Installation problems via windows installer

[klmarina]

Dear µ-SAM team,

We tried to install µSAM via the Windows installer on one of the workstations in our facility. We tried to install it via the miniforge conda prompt first but ran into an issue that the installer was not able to find a pytorch file which it tried to update.
We resorted to the windows installer since we cannot use the GPU anyways. However here we ran into an issue where after installing the software, we were given the error:
.
After hitting OK, the commandline produced an error " Freeype library not found".
We checked and the C.pyd file is present in the correct folder. We already removed napari and python from the workstation once after encountering the same error before.

Thank you for any advice you can give us in resolving this issue.
Best,
Marina

[anwai98]

Hi @klmarina,

Thanks for your interest in micro-sam!

We resorted to the windows installer since we cannot use the GPU anyways. However here we ran into an issue where after installing the software, we were given the error:

The installers are out-of-shape at the moment (please check the documentation for details). And the older version of the installers do not have GPU support (sorry for that, we are working on updating them and would finalize stuff there for updating the installers rather soonish - I have been procrastinating that for a while now)

For now, I suggest installing micro-sam using conda. If you are new to conda, we have a brief documentation in the FAQ section about how to get started with micromamba and install micro-sam from conda.

Let us know if installing this with conda works for you or if you need any further assistance. Happy to help!

[klmarina]

Thank you for your fast answer.

We tried to install it with the miniforge conda promp tin the first place. But the installer was not able to find a pytorch file which it tried to update. We tried several times, deleted the file and re-installed it, but the problem was not solved.

Thank you for any advice you can give us in resolving this issue.
Best,
Marina

[anwai98]

Hi @klmarina,

Thanks for checking it out via conda as well, and apologies that you had to go through such trouble.

Can you please pinpoint me the error? I might be able to help or ask relevant people around if I see an error trace for installation via conda.

On a good day, the installation in a new environment should simply work with: conda env create -n micro-sam -c conda-forge python=3.11 micro_sam.

Let's try it with the script given here by me and try to reinstall micro-sam and look at the error trace!

[klmarina]

Hi,

I tried again the script from the documentation and I tried your code, and both times the same error notification pops up.
Also the code you gave me initially didn't work, but this worked: conda create -n micro_sam_env python=3.11 micro_sam -c conda-forge. But also the same error notification.

This is the error with the the script from the documentation:

This is the error with you script:

And this ist the error with the modification of your code:

In the first picture you can also see, that the file which the installer was not able to find, is there.

[klmarina]

we also tried to install pytorch seperatly but it also resulted in the same error

[constantinpape]

Hi @klmarina , this is most likely due to an outdated version of your miniforge prompt. Can you try to update it?
Or, if possible, we recommend to use the latest version of micromamba, which is a lightweight replacement of conda.

[klmarina]

Hi, thank you for this tip. I tried it now with the latest version of micromamba, but sadly i got the same error notification regarding the pytorch file.

[anwai98]

Hi @klmarina,

Sorry to hear that the error prevails.

Could you please send a screenshot and the command you tried to install the environment?

(and as a rule of thumb, whenever trying things out, I would recommend to please share the command and error trace again - the error might be the same, but we might get better hints at the workflow)

[klmarina]

Thank you for the remark.

The installation of micromamba with windows powershell did not work, because I don't have admin rights

Then I installed micromamba in miniforge with: conda install -c conda-forge micromamba
Then i used to commands from the micro-SAM documentation to creat an environment
This is the error notifictaion:

[anwai98]

Hi @klmarina,

The problem is right there. You must install the micromamba as a package manager!

The installation of micromamba with windows powershell did not work, because I don't have admin rights

What do you mean by this? Is this your own PC or a remote desktop administered by local IT?

If it's your own PC, you can open Powershell as admin (right click in the start menu and open as admin) and that should give you admin rights!

[klmarina]

Yes, it is a desktop administered by local IT

[constantinpape]

Thanks for trying all the solutions and the feedback @klmarina . I will read through this more carefully later and follow up.