MedNIST Tutorial - PermissionError: [Errno 13] Permission denied: '/var/monai/output/output.json'

[Zrrr1997]

Hi all,

Thanks for this beautiful project! I am currently getting to know MONAI Deploy and followed all the instructions from the tutorial on MedNIST.

The code runs fine up until the container execution with:

monai-deploy run mednist_app:latest input output

I get the following output:

Checking dependencies...
--> Verifying if "docker" is installed...

--> Verifying if "mednist_app:latest" is available...

Checking for MAP "mednist_app:latest" locally
"mednist_app:latest" found.

Reading MONAI App Package manifest...
--> Verifying if "nvidia-docker" is installed...

/opt/conda/lib/python3.8/site-packages/scipy/__init__.py:138: UserWarning: A NumPy version >=1.16.5 and <1.23.0 is required for this version of SciPy (detected version 1.23.5)
  warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion} is required for this version of "
Going to initiate execution of operator LoadPILOperator
Executing operator LoadPILOperator (Process ID: 1, Operator ID: b01466ed-8498-4e89-a344-a0519a9836f0)
Done performing execution of operator LoadPILOperator

Going to initiate execution of operator MedNISTClassifierOperator
Executing operator MedNISTClassifierOperator (Process ID: 1, Operator ID: f4e03236-4413-4614-9bac-0d3719a3b01d)
/root/.local/lib/python3.8/site-packages/monai/utils/deprecate_utils.py:107: FutureWarning: <class 'monai.transforms.utility.array.AddChannel'>: Class `AddChannel` has been deprecated since version 0.8. please use MetaTensor data type and monai.transforms.EnsureChannelFirst instead.
  warn_deprecated(obj, msg, warning_category)
/root/.local/lib/python3.8/site-packages/monai/utils/type_conversion.py:134: UserWarning: The given NumPy array is not writeable, and PyTorch does not support non-writeable tensors. This means you can write to the underlying (supposedly non-writeable) NumPy array using the tensor. You may want to copy the array to protect its data or make it writeable before converting it to a tensor. This type of warning will be suppressed for the rest of this program. (Triggered internally at  /opt/pytorch/pytorch/torch/csrc/utils/tensor_numpy.cpp:175.)
  tensor = torch.as_tensor(tensor, **kwargs)
AbdomenCT
/var/monai/output/output.json
Traceback (most recent call last):
  File "/opt/monai/app/mednist_classifier_monaideploy.py", line 119, in <module>
    App(do_run=True)
  File "/root/.local/lib/python3.8/site-packages/monai/deploy/core/application.py", line 129, in __init__
    self.run(log_level=args.log_level)
  File "/root/.local/lib/python3.8/site-packages/monai/deploy/core/application.py", line 429, in run
    executor_obj.run()
  File "/root/.local/lib/python3.8/site-packages/monai/deploy/core/executors/single_process_executor.py", line 125, in run
    op.compute(op_exec_context.input_context, op_exec_context.output_context, op_exec_context)
  File "/opt/monai/app/mednist_classifier_monaideploy.py", line 94, in compute
    with open(output_path, "w") as fp:
PermissionError: [Errno 13] Permission denied: '/var/monai/output/output.json'

ERROR: MONAI Application "mednist_app:latest" failed.

Could anyone point me in the right direction to fix this? It might be a Docker-specific permissions issue, but I am not sure how to approach this.

Best,
Zdravko

[Zrrr1997]

The problem was incredibly simple to solve: the output folder should have write permissions to docker's GUID. Changing the permissions via the directory properties for groups/others solved the problem