To know R is to love R. RStudio Server is a popular IDE tool that makes the R experience even better. And OpenShift makes it even easier again. R is for Riki. This lab is another in the OpenShift MiniLabs series.
Let’s demonstrate hosting an RStudio Server instance as a container managed by OpenShift. Moreover, the guest account home directory is mapped to an external volume such that any installed packages are preserved on container restart.
To reset your environment to repeat this tutorial do the following:
$ cd ~/containersascode $ ./oc-cluster-wrapper/oc-cluster up containersascode $ oc login -u system:admin $ oc delete persistentvolumeclaim rstudioguestclaim $ oc delete persistentvolume rstudiovolume $ oc login -u developer -p developer $ oc delete project rstudio
This demonstration begins by creating a persistent volume that can be later claimed by a container instance. This step is something typically done by an Administrator.
Create the Persistent Volume
Replace $VOLUMEPATH below with your preferred host-path location, e.g. /Users/johndoe/oc/volumes
$ oc login -u system:admin $ oc get pv $ oc create -f - << EOF! apiVersion: v1 kind: PersistentVolume metadata: name: rstudiovolume spec: capacity: storage: 2Gi accessModes: - ReadWriteOnce - ReadWriteMany persistentVolumeReclaimPolicy: Recycle hostPath: path: $VOLUMEPATH EOF! $ oc get pv
Let’s create a project for our new application. The RStudio Server container needs some extra privileges so will assign that as follows:
$ oc login -u developer -p developer $ oc new-project rstudio --display-name='RStudio Server' --description='RStudio Server' $ oc login -u system:admin $ oc adm policy add-scc-to-user anyuid -z default
Create Application from Dockerfile
You can create an OpenShift container straight from a Docker file. Do the following for the pre-supplied Docker file that will build an RStudio Server instance on Centos:
$ oc login -u developer -p developer $ wget https://raw.githubusercontent.com/StefanoPicozzi/MLOps/master/rstudio/Dockerfile $ oc new-app . -l name='server' --name='server' $ oc deploy server --cancel $ oc expose service server
Claim the Storage
$ oc login -u developer -p developer $ oc project rstudio $ oc set volume dc/server --add \ --overwrite \ --name=work \ --type=persistentVolumeClaim \ --mount-path=/home/guest \ --claim-size=2Gi \ --claim-name=rstudioguestclaim \ --containers=server
Build the Image
Make sure you are in the same directory as the Dockerfile. The first build attempt will take some time. You can observe progress from the Console at https://127.0.0.1:8443/console/project/rstudio/browse/builds/server/server-2?tab=logs
$ oc login -u developer -p developer $ oc project rstudio $ oc start-build server --from-dir=. $ oc status -v
Verify Lab Success
Once deployed, visit your new RStudio Server instance at http://server-rstudio.127.0.0.1.nip.io/ using credentials guest/guest. Try and few R commands but more interestingly install a new package, e.g. plyr.
Now restart the container by scaling the pod down and up again at: https://127.0.0.1:8443/console/project/rstudio/overview . Then revisit the RStudio Console and verify the previously installed package remains by issuing the command
installed.packages() inside the RStudio console.
Some users on Chrome may encounter an “R Session Disconnected” problem after login to http://server-rstudio.127.0.0.1.nip.io/. The cause of this error is undetermined but a workaround is to just use an alternate browser such as Firefox instead.
Check sites such as https://www.rstudio.com/products/rstudio/ and https://support.rstudio.com/hc/en-us for more on RStudio Server. Managing R libraries in RStudio server is described at https://support.rstudio.com/hc/en-us/articles/215733837-Managing-libraries-for-RStudio-Server