oeway
commented
5 years ago Hi, thanks for the report.
For the plugin, I only tested on Ubuntu with GPU.
Unfortunately, i don’t have a windows machine with GPU here. @muellerflorian have you ever tried on a window machine? Maybe you can take a look see if you can reproduce it?
Also, we have some ongoing work on improving the DPN code base to work with the latest Pytorch and on GPU. I will try to make that available in a two or three days so you can test that.
On Wed 2 Oct 2019 at 18:53, Padoup-Padoup notifications@github.com wrote:
Hi @oeway https://github.com/oeway,
I just tried to open the DPNUnet plugin in Imjoy, and I am getting the following error in the Plugin Engine console. Can you reproduce the problem? Could you tell me what kind of information you would need me to provide?
Here is the log from the plugin engine console:
INFO:ImJoyPluginEngine:Initialize the plugin, name=DPNUnet, id=DPNUnetbwqzk5on9c, cmd=python, worksp ace=default INFO:ImJoyPluginEngine:Cloning repo https://github.com/oeway/DPNUnet-Segmentation to C:\Users\Coulon team/ImJoyWorkspace\default\DPNUnet-Segmentation INFO:ImJoyPluginEngine:Running env command: conda create -y -n dsb2018-gpu python=3.6.8 INFO:ImJoyPluginEngine:Running command ['conda', 'create', '-y', '-n', 'dsb2018-gpu', 'python=3.6.8']
Collecting package metadata (repodata.json): done Solving environment: done
Package Plan
environment location: C:\Users\Coulon_team\Anaconda3\envs\dsb2018-gpu
added / updated specs:
- python=3.6.8
The following packages will be downloaded:
package | build ---------------------------|----------------- certifi-2019.9.11 | py36_0 155 KB pip-19.2.3 | py36_0 1.9 MB python-3.6.8 | h9f7ef89_7 20.3 MB setuptools-41.2.0 | py36_0 685 KB wheel-0.33.6 | py36_0 58 KB wincertstore-0.2 | py36h7fe50ca_0 13 KB ------------------------------------------------------------ Total: 23.1 MBThe following NEW packages will be INSTALLED:
certifi pkgs/main/win-64::certifi-2019.9.11-py36_0 pip pkgs/main/win-64::pip-19.2.3-py36_0 python pkgs/main/win-64::python-3.6.8-h9f7ef89_7 setuptools pkgs/main/win-64::setuptools-41.2.0-py36_0 sqlite pkgs/main/win-64::sqlite-3.29.0-he774522_0 vc pkgs/main/win-64::vc-14.1-h0510ff6_4 vs2015_runtime pkgs/main/win-64::vs2015_runtime-14.16.27012-hf0eaf9b_0 wheel pkgs/main/win-64::wheel-0.33.6-py36_0 wincertstore pkgs/main/win-64::wincertstore-0.2-py36h7fe50ca_0
Downloading and Extracting Packages setuptools-41.2.0 | 685 KB | | 0% wincertstore-0.2 | 13 KB | | 0% certifi-2019.9.11 | 155 KB | | 0% pip-19.2.3 | 1.9 MB | | 0% wheel-0.33.6 | 58 KB | | 0% python-3.6.8 | 20.3 MB | | 0% INFO:ImJoyPluginEngine:Running requirements commands: ['activate dsb2018-gpu && pip install descartes palettable geojson read-roi gputil namedlist', 'activate dsb2018-gpu && pip install lightgbm imgaug pandas imageio', 'activate dsb2018-gpu && conda install -y opencv tqdm scipy=1.0.0', 'activate dsb201 8-gpu && conda install -y pytorch=0.4.1 torchvision==0.2.0 cuda90 -c pytorch', 'activate dsb2018-gpu && pip install tensorboardX', 'activate dsb2018-gpu && pip install imjoy[worker]==0.8.22'] Running command: activate dsb2018-gpu && pip install descartes palettable geojson read-roi gputil nam edlist Requirement already satisfied: descartes in c:\users\coulon_team\anaconda3\lib\site-packages (1.1.0) Requirement already satisfied: palettable in c:\users\coulon_team\anaconda3\lib\site-packages (3.3.0)
Requirement already satisfied: geojson in c:\users\coulon_team\anaconda3\lib\site-packages (2.5.0) Requirement already satisfied: read-roi in c:\users\coulon_team\anaconda3\lib\site-packages (1.5.2) Requirement already satisfied: gputil in c:\users\coulon_team\anaconda3\lib\site-packages (1.4.0) Requirement already satisfied: namedlist in c:\users\coulon_team\anaconda3\lib\site-packages (1.7) Requirement already satisfied: matplotlib in c:\users\coulon_team\anaconda3\lib\site-packages (from d escartes) (2.2.3) Requirement already satisfied: numpy>=1.7.1 in c:\users\coulon_team\anaconda3\lib\site-packages (from matplotlib->descartes) (1.15.1) Requirement already satisfied: cycler>=0.10 in c:\users\coulon_team\anaconda3\lib\site-packages (from matplotlib->descartes) (0.10.0) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in c:\users\coulon_team\anaco nda3\lib\site-packages (from matplotlib->descartes) (2.2.0) Requirement already satisfied: python-dateutil>=2.1 in c:\users\coulon_team\anaconda3\lib\site-packag es (from matplotlib->descartes) (2.7.3) Requirement already satisfied: pytz in c:\users\coulon_team\anaconda3\lib\site-packages (from matplot lib->descartes) (2018.5) Requirement already satisfied: six>=1.10 in c:\users\coulon_team\anaconda3\lib\site-packages (from ma tplotlib->descartes) (1.11.0) Requirement already satisfied: kiwisolver>=1.0.1 in c:\users\coulon_team\anaconda3\lib\site-packages (from matplotlib->descartes) (1.0.1) Requirement already satisfied: setuptools in c:\users\coulon_team\anaconda3\lib\site-packages (from k iwisolver>=1.0.1->matplotlib->descartes) (40.2.0) Running command: activate dsb2018-gpu && pip install lightgbm imgaug pandas imageio Collecting lightgbm Using cached https://files.pythonhosted.org/packages/c7/0b/a183c06e7778893b2f12bb3e2cdab57f142b4e49 cd25cc643047f714e74c/lightgbm-2.3.0-py2.py3-none-win_amd64.whl https://files.pythonhosted.org/packages/c7/0b/a183c06e7778893b2f12bb3e2cdab57f142b4e49cd25cc643047f714e74c/lightgbm-2.3.0-py2.py3-none-win_amd64.whl Collecting imgaug Using cached https://files.pythonhosted.org/packages/11/df/5a3bba95b4600d5ca7aff072082ef0d9837056dd 28cc4e738e7ce88dd8f8/imgaug-0.3.0-py2.py3-none-any.whl https://files.pythonhosted.org/packages/11/df/5a3bba95b4600d5ca7aff072082ef0d9837056dd28cc4e738e7ce88dd8f8/imgaug-0.3.0-py2.py3-none-any.whl Requirement already satisfied: pandas in c:\users\coulon_team\anaconda3\lib\site-packages (0.23.4) Requirement already satisfied: imageio in c:\users\coulon_team\anaconda3\lib\site-packages (2.4.1) Requirement already satisfied: scikit-learn in c:\users\coulon_team\anaconda3\lib\site-packages (from lightgbm) (0.19.2) Requirement already satisfied: scipy in c:\users\coulon_team\anaconda3\lib\site-packages (from lightg bm) (1.1.0) Requirement already satisfied: numpy in c:\users\coulon_team\anaconda3\lib\site-packages (from lightg bm) (1.15.1) Requirement already satisfied: Pillow in c:\users\coulon_team\anaconda3\lib\site-packages (from imgau g) (5.2.0) Requirement already satisfied: matplotlib in c:\users\coulon_team\anaconda3\lib\site-packages (from i mgaug) (2.2.3) Requirement already satisfied: six in c:\users\coulon_team\anaconda3\lib\site-packages (from imgaug) (1.11.0) Collecting scikit-image>=0.14.2 (from imgaug) Using cached https://files.pythonhosted.org/packages/79/16/c5a36a03f90d4a246791d4ff1879f1868e1c5db5 8fac9f03427395c5e2d6/scikit_image-0.15.0-cp37-none-win_amd64.whl https://files.pythonhosted.org/packages/79/16/c5a36a03f90d4a246791d4ff1879f1868e1c5db58fac9f03427395c5e2d6/scikit_image-0.15.0-cp37-none-win_amd64.whl Collecting Shapely (from imgaug) Using cached https://files.pythonhosted.org/packages/a2/fb/7a7af9ef7a35d16fa23b127abee272cfc483ca89 029b73e92e93cdf36e6b/Shapely-1.6.4.post2.tar.gz https://files.pythonhosted.org/packages/a2/fb/7a7af9ef7a35d16fa23b127abee272cfc483ca89029b73e92e93cdf36e6b/Shapely-1.6.4.post2.tar.gz ERROR:ImJoyPluginEngine:Failed to setup plugin virtual environment or its requirements: Traceback (mo st recent call last): File "c:\users\coulon_team\anaconda3\lib\site-packages\imjoy\runners\subprocess.py", line 729, in l aunch_plugin logging_callback, File "c:\users\coulon_team\anaconda3\lib\site-packages\imjoy\runners\helper.py", line 99, in instal l_reqs fail_install() File "c:\users\coulon_team\anaconda3\lib\site-packages\imjoy\runners\helper.py", line 71, in fail_i nstall f"Failed to install dependencies with exit code {code} and error: {errors}" Exception: Failed to install dependencies with exit code 1 and error: b'Could not find conda environm ent: dsb2018-gpu\r\nYou can list all discoverable environments with
conda info --envs.\r\n\r\n E RROR: Command errored out with exit status 1:\r\n command: \'c:\users\coulon_team\anaconda3\p ython.exe\' -c \'import sys, setuptools, tokenize; sys.argv[0] = \'"\'"\'C:\\Users\\COULON~1\\A ppData\\Local\\Temp\\pip-install-9ta87otg\\Shapely\\setup.py\'"\'"\'; file=\'"\'"\'C:\ \Users\\COULON~1\\AppData\\Local\\Temp\\pip-install-9ta87otg\\Shapely\\setup.py\'"\'"\ ';f=getattr(tokenize, \'"\'"\'open\'"\'"\', open)(file);code=f.read().replace(\'"\'"\'\r\n\'"\' "\', \'"\'"\'\n\'"\'"\');f.close();exec(compile(code, file, \'"\'"\'exec\'"\'"\'))\' egg_info -- egg-base pip-egg-info\r\n cwd: C:\Users\COULON~1\AppData\Local\Temp\pip-install-9ta87ot g\Shapely\\r\n Complete output (9 lines):\r\n Traceback (most recent call last):\r\n Fil e "", line 1, in \r\n File "C:\Users\COULON~1\AppData\Local\Temp\pip-insta ll-9ta87otg\Shapely\setup.py", line 80, in \r\n from shapely._buildcfg import geos_v ersion_string, geos_version, \\r\n File "C:\Users\COULON~1\AppData\Local\Temp\pip-install -9ta87otg\Shapely\shapely\_buildcfg.py", line 200, in \r\n lgeos = CDLL("geos_c.dll ")\r\n File "c:\users\coulon_team\anaconda3\lib\ctypes\init.py", line 356, in init \r\n self._handle = _dlopen(self._name, mode)\r\n OSError: [WinError 126] The specified mod ule could not be found\r\n ----------------------------------------\r\nERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.\r\n' INFO:ImJoyPluginEngine:Disconnecting from plugin (success: False, message: Plugin process failed to s tart: Traceback (most recent call last): File "c:\users\coulon_team\anaconda3\lib\site-packages\imjoy\runners\subprocess.py", line 729, in l aunch_plugin logging_callback, File "c:\users\coulon_team\anaconda3\lib\site-packages\imjoy\runners\helper.py", line 99, in instal l_reqs fail_install() File "c:\users\coulon_team\anaconda3\lib\site-packages\imjoy\runners\helper.py", line 71, in fail_i nstall f"Failed to install dependencies with exit code {code} and error: {errors}" Exception: Failed to install dependencies with exit code 1 and error: b'Could not find conda environm ent: dsb2018-gpu\r\nYou can list all discoverable environments with
conda info --envs.\r\n\r\n E RROR: Command errored out with exit status 1:\r\n command: \'c:\users\coulon_team\anaconda3\p ython.exe\' -c \'import sys, setuptools, tokenize; sys.argv[0] = \'"\'"\'C:\\Users\\COULON~1\\A ppData\\Local\\Temp\\pip-install-9ta87otg\\Shapely\\setup.py\'"\'"\'; file=\'"\'"\'C:\ \Users\\COULON~1\\AppData\\Local\\Temp\\pip-install-9ta87otg\\Shapely\\setup.py\'"\'"\ ';f=getattr(tokenize, \'"\'"\'open\'"\'"\', open)(file);code=f.read().replace(\'"\'"\'\r\n\'"\' "\', \'"\'"\'\n\'"\'"\');f.close();exec(compile(code, file, \'"\'"\'exec\'"\'"\'))\' egg_info -- egg-base pip-egg-info\r\n cwd: C:\Users\COULON~1\AppData\Local\Temp\pip-install-9ta87ot g\Shapely\\r\n Complete output (9 lines):\r\n Traceback (most recent call last):\r\n Fil e "", line 1, in \r\n File "C:\Users\COULON~1\AppData\Local\Temp\pip-insta ll-9ta87otg\Shapely\setup.py", line 80, in \r\n from shapely._buildcfg import geos_v ersion_string, geos_version, \\r\n File "C:\Users\COULON~1\AppData\Local\Temp\pip-install -9ta87otg\Shapely\shapely\_buildcfg.py", line 200, in \r\n lgeos = CDLL("geos_c.dll ")\r\n File "c:\users\coulon_team\anaconda3\lib\ctypes\init.py", line 356, in init \r\n self._handle = _dlopen(self._name, mode)\r\n OSError: [WinError 126] The specified mod ule could not be found\r\n ----------------------------------------\r\nERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.\r\n' )``` Any help would be very appreciated!
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/oeway/DPNUnet-Segmentation/issues/9?email_source=notifications&email_token=AADU3SYXVDICJ3AQGBIOJH3QMTGW3A5CNFSM4I4Y4HL2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HPF6BYA, or mute the thread https://github.com/notifications/unsubscribe-auth/AADU3S4EQ7WR5GUDZKAJN3DQMTGW3ANCNFSM4I4Y4HLQ .
Padoup-Padoup
Hi @oeway,
I just tried to open the DPNUnet plugin in Imjoy, and I am getting the following error in the Plugin Engine console. Can you reproduce the problem? Could you tell me what kind of information you would need me to provide?
Here is the log from the plugin engine console:
Any help would be very appreciated!