bc_rcc_rstudio_server

RStudio Server app for Open OnDemand

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

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. You might still need PRoot or Singularity depending on your HPC environment, so your mileage may vary.

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-1.2.5042-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`.