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Using simulation workspacesto “submit” jobs and workflows
Michael McLennanHUBzero® Platform for Scientific Collaboration
Purdue University
This work licensed underCreative Commons
See license online:by-nc-sa/3.0
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Launching workspaces
Find it on your dashboard:
Success!
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What is a workspace?
File server
• Full-featured Linux desktop• For tool developers• For researchers• Accessible from any web browser• Still running after you close your browser• Access to computational clusters• File storage provided by the hub
localclusters
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Accessing running workspaces
Close the browser
Still running, and listed under “my sessions”
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Closing workspaces
Click on “Terminate”
Click here to terminate
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Resize the screen
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Share your screen
johndoe
Share the sessionwith these people
Check this box ifyou don’t want to
share control
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Explore the desktop
“Start”menu
New terminalwindow
Editors:• geany• gedit• vim• emacs
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Choosing common utilities
Takes effect for the next newterminal window that you open
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Downloading files
Easy way to download:exportfile tool.xml
Tools can provide “download”function by exec’ing thiscommand
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Uploading files
Easy way to upload:importfile
IMG_1876.jpg
Tools can provide “upload”function by exec’ing thiscommand
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Research Computing Environment
NAMDAccess research codes and remote supercomputers
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Submit: Parameter Sweeps
If you normally run a command like this…spice3 –b circuit
Submit to remote resources like this…submit –v DiaGrid spice3 –b circuit
submit –p @@res=100,1k,10k spice3 –b @:circuit
submit –p @@res=100,1k,10k –p @@cap=1u,10u,100u spice3 –b @:circuit
submit –d indata.csv spice3 –b @:circuit
submit –p @@num=1:100 spice3 –b circuit@@num
submit –p @@file=glob:circuit* spice3 –b @@file
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Submit: Parameter Sweeps
If you normally run a command like this…spice3 –b circuit
Submit to remote resources like this…submit –v DiaGrid spice3 –b circuit
submit –p @@res=100,1k,10k spice3 –b @:circuit
submit –p @@res=100,1k,10k –p @@cap=1u,10u,100u spice3 –b @:circuit
submit –d indata.csv spice3 –b @:circuit
submit –p @@num=1:100 spice3 –b circuit@@num
submit –p @@file=glob:circuit* spice3 –b @@file
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Demo: BLASTX
submit blastx-2.2.28 -query test.fasta \ -db /group/diagrid/databases/ncbi/week-24-2014/nr \ -html -out output
exportfile output
submit -p @@seq=glob:seq* blastx-2.2.28 -query @@seq \ -db /group/diagrid/databases/ncbi/week-24-2014/nr \ -html -out output
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Automated Workflow
Ewa DeelmanUSC Information Sciences Institute
Development Team:Gideon Juve, Rajiv Mayani,
Mats Rynge, Karan Vahi
Pegasus Workflow Management System (est. 2001)
http://pegasus.isi.edu
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How does Pegasus work?
APIs forworkflow
specification
WorkflowSpec
DAX=
DAG in XML
Executable Workflow(After Pegasus Planning)
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Hub Web Server
Execution Host 1
Execution Host 2
. . .
Submitting Your Pegasus Workflow
Pegasus “DAX”Workflow
submit pegasus-plan --dax myworkflow.dax
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Two Audiences
Researchers Casual Users
Use “workspace” (remote desktop)Launch simulation jobs on grid/cloud
Share desktopsBuild and deploy tools
Use “tools” (app store)Simple, intuitive interfacesShare tools
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More Information
https://hubzero.org/documentation/1.2.2/tooldevshttps://hubzero.org/resources/779https://hubzero.org/resources/834https://hubzero.org/resources/pegtuthttp://pegasus.isi.edu