savio-singularity-rstudio

Materials for using (and creating) Singularity container for running RStudio server on Savio.

NOTE: While this should still work, using RStudio via this approach on Savio should be unnecessary as of spring 2021. We now have Open OnDemand in place on Savio, providing a browser-based front-end to Savio on which you can run RStudio. Please go here and select RStudio Server on the Interactive Apps menu.

Overview

This repository provides the materials needed to create a Singularity container that provides an RStudio server session to run on a compute node (or on the viz node) and for the Savio user to connect to that RStudio session from the viz node. It builds on the Rocker Dockerfile for RStudio/RStudio server, modified such that the RStudio server can start when not running as root.

To use the container on Savio

Using RStudio without authentication

These steps are for when you want to have RStudio running on a compute node and viewed via the viz node:

1. Start RStudio server on a compute node via srun or sbatch as follows. If you're using srun, start your interactive session via srun and then invoke the Singularity command below. If you're using sbatch, invoke Singularity command below within your submission script.

   singularity run /global/home/groups/consultsw/sl-7.x86_64/modules/rstudio-server-singularity/0.3/rstudio-server-0.3.simg

2. Note the name of the Savio node, e.g., n0070.savio2 on which the job started.

3. Login to the Savio visualization node, start a vncserver session, and connect to a VNC Viewer window (i.e., a remote desktop session) following these instructions.

4. From a terminal in the remote desktop session (also fine to do in a terminal started via ssh), run: From a terminal in the remote desktop session run the following (changing n0070.savio2 as needed to the node from step 2):

   • firefox http://n0070.savio2:8787

5. When you are done with RStudio, make sure to kill your srun or sbatch session so you are not charged for time you don't need.

6. End your VNCserver session with:

   • vncserver -kill :<port number>

To run RStudio directly on the viz node, do this:

1. Login to the Savio visualization node, start a vncserver session, and connect to a VNC Viewer window (i.e., a remote desktop session) following these instructions.

2. From a terminal in the remote desktop session (also fine to do in a terminal started via ssh), run the following:

   singularity run /global/home/groups/consultsw/sl-7.x86_64/modules/rstudio-server-singularity/0.3/rstudio-server-0.3.simg

3. From a terminal in the remote desktop session, run:

   • `firefox http://127.0.0.1:8787

4. End your VNCserver session with:

   • vncserver -kill :<port number>

Note that it's possible another user could connect to your RStudio session if you don't use authentication.

Using RStudio with authentication

These instructions are for running RStudio on a compute node. If you want to run directly on the viz node, modify the steps below per the instructions in the previous section.

1. Start RStudio server on a compute node via srun or sbatch as follows. If you're using srun, start your interactive session via srun and then invoke the Singularity command below. If you're using sbatch, invoke Singularity command below within your submission script. You can set the password (here 'foo') to whatever you desire.

   PASSWORD=foo singularity run /global/home/groups/consultsw/sl-7.x86_64/modules/rstudio-server-singularity/0.3/rstudio-server-0.3.simg --auth-pam-helper-path /usr/lib/rstudio-server/bin/pam-helper --auth-none 0

2. Note the name of the Savio node, e.g., n0070.savio2 on which the job started.

3. Login to the Savio visualization node, start a vncserver session, and connect to a VNC Viewer window (i.e., a remote desktop session) following these instructions.

4. From a terminal in the remote desktop session run the following (changing n0070.savio2 as needed to the node from step 2):

   • firefox http://n0070.savio2:8787

5. Authenticate with RStudio using your username (your Savio username) and the password you entered in step 1.

6. When you are done with RStudio, make sure to kill your srun or sbatch session so you are not charged for time you don't need.

Adding R packages to your container

While one could add additional R packages to the container itself, the easiest thing to do as a user is to install additional packages outside the container, which is easy to do because Singularity automatically gives you access to files on the host system.

One possibility is to simply use install.packages inside the container. That will likely install into the R subdirectory of your home directory on the host system (if ~/R/x86_64-pc-linux-gnu-library/3.6 exists, where 3.6 in this case is the version of R being used). This might be fine but runs the risk of conflicting with R packages that you've installed for use on the host system.

Here's an alternative that isolates the additional packages in a directory. In this example, we install the assertthat and testthat packages:

export SING_R_DIR=~/singularity_R
mkdir ${SING_R_DIR}
SINGULARITYENV_R_LIBS_USER=${SING_R_DIR} singularity exec  \
   rstudio-server-0.3.simg Rscript -e "install.packages(c('assertthat', 'testthat'))"

Now when you want to run R inside the container, make sure to set SINGULARITYENV_R_LIBS_USER (which sets R_LIBS_USER inside the container, such that R knows where to find the packages you've just installed), for example:

SINGULARITYENV_R_LIBS_USER=${SING_R_DIR} singularity run rstudio-server-0.3.simg

Using R without RStudio

You can also use R without using the RStudio interface. For interactive use, after invoking srun, you just tell the Singularity container to run R, like this:

singularity exec rstudio-server-0.3.simg R

Similarly for a batch job via sbatch, you tell the Singularity container to run R CMD BATCH:

singularity exec rstudio-server-0.3.simg R CMD BATCH --no-save file.R file.Rout

To build the container

You'll need access to a machine where you have administrative privileges (i.e., 'root' access).

sudo singularity build /tmp/rstudio-server-0.3.simg rstudio-server-0.3.def

Alternatively (i.e., without any special privileges), if you're using a newer version of Singularity, you may be able to build the container via Sylabs Cloud Remote Builder, like this:

singularity build --remote rstudio-server-0.3.simg rstudio-server-0.3.def

You'll need to create an account with Sylabs Cloud. More details are here.

Notes:

• Unlike the Rocker definition on which this is based, don't use /init in your container definition as that causes RStudio server to try to write to /var/run, which would only be possible with a writable image in which permissions on /var are modified; use rserver instead as the command to start RStudio server.
• Make sure you have pam-helper.sh copied into container (the Dockerfile does this as long as pam-helper.sh is in the build directory. That allows authentication to work by overriding usual pam authentication, which won't work on Savio: see nickjer/singularity-rstudio#1.
• Note that @paciorek can't figure out how to run the container as a service (using singularity instance.start). If I try to use rserver to start RStudio server inside the container, the user sees a login page, and I'm not sure why it is asking for authentication. If I try to run with rserver --auth-pam-helper-path /usr/lib/rstudio-server/bin/pam-helper --auth-none 0, I don't know how to pass PASSWORD into instance.start.