Dependency version requirements incompatible with environment

[Michael Zoberman]

Hi MAJIQ team,

I really appreciate the work that’s gone into MAJIQ and Voila. It has been very useful.

I’m trying to install it on an HPC system and running into issues with strict dependency version requirements. For example it seems that version 2.0.0 of numpy is required which I cannot install or access on my HPC environment.

Is it possible to run MAJIQ and Voila with newer dependency versions, or is there a recommended HPC deployment approach such as a Singularity or Apptainer?

I have also tried to clone the repository to see if I can manually change the hardcoded dependency requirements but it seems like a BitBucket account with access to the repository is required.

Thanks!

All the best,

Mike Zoberman

[San Jewell]

Hi Mike!

Thanks for reaching out and I'm glad the software has been helpful for you!

It would help me to know why exactly what the restrictions for your HPC are ; i.e. if you are able to access the internet to download majiq, are you then not able to access the internet to download the package dependencies? Are there certain python packages which are available on your HPC and not others? I'm sure I can help you here I just need more information. 

Are you installing majiq in a virtual environment as per the instructions in the post-registration page? Are you getting specific errors during this process? If the internet is blocked, there are methods to download all of the required packages at the correct versions from pypi on your personal laptop or another machine, and then transfer them to your hpc in order to install majiq, and I can help describe the technical procedure of this approach if it's what you are looking for. 

While I do not recommend changing the versions of dependencies as you ask, as this may cause bugs or undefined behavior in majiq, you are of course welcome to do so if you wish. In this case, I believe you are getting the bitbucket account requirement either because you are trying to clone the 'majiq' instead of the 'majiq_academic' repository, or because you are using the git+ssh clone protocol (which requires an account) instead of the https protocol (which can be pulled anonymously)

As far as container systems like singularity or docker, we have experimented with using them for some of our commercial deployments, but in general these tools require even more administrative access on most HPC systems than most users will have. I can share docker files if this is actually the approach you'd like to take, but I would not generally recommend it, espceially if you are going to use voila view which would require some more tedious networking setup. 

Please let me know if any of this helps, or a little more information about your situation so I can help you. 

Thanks!

-San