Test and known issues commissioning RStudio on OOD

[ChrisPWelsh]

Hi All,
RStudio server as a whole on out cluster has been a really valuable approach. We have some issues to resolve before we go live though.

A round of testing has just completed and I would like to seek help to resolve some issues users raised. I have numbered each issue and would welcome a responses with an example if poss. Thx.

Note: I have chosen to install and run from RPMs rather than run RStudio server and R in a container. (Rhel9.6

Issue:

1. The Rstudio server job submits and runs but after selecting the “Connect to RStudio Server” button the IDE starts and renders but a popup appears. This happens to all users. How can I prevent this from happening?

   

2. A user login’s in and get this error:
   Error – Warning: invalid configuration option “passenger_log_level”
   can’t find group for 40156
   Run ‘nginx_stage --help’ to see a full list of available command line options.

   My Comment: I don’t have “passenger_log_level” set at all - why is it complaining about an invalid config option? I suspect if I want to introduce an option I would add one to the “ood_portal.yml”?

   Can you please give me the exact option and where to put it to enable log level 3?

   [root@ood /etc/ood]# grep -R passenger_log_level *

   config/nginx_stage.yml:passenger_log_level: “0” # Or desired log level (e.g., 0 for errors, 3 for info, 7 for debug)

   3. Issue with ‘Projects’. When setting up a Project during one run, when I come back to it on another day the project is no longer writable. This is causing a lot of troubles with separating my different projects easily. I have set up new ones and the same occurs.
   

   4. After a period of inactivity, the tab the user was using may not let the user back in. To get back in, the user needs to go back to the “my interactive jobs” tab and press the “connect to Rstudio Server” button.

   5. Upon reconnecting, user’s are often presented with an error saying the session died unexpectedly.

   6. A redirect might be helpful when signing in to a session that is dead. How can I do this?

   7. I load a module “4.4.1-wz5qfuk.lua” that sets: :" “setenv(“R_LIBS_USER”, “~/R/mk4-library/%v”)”

   But in the “/var/www/ood/apps/sys/bc_rcc_rstudio_server/template/script.sh.erb”
   file, the following”
   exec rsession --r-libs-user ‘${R_LIBS_USER}’ “\${@}”

   results in creating a directory: “/home/chris/R/mk4-library”
   ”drwxr-xr-x. 2 chris chris.dg 4096 Oct 17 09:55 **%v”
   **
   in actual fact it should be “4.4” or representing the version of “r” I loaded as a module when submitting the form. How can I fix this?

[jeff.ohrstrom]

1. That is expected because the job (your scheduler) stops Rstudio and all other processes’ when the job completes. I think if you exit from Rstudio in the interface it wouldn’t happen, but most folks just let the job run to completion which will kill everything

@ChrisPWelsh

can’t find group for 40156

Not sure why it’s talking about log level here - but this is the actual error - some issue with this GID 40156 from your LDAP.

3. I have no idea, that seems to be an Rstudio issue. Rstudio keeps data in ~/.rstudio so you could fix something there or through the UI. In any case, I’m not really sure, but an rstudio forum may have the answer.
4. This is expected, but maybe you can set session-timeout-minutes=0 so that it’s allowed to never timeout?
   bc_osc_rstudio_server/template/etc/rsession.conf.erb at master · OSC/bc_osc_rstudio_server · GitHub
5. Same as number 1?
6. I’m not entirely sure, but I pulled this from our module file that appears to work for us:

append_path("R_LIBS_USER", pathJoin(os.getenv("HOME"), "R/rhel9", version))

For me that resolves to ~/R/rhel9/4.4.0. IIRC there’s some issue with %v, but in any case if you have the version variable in the lua file then maybe you should just use it.

[ChrisPWelsh]

Thx for the swift reply Jeff.

1. I will ask the users to test this case. I believe it hapens even when they hit the logout button. TBC

2. Yep, there is an LDAP error. But wondered:
   a). If there is somewhere I could turn the passenger error logging on to mode 3 in the ood_portal.yml file?
   b). Is there a way to send users to a nice error page for errors?

3. Thx

4. Thx I will try.

5. Thx

6. Thx. Will let you know.

[jeff.ohrstrom]

@ChrisPWelsh

Yep, there is an LDAP error. But wondered:
a). If there is somewhere I could turn the passenger error logging on to mode 3 in the ood_portal.yml file?
b). Is there a way to send users to a nice error page for errors?

a) I think you can use passenger_options to set passenger_log_level.

nginx_stage.yml — Open OnDemand 4.0.0 documentation

Configuration reference - Nginx - Passenger Library

b) Unfortunately, no I don’t think so.