high performance computing @ louisiana state university - loni hpc enablement workshop – latech...
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High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/
http://www.loni.org
LONI HPC Enablement Workshop – LaTech University, October 23, 2008
Introduction to Globus Procedures using LONI Resources
October 2009
Sirish TummalaLONI HPC Enablement Group
Email: [email protected]
High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/
http://www.loni.org
LONI HPC Enablement Workshop – LaTech University, October 23, 2008
So Far in the HPC Workshop
10/06/09
•About LONI•Machines•Allocation Procedures•Software Environment•Linux, Vi Tutorials•Using the Batch System (PBS, Loadleveler)
High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/
http://www.loni.org
LONI HPC Enablement Workshop – LaTech University, October 23, 2008
So Far Computing your Data
10/06/09
•Login to the Machine•Compile your Code using native compiler on the machine.•Write a submit file•Submit it to the Batch System (PBS, Loadleveler)
High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/
http://www.loni.org
LONI HPC Enablement Workshop – LaTech University, October 23, 2008
So Far Data Management
10/06/09
•Copy your data to the machine using SCP, SFTP•Create directories manually•After Computation, archive it without exceeding the disk quotas.
High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/
http://www.loni.org
LONI HPC Enablement Workshop – LaTech University, October 23, 2008
So Far: Workflows
10/06/09
•You write your own scripts to automate everything.•Stage in, Preprocessing, Processing, Post Processing, Stage out and Archival•Usually, without any fault tolerance (retrial from the point of failure, in case of one)
High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/
http://www.loni.org
LONI HPC Enablement Workshop – LaTech University, October 23, 2008
AIX•Bluedawg•Ducky•Zeke•Neptune•LacumbaLINUX•Eric•Oliver•Poseidon•Louie•Painter•Queenbee•Unnamed
10/06/09
Too many Options?
High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/
http://www.loni.org
LONI HPC Enablement Workshop – LaTech University, October 23, 2008
Constraint: Using one machine at a time
10/06/09
•You are more focused on your work than to use all the machines for your work.•You avoid playing with multiple machines and instead work on your code•Often, your code is not portable because you don’t use it on other machines.•So you end up working with one or very few machines (usually your favorite ones)
High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/
http://www.loni.org
LONI HPC Enablement Workshop – LaTech University, October 23, 2008
What are you missing out?
10/06/09
•Unused computational cycles on other machines. Get your work done fast. No more long queues.•Spread your risk of machine failure while you need to get your results in time.•See how your code scales on different machines and use that for improvement.
High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/
http://www.loni.org
LONI HPC Enablement Workshop – LaTech University, October 23, 2008
Use Globus Toolkit !
10/06/09
Using Globus you can:•There are 12 supercomputing machines on LONI. Use them all.•Submit jobs to all the machines, without going to each one.•When a machine goes down, throttle jobs to a different machine.•Get more computational throughput in a given amount of time, by spreading your allocation/computation over multiple machines.•Automate your data management. No more manual data peddling, disk quota exceeding = “no more annoying emails from us.”
High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/
http://www.loni.org
LONI HPC Enablement Workshop – LaTech University, October 23, 2008
LONI Grid Service Nodes
qb1.loni.orgeric1.loni.org
BLUEDAWG.LONI.ORGPAINTER1.LONI.ORG
UNNAMED(NEW)LACUMBA.LONI.ORG
NEPTUNE.LONI.ORGPOSEIDON1.LONI.ORGOLIVER1.LONI.ORG
ZEKE.LONI.ORG
LOUIE1.LONI.ORGDUCKY.LONI.ORG
QB1.LONI.ORGERIC1.LONI.ORG
High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/
http://www.loni.org
LONI HPC Enablement Workshop – LaTech University, October 23, 2008
Your Globus Grid Certificate• Globus uses the Grid Security Infrastructure
(GSI).
– Based on the Public-key infrastructure
– All Entities use certificates to estabilish trust and identity.
– A certificate contains:
• Entity's identity
• Public Key
• Certificate Authority Identity
– Delegation
• Services can act on behalf of users so that grid tasks can be automated and do not require entering a passphrase manually.
– GridMap File
• A list of Certificate subject entries and corresponding local unix accounts to correctly map certificate owners to local accounts.
High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/
http://www.loni.org
LONI HPC Enablement Workshop – LaTech University, October 23, 2008
LONI MyProxy Service• “proxy01.hpc.lsu.edu”
• MyProxy is an online credential repository.
• Users having certificates can store their credentials in the MyProxy repository with a password of their choice.
• Used for delegating grid credentials to other resources.– You can have your certificates
in one place and obtain the delegated proxy on other resources.
High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/
http://www.loni.org
LONI HPC Enablement Workshop – LaTech University, October 23, 2008
GridFTP Protocol
Basic TransferOne control channel, several parallel data channels
Basic TransferOne control channel, several parallel data channels
Third-partyTransferControl channels to each server, several parallel data channels between servers
High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/
http://www.loni.org
LONI HPC Enablement Workshop – LaTech University, October 23, 2008
Reliable File Transfer Service• Reliable File Transfer: RFT provides a
management layer over GridFTP to provide reliability and fault tolerance.
– Uses a database to maintain state.– All file operations in the Web services
implementation of globus use RFT.
High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/
http://www.loni.org
LONI HPC Enablement Workshop – LaTech University, October 23, 2008
Globus Pre-WSGRAM• DELEGATE, DELEGATE, DELEGATE !!!• A uniform service interface for remote
job submission and control– Includes file staging and I/O
management– Includes reliability features– Supports basic Grid security
mechanisms– Available in Pre-WS and WS forms
High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/
http://www.loni.org
LONI HPC Enablement Workshop – LaTech University, October 23, 2008
Language of Pre-WS GRAM• GRAM uses the Resource Specification
Language (RSL) to describe execution tasks that need to be submitted to GRAM. The GRAM service endpoint is called the gatekeeper.
High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/High Performance Computing @ Louisiana State University - http://www.hpc.lsu.edu/
http://www.loni.org
LONI HPC Enablement Workshop – LaTech University, October 23, 2008
10/06/09
Globus & PBS, Globus & Loadleveler, Globus & Workflows
•You submit Jobs and Data transfer tasks using Globus•It uses PBS/Loadleveler on the machine for Computation•It used GridFTP to manage your data•Gridway, DAGMan(Condor) to schedule your workflows.