PermissionError when run agml.synthetic.reinstall_helios()

[Vincent-WangCH]

I am running the AgML-Synthetic.ipynb in /AgML/examples and encountered this isse: I found the previous isse and solution as run:

agml.synthetic.reinstall_helios()

So I add a code cell above the troubled cell to run the above code. But I encouter another permission error as follow:

I am using conda environment as the kernel and window11 system

[Vincent-WangCH]

I have also tried

• run the vscode as admin,
• run the terminal as admin and open up python run following command:

  import agml
  agml.synthetic.reinstall_helios()

• run powershell
• I changed the secruity option of the folder with path agml/_helios/Helios like follow:

However, none of those solved the permission error issue

[masonearles]

@amogh7joshi or @dariojavo Any thoughts on this issue?

On Sun, Jan 29, 2023 at 13:21 Vincent-WangCH @.***> wrote:

I have also tried

• run the vscode as admin,
• run the terminal as admin and open up python run following command:

import agml agml.synthetic.reinstall_helios()

• run powershell
• I changed the secruity option of the folder with path agml/_helios/Helios like follow: [image: image] https://user-images.githubusercontent.com/74845578/215356301-fc7e7dd5-eaf9-45a4-829f-3e87462ae68d.png

However, none of those solved the permission error issue

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[dariojavo]

By seeing the first image, seems that the generated path is not correctly generated for windows. This need to be fix, in the meantime, @Vincent-WangCH can you try to use it on wsl/windows? You can install it from the app store.

[amogh7joshi]

@Vincent-WangCH Have you been able to resolve this?

[Vincent-WangCH]

Yes, I think use the wsl is the only option for the synthetic one. I assume this is the right output for synthetic. However I tried several time on window it returns me the same output as the image above.

[Vincent-WangCH]

I have encounter a new error when executing a cell below it. Can also check this out?

[masonearles]

It seems like this is a memory related issue based on your error, which I'm a little surprised about. What are the specifications of your machine in terms of available RAM and hard disk space?

Regardless, you can try editing some parameters to change plant geometry that will reduce the memory requirement. You can see how to do this in the example notebook at this link:

https://github.com/Project-AgML/AgML/blob/main/examples/AgML-Synthetic.ipynb

If your computer is memory constrained, you could try the following before generating the canopy which will reduce the number of geometric primitives.

opt.canopy.plant_count = [1, 1] opt.canopy.fruit_subdivisions = 4 opt.shoot_subdivisions = 4

I would also check what other applications you have running and how much memory they are currently consuming. You could try closing them down to free up memory.

Let us know if this helps and we can go from there.

On Fri, Mar 17, 2023 at 12:33 AM Vincent-WangCH @.***> wrote:

[image: image] https://user-images.githubusercontent.com/74845578/225841081-e5ab236c-82be-47dd-aacc-b2788971b6d7.png [image: image] https://user-images.githubusercontent.com/74845578/225841125-3b565c31-2184-434b-9ad4-2fbb9274597a.png I have encounter a new error when executing a cell below it. Can also check this out?

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[Vincent-WangCH]

I was using the WSL so I am not quite sure what is the process of checking the memory allocated to it. Do you have any suggestion? By the way I was trying to run this on google colab, but it pops out this error message. Is AgML avaliable on google colab?

[masonearles]

@amogh7joshi @dariojavo Will Helios currently run on Colab?

[dariojavo]

Hi @Vincent-WangCH,

The error that you are receiving in semantic segmention was due to a leak of memory in the synthetic annotation plugin in Helios, which has been solved by the Helios team. Can you check which was the latest version of Helios pulled from AgML?

Regarding Colab, I don't think you will be able to use it since Helios is installed locally, but @amogh7joshi may be able to answer this better.

[amogh7joshi]

I've been able to build Helios on Colab, but it always runs into issues with GLFW, so I don't think it will work (unless changes have been made recently).

[Vincent-WangCH]

Hi @dariojavo,

I have try to looking for the reinstall of helios but I think it is a exectubale that run when "pip install agml", This is the helios related installation I am not sure there is an version specified for Helios. Besides that there will be an helios_configure.json file created during the execution of AgML-Synthetic.ipynb which I also found no information about how to update to the latest version of Helios. Can you help me on that? I have try to reinstall the AgML github and reinstall agml though pip install and uninstall. Both doesn't work, it still run into this problem.