Primary informations
Username: bezrukov
Cluster: baobab
Description
The RStudio interactive app in OpenOnDemand does not work at the moment, using any Rstudio image suggested. Digging into the problem (in the output.log for hte session) I can see, that the reason is that /acanas/m-BioinfoSupport i snot mounted at the moment on the compute nodes.
- First, I guess that the problme will clean itself in a little while (at the login node this directory disappeared, but now I get it back mounted)
- Second, I would guess that probably adding the bind mount of
/acanas/m-BioinfoSupport to the singularity command should be done only if the requested image resides there? Or if this directory is present and mounted. Then the app whould happily start if /acanas has problems (if I use docker based images, or my own singularity images)
Steps to Reproduce
Start RStudio interactive App in baobab openondemand. The process completes nearly immediately and does not start the server.
Expected Result
Expecting the app to start and the link to connect to RStudio to appear.
Actual Result
You get the report of the form
Digging into the debug information into output.log you can find that the reason is:
FATAL: container creation failed: mount hook function failure: mount /acanas/m-BioinfoSupport->/acanas/m-BioinfoSupport error: while mounting /acanas/m-BioinfoSupport: mount source /acanas/m-BioinfoSupport doesn't exist
Oh, found the workaround 
Running
srun -p public-interactive-cpu ls /acanas/m-BioinfoSupport
trigered the automounter to mount the required directory on the compute node I was using.
However I would guess either attempting to trigger the automounter from the RStudio start script for openondemand (just by doing ls /acanas/m-BioinfoSupport before starting singularity) or mounting this directory optionally would improve stability of the service.
Best!
Hi @Fedor.Bezrukov
The storage team performed a migration on this NASAC share. We had to unmount it on every HPC server, resulting in the unavailability of /acanas/m-BioinfoSupport.
Since it’s a private share, I have only contacted the owners. (My bad)
It’s not a workaround; your srun command worked because the share has been re-mounted in the same time. 
In this case, You may try to use another R image in OpenOnDemand as described in the example value.
As the share is back again, you can use /acanas/m-BioinfoSupport with R-OpenOnDemand.
Hi @Adrien.Albert,
Thanks!
One note – while the mount was absent, the Rstudio app failed to work for any images, both those on /acanas/m-BioinfoSupport, and docker based, or stored in my home dir. The reason is that there singularity command in the app is invoked with --bind /acanas/m-BioinfoSupport opton, independent on what image is chosen, and not finding this directory it failed.
1 Like
Thanks for noticing, I will update it to make it more generic
