Creating and running an application on the NGS

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Creating and running an application on the NGS
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Policy for re-use

• This presentation can be re-used for academic
  purposes.
• However if you do so then please let
  training-support_at_nesc.ac.uk know. We need to
  gather statistics of re-use no. of events,
  number of people trained. Thank you!!

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Acknowledgements

• This presentation re-uses material
• on globus commands from Stephen Pickering
  (University of Leeds)

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Outline

• 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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Goals

• Youve got your proxy on a UI machine and want to
  know how to port and run an application
• Er.. Whats a UI machine?

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The UI machine

• 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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Our setup
Tutorial room machines
ssh
UI
Internet
Core NGS nodes
grid-data.rl.ac.uk
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Secure file copy
UI
NGS compute node
gsiscp copies file using proxy certificate to
allow AA
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Open shell on NGS CN
UI
NGS compute node
gsissh Can be an X-windows client
Compile, edit, recompile, build SHORT interactive
runs are ok (sequential) Totalview debugger.
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Establishing contact

• 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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Run jobs from the UI
UI
NGS compute node
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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PRACTICAL 2
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The UI machine

• 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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Globus Job Commands

• globus-job-run ltoptionsgt
• globus-job-submit ltoptionsgt
• globus-job-status URL
• globus-job-get-output URL
• BUILT on GSI

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globus_job_run
Job request
I.S.
the gatekeeper reads the gridmapfile to map the
users id from their proxy certificate to a
local account
head-node
Info system
Globus gatekeeper
gridmapfile
Forks process to run command.
Job runs on head-node
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globus_job_submit
Job request
I.S.
the gatekeeper reads the gridmapfile to map the
users id from their proxy certificate to a
local account
head-node
Info system
Globus gatekeeper
gridmapfile
Job queue PBSPro
Job runs on a cluster node
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Questions -1

• 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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Questions -2

• 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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Further information

• VDT documentationhttp//www.cs.wisc.edu/vdt/docum
  entation.html
• NGS user pageshttp//www.ngs.ac.uk/users/userguid
  e.html

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Extras for people who like MPI (outside scope of
today)
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.bashrc example, for MPI jobs

• ngs0255_at_grid-compute ngs0255 cat .bashrc
• .bashrc
• User specific aliases and functions
• Source global definitions
• if -f /etc/bashrc then
• . /etc/bashrc
• 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

Setting environment for globus and local batch
queue manager
Setting environment to use MPI with the GNU
compiler. Can then compile with mpicc
See user documentation on NGS website
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Check loaded modules

• ngs0255_at_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-g
  nu
• 5) /pbs/5.3.3

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globus-job-run Examples

• 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/jobmanag
  er-pbs \-np 8 -x (jobtypempi)(environment
  \(NGSMODULES clusteruser)) ./MPI/test
• globus-job-run grid-data.rl.ac.uk -s ./test

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globus-job-submit Examples

• globus-job-submit \grid-data.rl.ac.uk/jobmanager-
  pbs ./test
• globus-job-submit \grid-compute.leeds.ac.uk/jobma
  nager-pbs \-x (jobtypempi)(directory/home/bob/
  mpi) \(environment(NGSMODULES clusteruser))
  \(count8) ./mpi_program
• globus-job-submit \grid-data.man.ac.uk/jobmanager
  -pbs -s ./test

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• globus-job-submit grid-compute.leeds.ac.uk/jobmana
  ger-pbs -np
• 2 -x '(jobtypempi)(directory/home/data01_b/ngs02
  55)
• (environment(NGSMODULES clusteruser))
• ' ./M3