Adding R studio to OOD

[AMK13]

Seeking advise here. We have a cyclecloud cluster with OOD and Interactive Jupyter deployed. Now our aim is to get a R-Studio interactive OOD interactive app working on the cluster without interfering/impacting the current demo. Here is the links I found online

https://osc.github.io/ood-documentation/latest/how-tos/app-development.html

https://osc.github.io/ood-documentation/release-2.0/app-development/tutorials-interactive-apps/add-rstudio/copy-app.html

can you please advise what flow we need adapt to get OOD installed and working on OOD.

Kind Regards

[johrstrom]

I think the second link is about right - though since it's old it's likely a bit out of date. In any case, since you setup Jupyter, RStudio is going to be similar to it.

That said - you can always take a look at our production Rstudio app - https://github.com/OSC/bc_osc_rstudio_server. This is the Rstudio app we use in production at OSC.

[robertosussex]

Hi,

Before we add R I believe we need to make sure that OoD works fine.

1) We are currently use OoD to launch Jupyter app and although it works in principle, there are issues with Proxies.

2) When we try to connect to the jupyter session it gives:

What is the reason for the delay in the DNS resolution? Any settings we should check?

3) If I add IP FQDN to the /etc/hosts filr on the machine where OoD works it is able to connect to Jupyter

4) If I try to connect to the Terminal

We get:

Any reason for this?

Settings we can check?

[robertosussex]

any advice is appreciated Kind regards Roberto

[robertosussex]

Hi there,

With some help we were able to add Rstudio to OoD. The app appears in the list of the interactive apps:

We are using a singularity image that we are loading from the file script.sh.erb in /var/www/ood/apps/sys/rstudio/template

It is possible to submit a job. However, it terminates immediately meaning that something stops in using the singularity image

In trying to run the script directly on the login node we get:

Is it a matter of permissions/users IDs etc?

Please advice Roberto

[robertosussex]

While running as root .... gives

Many thanks Roberto

[robertosussex]

That is after loading the proper environment:

Please advice

Roberto

[robertosussex]

Regards Roberto

[robertosussex]

After adding the error disappeared ....however, the session still terminates ...immediately...

in

looking at output.log we get

no errors in

Any idea?

Many thanks Roberto

[robertosussex]

I tried submitting the job with Open on Demand invoking a session of Rstudio I got in the output log in my home directory

used script is:

====================================================

I suppose it is a network/authentication issue?

Any advice? Many thanks Roberto

[johrstrom]

You should look at our production application. One thing to note is that we reconfigure where the output logs should go. Inside the container, you're logging to /var/log

You can see from this configuration - we are logging to the staged_root instead of /var/lib. This log file will tell you what's going on/why it's crashing.

https://github.com/OSC/bc_osc_rstudio_server/blob/master/template/etc/logging.conf.erb

[robertosussex]

Now ...we are trying using a different repo and NOT the singularity container. We got the error after connecting to the "running" session.

depending on what we use for --auth-none

With --auth-none 1 we get a caching error

With --auth-none 0 we get a login session and we cannot get anywhere ... (csf errors and so on...)

..still investigating Roberto

[AMK13]

The repo we are using is

https://github.com/mcw-rcc/bc_rcc_rstudio_server

[robertosussex]

We are using Almalinux s our operating system. Would this create issues? Kind regards Roberto