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Ginsburg is currently running Red Hat Enterprise Linux release 8.2.

The table below shows software already installed on the cluster system-wide.

The list may be partial and not totally up-to-date at any given time.

Use the following command to verify whether unlisted software/packages can be found on Ginsburg otherwise:

$ module avail

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Ginsburg is currently running Red Hat Enterprise Linux release 8.2.

The table below shows software already installed on the cluster system-wide.

The list may be partial and not totally up-to-date at any given time.

Use the following command to verify whether unlisted software/packages can be found on Ginsburg otherwise:

$ module avail

...

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srun -X -A <GROUP> --pty -t 0-0102:00 -X /bin/bash

OR, if you want a GPU node

srun -X -A <GROUP> --pty -t 0-0102:00 -X --gres=gpu:1 /bin/bash

Load the Singularity module:

module load singularity

This next step will take a few minutes and will only NEXT, a number of steps need to be done the first time you launch this application. On subsequent sessions you skip this step as the container is downloaded:

singularity pull --name rstudio.simg docker://rocker/rstudio:4.3.1

In order for RStudio to start in a browser via an interactive session you will need the IP address of the compute node. Note that the IP below will likely be different for you:

IP_ADDR=`hostname -i`
echo $IP_ADDR
10.197.16.39

From RStudio 4.2 and later, some added security features require binding of a locally created database file to the database in the container. Don't forget to change the password.

mkdir -p run var-lib-rstudio-server

printf 'provider=sqlite\ndirectory=/var/lib/rstudio-server\n' > database.conf

PASSWORD='CHANGEME' singularity exec \
   --bind run:/run,var-lib-rstudio-server:/var/lib/rstudio-server,database.conf:/etc/rstudio/database.conf \
   rstudio.simg \
   /usr/lib/rstudio-server/bin/rserver --auth-none=0 --auth-pam-helper-path=pam-helper --server-user=$USER

This will run the Rstudio server in a Singularity container.

PART 2:  Port forwarding and access from your browser

Now open another Terminal and start the RStudio rserver session using Port Forwarding to connect a local port on your computer to a remote one on Ginsburg.

ssh -Nf -L 8787:10.197.16.39:8787 myUNI@burg.rcs.columbia.edu  

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NOTE FOR WINDOWS USERS:

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that have been collected into a simple script.

Type "RSserver.sh" (without the quotes) to execute the container setup script. For those interested, the script echos the commands it's running as it runs them.

PART 2:  Port forwarding and access from your browser

The Rstudio server is now running in a container in one window.  Now you will open another window and create a Port Forwarding connection so your web browser will be able to connect to a port on your local machine, that forwards the connection to the remote container.

If you're on a Mac or Linux machine, open a second Terminal and start the RStudio rserver port forwarding with the below command:

ssh -Nf -L 8787:10.197.16.39:8787 myUNI@burg.rcs.columbia.edu    <-- the "10.197.16.39" IP number is ONLY for demonstration. The above script will have given you the real IP you will be using.

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The above Port Forwarding line works on Linux/Unix/MacOS, or any virtual machine running Linux. For Windows, we are assuming you are using PuTTY and the above line would be accomplished using the alternative steps below:

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Next, use a web browser to connect to to your locally forwarded port.

In any web browser, e.g., Google Chrome, enter localhost:8787. The login screen for RStudio will appear and you enter your UNI (without the @columbia.edu) and whatever password you put from the above example (where it says CHANGME). If you need a session that last longer than an hour you can add --auth-timeout-minutes=0 --auth-stay-signed-in-days=30 to the end of the above singularity. command. A sample Slurm bash script is available at Rocker Project's Singularity page. If you run into an error such as [rserver] ERROR system error 98 (Address already in use), you can specify the port number as an additional option, e.g.,  --www-port 8788. The new command could look like this:

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Safari or Edge, enter localhost:8787 (or a different number after the colon, if you received an error above and had to choose another port).

The login screen for RStudio will appear and you enter your UNI (without the @columbia.edu) and whatever password you entered in the setup script.

A sample Slurm bash script is available at Rocker Project's Singularity page.

***IMPORTANT NOTE***

When you are finished with RStudio remember to stop the Singularity session via ctl-c, and you can kill the SSH forwarding session by finding the process ID (PID) with the following command, noting that the PID is the second column:

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Visual Studio Code is an Integrated Development Environment that some like to use on their laptops. If you are familiar with that, the HPC has a server-side version hosted on the compute nodes (NOT the login nodes) for users to connect their local VS Code application on their laptop to Ginsburg and open files from their Ginsburg folder directly.  To use it, do the following:

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