This repository includes a definition file for a singularity container and instructions for starting up an instance on CENTOS in a HPC environment.

1. SSH to the server
2. Run the following to select the target folder and download the current version of this container:

# cd to user singularity directory
cd /panasas/scratch/grp-adamw/singularity/$USER;
# download the most recent version of the container
wget -O singularity-geospatial-r_latest.sif \
   https://github.com/AdamWilsonLab/singularity-geospatial-r/releases/download/0.0.1/AdamWilsonLab-singularity-geospatial-r.latest.sif

3. Create symlinks to singularity folder in project storage to prevent disk space problems in the home directory. You should only have to do this once.

cd ~
mkdir -p /projects/academic/adamw/singularity/$USER/.singularity
ln -s /projects/academic/adamw/singularity/$USER/.singularity .singularity

# Symlinks for RStudio
mkdir -p /projects/academic/adamw/rstudio/$USER/rstudio
mv .local/share/rstudio /projects/academic/adamw/rstudio/$USER/

mkdir -p ~/.local/share
ln -s /projects/academic/adamw/rstudio/$USER/rstudio ~/.local/share/rstudio

4. Run the singularity_start.sh script to start up a singularity instance. You can just copy paste the code into the terminal. This includes a few system specific settings for the Buffalo CCR. This should only need to be done once (as long as the instance keeps running, server is not restarted, etc.). If the instance stops for any reason, you'll need to rerun this script. You can confirm it's running with singularity instance list or by checking htop.

After running the steps above, you should be able to do just the following to begin working. If the server restarts you will need to re-run step 4 above.

1. Connect to the instance via SSH with port Forwarding. You will need to be on campus or connected via VPN. See notes below for *nix and windows.
2. Open RStudio at localhost:8787 in your local browser and login with user/password from #4 above.

This container builds upon the rocker geospatial container, which I ported to Singularity here. This repository/collection then adds additional packages in this file. That's the file to modify if you want to add more linux packages, etc.

Use terminal to ssh to the server as explained in singularity_start.sh. Add something like the following to your .ssh/config file to simplify connecting with port forwarding via ssh. You will then have to update HOST to the host address and PORT_NUMBER to the updated port number.

Host rserver
HostName HOST
LocalForward 8787 HOST:PORT_NUMBER
User $USER
ForwardX11 yes
ForwardAgent yes

On Windows you will need to use PuTTY or a similar terminal program.

1. In PuTTY, enter the server address (host name) and "22" (port) on the "Session" tab.
2. On the "SSH/Tunnels" tab, enter the port number of the rsession under “Source port” and type in HOST:PORT (replace with the actual server IP address + the port number) as the destination address. Then, click "Add".
3. Connect and login as usual in the terminal.
4. Point the web browser to http://localhost:PORT (where PORT is the port number)" and log in with the user name and the previously generated password.

1. Separate container from startup and monitor script
2. Switch to a docker image

I started with nickjer's very helpful example and updated it to pull from the geospatial version of the versioned rocker stack instead of the repository based R. This should make it easier to keep up to date.

This error can appear in the web browser when connecting via localhost. This can be caused by RStudio not being able to write session files in the right place. Confirm that:

1. The directory /projects/academic/adamw/rstudio/$USER/rstudio exists
2. and is linked to ~/.local/share/rstudio

The error "Could not acquire revocation list file lock" resolved with help from here

Starting in early 2021, something changed that resulted in the following error when starting a new instance:

ERROR database error 7 (sqlite3_statement_backend::loadOne: attempt to write a readonly database) [description: Could not delete expired revoked cookies from the database, description: Could not read revoked cookies from the database]; OCCURRED AT virtual rstudio::core::Error rstudio::core::database::Connection::execute(rstudio::core::database::Query&, bool*) src/cpp/core/Database.cpp:480; LOGGED FROM: int main(int, char* const*) src/cpp/server/ServerMain.cpp:729

I solved this by binding an address outside the container to /var/lib/rstudio-server when starting the instance as follows:

--bind $RSTUDIO_DB:/var/lib/rstudio-server

where $RSTUDIO_DB is just a path outside the container. I got this idea from this post.

docker run -d -p 8787:8787 -e PASSWORD=really_clever_password -v ~/Documents:~/Documents rocker/rstudio

A few links I found useful while developing this container

• https://divingintogeneticsandgenomics.rbind.io/post/run-rstudio-server-with-singularity-on-hpc/
• https://hub.docker.com/r/rocker/geospatial
• https://singularity-hub.org/collections/4930
• https://pawseysc.github.io/singularity-containers/23-web-rstudio/index.html
• https://www.rocker-project.org/use/singularity/
• grst/rstudio-server-conda#3