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Helpful command line tools

Navigating the filesystem

• less FILENAME: Show the contents of a text file
  • Scroll up and down in file with arrow keys or page-up, page-down
  • Exit by pressing q
• ls DIRECTORY: List the contents of a directory
• cd DIRECTORY: Change into directory DIRECTORY
  • Note: Typing cd with no directory name given will change to your home directory
• cp FILENAME DESTINATION: Copy a file from FILENAME to DESTINATION
  • Note: To copy a directory you must include the -r flag. For example, cp -r DIRECTORY DESTINATION

Running DOUAR jobs

Editing and running a new job

To run a new simulation with DOUAR you should do the following:

cd
cd douar/inputs
cp OLDMODEL.txt NEWMODEL.txt
nano NEWMODEL.txt

(edit parameters)

~/bin/submitdouar.sh -i ~/douar/inputs/NEWMODEL.txt -n 32

Monitoring job status/cancelling a job

• squeue: Show a list of models running on the geo-hpcc cluster
• scancel JOB_ID: Cancel a job running on the cluster

Postprocessing job output

To create the VTK files for visualization in ParaView, you can do the following:

cd /globalscratch/introgm[N]/douar/NEWMODEL_yymmddhhmmss/OUT
~/bin/process_outbin.sh -n NUM

(tranfer .vtk files using WinSCP or scp)

(Visualize data in ParaView)

where [N] in introgm[N] should be replaced with your user number and NUM is the frequency of VTK output to produce. For example, ~/bin/process_outbin.sh -n 5 would produce output for every 5th DOUAR time step.