How to Run the Docker File

[Elizalll]

Dear organizers @Puzzled-Hui @yungu-imr :

I download the docker file from team neu204 and sanmed_ai, and try to run it using Singularity on the server.

First, I try singularity build neu204.sif docker-archive:neu204.tar.gz to turn tar.gz file into sif type, which is for Singularity.

Then, I try singularity exec --nv -B /Home/CODE/dataset/ATM/imagesVal/:/workspace/inputs/ -B $PWD/neu204_outputs/:/workspace/outputs/ neu204.sif /bin/bash -c "sh predict.sh" to run it.

However, it shows error sh: 0: Can't open predict.sh and stop.

So I try to put the predict.sh from https://github.com/EndoluminalSurgicalVision-IMR/ATM-22-Related-Work/blob/main/baseline-and-docker-example/predict.sh with the neu204.sif.

And this time it shows error python: can't open file 'predict.py': [Errno 2] No such file or directory, which is from python.

I think put predict.sh is not a correct way. How should I do to make things correct? I would appreciate your patient reply.

Yours sincerely, Eliza

[Puzzled-Hui]

Hi,

Thanks for reaching out.

We did not test by the Singularity but i think it should work because it has good compatibility with Docker.

Could you please try the docker command, and run the following commands, which we had tested successfully before to obtain the results in the ATM22 benchmark:

docker image load < teamname.tar.gz
docker container run --gpus "device=0" --name teamname --rm -v $PWD/inputs/:/workspace/inputs/ -v $PWD/teamname_outputs/:/workspace/outputs/ teamname:latest /bin/bash -c "sh predict.sh"

By the way, we would like to check the baseline and update it in time.

Best,