diffeqpy
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20 hours ago •
SciML
SciML
FileNotFoundError when trying to import diffeqpy from Jupyter
I have just installed Julia-1.2 on macOS (version 10.14.6 (18G3020)), and then installed diffeqpy. I tried to import it in a Jupyter notebook with the command from diffeqpy import de, but got this error message:
FileNotFoundError Traceback (most recent call last)
<ipython-input-5-65b37eb28595> in <module>
----> 1 from diffeqpy import de
2
3 def f(u,p,t):
4 return -u
5
/opt/anaconda3/lib/python3.7/site-packages/diffeqpy/de.py in <module>
2 import sys
3
----> 4 from julia import Main
5
6 script_dir = os.path.dirname(os.path.realpath(__file__))
/opt/anaconda3/lib/python3.7/importlib/_bootstrap.py in _find_and_load(name, import_)
/opt/anaconda3/lib/python3.7/importlib/_bootstrap.py in _find_and_load_unlocked(name, import_)
/opt/anaconda3/lib/python3.7/importlib/_bootstrap.py in _load_unlocked(spec)
/opt/anaconda3/lib/python3.7/importlib/_bootstrap.py in _load_backward_compatible(spec)
/opt/anaconda3/lib/python3.7/site-packages/julia/core.py in load_module(self, fullname)
244 if juliapath == 'Main':
245 return sys.modules.setdefault(fullname,
--> 246 JuliaMainModule(self, fullname))
247 elif self.julia.isafunction(juliapath):
248 return self.julia.eval(juliapath)
/opt/anaconda3/lib/python3.7/site-packages/julia/core.py in __init__(self, loader, *args, **kwargs)
146 def __init__(self, loader, *args, **kwargs):
147 super(JuliaModule, self).__init__(*args, **kwargs)
--> 148 self._julia = loader.julia
149 self.__loader__ = loader
150
/opt/anaconda3/lib/python3.7/site-packages/julia/core.py in julia(self)
236 @property
237 def julia(self):
--> 238 self.__class__.julia = julia = Julia()
239 return julia
240
/opt/anaconda3/lib/python3.7/site-packages/julia/core.py in __init__(self, init_julia, jl_init_path, runtime, jl_runtime_path, debug, **julia_options)
465 self.api = get_libjulia()
466 elif init_julia:
--> 467 jlinfo = JuliaInfo.load(runtime)
468 if jlinfo.version_info < (0, 7):
469 raise RuntimeError("PyJulia does not support Julia < 0.7 anymore")
/opt/anaconda3/lib/python3.7/site-packages/julia/juliainfo.py in load(cls, julia, **popen_kwargs)
71 stderr=subprocess.PIPE,
72 universal_newlines=True,
---> 73 **popen_kwargs
74 )
75
/opt/anaconda3/lib/python3.7/subprocess.py in __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, encoding, errors, text)
798 c2pread, c2pwrite,
799 errread, errwrite,
--> 800 restore_signals, start_new_session)
801 except:
802 # Cleanup if the child failed starting.
/opt/anaconda3/lib/python3.7/subprocess.py in _execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, restore_signals, start_new_session)
1549 if errno_num == errno.ENOENT:
1550 err_msg += ': ' + repr(err_filename)
-> 1551 raise child_exception_type(errno_num, err_msg, err_filename)
1552 raise child_exception_type(err_msg)
1553
FileNotFoundError: [Errno 2] No such file or directory: 'julia': 'julia'
I tried to install and build IJulia but it doesn't seem to make a difference... any help?
I think it means that IPython cannot find command line program julia inside Jupyter.
To check if IPython can find julia, you can run !which julia (with !) inside Jupyter. If it says julia not found or sometihng similar, you need to specify the path to julia explicitly when using PyJulia. To find out the absolute path to julia, you can do which julia (no ! here) in the system shell (e.g., bash). Once you get the path, you can then do
from julia import Julia
Julia(runtime="PATH/TO/bin/julia")
from diffeqpy import de
with PATH/TO/bin/julia replaced with the actual path printed by which julia.
Ref: https://pyjulia.readthedocs.io/en/latest/api.html
!which julia resulted in:
which julia julia
/usr/local/bin/julia
/usr/local/bin/julia
What seems to work is:
from julia.api import Julia
jl = Julia(compiled_modules=False)
#jl(runtime="/usr/local/bin/julia")
from diffeqpy import de
However it takes quite a long time to import the package...
Do you get the same stacktrace as in the first post if you:
- Restart the IPython kernel, and then
- Evaluate
from julia import Main
?
I've restarted the Kernel and used:
import time
start = time.time()
from julia import Main
end = time.time()
print(end - start)
But I have got FileNotFoundError:
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
<ipython-input-4-d6cf9f272d96> in <module>
1 import time
2 start = time.time()
----> 3 from julia import Main
4 end = time.time()
5 print(end - start)
/opt/anaconda3/lib/python3.7/importlib/_bootstrap.py in _find_and_load(name, import_)
/opt/anaconda3/lib/python3.7/importlib/_bootstrap.py in _find_and_load_unlocked(name, import_)
/opt/anaconda3/lib/python3.7/importlib/_bootstrap.py in _load_unlocked(spec)
/opt/anaconda3/lib/python3.7/importlib/_bootstrap.py in _load_backward_compatible(spec)
/opt/anaconda3/lib/python3.7/site-packages/julia/core.py in load_module(self, fullname)
244 if juliapath == 'Main':
245 return sys.modules.setdefault(fullname,
--> 246 JuliaMainModule(self, fullname))
247 elif self.julia.isafunction(juliapath):
248 return self.julia.eval(juliapath)
/opt/anaconda3/lib/python3.7/site-packages/julia/core.py in __init__(self, loader, *args, **kwargs)
146 def __init__(self, loader, *args, **kwargs):
147 super(JuliaModule, self).__init__(*args, **kwargs)
--> 148 self._julia = loader.julia
149 self.__loader__ = loader
150
/opt/anaconda3/lib/python3.7/site-packages/julia/core.py in julia(self)
236 @property
237 def julia(self):
--> 238 self.__class__.julia = julia = Julia()
239 return julia
240
/opt/anaconda3/lib/python3.7/site-packages/julia/core.py in __init__(self, init_julia, jl_init_path, runtime, jl_runtime_path, debug, **julia_options)
465 self.api = get_libjulia()
466 elif init_julia:
--> 467 jlinfo = JuliaInfo.load(runtime)
468 if jlinfo.version_info < (0, 7):
469 raise RuntimeError("PyJulia does not support Julia < 0.7 anymore")
/opt/anaconda3/lib/python3.7/site-packages/julia/juliainfo.py in load(cls, julia, **popen_kwargs)
71 stderr=subprocess.PIPE,
72 universal_newlines=True,
---> 73 **popen_kwargs
74 )
75
/opt/anaconda3/lib/python3.7/subprocess.py in __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, encoding, errors, text)
798 c2pread, c2pwrite,
799 errread, errwrite,
--> 800 restore_signals, start_new_session)
801 except:
802 # Cleanup if the child failed starting.
/opt/anaconda3/lib/python3.7/subprocess.py in _execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, restore_signals, start_new_session)
1549 if errno_num == errno.ENOENT:
1550 err_msg += ': ' + repr(err_filename)
-> 1551 raise child_exception_type(errno_num, err_msg, err_filename)
1552 raise child_exception_type(err_msg)
1553
FileNotFoundError: [Errno 2] No such file or directory: 'julia': 'julia'
