Batch Connect - OSC RStudio Server

An interactive app designed for OSC OnDemand that launches an RStudio Server within an Owens batch job.

Modifications made for CHPC's notchpeak-shared partition.

As of Mar20 we are using Docker containers from rocker and bioconductor:

• base R image, based on https://hub.docker.com/r/rocker/rstudio
• geospatial R image, based on https://hub.docker.com/r/rocker/geospatial - this has installed gdal and rgdal, among other things.
• bioinfomatics R image, based on https://hub.docker.com/r/bioconductor/bioconductor_docker - this has installed most if not all bioconductor system dependencies, like hdf5, udunits, gdal, ... Therefore user based R library installations should work as these system based dependencies are present.

We build the container images and store them locally as e.g. singularity build ood-rstudio-rocker_3.6.2.sif docker://rocker/rstudio. In the environment modules, we define paths to these containers, and also environment variables that set things like the user R libraries and environment file location, and the OOD's helper variables used in template/script.sh.erb.

Stuff below is deprecated now - the rocker and bioconductor based Docker images work without need to hand modify the container

As of Nov19 using Virginia Tech's R containers, as compared to previously used OSC's. The main reason for this is that VT includes some commonly used R packages in the container so users don't have to install them, and, they have different containers for different needs (Bioinformatics, Geospatial).

The containers are at: https://hub.docker.com/u/rsettlag
VT's OOD apps are at: https://github.com/rsettlage/ondemand2

Due to a few hard coded pieces we hand edit the containers as follows:

$ singularity build --sandbox ood-rstudio-bio_3.6.1 docker://rsettlag/ood-rstudio-bio:3.6.1  
sudo singularity shell --writable ood-rstudio-bio_3.6.1  
apt-get update && apt-get install apt-file -y && apt-file update && apt-get install vim -y  
vi /usr/local/lib/R/etc/Rprofile.site  

• remove:

 Sys.setenv(http_proxy="http://uaserve.cc.vt.edu:8080")  
 Sys.setenv(https_proxy="http://uaserve.cc.vt.edu:8080")  
 Sys.setenv(R_ENVIRON_USER="~/.Renviron.OOD")  
 Sys.setenv(R_LIBS_USER="~/R/OOD/3.6.1")  

$ sudo singularity build ood-rstudio-bio_3.6.1.sif ood-rstudio-bio_3.6.1/  

Prerequisites

This Batch Connect app requires the following software be installed on the compute nodes that the batch job is intended to run on (NOT the OnDemand node):

• Lmod 6.0.1+ or any other module restore and module load <modules> based CLI used to load appropriate environments within the batch job before launching the RStudio Server.

without Singularity

• R 3.3.2+ (earlier versions are untested but may work for you)
• RStudio Server 1.0.136+ (earlier versions are untested by may work for you)
• PRoot 5.1.0+ (used to setup fake bind mount)

or with Singularity

• Singularity 2.4.2+
• A Singularity image similar to nickjer/singularity-rstudio
• Corresponding module to launch the above Singularity image (see example_module)

Install

Use git to clone this app and checkout the desired branch/version you want to use:

scl enable git19 -- git clone <repo>
cd <dir>
scl enable git19 -- git checkout <tag/branch>

You will not need to do anything beyond this as all necessary assets are installed. You will also not need to restart this app as it isn't a Passenger app.

To update the app you would:

cd <dir>
scl enable git19 -- git fetch
scl enable git19 -- git checkout <tag/branch>

Again, you do not need to restart the app as it isn't a Passenger app.

Contributing

1. Fork it ( https://github.com/OSC/bc_osc_rstudio_server/fork )
2. Create your feature branch (git checkout -b my-new-feature)
3. Commit your changes (git commit -am 'Add some feature')
4. Push to the branch (git push origin my-new-feature)
5. Create a new Pull Request