Timed out waiting for Jupyter Notebook/permission denied


Been having some issues launching the interactive apps within OOD. The VM we are running OOD on was moved over to our dmz and set up as a “fresh” install with v1.7, so I am assuming I have a firewall issue as this worked perfectly before on the old dev system which stayed on our internal network. I did not entirely set things up from scratch but copied over the existing files from the old setup as appropriate. I keep getting this message when attempting to start an interactive app (Jupyter).

Script starting...
Waiting for Jupyter Notebook server to open port 34254...
/cm/local/apps/slurm/var/spool/job17731471/slurm_script: line 129: /home/testuser/ondemand/data/sys/dashboard/batch_connect/sys/jupyterlab/output/f7e37770-4c15-4b34-b611-83380895652c/script.sh: Permission denied
TIMING - Starting wait at: Thu May 21 13:01:49 CDT 2020
Timed out waiting for Jupyter Notebook server to open port 34254!
TIMING - Wait ended at: Thu May 21 13:02:51 CDT 2020
Cleaning up...

However I don’t know how to interpret the “permission denied” error after script.sh. Is something else going on here? As far as firewall are you allowing all traffic between the OOD node and the login node of your cluster(s) or what ports at a minimum should be open? If there are any general suggestions on this I would appreciate it.

That file needs to be executable. I don’t know how you copied or installed that jupyter application, but the file permissions didn’t seem to be preserved. You just need to chmod +x on the source file (/var/www/ood/apps/sys/jupyterlab/template/script.sh.erb?).

So however you’re saving this app (I know git saves mode bits) you just need to save the executable file. Just to be sure any template/*.sh.erb files should be executable.

Jeff, that did it! thanks again.