ssh_exec_wait: module command not found about ssh HOT 7 OPEN

Hi. This issues did not seem to get addressed, yet I am encountering it too about 1 year after the original post. I am happy to provide more information on demand.

from ssh.

What does module load R do ? That is not a shell command?

from ssh.

First, I wanted to thank you for this package, which has been very invaluable for me as I am really only familiar with R, and so having it has made my life much easier.

Here's the information I could find on module:
http://modules.sourceforge.net/
https://modules.readthedocs.io/en/stable/module.html
On my cluster I would be loading some modules as part of my SLURM script. I am using a custom R script to generate a SLURM script and a parameter files for a job on the cluster, and want to detect versions available for my favourite module. But while running module commands directly in PuTTY works for me, doing it through ssh_exec_wait fails.

from ssh.

Maybe you're using a different shell in putty? Does it work if you explicitly start bash? According to the docs you sent you might first have to run this?

. /usr/share/Modules/init/sh

I don't know what a slurm script is.

from ssh.

Ha, no problem. SLURM is a way to create queue jobs for a linux cluster.
I tried you suggestion already, and get:

ssh_exec_wait(sshsess, ". /usr/share/Modules/init/sh")
bash: /usr/share/Modules/init/sh: No such file or directory
[1] 1

from ssh.

has this been fixed? I am running into the same issue. Again it would be very useful to load modules prior to submitting a cluster job directly from R.

from ssh.

Hello,

I've tried the module init and it is working for me.

session <- ssh::ssh_connect(host = "[email protected]", passwd = "test", verbose = FALSE)

out <- ssh::ssh_exec_internal(session, command = c(
  '. /usr/share/Modules/init/sh', # init module on shell
  'module list'
))

cat(rawToChar(out$stdout))
cat(rawToChar(out$stderr))

from ssh.