After installing the Nest Neural Simulator, I keep getting the following error when trying to run any of the example python files that came in the installation. I've tried re-installing Nest, Python, and using Anaconda, but no go.
Python error:
ImportError: No module named nest
Suggestions?
At https://nest-simulator.org/documentation you now find many different install instructions and how to solve the "ImportError: no module named nest" depends on the way you installed NEST.
System Python
The problem with the nest python module not being found is usually, that NEST is installed for a specific Python version and you can not load it from another. So while many OS still use Python 2.7 you may need to explicitly run
$ python3
>>> import nest
Additionally, if you have multiple Python 3.x versions installed, modules may still be installed for a different version and you have to explicitly start python with python3.6 or python3.8, etc.
Conda package
As #nosratullah-mohammadi already mentioned, if you have a Conda flavour installed, using the pre-built package is a very quick solution. The link in his post is unfortunately broken; this one should work, then go to "Installation" in the side bar.
$ conda create --name nest -c conda-forge python3 nest-simulator
$ conda activate nest
$ python # this should load the Python from the conda env
>>> import nest # this loads nest which is installed explicitly for that Python
From Source
For every install from source, be sure to have Python and other prerequisites installed before building NEST. Then you can create your temporary build directory (can be deleted afterwards) and configure with the flags you need.
cd somewhere
mkdir nest-build
cd nest-build
cmake -DCMAKE_INSTALL_PREFIX:PATH=/install/path -Dwith-python=3 .../sources/of/nest-simulator
Replace somewhere, /install/path and .../sources/of/nest-simulator with the paths correct for your setup. (A popular choice when compiling from source in conjunction with Conda environments, for example, is to use -CMAKE_INSTALL_PREFIX=$CONDA_PREFIX, which installs NEST directly into the active environment. Conda is however in no way necessary for NEST.)
Add more -D... flags as you prefer. Possible flags you see with cmake -LA .../sources/of/nest-simulator, as pointed out here. You are probably interested in many of the with-xyz at the end. Check the aforementioned documentation for deatils.
Check that the paths and libraries reported in the Configuration Summary make sense (you may need to scroll up a bit to see). It could for example look something like this:
--------------------------------------------------------------------------------
NEST Configuration Summary
--------------------------------------------------------------------------------
[...]
Python bindings : Yes (Python 3.6.8: /home/yourname/miniconda3/envs/nest/bin/python3)
Includes : /home/yourname/miniconda3/envs/nest/include/python3.6m
Libraries : /home/yourname/miniconda3/envs/nest/lib/libpython3.6m.so
Cython bindings : Yes (Cython 0.27.3: /home/yourname/miniconda3/envs/nest/bin/cython)
[...]
--------------------------------------------------------------------------------
[...]
PyNEST will be installed to:
/home/yourname/miniconda3/envs/nest/lib/python3.6/site-packages
--------------------------------------------------------------------------------
In this example CMake configured everything for Python3.6 from my conda environment.
If you are satisfied with your settings and all the found Python versions match, run the usual
$ make # optionally with -j$(nproc)
$ make install
$ make installcheck
In case that works out fine you are done and can delete the build directory to free the space. Congratulations!
Also if things get too mixed up and it doesn't seem to do what you expect, it is sometimes useful to delete the build directory and start off clean.
there is a new method of installation added to other methods, wich is installing nest with conda package and it's in its beta version. but it works and it's really simple.
you can find the installation from here!
simply after install mini conda package run your terminal and type this :
conda create --name ENVNAME -c conda-forge nest-simulator python
then type :
conda activate ENVNAME
and you're good to go!
NEST now provide the solution to that problem and similar ones, by providing a script which automatically sets the relevant system variables:
If your operating system does not find the nest executable or Python
does not find the nest module, your path variables may not be set
correctly. This may also be the case if Python cannot load the nest
module due to missing or incompatible libraries. In this case, please
run
source </path/to/nest_install_dir>/bin/nest_vars.sh
to set the necessary environment variables. You may want to include
this line in your .bashrc file, so that the environment variables are
set automatically.
https://nest-simulator.readthedocs.io/en/latest/installation/linux_install.html
Turns out I needed to move the directory where I installed nest (Users/name/opt/nest) into a nest folder in the following directory in anaconda. Specifically, I moved the contents of the folder (from the nest installation):
/Users/name/opt/nest/lib/python2.7/site-packages/nest
Into this one:
/anaconda/lib/python2.7/site-packages/nest
Disclaimer: I could very well run into problems for not having copied all the contents of the Nest installation, but this little hack is helping me run example files now.
Related
I have recently tried to use pylearn2, a deep machin learning package for Python developed at University of Montreal.
I've just installed it and tried to run a simple example, but it did not work.
I have been using a pc with an Ubuntu 13.10 system, on which I found ipython installed.
I have installed Theano and later pylearn2, by following this webpage instructions:
http://deeplearning.net/software/pylearn2/
I have also modified the .bashrc file, as suggested
I thought that everything went well, and then I tried this Quick start example:
http://deeplearning.net/software/pylearn2/tutorial/index.html
I stopped at the first command:
python make_dataset.py
My terminal states:
Traceback (most recent call last): File "make_dataset.py", line 14,
in
Do you have any ideas on why it is not working?
Do you why these errors occur?
Thanks a lot
EDIT: the 14 line is the first non-commented line of the file. It states
from pylearn2.utils import serial
Without more information, I can only guess, but my first guess is…
You haven't actually installed pylearn2, because if you follow the linked docs to grab the git repo and add a PYLEARN2_DATA_PATH variable, nothing gets installed into site-packages (or dist-packages or anywhere else on sys.path).
This means that pylearn2 will only work when you start Python from within the top-level directory of the pylearn2 repo.
So, if you run a script like this:
$ cd /path/to/pylearn2
$ cd scripts/tutorials/grbm_smd/
$ python make_dataset.py
… it won't actually work.
It looks like there is a setup.py file in the repository. Does it work? I have no idea. Even though the docs don't mention using it, you might want to try. Either this:
$ pip install .
… or, if you don't have pip or it doesn't work on this package:
$ python setup.py install
Either way, of course, you may need sudo or a flag to install to your user site-packages instead of system, etc., as with any other Python package.
If that doesn't work, you might be able to just add /path/to/pylearn2 to your sys.path in some way. The most obvious way is by doing an export PYTHONPATH=/path/to/pylearn2:$PYTHONPATH in your ~/.bashrc.
Also, you will need to either source ~/.bashrc or create a new shell to get any effects of modifying the file.
If you're wondering why the instructions and the tutorial together don't give you enough information to make this work without a lot of hassle, I think that's covered in the very top of the documentation:
Pylearn2 is still undergoing rapid development. Don’t expect a clean road without bumps!
And the very fact that there is no PyPI download yet implies that this really is not ready for novices to use. If you don't know enough about using Python packages (and bash basics) to muddle through on your own, there's a good chance you won't be able to use this package.
Getting the following kinds of warnings when running most python scripts in the command line:
/Library/Python/2.6/site-packages/virtualenvwrapper/hook_loader.py:16: UserWarning: Module
pkg_resources was already imported from /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/pkg_resources.pyc, but /Library/Python/2.6/site-packages is being added to sys.path
import pkg_resources
/Library/Python/2.6/site-packages/virtualenvwrapper/hook_loader.py:16: UserWarning: Module site was already imported from /System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site.pyc, but /Library/Python/2.6/site-packages is being added to sys.path
import pkg_resources
I think it has to do with a combination of using distribute and virtualenv, but wanted to check if anyone else has run in to this or would know how to go about fixing it.
Perhaps use the virtualenv option --no-site-packages so you won't see any system site-packages within your virtual environment. Having items installed both in your virtualenv and on the system root may be the cause of this issue.
Using --no-site-packages when creating your virtualenv prevents any conflict between system packages. I almost always use that option when creating a new virtualenv to prevent any conflicts. Though I may have several copies of libraries, at least they don't mess with each other.
The python equivalent of putting a bit of electrical tape over the check engine light would be to use the -W command line flag or by adding a warning filter.
In my case reinstalling of anything did not help. There were some orphaned .pyc files (specifically pkg_resources.pyc) left in /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python
sudo find . -type f -name "*.pyc" -delete
made it work. This link helped me to track down the problem.
I had this sort of Python packaging hell visit today too.
Running Python 2.7.3 on Ubuntu, using namespace packages and using zc.buildout.
Finally, updating system wide Distribute from older version 0.6.30 to latest version 0.6.35 resolved the problem.
If the warning shows in a program you are modifying, try it this way (examply with pytz):
try:
import pytz
except ImportError:
from pkg_resources import require
require('pytz')
I'm just starting out with Python, and have found out that I can import various libraries. How do I find out what libraries exist on my Mac that I can import? How do I find out what functions they include?
I seem to remember using some web server type thing to browse through local help files, but I may have imagined that!
From the Python REPL (the command-line interpreter / Read-Eval-Print-Loop), type help("modules") to see a list of all your available libs.
Then to see functions within a module, do help("posix"), for example. If you haven't imported the library yet, you have to put quotes around the library's name.
For the web server, you can run the pydoc module that is included in the python distribution as a script:
python /path/to/pydoc.py -p 1234
where 1234 is the port you want the server to run at. You can then visit http://localhost:1234/ and browse the documentation.
Every standard python distribution has these libraries, which cover most of what you will need in a project.
In case you need to find out if a library exists at runtime, you do it like this
try:
import ObscureModule
except ImportError:
print "you need to install ObscureModule"
sys.exit(1) # or something like that
You can install another library: yolk.
yolk is a python package manager and will show you everything you have added via pypi. But it will also show you site-packages added through whatever local package manager you run.
just run the Python interpeter and type the command
import "lib_name"
if it gives an error, you don't have the lib installed...else you are good to go
On Leopard, depending on the python package you're using and the version number, the modules can be found in /Library/Python:
/Library/Python/2.5/site-packages
or in /Library/Frameworks
/Library/Frameworks/Python.framework/Versions/Current/lib/python2.6/site-packages
(it could also be 3.0 or whatever version)...
I guess it is quite the same with Tiger
Considering that in every operating system most of python's packages are installed using 'pip' (see pip documentation) you can also use the command 'pip freeze' on a terminal to print a list of all the packages you have installed through it.
Other tools like 'homebrew' for macOS (used when for some reason you can't install a package using pip) have similar commands, in this specific case 'brew list'.
I'm trying to install python to a 1and1.com shared linux hosting account.
There is a nice guide at this address:
http://www.jacksinner.com/wordpress/?p=3
However I get stuck at step 6 which is: "make install". The error I get is as follows:
(uiserver):u58399657:~/bin/python > make install
Creating directory /~/bin/python/bin
/usr/bin/install: cannot create directory `/~’: Permission denied
Creating directory /~/bin/python/lib
/usr/bin/install: cannot create directory `/~’: Permission denied
make: *** [altbininstall] Error 1
I look forward to some suggestions.
UPDATE:
Here is an alternative version of the configure step to fix the above error, however this time I'm getting a different error:
(uiserver):u58399657:~ > cd Python-2.6.3
(uiserver):u58399657:~/Python-2.6.3 > ./configure -prefix=~/bin/python
configure: error: expected an absolute directory name for --prefix: ~/bin/python
(uiserver):u58399657:~/Python-2.6.3 >
The short version is, it looks like you've set the prefix to /~/bin/python instead of simply ~/bin/python. This is typically done with a --prefix=path argument to configure or some other similar script. Try fixing this and it should then work. I'd suggest actual commands, but it's been a while (hence my request to see what you've been typing.)
Because of the above mistake, it is trying to install to a subdirectory called ~ of the root directory (/), instead of your home directory (~).
EDIT: Looking at the linked tutorial, this step is incorrect:
./configure --prefix=/~/bin/python
It should instead read:
./configure --prefix=~/bin/python
Note, this is addressed in the very first comment to that post.
EDIT 2: It seems that whatever shell you are using isn't expanding the path properly. Try this instead:
./configure --prefix=$HOME/bin/python
Failing even that, run echo $HOME and substitute that for $HOME above. It should look something like --prefix=/home/mscharley/bin/python
You really should consider using the AS binary package from Activestate for this kind of thing. Download the .tar.gz file, unpack it, change to the python directory and run the install shell script. This installs a completely standalone version of python without touching any of the system stuff. You don't need root permissions and you don't need to mess around with make.
Of course, maybe you are a C/C++ developer, make is a familiar tool and you are experienced at building packages from source. But if any of those is not true then it is worth your while to try out the Activestate AS binary package.
I was facing same issue with 1and1 shared hosting (Your provided linked tutorial is not available now). I followed Installing Python modules on Hostgator shared hosting using VirtualEnv tutorial with only one change for 1and1. That is:
Instead of:
> python virtualenv-1.11.6/virtualenv.py /home1/yourusername/public_html/yourdomain.com/env --no-site-package
I used:
> python virtualenv-1.11.6/virtualenv.py /kunden/homepages/29/yourusername/htdocs/env --no-site-package
Rest of the instructions worked and I successfully installed VirtualEnv.
Example: 1and1 does not provide Requests module and pip cannot be used in shared hosting. This screenshot demonstrates that after installing VirtualEnv, pip command can be used and at the end >>> import requests successfully worked.
The question is related to the answer to "Unable to install Python without sudo access".
I need to install python-setuptools to install python modules.
I have extracted the installation package.
I get the following error when configuring
[~/wepapps/pythonModules/setuptools-0.6c9]# ./configure --prefix=/home/masi/.local
-bash: ./configure: No such file or directory
I did not find the solution at the program's homepage.
How can I resolve this error?
As Noah states, setuptools isn't an automake package so doesn't use ‘./configure’. Instead it's a pure-Python-style ‘setup.py’ (distutils) script.
You shouldn't normally need to play with .pydistutils.cfg, as long as you run it with the right version of Python. So if you haven't added the .local/bin folder to PATH, you'd have to say explicitly:
/home/masi/.local/bin/python setup.py install
AIUI this should Just Work.
I did not find the solution at the program's homepage.
Yeah, they want you to install it from a shell script egg which uses the default version of Python. Which you don't want.
(Another approach if you can't get setuptools to work is to skip it and install each module and dependency manually. Personally I have a bit of an aversion to setuptools/egg, as it contains far too much “clever” magic for my tastes and makes a mess of my filesystem. But I'm an old curmudgeon like that. Most Python modules can be obtained as simple Python files or plain old distutils scripts, but unfortunately there are some that demand eggs.)
You might want to check http://peak.telecommunity.com/DevCenter/EasyInstall#custom-installation-locations.
EasyInstall is a python module with some shell scripts (or some shell scripts with a python module?) and does not use the unix make tool that gets configured with the "./configure" command. It looks like your best bet is to try editing ~/.pydistutils.cfg to include:
[install]
install_lib = /home/masi/.local/lib/python/site-packages/
install_scripts = /home/masi/.local/bin
You'll also presumably have made the ~/.local/bin/ folder part of your PATH so you can run the easy_install script. (I'm not sure exactly where the site-packages directory will be under .local, but it shouldn't be hard to find.)
Hope this helps.