RStudio Server app for Open OnDemand
Based on https://github.com/OSC/bc_osc_rstudio_server.
This guide is a help to install the OOD RStudio Server app without requiring PRoot and/or Singularity. Prior to RStudio Server 1.3###, some hard-coded file paths caused a conflict when running multiple RStudio Server instances on the same server, as is the case when more than one OOD job launches to the same compute node. PRoot/Singularity fixed this issue by creating a unique TMP_DIR which was mounted into the container at /tmp. This fix successfully separated multiple instances running on the same server. To my knowledge, this was the primary benefit of using PRoot/Singularity.
Starting in RStudio Server 1.3###, the developers added environment variables to control the location of those hard-coded files. This means that (in our case at least) PRoot/Singularity is no longer required for the OOD RStudio Server App.
- Lmod or any environment module system
- R
- RStudio Server 1.4 or higher (any of the recent date based releases will work)
RStudio Server 1.4.XXXX and above enables RStudio OOD app to run without PRoot or Singularity. The developers added two flags for rserver that allow control of previously hard-coded file paths. However, you might still need PRoot or Singularity for some other reason depending on your HPC environment.
The simplest way is to install using the RPM (we run CentOS 7) installer provided by RStudio.
wget https://download2.rstudio.org/server/centos7/x86_64/rstudio-server-rhel-2022.02.2-485-x86_64.rpm
sudo yum install rstudio-server-rhel-2022.02.2-485-x86_64.rpm
However, many HPC sites like to control installation prefix. The provided RPM is not relocatable, but you can extract the files and move them manually.
mkdir ~/rstudio_files && cd ~/rstudio_files
wget https://download2.rstudio.org/server/centos7/x86_64/rstudio-server-rhel-2022.02.2-485-x86_64.rpm
rpm2cpio rstudio-server-rhel-2022.02.2-485-x86_64.rpm | cpio -idmv
This creates a directory ~/rstudio_files/usr/lib/rstudio-server that contains the files. Move these files to your shared filesystem.
# Our shared filesystem for apps is /hpc/apps. Modify to suit your needs.
cp -R ~/rstudio_files/usr/lib/rstudio-server/* /hpc/apps/rstudio-server/2022.02.2-485
Optionally add a modulefile to load env.
To install the app:
cd /var/www/ood/apps/sys
git clone https://github.com/mcw-rcc/bc_rcc_rstudio_server.git
cd bc_rcc_rstudio_server
Modify manifest.yml, form.yml, and submit.yml.erb for your site. The template/script.sh.erb should also be modified to suit your site. For instance, we use a modulefile to load RStudio Server, which is specific by site and should be supplied by your site.
rserver \
--www-port ${port} \
--auth-none 0 \
--auth-pam-helper-path "${RSTUDIO_AUTH}" \
--auth-encrypt-password 0 \
--rsession-path "${RSESSION_WRAPPER_FILE}" \
--server-data-dir "${TMPDIR}" \
--secure-cookie-key-file "${TMPDIR}/rstudio-server/secure-cookie-key"
--database-config-file "${DBCONF}"
--server-user $(whoami)
--server-data-dir "${TMPDIR}" redirects output of PIDs from /var/run/rstudio-rsession to ${TMPDIR}.
--secure-cookie-key-file "${TMPDIR}/rstudio-server/secure-cookie-key" redirects output of secure-cookie-key from /tmp/rstudio-server to $TMPDIR. Necessary to avoid conflict where multiple RStudio Server instances are running and generate same hard-coded file.
--database-config-file "${DBCONF}" sets the path for a new database config requirement in 1.4.1717.
Your $TMPDIR location needs to be unique for this to work. We use our queueing system to set a unique $TMPDIR per job. You can also use export TMPDIR="$(mktemp -d)" within template/script.sh.erb.