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Project-MONAI / MONAILabel

MONAI Label is an intelligent open source image labeling and learning tool.
https://docs.monai.io/projects/label
Apache License 2.0
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I can't start server windows 10 with anaconda3 [MainThread] [ERROR] (uvicorn.error:56) - Application startup failed. Exiting. #1264

Closed varemenoscomputeras closed 1 year ago

varemenoscomputeras commented 1 year ago

(base) C:\Users\demos\anaconda3>monailabel start_server --app C:\Users\demos\apps\pathology --studies C:\Users\demos\datasets\Task05_Prostate\imagesTr Using PYTHONPATH=C:\Users\demos; "" 2023-01-25 23:13:08,555 - USING:: version = False 2023-01-25 23:13:08,555 - USING:: app = C:\Users\demos\apps\pathology 2023-01-25 23:13:08,555 - USING:: studies = C:\Users\demos\datasets\Task05_Prostate\imagesTr 2023-01-25 23:13:08,556 - USING:: verbose = INFO 2023-01-25 23:13:08,556 - USING:: conf = None 2023-01-25 23:13:08,557 - USING:: host = 0.0.0.0 2023-01-25 23:13:08,558 - USING:: port = 8000 2023-01-25 23:13:08,558 - USING:: uvicorn_app = monailabel.app:app 2023-01-25 23:13:08,558 - USING:: ssl_keyfile = None 2023-01-25 23:13:08,559 - USING:: ssl_certfile = None 2023-01-25 23:13:08,559 - USING:: ssl_keyfile_password = None 2023-01-25 23:13:08,560 - USING:: ssl_ca_certs = None 2023-01-25 23:13:08,560 - USING:: workers = None 2023-01-25 23:13:08,560 - USING:: limit_concurrency = None 2023-01-25 23:13:08,561 - USING:: access_log = False 2023-01-25 23:13:08,561 - USING:: log_config = None 2023-01-25 23:13:08,562 - USING:: dryrun = False 2023-01-25 23:13:08,562 - USING:: action = start_server 2023-01-25 23:13:08,562 - ENV SETTINGS:: MONAI_LABEL_API_STR = 2023-01-25 23:13:08,563 - ENV SETTINGS:: MONAI_LABEL_PROJECT_NAME = MONAILabel 2023-01-25 23:13:08,563 - ENV SETTINGS:: MONAI_LABEL_APP_DIR = 2023-01-25 23:13:08,563 - ENV SETTINGS:: MONAI_LABEL_STUDIES = 2023-01-25 23:13:08,564 - ENV SETTINGS:: MONAI_LABEL_AUTH_ENABLE = False 2023-01-25 23:13:08,564 - ENV SETTINGS:: MONAI_LABEL_AUTH_DB = 2023-01-25 23:13:08,565 - ENV SETTINGS:: MONAI_LABEL_APP_CONF = '{}' 2023-01-25 23:13:08,565 - ENV SETTINGS:: MONAI_LABEL_TASKS_TRAIN = True 2023-01-25 23:13:08,565 - ENV SETTINGS:: MONAI_LABEL_TASKS_STRATEGY = True 2023-01-25 23:13:08,566 - ENV SETTINGS:: MONAI_LABEL_TASKS_SCORING = True 2023-01-25 23:13:08,566 - ENV SETTINGS:: MONAI_LABEL_TASKS_BATCH_INFER = True 2023-01-25 23:13:08,566 - ENV SETTINGS:: MONAI_LABEL_DATASTORE = 2023-01-25 23:13:08,567 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_URL = 2023-01-25 23:13:08,567 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_USERNAME = 2023-01-25 23:13:08,568 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_PASSWORD = 2023-01-25 23:13:08,568 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_API_KEY = 2023-01-25 23:13:08,568 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_CACHE_PATH = 2023-01-25 23:13:08,569 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_PROJECT = 2023-01-25 23:13:08,572 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_ASSET_PATH = 2023-01-25 23:13:08,572 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_DSA_ANNOTATION_GROUPS = 2023-01-25 23:13:08,572 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_USERNAME = 2023-01-25 23:13:08,573 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_PASSWORD = 2023-01-25 23:13:08,573 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CACHE_PATH = 2023-01-25 23:13:08,573 - ENV SETTINGS:: MONAI_LABEL_QIDO_PREFIX = None 2023-01-25 23:13:08,574 - ENV SETTINGS:: MONAI_LABEL_WADO_PREFIX = None 2023-01-25 23:13:08,574 - ENV SETTINGS:: MONAI_LABEL_STOW_PREFIX = None 2023-01-25 23:13:08,574 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_FETCH_BY_FRAME = False 2023-01-25 23:13:08,575 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CONVERT_TO_NIFTI = True 2023-01-25 23:13:08,575 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_SEARCH_FILTER = '{"Modality": "CT"}' 2023-01-25 23:13:08,576 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CACHE_EXPIRY = 180 2023-01-25 23:13:08,576 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_PROXY_TIMEOUT = 30.0 2023-01-25 23:13:08,576 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_READ_TIMEOUT = 5.0 2023-01-25 23:13:08,577 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_AUTO_RELOAD = True 2023-01-25 23:13:08,577 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_READ_ONLY = False 2023-01-25 23:13:08,578 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_FILE_EXT = '[".nii.gz", ".nii", ".nrrd", ".jpg", ".png", ".tif", ".svs", ".xml"]' 2023-01-25 23:13:08,578 - ENV SETTINGS:: MONAI_LABEL_SERVER_PORT = 8000 2023-01-25 23:13:08,578 - ENV SETTINGS:: MONAI_LABEL_CORS_ORIGINS = '[]' 2023-01-25 23:13:08,579 - ENV SETTINGS:: MONAI_LABEL_SESSIONS = True 2023-01-25 23:13:08,579 - ENV SETTINGS:: MONAI_LABEL_SESSION_PATH = 2023-01-25 23:13:08,579 - ENV SETTINGS:: MONAI_LABEL_SESSION_EXPIRY = 3600 2023-01-25 23:13:08,580 - ENV SETTINGS:: MONAI_LABEL_INFER_CONCURRENCY = -1 2023-01-25 23:13:08,580 - ENV SETTINGS:: MONAI_LABEL_INFER_TIMEOUT = 600 2023-01-25 23:13:08,581 - ENV SETTINGS:: MONAI_LABEL_TRACKING_ENABLED = True 2023-01-25 23:13:08,581 - ENV SETTINGS:: MONAI_LABEL_TRACKING_URI = 2023-01-25 23:13:08,581 - ENV SETTINGS:: MONAI_ZOO_SOURCE = github 2023-01-25 23:13:08,582 - ENV SETTINGS:: MONAI_ZOO_REPO = Project-MONAI/model-zoo/hosting_storage_v1 2023-01-25 23:13:08,582 - ENV SETTINGS:: MONAI_ZOO_AUTH_TOKEN = 2023-01-25 23:13:08,582 - ENV SETTINGS:: MONAI_LABEL_AUTO_UPDATE_SCORING = True 2023-01-25 23:13:08,583 - Allow Origins: ['*'] [2023-01-25 23:13:09,498] [20076] [MainThread] [INFO] (uvicorn.error:75) - Started server process [20076] [2023-01-25 23:13:09,499] [20076] [MainThread] [INFO] (uvicorn.error:45) - Waiting for application startup. [2023-01-25 23:13:09,500] [20076] [MainThread] [INFO] (monailabel.interfaces.utils.app:38) - Initializing App from: C:\Users\demos\apps\pathology; studies: C:\Users\demos\datasets\Task05_Prostate\imagesTr; conf: {} [2023-01-25 23:13:09,508] [20076] [MainThread] [ERROR] (uvicorn.error:119) - Traceback (most recent call last): File "C:\Users\demos\anaconda3\lib\site-packages\starlette\routing.py", line 635, in lifespan async with self.lifespan_context(app): File "C:\Users\demos\anaconda3\lib\site-packages\starlette\routing.py", line 530, in aenter await self._router.startup() File "C:\Users\demos\anaconda3\lib\site-packages\starlette\routing.py", line 612, in startup await handler() File "C:\Users\demos\anaconda3\lib\site-packages\monailabel\app.py", line 106, in startup_event instance = app_instance() File "C:\Users\demos\anaconda3\lib\site-packages\monailabel\interfaces\utils\app.py", line 44, in app_instance c = get_class_of_subclass_from_file("main", main_py, "MONAILabelApp") File "C:\Users\demos\anaconda3\lib\site-packages\monailabel\utils\others\class_utils.py", line 55, in get_class_of_subclass_from_file return get_class_of_subclass(module_from_file(module_name, file_path), class_c) File "C:\Users\demos\anaconda3\lib\site-packages\monailabel\utils\others\class_utils.py", line 27, in module_from_file spec.loader.exec_module(module) File "", line 850, in exec_module File "", line 228, in _call_with_frames_removed File "C:\Users\demos\apps\pathology\main.py", line 18, in import lib.configs File "C:\Users\demos\apps\pathology\lib__init.py", line 18, in cdll.LoadLibrary(str(ctypes.util.find_library("libopenslide-0.dll"))) File "C:\Users\demos\anaconda3\lib\ctypes__init__.py", line 460, in LoadLibrary return self._dlltype(name) File "C:\Users\demos\anaconda3\lib\ctypes\init.py", line 382, in init__ self._handle = _dlopen(self._name, mode) FileNotFoundError: Could not find module 'None' (or one of its dependencies). Try using the full path with constructor syntax.

[2023-01-25 23:13:09,509] [20076] [MainThread] [ERROR] (uvicorn.error:56) - Application startup failed. Exiting.

SachidanandAlle commented 1 year ago

You need to install openslide library.. some instructions are mentioned on the pathology app readme

diazandr3s commented 1 year ago

Hi @varemenoscomputeras,

Here you can find more instructions: https://github.com/Project-MONAI/MONAILabel/issues/683#issuecomment-1348234061

varemenoscomputeras commented 1 year ago

thank you, I did it but now application startup failed for other reason...

(base) C:\pathology\openslide\bin>monailabel start_server --app C:\Users\demos\apps\pathology --studies C:\Users\demos\datasets\Task05_Prostate\imagesTr Using PYTHONPATH=C:\Users\demos; "" 2023-01-26 01:26:42,030 - USING:: version = False 2023-01-26 01:26:42,030 - USING:: app = C:\Users\demos\apps\pathology 2023-01-26 01:26:42,030 - USING:: studies = C:\Users\demos\datasets\Task05_Prostate\imagesTr 2023-01-26 01:26:42,030 - USING:: verbose = INFO 2023-01-26 01:26:42,030 - USING:: conf = None 2023-01-26 01:26:42,030 - USING:: host = 0.0.0.0 2023-01-26 01:26:42,030 - USING:: port = 8000 2023-01-26 01:26:42,030 - USING:: uvicorn_app = monailabel.app:app 2023-01-26 01:26:42,030 - USING:: ssl_keyfile = None 2023-01-26 01:26:42,030 - USING:: ssl_certfile = None 2023-01-26 01:26:42,030 - USING:: ssl_keyfile_password = None 2023-01-26 01:26:42,030 - USING:: ssl_ca_certs = None 2023-01-26 01:26:42,046 - USING:: workers = None 2023-01-26 01:26:42,046 - USING:: limit_concurrency = None 2023-01-26 01:26:42,046 - USING:: access_log = False 2023-01-26 01:26:42,046 - USING:: log_config = None 2023-01-26 01:26:42,046 - USING:: dryrun = False 2023-01-26 01:26:42,046 - USING:: action = start_server 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_API_STR = 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_PROJECT_NAME = MONAILabel 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_APP_DIR = 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_STUDIES = 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_AUTH_ENABLE = False 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_AUTH_DB = 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_APP_CONF = '{}' 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_TASKS_TRAIN = True 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_TASKS_STRATEGY = True 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_TASKS_SCORING = True 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_TASKS_BATCH_INFER = True 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_DATASTORE = 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_URL = 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_USERNAME = 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_PASSWORD = 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_API_KEY = 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_CACHE_PATH = 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_PROJECT = 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_ASSET_PATH = 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_DSA_ANNOTATION_GROUPS = 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_USERNAME = 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_PASSWORD = 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CACHE_PATH = 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_QIDO_PREFIX = None 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_WADO_PREFIX = None 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_STOW_PREFIX = None 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_FETCH_BY_FRAME = False 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CONVERT_TO_NIFTI = True 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_SEARCH_FILTER = '{"Modality": "CT"}' 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CACHE_EXPIRY = 180 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_PROXY_TIMEOUT = 30.0 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_READ_TIMEOUT = 5.0 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_AUTO_RELOAD = True 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_READ_ONLY = False 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_FILE_EXT = '[".nii.gz", ".nii", ".nrrd", ".jpg", ".png", ".tif", ".svs", ".xml"]' 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_SERVER_PORT = 8000 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_CORS_ORIGINS = '[]' 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_SESSIONS = True 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_SESSION_PATH = 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_SESSION_EXPIRY = 3600 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_INFER_CONCURRENCY = -1 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_INFER_TIMEOUT = 600 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_TRACKING_ENABLED = True 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_TRACKING_URI = 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_ZOO_SOURCE = github 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_ZOO_REPO = Project-MONAI/model-zoo/hosting_storage_v1 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_ZOO_AUTH_TOKEN = 2023-01-26 01:26:42,046 - ENV SETTINGS:: MONAI_LABEL_AUTO_UPDATE_SCORING = True 2023-01-26 01:26:42,046 - Allow Origins: ['*'] [2023-01-26 01:26:43,148] [24944] [MainThread] [INFO] (uvicorn.error:75) - Started server process [24944] [2023-01-26 01:26:43,148] [24944] [MainThread] [INFO] (uvicorn.error:45) - Waiting for application startup. [2023-01-26 01:26:43,148] [24944] [MainThread] [INFO] (monailabel.interfaces.utils.app:38) - Initializing App from: C:\Users\demos\apps\pathology; studies: C:\Users\demos\datasets\Task05_Prostate\imagesTr; conf: {} [2023-01-26 01:26:43,223] [24944] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for MONAILabelApp Found: <class 'main.MyApp'> [2023-01-26 01:26:43,254] [24944] [MainThread] [ERROR] (uvicorn.error:119) - Traceback (most recent call last): File "C:\Users\demos\anaconda3\lib\site-packages\starlette\routing.py", line 635, in lifespan async with self.lifespan_context(app): File "C:\Users\demos\anaconda3\lib\site-packages\starlette\routing.py", line 530, in aenter await self._router.startup() File "C:\Users\demos\anaconda3\lib\site-packages\starlette\routing.py", line 612, in startup await handler() File "C:\Users\demos\anaconda3\lib\site-packages\monailabel\app.py", line 106, in startup_event instance = app_instance() File "C:\Users\demos\anaconda3\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\demos\apps\pathology\main.py", line 46, in init candidates = get_class_names(lib.configs, "TaskConfig") File "C:\Users\demos\anaconda3\lib\site-packages\monailabel\utils\others\class_utils.py", line 144, in get_class_names module = importlib.import_module("." + name, package=current_module_name) File "C:\Users\demos\anaconda3\lib\importlib__init.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 1030, in _gcd_import File "", line 1007, in _find_and_load File "", line 986, in _find_and_load_unlocked File "", line 680, in _load_unlocked File "", line 850, in exec_module File "", line 228, in _call_with_frames_removed File "C:\Users\demos\apps\pathology\lib\configs\classification_nuclei.py", line 17, in import lib.trainers File "C:\Users\demos\apps\pathology\lib\trainers\init.py", line 15, in from .segmentation_nuclei import SegmentationNuclei File "C:\Users\demos\apps\pathology\lib\trainers\segmentation_nuclei.py", line 17, in from ignite.metrics import Accuracy File "C:\Users\demos\anaconda3\lib\site-packages\ignite\init.py", line 3, in import ignite.engine File "C:\Users\demos\anaconda3\lib\site-packages\ignite\engine\init.py", line 10, in from ignite.metrics import Metric File "C:\Users\demos\anaconda3\lib\site-packages\ignite\metrics\init.py", line 7, in from ignite.metrics.frequency import Frequency File "C:\Users\demos\anaconda3\lib\site-packages\ignite\metrics\frequency.py", line 7, in from ignite.handlers.timing import Timer File "C:\Users\demos\anaconda3\lib\site-packages\ignite\handlers\init.py", line 5, in from ignite.handlers.checkpoint import Checkpoint, DiskSaver, ModelCheckpoint File "C:\Users\demos\anaconda3\lib\site-packages\ignite\handlers\checkpoint.py", line 17, in from torch.distributed.optim import ZeroRedundancyOptimizer File "C:\Users\demos\AppData\Roaming\Python\Python39\site-packages\torch\distributed\optim\init.py", line 8, in from .optimizer import DistributedOptimizer File "C:\Users\demos\AppData\Roaming\Python\Python39\site-packages\torch\distributed\optim\optimizer.py", line 9, in from torch.distributed.rpc import RRef ImportError: cannot import name 'RRef' from 'torch.distributed.rpc' (C:\Users\demos\AppData\Roaming\Python\Python39\site-packages\torch\distributed\rpc\init__.py)

[2023-01-26 01:26:43,254] [24944] [MainThread] [ERROR] (uvicorn.error:56) - Application startup failed. Exiting.

varemenoscomputeras commented 1 year ago

this is my $Env:PATH

C:\Program Files (x86)\Common Files\Oracle\Java\javapath;C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v10.1\bin;C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v10.1\libnvvp;C:\Program Files\AdoptOpenJDK\jdk-8.0.242.08-hotspot\bin;C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v11.6\bin;C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v11.6\libnvvp;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Windows\System32\OpenSSH\;C:\Program Files\NVIDIA Corporation\NVIDIA NvDLISR;C:\Program Files (x86)\NVIDIA Corporation\PhysX\Common;C:\Program Files\dotnet\;C:\Program Files\NVIDIA Corporation\Nsight Compute 2019.4.0\;C:\Program Files\MATLAB\MATLAB Runtime\v911\runtime\win64;C:\Program Files\Docker\Docker\resources\bin;C:\Users\demos\anaconda3\Lib\site-packages\monailabel\scripts;C:\Users\demos\AppData\Local\Microsoft\WindowsApps;C:\Users\demos.dotnet\tools;;C:\pathology\openslide\bin

diazandr3s commented 1 year ago

this is my $Env:PATH

C:\Program Files (x86)\Common Files\Oracle\Java\javapath;C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v10.1\bin;C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v10.1\libnvvp;C:\Program Files\AdoptOpenJDK\jdk-8.0.242.08-hotspot\bin;C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v11.6\bin;C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v11.6\libnvvp;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0;C:\Windows\System32\OpenSSH;C:\Program Files\NVIDIA Corporation\NVIDIA NvDLISR;C:\Program Files (x86)\NVIDIA Corporation\PhysX\Common;C:\Program Files\dotnet;C:\Program Files\NVIDIA Corporation\Nsight Compute 2019.4.0;C:\Program Files\MATLAB\MATLAB Runtime\v911\runtime\win64;C:\Program Files\Docker\Docker\resources\bin;C:\Users\demos\anaconda3\Lib\site-packages\monailabel\scripts;C:\Users\demos\AppData\Local\Microsoft\WindowsApps;C:\Users\demos.dotnet\tools;;C:\pathology\openslide\bin

Sorry, are you trying to start the pathology app on the CT images?

monailabel start_server --app C:\Users\demos\apps\pathology --studies C:\Users\demos\datasets\Task05_Prostate\imagesTr

Are you sure you want to use the pathology app? Please specify the model as it's suggested here: https://github.com/Project-MONAI/MONAILabel/tree/main/sample-apps/radiology#how-to-use

varemenoscomputeras commented 1 year ago

I want to use the pathology app with QuPath. I tried to run monailabel start_server --app C:\Users\demos\anaconda3\monailabel\sample-apps\pathology --studies http://0.0.0.0:8080/api/v1 monailabel start_server --app C:\Users\demos\apps\pathology --studies C:\Users\demos\datasets\wsi monailabel start_server --app sample-apps/pathology --studies datasets/wsi

and all with the same results [MainThread] [ERROR] (uvicorn.error:56) - Application startup failed. Exiting.

Thank you

diazandr3s commented 1 year ago

I want to use the pathology app with QuPath. I tried to run monailabel start_server --app C:\Users\demos\anaconda3\monailabel\sample-apps\pathology --studies http://0.0.0.0:8080/api/v1 monailabel start_server --app C:\Users\demos\apps\pathology --studies C:\Users\demos\datasets\wsi monailabel start_server --app sample-apps/pathology --studies datasets/wsi

and all with the same results [MainThread] [ERROR] (uvicorn.error:56) - Application startup failed. Exiting.

Thank you

Sorry, I'm a bit confused. Where are you hosting the histopathological images? Locally on your PC? if yes, this command won't work as you're telling the MONAI Label server that images are hosted on a server.

monailabel start_server --app C:\Users\demos\anaconda3\monailabel\sample-apps\pathology --studies http://0.0.0.0:8080/api/v1

If images are local, the command that should work is this:

monailabel start_server --app C:\Users\demos\apps\pathology --studies C:\Users\demos\datasets\wsi

As long the histopathological image is in this folder:

C:\Users\demos\datasets\wsi

and the pathology app is in this folder:

C:\Users\demos\apps\pathology

The logs that you sent before showed you were using CT images with the pathology app.

This error tells very little:

[MainThread] [ERROR] (uvicorn.error:56) - Application startup failed. Exiting.

Can you send the full logs?

varemenoscomputeras commented 1 year ago

I tried may compinations. The images are local,

(base) C:\pathology\openslide\bin>monailabel start_server --app C:\Users\demos\apps\pathology --studies C:\Users\demos\datasets\wsi Using PYTHONPATH=C:\Users\demos; "" 2023-01-26 08:26:13,124 - USING:: version = False 2023-01-26 08:26:13,124 - USING:: app = C:\Users\demos\apps\pathology 2023-01-26 08:26:13,124 - USING:: studies = C:\Users\demos\datasets\wsi 2023-01-26 08:26:13,124 - USING:: verbose = INFO 2023-01-26 08:26:13,124 - USING:: conf = None 2023-01-26 08:26:13,124 - USING:: host = 0.0.0.0 2023-01-26 08:26:13,124 - USING:: port = 8000 2023-01-26 08:26:13,124 - USING:: uvicorn_app = monailabel.app:app 2023-01-26 08:26:13,124 - USING:: ssl_keyfile = None 2023-01-26 08:26:13,124 - USING:: ssl_certfile = None 2023-01-26 08:26:13,124 - USING:: ssl_keyfile_password = None 2023-01-26 08:26:13,124 - USING:: ssl_ca_certs = None 2023-01-26 08:26:13,124 - USING:: workers = None 2023-01-26 08:26:13,124 - USING:: limit_concurrency = None 2023-01-26 08:26:13,124 - USING:: access_log = False 2023-01-26 08:26:13,124 - USING:: log_config = None 2023-01-26 08:26:13,124 - USING:: dryrun = False 2023-01-26 08:26:13,124 - USING:: action = start_server 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_API_STR = 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_PROJECT_NAME = MONAILabel 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_APP_DIR = 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_STUDIES = 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_AUTH_ENABLE = False 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_AUTH_DB = 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_APP_CONF = '{}' 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_TASKS_TRAIN = True 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_TASKS_STRATEGY = True 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_TASKS_SCORING = True 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_TASKS_BATCH_INFER = True 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_DATASTORE = 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_URL = 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_USERNAME = 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_PASSWORD = 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_API_KEY = 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_CACHE_PATH = 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_PROJECT = 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_ASSET_PATH = 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_DSA_ANNOTATION_GROUPS = 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_USERNAME = 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_PASSWORD = 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CACHE_PATH = 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_QIDO_PREFIX = None 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_WADO_PREFIX = None 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_STOW_PREFIX = None 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_FETCH_BY_FRAME = False 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CONVERT_TO_NIFTI = True 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_SEARCH_FILTER = '{"Modality": "CT"}' 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CACHE_EXPIRY = 180 2023-01-26 08:26:13,124 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_PROXY_TIMEOUT = 30.0 2023-01-26 08:26:13,139 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_READ_TIMEOUT = 5.0 2023-01-26 08:26:13,139 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_AUTO_RELOAD = True 2023-01-26 08:26:13,139 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_READ_ONLY = False 2023-01-26 08:26:13,139 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_FILE_EXT = '[".nii.gz", ".nii", ".nrrd", ".jpg", ".png", ".tif", ".svs", ".xml"]' 2023-01-26 08:26:13,139 - ENV SETTINGS:: MONAI_LABEL_SERVER_PORT = 8000 2023-01-26 08:26:13,139 - ENV SETTINGS:: MONAI_LABEL_CORS_ORIGINS = '[]' 2023-01-26 08:26:13,139 - ENV SETTINGS:: MONAI_LABEL_SESSIONS = True 2023-01-26 08:26:13,139 - ENV SETTINGS:: MONAI_LABEL_SESSION_PATH = 2023-01-26 08:26:13,139 - ENV SETTINGS:: MONAI_LABEL_SESSION_EXPIRY = 3600 2023-01-26 08:26:13,139 - ENV SETTINGS:: MONAI_LABEL_INFER_CONCURRENCY = -1 2023-01-26 08:26:13,139 - ENV SETTINGS:: MONAI_LABEL_INFER_TIMEOUT = 600 2023-01-26 08:26:13,139 - ENV SETTINGS:: MONAI_LABEL_TRACKING_ENABLED = True 2023-01-26 08:26:13,139 - ENV SETTINGS:: MONAI_LABEL_TRACKING_URI = 2023-01-26 08:26:13,139 - ENV SETTINGS:: MONAI_ZOO_SOURCE = github 2023-01-26 08:26:13,139 - ENV SETTINGS:: MONAI_ZOO_REPO = Project-MONAI/model-zoo/hosting_storage_v1 2023-01-26 08:26:13,139 - ENV SETTINGS:: MONAI_ZOO_AUTH_TOKEN = 2023-01-26 08:26:13,139 - ENV SETTINGS:: MONAI_LABEL_AUTO_UPDATE_SCORING = True 2023-01-26 08:26:13,139 - Allow Origins: ['*'] [2023-01-26 08:26:14,309] [2692] [MainThread] [INFO] (uvicorn.error:75) - Started server process [2692] [2023-01-26 08:26:14,309] [2692] [MainThread] [INFO] (uvicorn.error:45) - Waiting for application startup. [2023-01-26 08:26:14,309] [2692] [MainThread] [INFO] (monailabel.interfaces.utils.app:38) - Initializing App from: C:\Users\demos\apps\pathology; studies: C:\Users\demos\datasets\wsi; conf: {} [2023-01-26 08:26:14,375] [2692] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for MONAILabelApp Found: <class 'main.MyApp'> [2023-01-26 08:26:14,393] [2692] [MainThread] [ERROR] (uvicorn.error:119) - Traceback (most recent call last): File "C:\Users\demos\anaconda3\lib\site-packages\starlette\routing.py", line 635, in lifespan async with self.lifespan_context(app): File "C:\Users\demos\anaconda3\lib\site-packages\starlette\routing.py", line 530, in aenter await self._router.startup() File "C:\Users\demos\anaconda3\lib\site-packages\starlette\routing.py", line 612, in startup await handler() File "C:\Users\demos\anaconda3\lib\site-packages\monailabel\app.py", line 106, in startup_event instance = app_instance() File "C:\Users\demos\anaconda3\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\demos\apps\pathology\main.py", line 46, in init candidates = get_class_names(lib.configs, "TaskConfig") File "C:\Users\demos\anaconda3\lib\site-packages\monailabel\utils\others\class_utils.py", line 144, in get_class_names module = importlib.import_module("." + name, package=current_module_name) File "C:\Users\demos\anaconda3\lib\importlib__init.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 1030, in _gcd_import File "", line 1007, in _find_and_load File "", line 986, in _find_and_load_unlocked File "", line 680, in _load_unlocked File "", line 850, in exec_module File "", line 228, in _call_with_frames_removed File "C:\Users\demos\apps\pathology\lib\configs\classification_nuclei.py", line 17, in import lib.trainers File "C:\Users\demos\apps\pathology\lib\trainers\init.py", line 15, in from .segmentation_nuclei import SegmentationNuclei File "C:\Users\demos\apps\pathology\lib\trainers\segmentation_nuclei.py", line 17, in from ignite.metrics import Accuracy File "C:\Users\demos\anaconda3\lib\site-packages\ignite\init.py", line 3, in import ignite.engine File "C:\Users\demos\anaconda3\lib\site-packages\ignite\engine\init.py", line 10, in from ignite.metrics import Metric File "C:\Users\demos\anaconda3\lib\site-packages\ignite\metrics\init.py", line 7, in from ignite.metrics.frequency import Frequency File "C:\Users\demos\anaconda3\lib\site-packages\ignite\metrics\frequency.py", line 7, in from ignite.handlers.timing import Timer File "C:\Users\demos\anaconda3\lib\site-packages\ignite\handlers\init.py", line 5, in from ignite.handlers.checkpoint import Checkpoint, DiskSaver, ModelCheckpoint File "C:\Users\demos\anaconda3\lib\site-packages\ignite\handlers\checkpoint.py", line 17, in from torch.distributed.optim import ZeroRedundancyOptimizer File "C:\Users\demos\AppData\Roaming\Python\Python39\site-packages\torch\distributed\optim\init.py", line 8, in from .optimizer import DistributedOptimizer File "C:\Users\demos\AppData\Roaming\Python\Python39\site-packages\torch\distributed\optim\optimizer.py", line 9, in from torch.distributed.rpc import RRef ImportError: cannot import name 'RRef' from 'torch.distributed.rpc' (C:\Users\demos\AppData\Roaming\Python\Python39\site-packages\torch\distributed\rpc\init__.py)

[2023-01-26 08:26:14,393] [2692] [MainThread] [ERROR] (uvicorn.error:56) - Application startup failed. Exiting.

SachidanandAlle commented 1 year ago

Check your pytorch version.. it should support GPU

varemenoscomputeras commented 1 year ago

I think it support GPU

import torch torch.cuda.is_available() True torch.cuda.current_device() 0 torch.cuda.device_count() 1 torch.cuda.get_device_name(0) 'NVIDIA GeForce GTX 1650'

device = torch.device('cuda' if torch.cuda.is_available() else 'cpu') print('Using device:', device) Using device: cuda print()

if device.type == 'cuda': print(torch.cuda.get_device_name(0)) NVIDIA GeForce GTX 1650 print('Allocated:', round(torch.cuda.memory_allocated(0)/10243,1), 'GB') Allocated: 0.0 GB print('Cached: ', round(torch.cuda.memory_cached(0)/10243,1), 'GB') Cached: 0.0 GB

Name: torch Version: 1.9.1+cu102 Summary: Tensors and Dynamic neural networks in Python with strong GPU acceleration Home-page: https://pytorch.org/ Author: PyTorch Team Author-email: packages@pytorch.org License: BSD-3 Location: c:\users\demos\appdata\roaming\python\python39\site-packages Requires: typing-extensions Required-by: monai, monailabel, pytorch-ignite, torchaudio, torchvision

SachidanandAlle commented 1 year ago

ImportError: cannot import name 'RRef' from 'torch.distributed.rpc'

This is the error you have got.. and this is very much related to your pytorch + gpu setup/env.

SachidanandAlle commented 1 year ago

I see you have pytorch with cu102 (cuda 10x.. pretty old).. what is the output of nvidia-smi (u will see it's installed in some programs folder)

varemenoscomputeras commented 1 year ago

nvidia-smi.exe Thu Jan 26 09:38:07 2023 +-----------------------------------------------------------------------------+ | NVIDIA-SMI 528.24 Driver Version: 528.24 CUDA Version: 12.0 | |-------------------------------+----------------------+----------------------+ | GPU Name TCC/WDDM | Bus-Id Disp.A | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | | | | MIG M. | |===============================+======================+======================| | 0 NVIDIA GeForce ... WDDM | 00000000:01:00.0 Off | N/A | | N/A 39C P8 1W / 50W | 86MiB / 4096MiB | 0% Default | | | | N/A | +-------------------------------+----------------------+----------------------+

+-----------------------------------------------------------------------------+ | Processes: | | GPU GI CI PID Type Process name GPU Memory | | ID ID Usage | |=============================================================================| | 0 N/A N/A 2984 C+G ...e\PhoneExperienceHost.exe N/A | | 0 N/A N/A 4508 C+G ...8wekyb3d8bbwe\GameBar.exe N/A | | 0 N/A N/A 9820 C+G ...artMenuExperienceHost.exe N/A | | 0 N/A N/A 10252 C+G ...2txyewy\TextInputHost.exe N/A | | 0 N/A N/A 10600 C+G ...5n1h2txyewy\SearchApp.exe N/A | | 0 N/A N/A 11416 C+G ...top\WDADesktopService.exe N/A | | 0 N/A N/A 11892 C+G ...cw5n1h2txyewy\LockApp.exe N/A | | 0 N/A N/A 14436 C+G ...8wekyb3d8bbwe\Cortana.exe N/A | | 0 N/A N/A 15040 C+G ...ekyb3d8bbwe\HxOutlook.exe N/A | +-----------------------------------------------------------------------------+

varemenoscomputeras commented 1 year ago

I installed pytorch with Compute Platform cpuonly and it worked. I tried to use gpu cuda=11.6 and cuda=11.7 without success.

SachidanandAlle commented 1 year ago

I do have a laptop with smaller GPU and windows.. I can run basic train/inference using latest monailabel (or github) I believe it's more of your python env (I normally use pip) issue

PS C:\Projects\MONAILabel> nvidia-smi
Sun Mar 19 23:26:24 2023
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 527.37       Driver Version: 527.37       CUDA Version: 12.0     |
|-------------------------------+----------------------+----------------------+
| GPU  Name            TCC/WDDM | Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
|                               |                      |               MIG M. |
|===============================+======================+======================|
|   0  Quadro RTX 3000    WDDM  | 00000000:01:00.0 Off |                  N/A |
| N/A   51C    P8     3W /  N/A |   5056MiB /  6144MiB |      0%      Default |
|                               |                      |                  N/A |
+-------------------------------+----------------------+----------------------+

+-----------------------------------------------------------------------------+
| Processes:                                                                  |
|  GPU   GI   CI        PID   Type   Process name                  GPU Memory |
|        ID   ID                                                   Usage      |
|=============================================================================|
|    0   N/A  N/A     21612      C   ...ython\Python39\python.exe    N/A      |
+-----------------------------------------------------------------------------+
P
SachidanandAlle commented 1 year ago

No further updates/comments on this issue. I believe things are resolved. Closing it for now. Feel free to reopen if needed.