Windows OS error while running caiman - FileNotFound #56
Comments
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thanks! making a fix for this here #57 On your local workstation if you go into the git pull origin fix-56-windows-runfile
git checkout fix-56-windows-runfileand then try it out it should have fixed it, I will merge if the tests on that PR pass. |
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Done and done. Looks like the file path is good now, but still returning an error: File c:\users\gjb326\mesmerize-core\mesmerize_core\caiman_extensions\common.py:184, in CaimanSeriesExtensions._run_subprocess(self, runfile_path, callbacks_finished, callback_std_out) File ~\Anaconda3\envs\mesmerize-core\lib\subprocess.py:951, in Popen.init(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, user, group, extra_groups, encoding, errors, text, umask) File ~\Anaconda3\envs\mesmerize-core\lib\subprocess.py:1420, in Popen._execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, unused_restore_signals, unused_gid, unused_gids, unused_uid, unused_umask, unused_start_new_session) OSError: [WinError 193] %1 is not a valid Win32 application During handling of the above exception, another exception occurred: ValueError Traceback (most recent call last) File c:\users\gjb326\mesmerize-core\mesmerize_core\caiman_extensions\common.py:253, in CaimanSeriesExtensions.run(self, backend, callbacks_finished, callback_std_out) ValueError: $env:ALLUSERSPROFILE="C:\ProgramData"; |
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Looks like I'm going to need a windows machine to figure this out, I'll get
to this in a few days. Thanks for trying it out!
…On Tue, Jun 21, 2022, 13:10 Garrett Blair ***@***.***> wrote:
Done and done.
Looks like the file path is good now, but still returning an error:
---------------------------------Begin
error------------------------------------------
OSError Traceback (most recent call last)
File
c:\users\gjb326\mesmerize-core\mesmerize_core\caiman_extensions\common.py:248,
in CaimanSeriesExtensions.run(self, backend, callbacks_finished,
callback_std_out)
247 try:
--> 248 self.process = getattr(self, f"*run*{backend}")(
249 runfile_path, callbacks_finished, callback_std_out
250 )
251 except:
File
c:\users\gjb326\mesmerize-core\mesmerize_core\caiman_extensions\common.py:184,
in CaimanSeriesExtensions._run_subprocess(self, runfile_path,
callbacks_finished, callback_std_out)
182 parent_path =
self._series.paths.resolve(self._series.input_movie_path).parent
--> 184 self.process = Popen(runfile_path, cwd=parent_path)
185 return self.process
File ~\Anaconda3\envs\mesmerize-core\lib\subprocess.py:951, in Popen.
*init*(self, args, bufsize, executable, stdin, stdout, stderr,
preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo,
creationflags, restore_signals, start_new_session, pass_fds, user, group,
extra_groups, encoding, errors, text, umask)
948 self.stderr = io.TextIOWrapper(self.stderr,
949 encoding=encoding, errors=errors)
--> 951 self._execute_child(args, executable, preexec_fn, close_fds,
952 pass_fds, cwd, env,
953 startupinfo, creationflags, shell,
954 p2cread, p2cwrite,
955 c2pread, c2pwrite,
956 errread, errwrite,
957 restore_signals,
958 gid, gids, uid, umask,
959 start_new_session)
960 except:
961 # Cleanup if the child failed starting.
File ~\Anaconda3\envs\mesmerize-core\lib\subprocess.py:1420, in
Popen._execute_child(self, args, executable, preexec_fn, close_fds,
pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite,
c2pread, c2pwrite, errread, errwrite, unused_restore_signals, unused_gid,
unused_gids, unused_uid, unused_umask, unused_start_new_session)
1419 try:
-> 1420 hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
1421 # no special security
1422 None, None,
1423 int(not close_fds),
1424 creationflags,
1425 env,
1426 cwd,
1427 startupinfo)
1428 finally:
1429 # Child is launched. Close the parent's copy of those pipe
1430 # handles that only the child should have open. You need
(...)
1433 # pipe will not close when the child process exits and the
1434 # ReadFile will hang.
*OSError: [WinError 193] %1 is not a valid Win32 application*
During handling of the above exception, another exception occurred:
ValueError Traceback (most recent call last)
Input In [6], in <cell line: 3>()
1 # run the first "batch item"
2 # this will run in a subprocess by default
----> 3 process = df.iloc[0].caiman.run()
4 process.wait()
File
c:\users\gjb326\mesmerize-core\mesmerize_core\caiman_extensions\common.py:253,
in CaimanSeriesExtensions.run(self, backend, callbacks_finished,
callback_std_out)
251 except:
252 with open(runfile_path, "r") as f:
--> 253 raise ValueError(f.read())
255 return self.process
ValueError: $env:ALLUSERSPROFILE="C:\ProgramData";
$env:APPDATA="C:\Users\gjb326\AppData\Roaming";
$env:COMMONPROGRAMFILES="C:\Program Files\Common Files";
$env:COMMONPROGRAMFILES(X86)="C:\Program Files (x86)\Common Files";
$env:COMMONPROGRAMW6432="C:\Program Files\Common Files";
$env:COMPUTERNAME="030B2110005877";
$env:COMSPEC="C:\Windows\system32\cmd.exe";
$env:CONDA_DEFAULT_ENV="mesmerize-core";
$env:CONDA_EXE="C:\Users\gjb326\Anaconda3\Scripts\conda.exe";
$env:CONDA_PREFIX="C:\Users\gjb326\Anaconda3\envs\mesmerize-core";
$env:CONDA_PREFIX_1="C:\Users\gjb326\Anaconda3";
$env:CONDA_PROMPT_MODIFIER="(mesmerize-core) ";
$env:CONDA_PYTHON_EXE="C:\Users\gjb326\Anaconda3\python.exe";
$env:CONDA_SHLVL="2";
$env:CUDA_PATH="C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v11.6";
$env:CUDA_PATH_V11_6="C:\Program Files\NVIDIA GPU Computing
Toolkit\CUDA\v11.6";
$env:DRIVERDATA="C:\Windows\System32\Drivers\DriverData";
$env:FPS_BROWSER_APP_PROFILE_STRING="Internet Explorer";
$env:FPS_BROWSER_USER_PROFILE_STRING="Default";
$env:HOMEDRIVE="C:";
$env:HOMEPATH="\Users\gjb326";
$env:LOCALAPPDATA="C:\Users\gjb326\AppData\Local";
$env:LOGONSERVER="\ITS09-WDC";
$env:MKL_NUM_THREADS="1";
$env:NUMBER_OF_PROCESSORS="24";
$env:NVTOOLSEXT_PATH="C:\Program Files\NVIDIA Corporation\NvToolsExt";
$env:ONEDRIVE="C:\Users\gjb326\OneDrive";
$env:OPENBLAS_NUM_THREADS="1";
$env:OS="Windows_NT";
$env:PATH="C:\Users\gjb326\Anaconda3\envs\mesmerize-core;C:\Users\gjb326\Anaconda3\envs\mesmerize-core\Library\mingw-w64\bin;C:\Users\gjb326\Anaconda3\envs\mesmerize-core\Library\usr\bin;C:\Users\gjb326\Anaconda3\envs\mesmerize-core\Library\bin;C:\Users\gjb326\Anaconda3\envs\mesmerize-core\Scripts;C:\Users\gjb326\Anaconda3\envs\mesmerize-core\bin;C:\Users\gjb326\Anaconda3\condabin;C:\Program
Files\NVIDIA\CUDNN\v 8.4.0.27;C:\Program
Files\Git\cmd;"C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem";C:\Windows\system32;C:\Users\gjb326\Anaconda3;C:\Users\gjb326\Anaconda3\Library\mingw-w64\bin;C:\Users\gjb326\Anaconda3\Library\usr\bin;C:\Users\gjb326\Anaconda3\Library\bin;C:\Users\gjb326\Anaconda3\Scripts;C:\Users\gjb326\AppData\Local\Microsoft\WindowsApps;C:\Users\gjb326\AppData\Local\GitHubDesktop\bin;C:\Users\gjb326\AppData\Local\Programs\Microsoft
VS
Code\bin;C:\Users\gjb326\AppData\Roaming\npm;"C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0";C:\Windows\system32;.";
$env:PATHEXT=".COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC";
$env:PROCESSOR_ARCHITECTURE="AMD64";
$env:PROCESSOR_IDENTIFIER="Intel64 Family 6 Model 151 Stepping 2,
GenuineIntel";
$env:PROCESSOR_LEVEL="6";
$env:PROCESSOR_REVISION="9702";
$env:PROGRAMDATA="C:\ProgramData";
$env:PROGRAMFILES="C:\Program Files";
$env:PROGRAMFILES(X86)="C:\Program Files (x86)";
$env:PROGRAMW6432="C:\Program Files";
$env:PROMPT="(mesmerize-core) $P$G";
$env:PSMODULEPATH="C:\Program
Files\WindowsPowerShell\Modules;C:\Windows\system32\WindowsPowerShell\v1.0\Modules";
$env:PUBLIC="C:\Users\Public";
$env:SESSIONNAME="Console";
$env:SYSTEMDRIVE="C:";
$env:SYSTEMROOT="C:\Windows";
$env:TEMP="C:\Users\gjb326\AppData\Local\Temp";
$env:TMP="C:\Users\gjb326\AppData\Local\Temp";
$env:USERDNSDOMAIN="AD.NYU.EDU";
$env:USERDOMAIN="AD";
$env:USERDOMAIN_ROAMINGPROFILE="AD";
$env:USERNAME="gjb326";
$env:USERPROFILE="C:\Users\gjb326";
$env:VBOX_MSI_INSTALL_PATH="C:\Program Files\Oracle\VirtualBox";
$env:WINDIR="C:\Windows";
$env:ZES_ENABLE_SYSMAN="1";
$env:PYDEVD_USE_FRAME_EVAL="NO";
$env:JPY_INTERRUPT_EVENT="2724";
$env:IPY_INTERRUPT_EVENT="2724";
$env:JPY_PARENT_PID="2720";
$env:TERM="xterm-color";
$env:CLICOLOR="1";
$env:PAGER="cat";
$env:GIT_PAGER="cat";
$env:MPLBACKEND="module://matplotlib_inline.backend_inline";
$env:KMP_DUPLICATE_LIB_OK="True";
$env:KMP_INIT_AT_FORK="FALSE";
$env:TF2_BEHAVIOR="1";
$env:QT_API="pyqt5";
python c:\users\gjb326\mesmerize-core\mesmerize_core\algorithms\mcorr.py
--batch-path C:\Users\gjb326\caiman_data\mesmerize-core-batch\batch.pickle
--uuid d6d30735-2a5b-4034-b692-4b0966f489bb --data-path
C:\Users\gjb326\caiman_data
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@GarrettBlair windows compatibility has finally been merged and it works on GitHub's CI pipelines, so if you install the latest master branch it should work for you! Note that you'll still need to install pandas either directly from github or the nightly wheels (see below) since they still haven't released v1.5. If you're on python3.10 you should be able to install this pre-built wheel for pandas 1.5: pip install https://pypi.anaconda.org/scipy-wheels-nightly/simple/pandas/1.5.0.dev0%2B1172.ga7c5773d19/pandas-1.5.0.dev0%2B1172.ga7c5773d19-cp310-cp310-win_amd64.whlor if you're on python3.9: pip install https://pypi.anaconda.org/scipy-wheels-nightly/simple/pandas/1.5.0.dev0%2B1172.ga7c5773d19/pandas-1.5.0.dev0%2B1172.ga7c5773d19-cp39-cp39-win_amd64.whlNew docs are also up: https://mesmerize-core.readthedocs.io/ |
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Awesome, thanks for the thorough response Kushal! |
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closing, |
Running Windows 11 x64, running caiman gives a couple errors:
I can confirm the file is there -
os.path.isfile('C:/Users/gjb326/caiman_data/mesmerize-core-batch/f1f56d3d-53b9-4e80-a92c-a34a635b28da.runfile.ps1')returns True, but only when the '.ps1' is appendedBut
os.path.isfile(r'C:\Users\..\..a.runfile.ps1')andos.path.isfile('C:\\Users\\..\\..a.runfile.ps1')return False---------------------------------Begin error------------------------------------------
OSError Traceback (most recent call last)
File c:\users\gjb326\mesmerize-core\mesmerize_core\caiman_extensions\common.py:248, in CaimanSeriesExtensions.run(self, backend, callbacks_finished, callback_std_out)
247 try:
--> 248 self.process = getattr(self, f"run{backend}")(
249 runfile, callbacks_finished, callback_std_out
250 )
251 except:
File c:\users\gjb326\mesmerize-core\mesmerize_core\caiman_extensions\common.py:184, in CaimanSeriesExtensions._run_subprocess(self, runfile_path, callbacks_finished, callback_std_out)
182 parent_path = self._series.paths.resolve(self._series.input_movie_path).parent
--> 184 self.process = Popen(runfile_path, cwd=parent_path)
185 return self.process
File ~\Anaconda3\envs\mesmerize-core\lib\subprocess.py:951, in Popen.init(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, user, group, extra_groups, encoding, errors, text, umask)
948 self.stderr = io.TextIOWrapper(self.stderr,
949 encoding=encoding, errors=errors)
--> 951 self._execute_child(args, executable, preexec_fn, close_fds,
952 pass_fds, cwd, env,
953 startupinfo, creationflags, shell,
954 p2cread, p2cwrite,
955 c2pread, c2pwrite,
956 errread, errwrite,
957 restore_signals,
958 gid, gids, uid, umask,
959 start_new_session)
960 except:
961 # Cleanup if the child failed starting.
File ~\Anaconda3\envs\mesmerize-core\lib\subprocess.py:1420, in Popen._execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, unused_restore_signals, unused_gid, unused_gids, unused_uid, unused_umask, unused_start_new_session)
1419 try:
-> 1420 hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
1421 # no special security
1422 None, None,
1423 int(not close_fds),
1424 creationflags,
1425 env,
1426 cwd,
1427 startupinfo)
1428 finally:
1429 # Child is launched. Close the parent's copy of those pipe
1430 # handles that only the child should have open. You need
(...)
1433 # pipe will not close when the child process exits and the
1434 # ReadFile will hang.
OSError: [WinError 193] %1 is not a valid Win32 application
During handling of the above exception, another exception occurred:
FileNotFoundError Traceback (most recent call last)
Input In [5], in <cell line: 3>()
1 # run the first "batch item"
2 # this will run in a subprocess by default
----> 3 process = df.iloc[0].caiman.run()
4 process.wait()
File c:\users\gjb326\mesmerize-core\mesmerize_core\caiman_extensions\common.py:252, in CaimanSeriesExtensions.run(self, backend, callbacks_finished, callback_std_out)
248 self.process = getattr(self, f"run{backend}")(
249 runfile, callbacks_finished, callback_std_out
250 )
251 except:
--> 252 with open(runfile_path, "r") as f:
253 raise ValueError(f.read())
255 return self.process
FileNotFoundError: [Errno 2] No such file or directory: 'C:\Users\gjb326\caiman_data\mesmerize-core-batch\f1f56d3d-53b9-4e80-a92c-a34a635b28da.runfile'
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