Exercise 10: Downloading Workspaces with Cyberduck

The HPC cluster is a powerful tool which enables researchers to improve their efficiency. However, users of the HPC clusters cannot always use certain packages which they might otherwise be able to on their Local PCs since the TG determines the version of programs (R in this instance). On the HPC cluster, the installed version of R is not compatible with the effects package. We have created an lme object called fit which we want to plot the effects of using the effect function in the effects package to visualize the interaction between trial number and condition on reaction time. We’ve saved our workspace to RDM_Workshop_Analysis.RData and now we can download this from the HPC cluster and plot the fit object.

  1. Connect to Trigon via eduVPN or a hardwired connnection
  2. Connect to an Access Node
  • Open Cyberduck
  • Click Open Connection at the top left of the window
  • Click on the dropdown menu (which defaults to File Transfer Protocol (FTP)) and select SSH File Transfer Protocol (SFTP)
  • At the Server: field type in mentat001.dccn.nl
  • Enter your DCCN username (firlas@dccn.nl) and password and then click Connect at the bottom right side of the window
  1. Locate the RDM_Workshop_Analysis.RData file
  • Double-click on the results directory
  • Double-click on the firlas directory where firlas is your DCCN username
  • Single-click on the RDM_Workshop_Analysis.RData file
  1. Download the RDM_Workshop_Analysis.RData file
  • Click Action then Download To in the dropdown menu
  • Single-click the folder you want to download the RDM_Workshop_Analysis.RData file to
  • Push OK
  1. Disconnect

Now, if you want, you can open R on your Local PC, open the local_analysis.R file and open the RDM_Workshop_Analysis.RData workspace. Then, run the script. You should see a plot as an output.