Underworld Test Case

These files are provided for use as a  smoke test of the  ARCS Grid submission client  Grisu prior to release(s), using the latest Underworld-1.2.0 release.  Underworld is a 3D-parallel geodynamic modelling framework, under collaborative development by  Monash University and  VPAC, as part of the NCRIS AuScope capability in the  Simulation and Modelling Victoria program. The Underworld user community is one of the two target groups for the initial Grisu release.

Thanks to Wendy Mason for preparing this test case:

Wendy Mason
PhD Candidate, Computational Geodynamics
AuScope Research Assistant (Underworld E-Research Officer)
School of Geosciences / School of Mathematical Sciences
Monash University

Login and VO Selection

• launch Grisu
• select the "Shibboleth login" panel, enter your local institution username and password, ensure that "ServiceInterface to connect to" is set to "https://grisu.vpac.org/grisu-ws/services/grisu" and click on the "Login" button
• click on "Change" button, select /ACC and click on the "OK" button

Job Submission Template Selection

[Job submission panel]

• click on the "+" button, select the "underworld" template, click on the "Add" button, and select the "underworld" template in the "Applications" list to load it

Underworld Job Parameter Selection

[Job Submission > Basic job properties sub-panel]

• "Jobname": overwrite "underworld_job" with "underworld_smoketest"
• "Walltime" in the "Minutes" field overwrite "10" with "4"
• "CPUs": check the "Parallel" box, and in the "No. of cpus" field click on the down arrow and select "4" (note the job should actually take less time than this to run)
• "Submission details": click on the "Site" drop-down box and select "VPAC"; click on the "Queue" drop-down box and select "dque@tango-m"; in the "Version" section check the "Select version" box, click on the drop-down box below (which should now be active) and select "1.2.0"
• "Notify me when job": check both the "starts" and "finishes" boxes, and enter an email address into the "Email" field, which should have appeared below

Underworld File Selection

[Job Submission > Job parameters sub-panel]

• click on the "Job parameters" sub-panel
• "InputFile": click on the "Browse" button and select the file RayleighTaylorBenchmark_1.2.0_smoketest.xml
• "Additional File(s)": select the file "window_1.2.0_smoketest.xml and double-click on it so that it appears in the pane on the right-hand-side

Job Submission

[Job submission > Job parameters sub-panel]

• click on the "Submit" button (both subpanels should be replaced with a progress bar and progress pane detailing each step of the job submission progress)
• once the progress bar is full and the text "Job submission successful" has appeared in the progress pane, click on the "OK" button (the subpanels should reappear)

Job Monitoring

[Monitoring panel]

• click on the "Monitoring" panel
• the submitted job should be listed (jobs will be listed in alphabetical order by Jobname)
• click on the "Submission Time" column header to reorder the list by submission time (order should change if there is more than one job in the list)
• click on the "Refresh all" button to refresh the job status (order should still be by submission time)
• right-click on the job's name in the "Jobname" column and select "View job details" (a new window should appear in front of the main Grisu window, containing the panels "underworld", "Job directory" and "Job details" - if there is no "underworld" panel, close this window, wait a few seconds and repeat until it appears)

Underworld Post-processing Panel

[Monitoring > Job details > (new window) underworld panel]

• click on the "x-Axis" drop-down-menu and select "Time" (the x axis of the graph should change accordingly)
• click on the "y-Axis" drop-down-menu and select "Vrms" (the y axis of the graph should change accordingly)
• note the "Timestep" number above the status bar (which reflects the number of timesteps run out of the maxTimesteps specified in the input file), the shape of the graph plot and the FrequentOutput.dat file preview contents, then click on the refresh button and verify that these three features update (FrequentOutput.dat has been downloaded to ~/.grisu/cache/ng2.vpac.org (StartUp)/grisu-jobs-dir/underworld_smoketest on your local drive)

Output preview and file download

[Monitoring > Job details > (new window) Job directory panel]

• click on the "Job directory" panel (a "Preview" drop-down box should appear in the bottom right-hand corner of the window)
• ensure that these are listed in the pane on the left:
  • smoketestoutput directory (contains the model output files)
  • RayleighTaylorBenchmark_1.2.0_smoketest.xml (the first input file uploaded)
  • stderr.txt (error file, red and bold to denote content - this is OK for this test)
  • stdout.txt (journal output file, bold to denote content - this is expected)
  • window_1.2.0_smoketest.xml (the second input file uploaded)
• double-click on the smoketestoutput directory to open it (you will now see its contents)
• click on the refresh button (more files should appear if the job is still running)
• ensure that you can scroll down to view the full list of output files, once the list extends beyond the pane's view
• double-click on window.00005.png (a preview should appear in a new pane on the right - you may like to expand the window to view the whole image; this file has downloaded to ~/.grisu/cache/ng2.vpac.org (StartUp)/grisu-jobs-dir/underworld_smoketest on your local drive)
• click on the "Preview" drop-down box and change to "Files" (the preview pane should change to a file transfer pane, and the "copy →" button should become active)
• in the file transfer pane on the right, select a suitable location on your local drive, and click on the "copy →" button (the already highlighted window.00005.png file should be transferred to the selected local directory)
• double-click on ".." in the left pane to go up one directory level
• right-click on the smoketestoutput directory and select "Download", select a suitable location on your local drive, and click on the "Save" button (the directory will be saved with its original name; this may take a little while) (Note for mac laptops: verify that you can do this using ctrl-click on the laptop, in addition to using an external mouse)

Job Details

[Monitoring > Job details > (new window) Job details panel]

• click on the "Job details" panel to view some basic details of the job submission
• close this window and return to the main Grisu client window

File Management

[File management panel]

• click on the "File management" panel
• in the pane on the left:
  • Site: VPAC
  • Share: ng2.vpac.org (!ACC)
  • navigate into grisu-jobs/underworld_smoketest/smoketestoutput
  • select window.mpeg
• in the pane on the right, select a suitable location on your local drive
• click on the "copy →" button (window.mpeg should be transferred to the selected local directory)

File Transfers

[File transfers panel]

• click on the "File transfers" panel to see a list of files you have downloaded (as opposed to those previewed and downloaded to your local cache)

Deleting the Job Directory

[Monitoring and File management panels]

• click on the "Monitoring" panel
• right-click on the Jobname "underworld_smoketest" and select "Kill & clean job(s)", and when prompted for confirmation click on the Yes" button (the job directory should disappear)
• click on the File management panel:
  • Site: VPAC
  • Share: ng2.vpac.org (!ACC)
  • navigate into grisu-jobs/
• verify that the "underworld_smoketest" job directory has indeed been deleted from your home directory

Job Notification

• verify that a job execution email advice was received at the nominated email address, resembling (the job name is truncated):

PBS Job Id: ******.tango-m.vpac.org
Job Name:   Grid_ng2_ketest
Exec host:  tango***/*+tango***/*
Begun execution

• verify that a job terminaton email advice was received at the nominated email address, resembling (the job name is truncated):

PBS Job Id: ******.tango-m.vpac.org
Job Name:   Grid_ng2_ketest
Exec host:  tango***/*+tango***/*
Execution terminated
Exit_status=0
resources_used.cput=00:03:37
resources_used.mem=92288kb
resources_used.vmem=1261184kb
resources_used.walltime=00:01:58