Please help to load plumed

[debanjansen48]

i used the command !pip install plumed from Jupiter notebook to install plumed. and installed successfully. From terminal I checked its working. but during import, it returns following error.

ModuleNotFoundError Traceback (most recent call last)
/tmp/ipykernel_4222/276985268.py in
----> 1 import plumed
2 import matplotlib.pyplot as plt

ModuleNotFoundError: No module named 'plumed'

[GiovanniBussi]

Usually this means that you installed plumed in another python version. Maybe you can try to use pip3 instead of pip Il giorno sab 16 apr 2022 alle 16:55 debanjansen48 ***@***.***> ha scritto:

i used the command !pip install plumed from Jupiter notebook to install plumed. and installed successfully. From terminal I checked its working. but during import, it returns following error. ModuleNotFoundError Traceback (most recent call last) /tmp/ipykernel_4222/276985268.py in ----> 1 import plumed 2 import matplotlib.pyplot as plt ModuleNotFoundError: No module named 'plumed' — Reply to this email directly, view it on GitHub <#1>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABBNCXV7PPRE6FB2R53NRCTVFLIG5ANCNFSM5TSPIQ4Q> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

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[debanjansen48]

sir I changed the linux system and tried to install it on a windows laptop. but encountered the following error. PS C:\Users\HP> pip3 install plumed WARNING: Ignoring invalid distribution -tkinter-pymol (c:\pymol\dlls) WARNING: Ignoring invalid distribution -ip (c:\pymol\lib\site-packages) WARNING: Ignoring invalid distribution -tkinter-pymol (c:\pymol\dlls) WARNING: Ignoring invalid distribution -ip (c:\pymol\lib\site-packages) Collecting plumed Using cached plumed-2.8.0.tar.gz (273 kB) Preparing metadata (setup.py) ... error error: subprocess-exited-with-error × python setup.py egg_info did not run successfully. │ exit code: 1 ╰─> [14 lines of output] Traceback (most recent call last): File "<string>", line 36, in <module> File "<pip-setuptools-caller>", line 34, in <module> File "C:\Users\HP\AppData\Local\Temp\pip-install-v0sbs08m\plumed_7437cffb58784ae996155b1f0280c874\setup.py", line 56, in <module> plumedversion = subprocess.check_output(['grep','-v','#','./VERSION']).decode("utf-8").rstrip() File "C:\PyMol\lib\subprocess.py", line 411, in check_output **kwargs).stdout File "C:\PyMol\lib\subprocess.py", line 488, in run with Popen(*popenargs, **kwargs) as process: File "C:\PyMol\lib\subprocess.py", line 800, in __init__ restore_signals, start_new_session) File "C:\PyMol\lib\subprocess.py", line 1207, in _execute_child startupinfo) FileNotFoundError: [WinError 2] The system cannot find the file specified [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed × Encountered error while generating package metadata. ╰─> See above for output. note: This is an issue with the package mentioned above, not pip. hint: See above for details. WARNING: Ignoring invalid distribution -tkinter-pymol (c:\pymol\dlls) WARNING: Ignoring invalid distribution -ip (c:\pymol\lib\site-packages) WARNING: Ignoring invalid distribution -tkinter-pymol (c:\pymol\dlls) WARNING: Ignoring invalid distribution -ip (c:\pymol\lib\site-packages) WARNING: Ignoring invalid distribution -tkinter-pymol (c:\pymol\dlls) WARNING: Ignoring invalid distribution -ip (c:\pymol\lib\site-packages)

…

On Sat, Apr 16, 2022 at 8:43 PM Giovanni ***@***.***> wrote: Usually this means that you installed plumed in another python version. Maybe you can try to use pip3 instead of pip Il giorno sab 16 apr 2022 alle 16:55 debanjansen48 ***@***.***> ha scritto: > i used the command !pip install plumed from Jupiter notebook to install > plumed. and installed successfully. From terminal I checked its working. > but during import, it returns following error. > > ModuleNotFoundError Traceback (most recent call last) > /tmp/ipykernel_4222/276985268.py in > ----> 1 import plumed > 2 import matplotlib.pyplot as plt > > ModuleNotFoundError: No module named 'plumed' > > — > Reply to this email directly, view it on GitHub > <#1>, or unsubscribe > < https://github.com/notifications/unsubscribe-auth/ABBNCXV7PPRE6FB2R53NRCTVFLIG5ANCNFSM5TSPIQ4Q > > . > You are receiving this because you are subscribed to this thread.Message > ID: ***@***.***> > -- Sent from Gmail mobile — Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOJ7Q4R5R36NHOWI6Y3WGZTVFLKIFANCNFSM5TSPIQ4Q> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[debanjansen48]

in the windows system i uninstalled all possiable pythons. then installed python 3.10 and pip but returens following error

Successfully installed pip-22.0.4 wheel-0.37.1
PS C:\Users\HP> pip -V
pip 22.0.4 from C:\Users\HP\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.10_qbz5n2kfra8p0\LocalCache\local-packages\Python310\site-packages\pip (python 3.10)
PS C:\Users\HP> pip3 install plumed
Collecting plumed
Using cached plumed-2.8.0.tar.gz (273 kB)
Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error

× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [14 lines of output]
File "", line 2, in
File "", line 34, in
File "C:\Users\HP\AppData\Local\Temp\pip-install-auay_m25\plumed_fb13f8b35be04147b0857698a73e4ca7\setup.py", line 56, in
plumedversion = subprocess.check_output(['grep','-v','#','./VERSION']).decode("utf-8").rstrip()
File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.10_3.10.1264.0_x64__qbz5n2kfra8p0\lib\subprocess.py", line 420, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.10_3.10.1264.0_x64__qbz5n2kfra8p0\lib\subprocess.py", line 501, in run
with Popen(*popenargs, **kwargs) as process:
File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.10_3.10.1264.0_x64__qbz5n2kfra8p0\lib\subprocess.py", line 966, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.10_3.10.1264.0_x64__qbz5n2kfra8p0\lib\subprocess.py", line 1435, in _execute_child
hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
FileNotFoundError: [WinError 2] The system cannot find the file specified
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
PS C:\Users\HP> pip install plumed
Collecting plumed
Using cached plumed-2.8.0.tar.gz (273 kB)
Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error

× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [14 lines of output]
Traceback (most recent call last):
File "", line 2, in
File "", line 34, in
File "C:\Users\HP\AppData\Local\Temp\pip-install-aszyx_74\plumed_01cf0862f92e47e3b871724c183532cf\setup.py", line 56, in
plumedversion = subprocess.check_output(['grep','-v','#','./VERSION']).decode("utf-8").rstrip()
File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.10_3.10.1264.0_x64__qbz5n2kfra8p0\lib\subprocess.py", line 420, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.10_3.10.1264.0_x64__qbz5n2kfra8p0\lib\subprocess.py", line 501, in run
with Popen(*popenargs, **kwargs) as process:
File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.10_3.10.1264.0_x64__qbz5n2kfra8p0\lib\subprocess.py", line 966, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.10_3.10.1264.0_x64__qbz5n2kfra8p0\lib\subprocess.py", line 1435, in _execute_child
hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
FileNotFoundError: [WinError 2] The system cannot find the file specified
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

[debanjansen48]

in Linux system..
using jupyter notebook
!pip3 install plumed
Requirement already satisfied: plumed in /home/debanjan/amber20/miniconda/lib/python3.9/site-packages (2.8.0)
import plumed
ModuleNotFoundError Traceback (most recent call last)
/tmp/ipykernel_3014/1864219554.py in
----> 1 import plumed

ModuleNotFoundError: No module named 'plumed'

From command line
~$ python
Python 3.9.5 (default, Jun 4 2021, 12:28:51)
[GCC 7.5.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.

import plumed

[GiovanniBussi]

This problem is not related to plumed but to jupyter. See for instance here.

You can try this:

import sys
!{sys.executable} -m pip install <package_name>

However, please read carefully the link above

[GiovanniBussi]

This also seems relevant and well explained.