BraTS-preprocess stuck at "status reveived: { 'code': 201, 'message': 'nifti examination queued!'}."

[Lucas-rbnt]

Hi everyone,
I work on a computing server. And by wanting to use single preprocessing I get stuck at:

status reveived: {'code': 201, 'message': 'input inspection queued!'}
status reveived: { 'code': 201, 'message': 'nifti examination queued!'}.

I assume the BraTS server is running locally?
If yes then I guess it's due to the lack of a web server on the computing server, is it possible to disable it and use the Python API only?

Sorry for the inconvenience,
Lucas Robinet.

[neuronflow]

Thank for your interest in BraTS Toolkit.

"I assume the BraTS server is running locally?"
it should 🙈

What happens if you start the nvidia docker hello-world?
https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html

[Lucas-rbnt]

Hi,

Sorry for the answer delay.
I'm using Docker daily so I stuck with my workflow.

I assumed it was possible since NVIDIA docker is a wrapper around but maybe I am wrong here ?

Thanks again for your answer,
Lucas.

[neuronflow]

What happens if you start the nvidia docker hello-world?
https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html

[Lucas-rbnt]

Hello from Docker!
This message shows that your installation appears to be working correctly.

....

[neuronflow]

Can you please show the full output, including GPU and cuda version?

"If yes then I guess it's due to the lack of a web server on the computing server, is it possible to disable it and use the Python API only?"

Can you elaborate what you mean here? :)

[Lucas-rbnt]

I'm working on a computing server with no web server, I thought that maybe the problem comes from here ?

You mean the BraTS output ?
Because even trying to work with cpu-only mode, I'm still stuck at this part of the process.

Otherwise,
The compute server has 4 GeForce 2080 Ti, Cuda 11.6.

[neuronflow]

"I'm working on a computing server with no web server,"
Cannot follow you, sorry, please elaborate.

What happens internally: The backend is started in a docker, and it opens a local flask server that is communicating with the python frontend via WebSockets.

We do have another preprocessing pipeline not requiring docker that will be published soon.

[Lucas-rbnt]

Thank you for your answer.

So I guess, my problem might come from the lack of a graphics server on my compute server.

[neuronflow]

No, BraTS Toolkit can run headless without trouble.

[Lucas-rbnt]

Oh thanks again.

Then I have no idea why it's blocked at this stage.

[neuronflow]

Are other dockers running on the system, which ports are taken already?
Can you show the full output from the hello-world?

https://github.com/neuronflow/BraTS-Toolkit/blob/master/0_preprocessing_single.py
did you confirm processing of the exam? otherwise try setting the confirm parameter to False.

[Lucas-rbnt]

Hello from Docker!
This message shows that your installation appears to be working correctly.

To generate this message, Docker took the following steps:
 1. The Docker client contacted the Docker daemon.
 2. The Docker daemon pulled the "hello-world" image from the Docker Hub.
    (amd64)
 3. The Docker daemon created a new container from that image which runs the
    executable that produces the output you are currently reading.
 4. The Docker daemon streamed that output to the Docker client, which sent it
    to your terminal.

To try something more ambitious, you can run an Ubuntu container with:
 $ docker run -it ubuntu bash

Share images, automate workflows, and more with a free Docker ID:
 https://hub.docker.com/

For more examples and ideas, visit:
 https://docs.docker.com/get-started/

Some ports are already taken of course but not the 5000 dedicated to Flask. No container are running currently on the system.
I tried both cpu and gpu mode and confirm=True and confirm=False

Is BraTS-Toolkit using a docker image that needs login to be pulled ?

[neuronflow]

This appears to be the wrong hello world.

What happens if you start the nvidia docker hello-world? https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html

[Lucas-rbnt]

Can you elaborate "wrong hello world" ?

I tried my regular Docker installation and I also change my config to do it the nvidia-ctk way.
Everything works as expected in their documentation and my outputs (including the hello-world one) match the documentation ones

[neuronflow]

Please read the link:
https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html

Perhaps the hello world is confusing you, please run with and without sudo:

sudo docker run --rm --runtime=nvidia --gpus all nvidia/cuda:11.6.2-base-ubuntu20.04 nvidia-smi

and post the output.