Using Local Storage

The HPC cluster is a powerful tool which enables researchers to improve their efficiency. However, users of the HPC cluster cannot always use certain packages which they might otherwise be able to with Local Storage. 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. If you are using a Desktop PC in the DCCN, you can simply run your analysis on the local instance of RStudio (or whatever analysis platform you are using). However, if you are not in Trigon or do not have a hardwired connection, you can do so by following the exercises below.

Practice Using Local Storage

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 project directory

  • Double-click on the 3010000.05 directory

  • Double-click on the XXXXXXX.XX directory

  • Double-click on the results directory

  • Single-click on the RDM_Workshop_Analysis.RData file

  1. Download the RDM_Workshop_Analysis.RData file onto your DCCN or RU Managed device

  • 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.

Note

When a package is not available on the HPC Cluster or cannot be installed by the user, you can arrange this by contacting the DCCN TG.