"connection refused" on mox for R Studio server

[yaaminiv]

I'm following @kubu4's instructions to access the R Studio server on mox in this discussion. I am trying to tunnel into mox with the following command:

ssh -N -L 8787:n2221:33264 yaaminiv@mox.hyak.uw.edu

I'm able to log into mox, but I get the following "connection refused" error:

Subsequently I cannot access http://localhost:8787/. Is there a reason why the connection is refused?

[kubu4]

When I check the Mox queue, your script isn't currently running. That'd be my guess.

[kubu4]

Can you describe what you did to get these error messages? I just did some testing (where I ran the Sys.sleep(), followed by a print statement).

1. Closed the browser.

2. Killed the SSH tunnel.

3. After the set time in the Sys.sleep() command (120 seconds), I re-established the SSH connection and re-opened the browser.

The job completed without errors.

[kubu4]

Doing some poking around, is it possible your home directory quota is used up? This is my suspicion. It looks like RStudio Server is set up to save the Global Environment info in ~/.rstudio. If you're methylkit commands are generating large objects (which I would expect), I'm guessing that these are trying to get saved in ~/.rstudio which is using up all of your quota in your home directory.

The above is based on this article:

https://support.rstudio.com/hc/en-us/articles/218417097-Filling-up-the-home-directory-with-RStudio-Server

I'll see if I can update the container to get around this issue.

[kubu4]

Also, if space usage on your login node is the issue, it could be related to your ~/.Rdata file. Did you elect to save this file (if/when prompted by RStudio)? If yes, this, too, could end up being a very large file, depending on what you're doing/running.

[kubu4]

Also, as it turns out, the srlab is over our Mox quota! This could also be causing issues... Will try to free up some space.

[yaaminiv]

Can you describe what you did to get these error messages? I just did some testing (where I ran the Sys.sleep(), followed by a print statement).

All I did was close my browser window with R Studio server! That ended up killing my SSH tunnel (totally forgot to take a screenshot). When I logged in again, I saw that error message in R Studio. Maybe I did not follow the correct protocol for closing a session to still have it run?

[yaaminiv]

Doing some poking around, is it possible your home directory quota is used up? This is my suspicion.

I don't know if my home directory quota is used up! How do I check?

Also, I set my working directory to be /gscratch/scrubbed/yaaminiv/Manchester/analyses/methylKit when I started my R Studio session. Do I need to set up R Studio server to save ~/.rstudio in that folder instead?

Also, if space usage on your login node is the issue, it could be related to your ~/.Rdata file. Did you elect to save this file (if/when prompted by RStudio)?

I have not elected to save my ~/.Rdata, and manually write out my data to /gscratch/scrubbed/yaaminiv/Manchester/analyses/methylKit/methylKit.Rdata instead!

[yaaminiv]

Last night I set up R Studio server to run on genefish since closing my browser window killed my R Studio session. I just logged onto genefish to check my R Studio server session. I found that I had been automatically logged out due to 60 min of inactivity! When I logged back in, I saw the several error messages:

1. There were 50 or more warnings (use warnings() to see the first 50): Checked warnings(), they're glm.fit errors (not related to the issue at hand)

2. Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'head': object 'differentialMethylationStatsTreatment' not found: My fault, didn't reference the correct data frame

3. Same error writing to connection I posted above! However, it seems like my calculateDiffMeth command finished running, and my global environment was loaded again when I logged back into the R Studio server? So now I'm just not sure what these errors mean...

[kubu4]

Check quota:

mmlsquota --block-size G gscratch:home

Also, from a build node, please run the following commands and copy/paste results:

cd
du -hs .[^.]*

[yaaminiv]

Check quota

[yaaminiv]

Also, from a build node, please run the following commands and copy/paste results

128K .bash_history
0 .bash_profile
0 .bashrc
1.7M .cache
0 .conda
0 .condarc
0 .config
0 .cshrc
0 .gitconfig
640K .java
3.9M .local
0 .login
0 .pki
0 .Renviron
0 .rnd
2.0M .rstudio
0 .singularity
0 .ssh
0 .Xauthority

[kubu4]

Cool, ruled out storage space in ${HOME} as a potential culprit. Thanks!

We're still dealing with exceeding quota on /gscratch/srlab ATM. This could be the issue. Will report back once that's resolved...

[kubu4]

Mox storage has been expanded and we're no longer over quota. Give it another rip when you have a chance.