Improvements for clusters

open

#1

Hi

I would like to request some features that will make our life easier on clusters.

I like the lane approach that we can have multiple submission scripts as templates. However I think it will be useful to also include some variables that can be passed through GUI to the submission script. For example like in relion, if you can have a XXXextra1XXX variable (actually multiple of them) that can be replaced with any parameter user wants, this variable can be entered during submit to lane process.

Second request is more complicated.
I am using ssh tunnel to interact with GUI. The cluster that I am using at Stanford University offers another browser based method to reach the compute nodes (OnDemand). I would like to use that method for several reasons. However, web browser cannot communicate properly with the GUI. The URL to reach the node is as follows

https:// login sherlock stanford.edu/node/“host-name”/“port-name”/

As I consulted with the cluster admin, the issue is that CryoSPARC tries to load a Javascript file from the root of the webserver: /bee123456789123456789123456789aa.js?meteor_js_resource=true

It works fine with a SSH tunnel, but with OnDemand, it tries to load:

https:// login sherlock stanford.edu/bee123456789123456789123456789a.js?meteor_js_resource=true"

where the file is actually at:

https:// login sherlock stanford.edu/node/<nodename>/<port>/bee123456789123456789123456789aa.js?meteor_js_resource=true

Therefore I see a blank page.

If CryoSPARC does not use absolute paths when loading resources, but relative URLs, this problem should be resolved.

Can you implement these?

Thank you


#2

Hi, as for your second request, can’t use solve it by connecting with VPN rather than using SSH tunnel?


#3

Thank you Marino for your reply.

Standord cluster, probably many other clusters has a saperate 2 tier authentication system. Even on campus we need to tunnel and authenticate. Their web based system allows a computer to stay authenticated for 30days, which cuts down a lot of smartphone interaction. But for that, the javascript on cryosparc web app should load resources properly.
Is not it anyway better to use relative paths for web based applications? (The java script when we try to load cryosparc on web browser asking for an absolute path)

Alpay


#4

More importantly, is it possible to install and run cryosparc host-name free? The nodes on our cluster are stateless, and I would like to be able to run the background instance in any node I want. Many people cannot use cryosparc on our cluster because they do not own a node and they cannot practically request the same node.