RStudio may not show SSH password prompt on macOS

[mhesselbarth]

The HPC cluster I'm using does not allow to use a SSH key pair unfortunately. I know that some packages allow an interactive password prompt. Would something also be possible for the clustermq package?

Thanks a lot for the help!

[mschubert]

If I remember correctly, it already asked for a password on the console if no keys are set up.

Does it not work? If no, can you describe you setup and what you see?

[mhesselbarth]

Okay, so I think the problem is that ZeroMQ is not installed on the cluster. I talked to the admin and they were not super excited about installing it unfortunately.

Are there any resources which explain a bit more why clustermq need zeroMQ and what zeroMQ is actually used for within the package? This would hopefully help me explaining to them why it would be cool if they could install the library.

[mschubert]

ZeroMQ provides that TCP/IP sockets that clustermq communicates with its workers.

There is a high chance the library is already installed on your cluster, e.g. as part of any IPython/Jupyter setup.

If not, it should be as simple as downloading the release and:

# tar -xf ... and change into directory
./configure
make
make install # probably "make DESTDIR=/somewhere/in/your/home/dir install"

followed by:

# if you find the library installed somewhere you can just add that path here
LD_LIBRARY_PATH=/somewhere/in/your/home/dir/lib R -e "install.packages('clustermq')"

I should probably still write this down step-by-step in the docs. Please let me know if this works and if you run into any problems!

[mhesselbarth]

Okay, ZeroMQ should be now installed on the HPC and I can also load the package on the HPC without any errors.

But trying to connect from my local R session I get the following errors and the password prompt never shows up. Not sure if that is a problem with my laptop and the SSH though. I did re-install ssh-askpass but that did not help.

Connecting mhessel@greatlakes.arc-ts.umich.edu via SSH ...

ssh_askpass: exec(/usr/X11R6/bin/ssh-askpass): No such file or directory

Error in .subset2(public_bind_env, "initialize")(...) : publickey,keyboard-interactive).
  Remote R process did not respond after 5000 seconds. Check your SSH server log.

I'm on macOS Catalina 10.15.6

[mschubert]

Please have a look at this and see if it helps: https://mschubert.github.io/clustermq/articles/userguide.html#ssh-1

[mhesselbarth]

So ssh -R 54709:localhost:6687 <user@host> R --vanilla did run without any problems and started an R session.

I also have a .log-file setup in my local .Rprofile options but can't find it anywhere if I try to excuse the Q function from RStudio

[mschubert]

My guess is that ssh-askpass is incorrectly set up in RStudio.

What is your:

echo SSH_ASKPASS # shell

Sys.getenv("SSH_ASKPASS") # R and RStudio

Does the file /usr/X11R6/bin/ssh-askpass actually exist?

Does the clustermq example work if you start it from R instead of RStudio?

[mhesselbarth]

I tried R and RStudio and both do not work.

Here is what the two commands returned.

echo SSH_ASKPASS
SSH_ASKPASS

> Sys.getenv("SSH_ASKPASS") # R and RStudio
[1] "rpostback-askpass"

[mschubert]

I've updated the SSH troubleshooting page to also test

system("ssh -R 54709:localhost:6687 <user@host> R --vanilla")

from R so we can see if the SSH connection works that way.

Above, echo SSH_ASKPASS should have been echo $SSH_ASKPASS.

[mhesselbarth]

Okay, so echo $SSH_ASKPASS returns nothing. Could that be the problem that ASKPASS is not setup correctly?

[mschubert]

I think SSH_ASKPASS within R is trying to use a client that does not exist (/usr/X11R6/bin/ssh-askpass)

You could try and fix that, or try unsetting SSH_ASKPASS within R and see if this changes anything

These may also be a solution/workaround: (1) microsoft/vscode#32097, (2) http://it.gerull.nl/blog/2018/ssh-agent-on-mac/

[mschubert]

@mhesselbarth Did any of the hints help?

[mhesselbarth]

Not really...I was able to reach another cluster that I have access to from the machine. So it's seems to be a problem on the cluster side I think..