Cannot start_server for MONAILABEL

[borantolic]

Hi! I hope someone could help me with my problem. I successfully installed Monailabel on my home (Mac)computer, started the server, and it works inside 3D Slicer. I followed same steps to install it on my work Windows computer - which is more powerful - but I cannot seem to start the server.
Can anyone please look at the output bellow and suggest a solution?

(monailabel-env) C:\Users\EchoPac>monailabel start_server --app apps/radiology --studies datasets/Task02_Heart/ImagesTr --conf models deepedit
Using PYTHONPATH=C:\Users\EchoPac.conda\envs;
""
2023-01-20 17:48:12,913 - USING:: version = False
2023-01-20 17:48:12,913 - USING:: app = C:\Users\EchoPac\apps\radiology
2023-01-20 17:48:12,913 - USING:: studies = C:\Users\EchoPac\datasets\Task02_Heart\imagesTr
2023-01-20 17:48:12,913 - USING:: verbose = INFO
2023-01-20 17:48:12,913 - USING:: conf = [['models', 'deepedit']]
2023-01-20 17:48:12,913 - USING:: host = 0.0.0.0
2023-01-20 17:48:12,913 - USING:: port = 8000
2023-01-20 17:48:12,913 - USING:: uvicorn_app = monailabel.app:app
2023-01-20 17:48:12,913 - USING:: ssl_keyfile = None
2023-01-20 17:48:12,913 - USING:: ssl_certfile = None
2023-01-20 17:48:12,913 - USING:: ssl_keyfile_password = None
2023-01-20 17:48:12,913 - USING:: ssl_ca_certs = None
2023-01-20 17:48:12,913 - USING:: workers = None
2023-01-20 17:48:12,913 - USING:: limit_concurrency = None
2023-01-20 17:48:12,913 - USING:: access_log = False
2023-01-20 17:48:12,913 - USING:: log_config = None
2023-01-20 17:48:12,913 - USING:: dryrun = False
2023-01-20 17:48:12,913 - USING:: action = start_server
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_API_STR =
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_PROJECT_NAME = MONAILabel
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_APP_DIR =
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_STUDIES =
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_AUTH_ENABLE = False
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_AUTH_DB =
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_APP_CONF = '{}'
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_TASKS_TRAIN = True
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_TASKS_STRATEGY = True
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_TASKS_SCORING = True
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_TASKS_BATCH_INFER = True
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_DATASTORE =
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_URL =
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_USERNAME =
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_PASSWORD =
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_API_KEY =
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_CACHE_PATH =
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_PROJECT =
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_ASSET_PATH =
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_DSA_ANNOTATION_GROUPS =
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_USERNAME =
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_PASSWORD =
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CACHE_PATH =
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_QIDO_PREFIX = None
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_WADO_PREFIX = None
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_STOW_PREFIX = None
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_FETCH_BY_FRAME = False
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CONVERT_TO_NIFTI = True
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_SEARCH_FILTER = '{"Modality": "CT"}'
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CACHE_EXPIRY = 180
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_PROXY_TIMEOUT = 30.0
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_READ_TIMEOUT = 5.0
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_AUTO_RELOAD = True
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_READ_ONLY = False
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_FILE_EXT = '[".nii.gz", ".nii", ".nrrd", ".jpg", ".png", ".tif", ".svs", ".xml"]'
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_SERVER_PORT = 8000
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_CORS_ORIGINS = '[]'
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_SESSIONS = True
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_SESSION_PATH =
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_SESSION_EXPIRY = 3600
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_INFER_CONCURRENCY = -1
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_INFER_TIMEOUT = 600
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_TRACKING_ENABLED = True
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_TRACKING_URI =
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_ZOO_SOURCE = github
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_ZOO_REPO = Project-MONAI/model-zoo/hosting_storage_v1
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_ZOO_AUTH_TOKEN =
2023-01-20 17:48:12,913 - ENV SETTINGS:: MONAI_LABEL_AUTO_UPDATE_SCORING = True
2023-01-20 17:48:12,913 -
Allow Origins: ['*']
[2023-01-20 17:48:14,147] [11612] [MainThread] [INFO] (uvicorn.error:75) - Started server process [11612]
[2023-01-20 17:48:14,147] [11612] [MainThread] [INFO] (uvicorn.error:45) - Waiting for application startup.
[2023-01-20 17:48:14,147] [11612] [MainThread] [INFO] (monailabel.interfaces.utils.app:38) - Initializing App from: C:\Users\EchoPac\apps\radiology; studies: C:\Users\EchoPac\datasets\Task02_Heart\imagesTr; conf: {'models': 'deepedit'}
[2023-01-20 17:48:14,584] [11612] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for MONAILabelApp Found: <class 'main.MyApp'>
[2023-01-20 17:48:14,600] [11612] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.deepedit.DeepEdit'>
[2023-01-20 17:48:14,600] [11612] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.deepgrow_2d.Deepgrow2D'>
[2023-01-20 17:48:14,600] [11612] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.deepgrow_3d.Deepgrow3D'>
[2023-01-20 17:48:14,600] [11612] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.localization_spine.LocalizationSpine'>
[2023-01-20 17:48:14,600] [11612] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.localization_vertebra.LocalizationVertebra'>
[2023-01-20 17:48:14,600] [11612] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation.Segmentation'>
[2023-01-20 17:48:14,600] [11612] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_spleen.SegmentationSpleen'>
[2023-01-20 17:48:14,600] [11612] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_vertebra.SegmentationVertebra'>
[2023-01-20 17:48:14,600] [11612] [MainThread] [INFO] (main:93) - +++ Adding Model: deepedit => lib.configs.deepedit.DeepEdit
[2023-01-20 17:48:14,600] [11612] [MainThread] [INFO] (monailabel.utils.others.generic:185) - Downloading resource: C:\Users\EchoPac\apps\radiology\model\pretrained_deepedit_dynunet.pt from https://github.com/Project-MONAI/MONAILabel/releases/download/pretrained/radiology_deepedit_dynunet_multilabel.pt
pretrained_deepedit_dynunet.pt: 0.00B [00:00, ?B/s]
2023-01-20 17:48:14,727 - ERROR - Download failed from https://github.com/Project-MONAI/MONAILabel/releases/download/pretrained/radiology_deepedit_dynunet_multilabel.pt to C:\Users\EchoPac\AppData\Local\Temp\tmp6fkuh0c8\pretrained_deepedit_dynunet.pt.
[2023-01-20 17:48:14,806] [11612] [MainThread] [ERROR] (uvicorn.error:119) - Traceback (most recent call last):
File "C:\Users\EchoPac.conda\envs\monailabel-env\lib\urllib\request.py", line 1346, in do_open
h.request(req.get_method(), req.selector, req.data, headers,
File "C:\Users\EchoPac.conda\envs\monailabel-env\lib\http\client.py", line 1285, in request
self._send_request(method, url, body, headers, encode_chunked)
File "C:\Users\EchoPac.conda\envs\monailabel-env\lib\http\client.py", line 1331, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "C:\Users\EchoPac.conda\envs\monailabel-env\lib\http\client.py", line 1280, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "C:\Users\EchoPac.conda\envs\monailabel-env\lib\http\client.py", line 1040, in _send_output
self.send(msg)
File "C:\Users\EchoPac.conda\envs\monailabel-env\lib\http\client.py", line 980, in send
self.connect()
File "C:\Users\EchoPac.conda\envs\monailabel-env\lib\http\client.py", line 1454, in connect
self.sock = self._context.wrap_socket(self.sock,
File "C:\Users\EchoPac.conda\envs\monailabel-env\lib\ssl.py", line 501, in wrap_socket
return self.sslsocket_class._create(
File "C:\Users\EchoPac.conda\envs\monailabel-env\lib\ssl.py", line 1041, in _create
self.do_handshake()
File "C:\Users\EchoPac.conda\envs\monailabel-env\lib\ssl.py", line 1310, in do_handshake
self._sslobj.do_handshake()
ConnectionResetError: [WinError 10054] An existing connection was forcibly closed by the remote host

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "C:\Users\EchoPac.conda\envs\monailabel-env\lib\site-packages\starlette\routing.py", line 635, in lifespan
async with self.lifespan_context(app):
File "C:\Users\EchoPac.conda\envs\monailabel-env\lib\site-packages\starlette\routing.py", line 530, in aenter
await self._router.startup()
File "C:\Users\EchoPac.conda\envs\monailabel-env\lib\site-packages\starlette\routing.py", line 612, in startup
await handler()
File "C:\Users\EchoPac.conda\envs\monailabel-env\lib\site-packages\monailabel\app.py", line 106, in startup_event
instance = app_instance()
File "C:\Users\EchoPac.conda\envs\monailabel-env\lib\site-packages\monailabel\interfaces\utils\app.py", line 51, in app_instance
app = c(app_dir=app_dir, studies=studies, conf=conf)
File "C:\Users\EchoPac\apps\radiology\main.py", line 95, in init
self.models[k].init(k, self.model_dir, conf, self.planner)
File "C:\Users\EchoPac\apps\radiology\lib\configs\deepedit.py", line 74, in init
download_file(url, self.path[0])
File "C:\Users\EchoPac.conda\envs\monailabel-env\lib\site-packages\monailabel\utils\others\generic.py", line 187, in download_file
download_url(url, path)
File "C:\Users\EchoPac.conda\envs\monailabel-env\lib\site-packages\monai\apps\utils.py", line 203, in download_url
_download_with_progress(url, tmp_name, progress=progress)
File "C:\Users\EchoPac.conda\envs\monailabel-env\lib\site-packages\monai\apps\utils.py", line 114, in _download_with_progress
raise e
File "C:\Users\EchoPac.conda\envs\monailabel-env\lib\site-packages\monai\apps\utils.py", line 107, in _download_with_progress
urlretrieve(url, filepath, reporthook=t.update_to)
File "C:\Users\EchoPac.conda\envs\monailabel-env\lib\urllib\request.py", line 239, in urlretrieve
with contextlib.closing(urlopen(url, data)) as fp:
File "C:\Users\EchoPac.conda\envs\monailabel-env\lib\urllib\request.py", line 214, in urlopen
return opener.open(url, data, timeout)
File "C:\Users\EchoPac.conda\envs\monailabel-env\lib\urllib\request.py", line 517, in open
response = self._open(req, data)
File "C:\Users\EchoPac.conda\envs\monailabel-env\lib\urllib\request.py", line 534, in _open
result = self._call_chain(self.handle_open, protocol, protocol +
File "C:\Users\EchoPac.conda\envs\monailabel-env\lib\urllib\request.py", line 494, in _call_chain
result = func(*args)
File "C:\Users\EchoPac.conda\envs\monailabel-env\lib\urllib\request.py", line 1389, in https_open
return self.do_open(http.client.HTTPSConnection, req,
File "C:\Users\EchoPac.conda\envs\monailabel-env\lib\urllib\request.py", line 1349, in do_open
raise URLError(err)
urllib.error.URLError: <urlopen error [WinError 10054] An existing connection was forcibly closed by the remote host>

[2023-01-20 17:48:14,806] [11612] [MainThread] [ERROR] (uvicorn.error:56) - Application startup failed. Exiting.

[diazandr3s]

Hi @borantolic,

Thanks for trying MONAI Label.

The library is being tested on both Linux and Windows: https://github.com/Project-MONAI/MONAILabel#installation

One thing you could do is run the server on either Linux or Windows and the 3D Slicer on MAC.

BTW, this Wednesday, the 25th of Jan 2023 we're running a workshop for MONAI Label. It is free to participate and you can try different pretrained models on the AWS platform: https://projectweek.na-mic.org/PW38_2023_GranCanaria/MONAILabel_Workshop.html

[borantolic]

Hi! I am not really sure I explained my problem sufficiently.
I have a working installation (3d Slicer+Monai) on Mac, the problem is with the Windows installation. I would like to use the server and 3d Slicer on Windows, since the computer is much more powerful. In my original post I pasted the log of what get when I try to start the server on my Windows computer. Is there anything there that you see that could cause the problems? I went through the log, try to Google some of the errors, but I haven't been successful.
Thanks!

[SachidanandAlle]

The log says model failed to download from Internet.. the pretrained models are one of the GitHub releases section.. u can see the errors on the log saying http connect error

[borantolic]

I have seen that. I tried going to the specified address through my browser and it downloads the file with no problem. I don't know why it fails to download it when it is run via this star_server command. Any ideas? Can I manually download the file and change the command in some way so it wouldn't rely on the file from the net?

[SachidanandAlle]

No idea why it's happening on your box.. if u have another one try it.. or just download it and place it manually

[borantolic]

I could download it manually, but where should I put the file? When it downloads it, it always uses a different temporary directory.
I would somehow need to disable this download and tell the script to look for this file locally?

[SachidanandAlle]

Models folder against corresponding pretrained file name

[borantolic]

It works! Thanks a lot!