taiwan unigrid
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Taiwan UniGrid. Yeh-Ching Chung Department of Computer Science National Tsing Hua University Hsin-Chu, 300, Taiwan. Outline. Introduction Portal Broker and Scheduler Resource Information Service Storage Service Applications Conclusion. Introduction (1). - PowerPoint PPT PresentationTRANSCRIPT
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
• Introduction• Portal• Broker and Scheduler• Resource Information Service• Storage Service• Applications• Conclusion
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)
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.
User Workflow Management (2)
User Workflow Management (2)
• Structure of a workflow
sequentialexecution
parallelexecution
Workflow
User Workflow Management (3)
User Workflow Management (3)
• 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>
User Workflow Management (4)
User Workflow Management (4)
• Screenshot of the workflow editing web page
User Workflow Management (5)
User Workflow Management (5)
• 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.
User Workflow Management (6)
User Workflow Management (6)
UniGrid User
UniGrid PortalWorkflow Database
BrokerJob Status Database
WorkflowXML
Job Status
Scheduler Scheduler
User Workflow Management (7)
User Workflow Management (7)
• 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.
User Workflow Management (8)
User Workflow Management (8)
• Screenshot of the workflow monitoring web page
User Workflow Management (9)
User Workflow Management (9)
• Screenshot of the UniGrid workflow management web page
OutlineOutline
• Introduction• Portal• Broker and Scheduler• Resource Information Service• Storage Service• Applications• Conclusion
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 & Scheduler (2)Broker & Scheduler (2)
• Broker workflow
Broker & Scheduler (3)Broker & Scheduler (3)
• 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
Related Research (3)Related Research (3)
• 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
Related Research (4)Related Research (4)
• 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
Related Research (5)Related Research (5)
– Two-Level Scheduling (Empty-Queue-Only Multi-Pool Grid)• Global queue in the broker, local queues in the l
ocal queuing systems
Related Research (6)Related Research (6)
• 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
Single-pool centralized queue(slowdown ratio: 5)
200.71 2845.86 1.88 37.81
Single-pool centralized queue(slowdown ratio: 4)
117.57 1749.76 0.90 19.42
Single-pool centralized queue(slowdown ratio: 2)
61.71 946.55 0.47 13.88
Single-pool centralized queue(no slowdown)
50.36 774.95 0.37 11.00
Related Research (7)Related Research (7)
• 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
Related Research (8)Related Research (8)
• 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
Information System (2)Information System (2)
• 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
Information System (3)Information System (3)
UniGrid Nodes
NWS
MDSNWS
MDS
NWS
MDS
Resource Information Service
Other UniGrid Services
Information System (4)Information System (4)
• Screenshot of the node status webpage
Performance Visualization of MPI Programs (1)
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
Performance Visualization of MPI Programs (2)
Performance Visualization of MPI Programs (2)
• Execution of a Parallel Application using 4 computing nodes
Related Research (1)Related Research (1)
• 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
Related Research (3)Related Research (3)
• Communication localization techniques for non-identical cluster
Original communication table
Related Research (4)Related Research (4)
• Communication localization techniques for non-identical cluster (cont’d.)
Localized communication table
OutlineOutline
• Introduction• Portal• Broker and Scheduler• Resource Information Service• Storage Service• Applications• Conclusion
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
Virtual Storage System (2)Virtual Storage System (2)
• 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
Virtual Storage System (3)Virtual Storage System (3)
Master file server
UniGrid storage resources
Storage Service
UniGrid Service
UniGrid User
Virtual Storage System (4)Virtual Storage System (4)
• 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)
Replica1(address,timestamp)
OriginalFile
Replica Replica
OriginalFile
Replica Replica
Home(address,timestamp)
Replica0(address,timestamp)
Replica1(address,timestamp)
Data Management (3)Data Management (3)
• 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 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
Data Management (4)Data Management (4)
• 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
• 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 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
Data Management (5)Data Management (5)
• 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
• 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 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
OutlineOutline
• Introduction• Portal• Broker and Scheduler• Resource Information Service• Storage Service• Applications• Conclusion
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