R is available on C4 via a contributed
environment module. It can be run interactively in the terminal via R
on a development node, as explain on the how-to ‘Work with R’ page.
To run R via the RStudio IDE, there are three options:
The RStudio Server in the web browser via OnDemand
(temporarily retired as of 2022-12-28)
The RStudio Server in the web browser over SSH (recommended)
The RStudio Desktop over X11 Forwarding
Running desktop applications over X11 forwarding works, but depending on your network connection, you will experience more or less lag. For instance, you might see a small delay between a key is pressed and it is echoed at the R prompt. Similarly, plotted graphics might take some time to render. This is also true for the RStudio Desktop. Because of this, we recommend running a personal RStudio Server instance, either via OnDemand or over SSH, because that is designed to run remotely.
Regardless which one you use, you will be running the same version of R as you would when running from the terminal and all your installed packages will be available in either.
Please see the OnDemand page on how to access OnDemand.
You can run a personal RStudio Server instance, which you, and only you, can access via your local web browser. Contrary to RStudio Desktop, this approach does not require X11 forwarding. Instead, it does require running two separate SSH connections to the cluster: (i) one to launch RStudio Server, and (ii) one to connect to it.
Assuming you are already logged on to a development node, launch your personal RStudio Server instance as:
[alice@c4-dev1 ~]$ module load CBI rstudio-server-controller
[alice@c4-dev1 ~]$ rsc start
alice, your personal RStudio Server 2023.03.0+386 running R 4.2.2 is available on:
<http://127.0.0.1:20612>
Importantly, if you are running from a remote machine without direct access
to c4-dev1, you need to set up SSH port forwarding first, which you can do by
running:
ssh -L 20612:c4-dev1:20612 alice@c4-log1.ucsf.edu
in a second terminal from you local computer.
Any R session started times out after being idle for 120 minutes.
WARNING: You now have 10 minutes, until 2023-03-31 11:04:13-07:00, to
connect and log in to the RStudio Server before everything times out.
There is one things you should pay extra attention to here:
You will need it below.
On your local computer, log into the cluster in a second terminal
following the instruction above. Make sure to use your own username
and make sure to use the port number (e.g. 20612) that was assigned
to you.
{local}$ ssh -L 20612:c4-dev1:20612 alice@c4-log1.ucsf.edu
alice1@c4-log1.ucsf.edu:s password: XXXXXXXXXXXXXXXXXXX
[alice@c4-log1 ~]$
If you successfully completed the above two steps, and you made sure to use the correct port, then you should be able to open your personal RStudio Server in your local web browser by going to:
You will be presented with a ‘Sign in to RStudio’ web page. Use your C4 credentials to log in.
After clicking ‘Sign In’, you should be redirected to the RStudio interface.
To terminate the RStudio Server, start by exiting R by typing quit()
at the R prompt. Then press Ctrl-C in the terminal where
you called rsc start. Alternatively, run rsc stop in another
terminal, e.g. the second one used in Step 2.
Some users report that they stuck when they try to log in to RStudio.
After they enter their username and password, and click ‘Sign In’,
they get to a page “R is taking longer to start than usual” with a
spinner that never ends. The user is presented with three options
‘Reload’, ‘Safe Mode’, and ‘Terminate R’. Ideally, ‘Safe Mode’ or
‘Terminate R’ would solve the problem and let the user access the
RStudio GUI. Unfortunately, for some users, none of these options
help. Consecutive attempts to use rsc stop and rsc start fail for
same reasons.
As of 2023-12-04, it is not clear why and when this happens. The one workaround we have found is to wipe the user’s RStudio set up. For this, we recommend the to use:
$ tar -cvf ~/rstudio-config.tar ~/.local/share/rstudio && rm -rf ~/.local/share/rstudio
This will create a local copy of your problematic RStudio set up in
file ~/rstudio-config.tar, and, only then, remove the actually
settings. The next time you call rsc start, you should start out
with a fresh RStudio set up, and the login issue should be gone.
It is not possible to run RStudio Desktop via X2Go, because X2Go does not support the modern graphical protocols that RStudio Desktop requires.
To run the RStudio Desktop client, you must be logged via SSH with
X11 forwarding enabled. Then load the rstudio (Desktop) module from
the CBI stack and launch rstudio:
[alice@c4-dev1 ~]$ module load CBI rstudio
[alice@c4-dev1 ~]$ rstudio
TTY detected. Printing informational message about logging configuration.
Logging configuration loaded from '/etc/rstudio/logging.conf'. Logging to
'/c4/home/alice/.local/share/rstudio/log/rdesktop.log'.
You should see the RStudio Desktop interface appear after a few seconds. If you get a blank window, which some macOS users have reported, retry with:
[alice@c4-dev1 ~]$ QMLSCENE_DEVICE=softwarecontext rstudio
To exit the RStudio Desktop, type quit() at the R prompt, or press
Ctrl-C in the above terminal.