-pool grid

67.86 1239.00 0.22 6.34

Shortest-queue-first multi-pool grid

75.23 1361.69 0.23 5.14

Least-load-first multi-pool grid

73.22 1331.80 0.28 8.50

Methods with two local queues

Forwarding to shortest-queue site

94.51 1764.42 0.34 10.47


• Discussion– Non-FCFS methods can effectively improve the

overall system utilization and performance.– The smallest first non-FCFS policy outperforms

all other policies in terms of waiting time and waiting ratio.

– As the worst case is concerned, the backfilling policy is superior because it does not allow jobs to be delayed by the backfilling activities

OutlineOutline

• Introduction• Portal• Broker & Scheduler• Resource Information Service• Storage Service• Applications• Conclusion

Resource Information ServicesResource Information Services

• The resource information service provides information about current resource status, these information can be used by other services of the system

• Functionalities of the resource information service– Information system– Performance visualization of MPI parallel

program’s execution

Information System (1)Information System (1)

• Provides an interface for other services to query various information about computing nodes– The statistics about the individual nodes are

obtained using MDS (Monitoring & Discovery Service) provided by the Globus Toolkit

– The current network status between machines are gathered using NWS (Network Weather Service)

• Automatic update of node information– When a new computing nodes is added/removed


• The Network Weather Service (NWS)– A distributed system that periodically monitors

and dynamically forecasts the performance various network and computational resources can deliver over a given time interval

– Developed by the researchers at UCSB– It uses numerical models to generate forecasts

of what the conditions will be for a given time frame

– Because this functionality is analogous to weather forecasting, the system is called Network Weather Service


UniGrid Nodes

NWS

MDSNWS

MDS

NWS

MDS

Resource Information Service

Other UniGrid Services


• Screenshot of the node status webpage

Performance Visualization of MPI Programs (1)


• Input: any application (depending on the availability of compiler in grid platform)

• Output: performance visualization of the execution of this application



• Execution of a Parallel Application using 4 computing nodes


• Communication localization & data partitioning techniques in cluster-based grid system– Localized communication enhances

performance of parallel applications on grid

– Adaptive data partitioning for identical cluster & non-identical cluster grid topology

– In-core & out-of-core applications

Related Research (2)Related Research (2)• Communication localization techniques for

identical cluster

Original communication patterns Localized communication patterns


• Communication localization techniques for non-identical cluster

Original communication table


• Communication localization techniques for non-identical cluster (cont’d.)

Localized communication table

OutlineOutline


Storage ServiceStorage Service

• The goal of storage service is to provide a collaborative space where UniGrid users can share their data and resources with others.

• Components of the storage service– Virtual storage system– Data management system

Virtual Storage System (1)Virtual Storage System (1)

Clients

Grid Applications(Web Start)

StorageService

Stub

Web Server

SOAPEngine

Data Management

ServicePVFS Native API/ Linux

Kernel

PVFSs

ComputingService

CompilationService

AuthorizationService

AuthenticationService

Data Registry

User ProfileGroup Profile

Data RegistryService

PersonalWorkspace

GroupWorkspace

• Virtual storage system architecture


• The virtual storage system is implemented with Java as a web service

• UniGrid services access the virtual storage system when they need to fetch/modify users’ data files

• A client program is available for users to manage his own storage space

• The files are stored in a master file server and replicas of the files are distributed to other machines


Master file server

UniGrid storage resources

Storage Service

UniGrid Service

UniGrid User


• Screenshot of the storage service client program

Data Management (1)Data Management (1)• The Data Management is the

Web-based Replica Access and Management System

• It consists of the Registration, Search and Manager system– The registration system is

used in managing the user for accessing the UniGrid System

– The search system combines with the RLS and Web technique

– The manager system offers a friendly interface for manager, it will be easy to maintain the contents of database

• Structure of the Data Management System

Data Management (2)Data Management (2)

• Replica Location Service

Broker

user user user

Local Replica Catalog Server & Replica Location Index Server

Open DataBase Connectivity (ODBC)

MySQL

Replica Location Service

RLI RLI RLI

LRC LRC LRCLRC

RLI

RLI

LRC

LRC

RLI indexing over the full namespace

RLI indexing over a subset of LRCs

LRC being indexed only by one RLI

Multi-Indexed LRC for higher availability

OriginalFile

Replica Replica

Home(address,timestamp)

Replica0(address,timestamp)


OriginalFile

Replica Replica

OriginalFile

Replica Replica

Home(address,timestamp)




• The Registration System– In Security

• We design a web registration system

• User need to be registered in portal and logged in by CA (Proxy-init)

– In account manage• Administrator• User

• The detailed structure of Web Service System

Web Service SystemWeb Portal

Web Portal

Registration Search Manager

User Registration

Authentication

Authorization

Replica Management

Account Management

Accounting

Replica Indexing

Replica Location

Replica Download

Metadata Service

Replica Indexing

Replica Location

Replica Download

Metadata Service


Web Portal


User Registration

Authentication

Authorization

Replica Management

Account Management

Accounting

Replica Indexing

Replica Location

Replica Download

Metadata Service

Replica Indexing

Replica Location

Replica Download

Metadata Service


• The Search System– Replica Index and

Replica Location• In LRC Sever, we can

execute the basic command.

• We can update information of LRI server use the batch command

– Services• We offer the service of

the Job submit, files list, files upload and data replication in single server



Web Portal


User Registration

Authentication

Authorization

Replica Management

Account Management

Accounting

Replica Indexing

Replica Location

Replica Download

Metadata Service

Replica Indexing

Replica Location

Replica Download

Metadata Service


Web Portal


User Registration

Authentication

Authorization

Replica Management

Account Management

Accounting

Replica Indexing

Replica Location

Replica Download

Metadata Service

Replica Indexing

Replica Location

Replica Download

Metadata Service


• The Manager System– We plan to design a

friendly interface for manager, it will be easy to maintain the contents of Metadata database, update the RLS database and manage user’s account



Web Portal


User Registration

Authentication

Authorization

Replica Management

Account Management

Accounting

Replica Indexing

Replica Location

Replica Download

Metadata Service

Replica Indexing

Replica Location

Replica Download

Metadata Service


Web Portal


User Registration

Authentication

Authorization

Replica Management

Account Management

Accounting

Replica Indexing

Replica Location

Replica Download

Metadata Service

Replica Indexing

Replica Location

Replica Download

Metadata Service

OutlineOutline


Simulations of atmospheric circulations with the NTU/Purdue nonhydrostatic numerical model.

Model characteristics:NonhydrostaticExplicit forward-backward integration for both high-frequency waves and gravity wavesImplicit diffusion scheme with a TKE prognostic equationTime split schemes for high-frequency waves, gravity waves, diffusion, and surface processes.

Physical processes:Cloud microphysicsSurface similarity equation3-layer soil modelCoriolis force

Applications 1Applications 1

Machine name

NCHC-unigrid

Ntu-Cluster

Physical time

Runningtime

2 Dimension 3 Dimension

Physical time

Runningtime

50 sec 30 min

50 sec 31 min

5 hr17 min

12 hr

5 hr35 min

12 hr

Performance with the UniGridPerformance with the UniGrid

#NTUuninode11 2uninode12 2uninode14 2uninode15 2

host

uninode11uninode11uninode10uninode10uninode12uninode12uninode14uninode14uninode15uninode15uninode5uninode5uninode7uninode7uninode9uninode9

host1

/opt/mpich/pgi/bin/mpirun –nolocal –machinefile host –np 8 nonh3d.exe > test &

OBJ = nonh3d.o tograds.o copy.o update.o sound.o adv.o cloud1.o dampini.o\ initial.o restart.o nbr2d.o startend.o tkeeq.o updtrp.o\ sprogi4.o sprogi2.o diffxy.o diffz.o pbl.oEXE = ../nonh3d.exeOPT = -O3 -Mextend -Msave -Bstatic -byteswapio#OPT = -O3 -static -ffixed-line-length-80#OPT = -O3 -static#OPT = -O3

#OPT = -static$(EXE) : $(OBJ) /opt/mpich/pgi/bin/mpif77 $(OPT) -o $(EXE) $(OBJ).f.o : /opt/mpich/pgi/bin/mpif77 $(OPT) -c $<clean: rm -f *.o ../nonh3d.exe

makefile

Commands for submitting jobsCommands for submitting jobs

Initial spherical bubble develops into a mushroom-like shape. Two isentropic surfaces are shown. The isentropic surface corresponding to a higher potential temperature is in pink.

Three-dimension simulation of a thermal bubble in an isentropic environment

Three-dimension simulation of a thermal bubble in an isentropic environment

0 15km 30SBF

z

10

5km

0

xThe figure shows the total water mixing ratio (vapor plus liquid) over land after 2.5 hr. The label under the x-axis is the distance from the coastline. Water vapor is pumped up from the ground surface in the convective boundary layer (with the red/orange color representing high water vapor content in the air). The location of the sea breeze front (SBF) is shown.

Two-dimensional simulation of a sea breeze Two-dimensional simulation of a sea breeze

Applications 2Applications 2• FASTA

– Compares a protein sequence to another protein sequence or to a protein database, or a DNA sequence to another DNA sequence or a DNA library

Applications 3Applications 3

• ClustalW– A general purpose multiple sequence alignment program for

DNA or proteins.

Conclusions and Future WorkConclusions and Future Work

• A prototype of UniGrid system has been developed

• Enhance the data grid part of UniGrid

• Promote the UniGrid system to universities in Taiwan

Date post:	20-Jan-2016
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Taiwan UniGrid

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