http://www.grid-support.ac.uk
http://www.ngs.ac.uk
http://www.nesc.ac.uk/ http://www.pparc.ac.uk/ http://www.eu-egee.org/

• A “User interface” machine and our set-up today
• Commands to be used
• Practical:
– Port code and data from desktop/UI to the NGS compute nodes
– Compile and run code
– Invoke your application from the UI machine
• Summary
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• You’ve got your proxy on a UI machine and want to know how to port and run an application
• Er.. What’s a UI machine?
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• The users interface to the grid
– Where you upload your certificate for your session
– Where you create proxy certificates
– Where you can run the various commands
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ssh
UI
Internet
Core NGS nodes grid-data.rl.ac.uk
Tutorial room machines
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UI
NGS compute node gsiscp: copies file using proxy certificate to allow
AA
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UI
Code and data
NGS compute node
Code and data gsissh
Can be an Xwindows client
Compile, edit, recompile, build
SHORT interactive runs are ok (sequential)
Totalview debugger.
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• Connecting to the NGS compute node
• gsissh via port 2222
• Modify environment on the NGS account
(note which node you use and keep using it, or repeat commands on other nodes)
– .bashrc
• Used when you connect with gsissh
• Used by globus
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• gsissh -X -p 2222 grid-compute.leeds.ac.uk
• -X: enables forwarding of X11 connections
• -p: sets port through which gsissh works
• [ can set –X –p 2222 as defaults in config files]
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UI
Code and data
NGS compute node
Code and data
Executables globus_job_run
Or globus_job_submit / globus_get_output
Can pass files with these commands: e,g, parameters for a job.
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• The users interface to the grid
– Where you upload your certificate for your session
– Where you create proxy certificates
– Where you can run the various commands
• That was the good news.
• The bad news: install your own (currently!)
– May be your desktop with additional software
(GT2) – if you run UNIX derivative
– Note: 31 March - a 1 day course on this.
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the gatekeeper reads the gridmapfile to map the user’s id from their proxy certificate to a local account
Job request head-node
Globus gatekeeper
Forks process to run command.
Info system gridmapfile
I.S.
Job runs on head-node
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the gatekeeper reads the gridmapfile to map the user’s id from their proxy certificate to a local account
Job request head-node
Globus gatekeeper
Job queue: PBSPro
Info system gridmapfile
I.S.
Job runs on a cluster node
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• “How do I know which compute node to use?”
– As more nodes join the NGS, use the Information Service
(next talk)
– You should find that the Core nodes of the NGS all run the same software
– In general you are likely to use the same machine
• Is my NGS Compute Node account shared across all machines??
– NO – You must synchronise your accounts on different machines yourself. Your account names may be different on each machine. Use GridFTP (from portal) or gsi-scp
– You can hold files in the SRB,(Storage Resource Broker –see tomorrow) and read/write these from any compute node
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• “Should I stage an executable?” (stage = Send it to a compute node from my desktop/UI)
– Only if the UI produces a binary-compatible file!
– Safer to
• Check it compiles locally
• Copy to a compute node
• Compile it there
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• VDT documentation http://www.cs.wisc.edu/vdt/documentation.html
• NGS user pages http://www.ngs.ac.uk/users/userguide.html
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(outside scope of today)
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• [ngs0255@grid-compute ngs0255]$ cat .bashrc
• # .bashrc
•
• # Source global definitions
• if [ -f /etc/bashrc ]; then
. /etc/bashrc batch queue manager
Setting environment to use MPI with the
• fi
• module add clusteruser
• module remove mpich-gm
• module remove intel-compiler
• module remove intel-math
• module add mpich-gm/1.2.5..10-gnu
GNU compiler.
Can then compile with mpicc
See user documentation on NGS website
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[ ngs0255@grid-compute ngs0255]$ module list
Currently Loaded Modulefiles:
1) /dot 6) /gm/2.0.8
2) /null 7) /globus/2.4.3
3) /modules 8) /clusteruser
4) /cluster-tools/0.9 9) /mpich-gm/1.2.5..10-gnu
5) /pbs/5.3.3
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• globus-job-run grid-data.man.ac.uk /bin/date
• globus-job-run grid-data.rl.ac.uk ./test
• globus-job-run \ grid-compute.leeds.ac.uk/jobmanager-pbs \
-np 8 -x ‘(jobtype=mpi)(environment= \
(NGSMODULES clusteruser))’ ./MPI/test
• globus-job-run grid-data.rl.ac.uk -s ./test
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• globus-job-submit \ grid-data.rl.ac.uk/jobmanager-pbs ./test
• globus-job-submit \ grid-compute.leeds.ac.uk/jobmanager-pbs \
-x ‘(jobtype=mpi)(directory=/home/bob/mpi) \
(environment=(NGSMODULES clusteruser)) \
(count=8)’ ./mpi_program
• globus-job-submit \ grid-data.man.ac.uk/jobmanager-pbs -s ./test
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• globus-job-submit gridcompute.leeds.ac.uk/jobmanager-pbs -np
• 2 -x
'(jobtype=mpi)(directory=/home/data01_b/ng s0255)
• (environment=(NGSMODULES clusteruser))
• ' ./M3
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