Part 1 - Using R on the Network

NEFSC has moved to a container setup. Open a ticket using the helpdesk and IT will setup a container.

1. Containers sometimes need to be restarted or updated. The files in the root directory will not persist, so save your results somewhere else
2. Persistent startup scripts can be handled on request. Put your .Rprofile into your root directory on NEFSCFILE. Ask to have it copied into the root of your container every time the container is re-started or reconfigured. Be mindful of the leading period in ``.Rprofile''.
3. You will have access to an Rstudio development environment. If you so desire, you can execute scripts or unix commands from the Terminal tab.

Part 2 - Other tips

Terminal (Command line) access

You have access to a unix terminal from inside Rstudio. Use the "Terminal" tab (next to console).

One of your processes is frozen?

1. Use top -u <yourid> to lookup the process id. Replace <yourid> with your network id.
2. Use kill -9 <pid> to kill the process number <pid>

This also might be useful if Rstudio hangs indefinitely on loading

How much memory is available?

To see the amount of memory available use "free -g"

Only look at the available column, in this case that's 115 gigabytes.

Play nicely with others

If there are alot of other things running on the server, you can do this:

nice R < "your script here.R" --no-save

or

nice Rscript my_fancy_rcode.R

There's a way to set the exact level of depriortiziation, but I've not gotten it right. Default is 0. Positive numbers make your script "more nice" (so lower priority). You can't set negative numbers as a regular user.

Moving files with SCP

You might want to move files around on the network. SCP from the command line might be nice, because you can automate it. The syntax is

scp /full/path/of/files/to/move server:/full/path/of/destination

this might useful to put something onto the ftp server or put it into someone else's network folder.

Use batch files to do jobs

For Rscripts that take along time to run, you should either run them from the command line with:

Rscript my_fancy_rcode.R

Or put them into a batch file and execute a batch file.

Stuff

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