bc_rcc_rstudio_server

RStudio Server app for Open OnDemand

Based on https://github.com/OSC/bc_osc_rstudio_server.

Description

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.

Setup without PRoot/Singularity

RStudio Server 1.3.959 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.

Install RStudio Server 1.3.959 CentOS 6/7

The simplest way is to install using the RPM installer provided by RStudio.

wget https://download2.rstudio.org/server/centos6/x86_64/rstudio-server-rhel-1.3.959-x86_64.rpm
sudo yum install rstudio-server-rhel-1.3.959-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/centos6/x86_64/rstudio-server-rhel-1.3.959-x86_64.rpm
rpm2cpio rstudio-1.3.959-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.

# we use BCM so our shared filesystem for apps is /cm/shared/apps. Modify to suit your needs.
cp -R ~/rstudio_files/usr/lib/rstudio-server/* /cm/shared/apps/rstudio-server/1.3.959

Optionally add a modulefile to load env.

RStudio Server OOD App

To install the app:

cd /var/www/ood/apps/sys 
git clone https://github.com/mcw-rcc/bc_rcc_rstudio_server.git

Modify manifest.yml, form.yml, and submit.yml 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. The rserver command in template/script.sh.erb contains two new flags that allow 1.3.959 to function in a multi-user environment without PRoot or Singularity.

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"

--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.

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)"withintemplate/script.sh.erb`.