drylab:knitting_large_rmarkdowns_with_ciscovpn
When users work connected to the CiscoVPN it is often the case the connection abruptly ceases after a few hours. This can be rather inconvenient for instance for knitting large scripts that exceed this time.
An alternative approach to circumvent the issue would be as follows:
- Access Piggeldy or Frederick.
- Run htop and assess if the server is being intensely used before running.
- Open a screen with screen -S screen_name.
- Deactivate your conda base environment and open your conda working environment.
- Open an R terminal.
- Load library knitr.
- Knit your script with the command knit(“path_to_file.Rmd”).
- Detach from the screen pressing cntrl+a + d.
- You can check if the screen still exists with screen -list.
- You can access the screen anytime with screen -r screen_id. It will run on the background without needing the user to be connected to the server.
- Once the knitting is completed a file called path_to_file.md is created.
- Open it inside Rstudio and click Preview to quickly generate the html object.
- Remember to kill your screen. To do so detach as explained above and then run screen -S screen_name -X quit.
/opt/bitnami/dokuwiki/data/pages/drylab/knitting_large_rmarkdowns_with_ciscovpn.txt · Last modified: 2024/09/03 08:47 by dsoto