4. Customize Attributes¶

Now we will customize the app to work on a given cluster. Be sure that you walk through Software Requirements for the given cluster ahead of time.

The main responsibility of the form.yml file (User Form) located in the root of the app is for defining the attributes (their values or HTML form elements) used when generating the batch script.

  1. We will begin by adding a cluster for the RStudio app to use. You do this by editing the form.yml in your favorite editor as such:

# ~/ondemand/dev/bc_example_rstudio/form.yml
---
cluster: "my_cluster"
form:
  - bc_account
  - bc_queue
  - bc_num_hours
  - bc_num_slots
  - bc_email_on_started

where we replace my_cluster with a valid cluster that corresponds to a cluster configuration file located under /etc/ood/config/clusters.d/my_cluster.yml.

  1. Next we will modify the runtime environment to allow RStudio to launch inside a Singularity container. There are two ways to accomplish this, and both modify the file ~/ondemand/dev/bc_example_rstudio/template/script.sh.erb.

If you are not using LMod, then in the function setup_env replace the value for RSTUDIO_SERVER_IMAGE with the absolute path to the Singularity image, and SINGULARITY_BINDPATH with all the directories that contain dependencies for RStudio server and R. Discovering those paths may benefit from using ptrace or lsof. Finally ensure that R and rserver are in the PATH.

If you are using LMod then create a module like the following:

-- $path/to/lmodfiles/rstudio_container/v0.0.1.lua
help([[ rstudio - loads rstudio with singularity environment for ondemand apps ]])
whatis("loads rstudio with singularity environment for ondemand")
setenv("RSTUDIO_SERVER_IMAGE","/usr/local/project/ondemand/singularity/rstudio/rstudio_launcher_centos7.simg")
setenv("SINGULARITY_BINDPATH","/etc,/media,/mnt,/opt,/srv,/usr,/var")
append_path("PATH", "/usr/lib/rstudio-server/bin)

Then replace the exports in the function setup_env with the appropriate module use $module_path and module load rstudio_container/v0.0.1.

setup_env () {
  # Additional environment which could be moved into a module
  # Change these to suit
  # export RSTUDIO_SERVER_IMAGE="/apps/rserver-launcher-centos7.simg"
  # The most robust SINGULARITY_BINDPATH appears to be: /etc,/media,/mnt,/opt,/srv,/usr,/var.
  # That, plus Singularity's standard auto-mounts, covers most of the Filesystem Hierarchy Standard.
  #
  # Notable exceptions include:
  #
  #     - /tmp which we are explicitly overriding
  #     - those directories which in Centos 7 are commonly symlinks to/usr
  #     - root's home directory
  #
  # export SINGULARITY_BINDPATH="/etc,/media,/mnt,/opt,/srv,/usr,/var"
  # export PATH="$PATH:/usr/lib/rstudio-server/bin"
  # export SINGULARITYENV_PATH="$PATH"
  module use "$path/to/lmodfiles"
  module load rstudio_container/v0.0.1
}
setup_env

Note

It is possible to set the environment without using a module system, by setting the variables in ~/ondemand/dev/bc_example_rstudio/template/script.sh.erb.

Warning

There was a breaking change between Singularity 2.x and 3.x with how a host PATH may be propagated to the guest. In version 2.x you must export PATH as SINGULARITYENV_PATH in order for the PATH inside the container to include rserver. In version 3.x PATH alone is sufficient.

Warning

There was a breaking change between Singularity 3.4.x and 3.5.x with how a host LD_LIBRARY_PATH is propagated to the guest. In version 3.5.x you must export LD_LIBRARY_PATH as SINGULARITYENV_LD_LIBRARY_PATH.