LHAPDF: undefined symbol when running in Python - python

I'm trying to use the Python interface for LHAPDF, but I receive the following error message:
Traceback (most recent call last):
File "test.py", line 2, in <module>
import lhapdf
ImportError: /home/n17182559/LHAPDF/lib/python2.7/site-packages/lhapdf.so: undefined symbol: _ZN6LHAPDF6ConfigD1Ev
I'm running on Ubuntu 17.04, using Python 2.7, have Boost installed and have a working C++ compiler (g++). I believe I have successfully installed LHAPDF, as I followed the instructions on their website and got no error message (only warnings that auto_ptr is deprecated, but I don't think I have control over that). I did add the ~/LHAPDF/lib/python2.7/sitepackages/ directory to $PYTHONPATH and ~/LHAPDF/bin/ directory to $PATH. I am using LHAPDF 6.1.6 (latest version as of writing this).
I get this error message from a test.py file that merely contains
#!/usr/bin/python
import lhapdf
If it can help you help me, I have found someone with a similar problem, but the cause seems not to be the same thing (I don't have Anaconda installed). As they solved their problem by removing Anaconda from $PATH, here are my $PATH and $PYTHONPATH as they might be the source of the problem (although I don't see how):
$PATH
/home/n17182559/LHAPDF/bin:/opt/applications/geant4/geant4.10.02-install/bin:/home/n17182559/ROOT/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:
$PYTHONPATH
/home/n17182559/ROOT/lib:/home/n17182559/LHAPDF/lib/python2.7/site-packages:
Hope you guys can help!

I solved it (with external help), if anyone wants the solution. The problem was that the main LHAPDF lib directory was not linked to my LD_LIBRARY_PATH. This command line solved it:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/LHAPDF/lib/libLHAP‌​DF.so
(which I added to my ~/.bashrc file).

I can't speak to your specific problem, but when I get this class of error, it stems from a version mismatch between packages: lhapdf depends on another package to define that arcane "semi-hidden" symbol, but the package on which it depends is of a version different from the one expected; the older/newer version doesn't provide that symbol.

It is a version mismatch (of Python), which is likely caused by upgrading Python after LHAPDF is installed.
Therefore you may have to reinstall LHAPDF, or you could install a second LHAPDF if you use two versions of Python (as of now I am not aware of a solution other than this).
Let us assume you use LHAPDF of version 6.2 or higher, which is much simpler. First you would like to set the path in your shell profile so that it points to the version of Python you want to install LHAPDF for. For bash, you could do
export PATH=path/to/python
then you would like to follow the instruction and do
tar xf LHAPDF-6.X.Y.tar.gz
cd LHAPDF-6.X.Y
./configure --prefix=/path/for/installation
make
make install
After the installation is done, you can add LHAPDF to the path by
export PYTHONPATH=path/to/lhapdf/lib/pythonx.y/site-packages/
export LD_LIBRARY_PATH=path/to/lhapdf/lib
export PATH=path/to/lhapdf/bin/:$PATH
export LHAPDF_DATA_PATH=path/to/lhapdf/share/LHAPDF

Related

ImportError: No module named twisted.persisted.styles

From IDLE, I tried to run a script with a newly installed scrapy 1.0.3.
I'm using a script from a friend whom it worked for (but on Windows, I'm on a Mac).
From the import of scrapy on the first line, I get this error when running the program:
ImportError: No module named twisted.persisted.styles
The whole script, if it's helpful, points to this:
Traceback (most recent call last):
File "/Users/eliasfong/tutorial/tutorial/spiders/medspider.py", line 1, in <module>
import scrapy
File "/Library/Python/2.7/site-packages/scrapy/__init__.py", line 27, in <module>
from . import _monkeypatches
File "/Library/Python/2.7/site-packages/scrapy/_monkeypatches.py", line 20, in <module>
import twisted.persisted.styles # NOQA
ImportError: No module named twisted.persisted.styles
Any suggestions on how to tackle this problem?
Just try to force the update of twisted :
pip install twisted --upgrade
That works for me with python3.4 and Scrapy==1.1.0rc1
Either twisted is installed on your mac (I highly doubt it since it's not a standard library) and for whatever reason the IDE (i'm assuming that's what you mean since you typed "idle") or the terminal you are in doesn't have your updated environment variables, meaning it doesn't understand where your default python libraries are (again I highly doubt it), or you simple do not have twisted installed on your mac. If it's not installed you have a couple of options:
The easiest way to install a python package is through pip.
If that not an option you can try homebrew which is another package manager for macs. It offers an easy way to install packages correctly.
If that still is not an option for you or you simply don't want to attempt that you can download twisted directly from here (the .bz2 since you're on a mac), click on it and it should unzip it for you. Then just run setup.py and it should install it in the correct location on your mac.
If that still doesn't work and you have decent knowledge of unix. Use the "locate" command on the terminal and find out where your dist-packages directory is and put the source for twisted in there directly and then attempt to import twisted in your IDE or in the python interpreter to verify that it is installed.
note: If you're still having problems after it is installed trying restarting your IDE or messing with some setting to make sure your IDE has the right environment and python path. Hope that helps!
It could be related to having installed Python without bzip2. I had the same error and this helped me, see the accepted answer here:
Installing Twisted through pip broken on one server
Had this exact thing on FreeBSD. Solution (as root/sudo):
chmod -R go+rX /usr/local/lib/python2.7/site-packages
Some directory permissions weren't set up right on install.

Installing python server for emacs-jedi

I am trying to install Jedi for emacs using marmalade package manager by following instructions here -- http://tkf.github.io/emacs-jedi/latest/. The package manger installs Jedi along with its dependencies. But I cannot install python server using:
M-x jedi:install-server
because that command is not available even after restarting emacs after jedi installation. The only available commands are:
Possible completions are:
jedi:ac-setup jedi:complete
jedi:dot-complete jedi:get-in-function-call
jedi:goto-definition jedi:goto-definition-next
jedi:goto-definition-pop-marker jedi:setup
jedi:show-doc jedi:show-jedi-version
jedi:start-dedicated-server jedi:stop-server
jedi:toggle-debug-server
My .emacs has the following:
(autoload 'jedi:setup "jedi" nil t)
(add-hook 'python-mode-hook 'jedi:setup)
(setq jedi:complete-on-dot t)
I am using emacs on Mac OS X.
At this current state when I open any python file (I use python 2.7), I see the following appear automatically in the minibuffer:
deferred error : (error Server may raise an error : Traceback (most recent call last):
File "/Users/t_nithyanandan/.emacs.d/elpa/jedi-0.1.2/jediepcserver.py", line 302, in <module>
main()
File "/Users/t_nithyanandan/.emacs.d/elpa/jedi-0.1.2/jediepcserver.py", line 298, in main
jedi_epc_server(**vars(ns))
File "/Users/t_nithyanandan/.emacs.d/elpa/jedi-0.1.2/jediepcserver.py", line 210, in jedi_epc_server
import_jedi()
File "/Users/t_nithyanandan/.emacs.d/elpa/jedi-0.1.2/jediepcserver.py", line 249, in import_jedi
import jedi
ImportError: No module named jedi
)
I tried installing jedi using other methods such as el-get and also manually but those seem to not even go this far. I see that the jedi commands available are even lesser than listed above.
Could someone help point out what I am missing?
Thanks.
Edit: The primary purpose I would like to use Jedi is to use auto-completion features for python programming although I believe Jedi has many powerful features. For such a purpose, is the python server essential or could one work around it? Eventually, of course, I'd like to take advantage of many more features in Jedi.
I managed to fix the problem thanks to help from Chris and syohex from emacs-jedi github. Credit goes to them in tracing this to Jedi version.
I am just linking the discussion on emacs-jedi issue #177 and pasting the workaround I found including other problems I encountered along the way.
I was using the Marmalade version which installs a much older version. So I uninstalled jedi and associated dependencies. I set my repository to MELPA and installed a much more recent version of jedi. This made the command
M-x jedi:install-server
available which wasn't the case earlier.
However, issuing that command gave an error
python-environment--make-with-runner: Program named "virtualenv" does not exist.
I made sure I added the location of virtualenv to PATH in my .bashrc.
So I looked up emacs-jedi issue #158 which suggests installing exec-path-from-shell. I installed it from MELPA and added the lines
(when (memq window-system '(mac ns))
(exec-path-from-shell-initialize))
following instructions.
Restarting Emacs with the above lines gave an error:
Symbol's function definition is void: exec-path-from-shell-initialize
So I looked up Autoload issue #3 under exec-path-from-shell development (the link to this can be found in the link for emacs-jedi issue #177). Following one of the solutions, I restarted my computer, uninstalled and reinstalled exec-path-from-shell which magically did solve the problem that existed before the reboot.
Now I checked in emacs if virtualenv could be found using
M-! which virtualenv
It gave the right location.
Then I ran:
M-x jedi:install-server
which now seemed to run without trouble. The first time, there were messages about setting up a
default virtual environment under
/Users/XXX/.emacs.d/.python-environments
besides
Running: pip install --upgrade /Users/XXX/.emacs.d/elpa/jedi-20140321.1323/...Done
but in subsequent trials only the pip upgrade message was displayed.
Having seen that the server installed without trouble, I closed and restarted Emacs and opened a python script file. When I started editing, I got these messages in the minibuffers:
Error (jedi): Failed to start Jedi EPC server.
*** You may need to run "M-x jedi:install-server". ***
This could solve the problem especially if you haven't run the command yet
since Jedi.el installation or update and if the server complains about
Python module imports.
and
auto-complete error: (error Server may raise an error. Use "M-x epc:pop-to-last-server-process-buffer RET" to see full traceback:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python: can't open file '/Users/XXX/.emacs.d/elpa/jedi-0.1.2/jediepcserver.py': [Errno 2] No such file or directory`
)
Thus, I realized that I have to issue the command:
M-x jedi:install-server
every time I start Emacs before opening any python file. Then I was finally able to see the auto-completion features being available during editing.
Though I can run the above command every time manually, I wanted to automate it from my .emacs whenever Emacs is launched. It turned out that I had the following line in my .emacs
(setq jedi:server-command (list "python" "/Users/XXX/.emacs.d/elpa/jedi-0.1.2/jediepcserver.py"))
Upon removing this line in my .emacs, the problem went away and jedi is functional now.
Marmalade currently contains jedi version 0.1.2, but you're looking at documentation for version 0.2.0alpha2.
The documentation for 0.1.2 has different instructions:
package.el (Marmalade or MELPA)
You can install Jedi.el using package.el interface from Marmalade or MELPA. As package.el does not support installing non-elisp packages, you need to install Python part manually (see the next section).
And then in that next section, the imporant bit:
Install Jedi and python-epc by
make requirements (no need for root privileges) or
pip install -r requirements.txt if you want to determine where to install Python modules. You need root privileges (i.e., sudo) to install it in system directory.
You should be able to do make requirements from the ~/.emacs.d/elpa/jedi-0.1.2/ directory, but something like pip install epc jedi should work too.

Nvim setup instructions for the layman?

I'm trying to install vim and nvim as a replacement for Notational Velocity. I recently migrated to Ubuntu (14.04) and I'm very new to how everything works. The instructions for installing nvim are kind of elliptic and not entirely clear to me as a beginner. I manage to get it running if I enter vim and then type :Nvim inside the directory where I store my .txt notes. However, the notes aren't visible in nvim and here's where I run into trouble. As a beginner I simply do not understand the instructions regarding PATH and :python that are given on the installation page. I've tried (successfully, I think) to install xapian as well (after having installed vim) but nothing changed. That is, I cannot specify a PATH for my nvim and I cannot get the nvim script to work as a command anywhere in the terminal.
More consequentially, when I type
:python nvimdb.rebuild_database()
inside vim, I get:
Traceback (most recent call last):
File "", line 1, in
NameError: name 'nvimdb' is not defined
What I would like to ask for are step by step instructions for making nvim work with an existing library of .txt notes targeted at the vim and linux novice.
The program looks great and appears to be exactly what I need for my note taking needs, and I would really appreciate your help! Thank you so much.
I believe this is probably because you haven't installed the xapian library as that is a required mentioned by nvim. You need to install the package xapian-core I believe, you can do that in ubuntu with something like this : sudo apt-get install xapian-core

PySide's shiboken python module not found

PySide is installed successfully, and it works perfectly, but I can't find a way to import the shiboken module. Now I found the discussion about the feature request to expose shiboken functions through a python module (http://bugs.pyside.org/show_bug.cgi?id=902), but the issue is resolved. It was implemented in january 2012, if I understood correctly.
Even though after the installation of PySide 1.1.1 when I try:
>>> import shiboken
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: No module named shiboken
I get an ImportError exception. How can I install the shiboken python module?
Looks like someone forgot to update cmake: bugs-PYSIDE-55.
However, I've just compiled shiboken-1.1.2, and the issue seems to be fixed.
I beleive under ideal circumstances ekhumoro's answer is totally correct, unfortunately I was not that lucky, and the binary packages still didn't allow the usage of the shiboken python module. I had to compile it manually, but that part became tricky too as it didn't work by the default instructions found on their homepage, probably because I'm using ubuntu 12.04, or I'm not sure why else.
As the target was the usage from withing a virtualenv I followed these instructions:
export PYSIDESANDBOXPATH=/path/to/my/virtualenv
export PATH=$PYSIDESANDBOXPATH/bin:$PATH
export PYTHONPATH=$PYSIDESANDBOXPATH/lib/python2.6/site-packages:$PYTHONPATH
export LD_LIBRARY_PATH=$PYSIDESANDBOXPATH/lib:$LD_LIBRARY_PATH
export PKG_CONFIG_PATH=$PYSIDESANDBOXPATH/lib/pkgconfig:$PKG_CONFIG_PATH
mkdir build
cd build
cmake .. -DCMAKE_INSTALL_PREFIX=$PYSIDESANDBOXPATH -DCMAKE_BUILD_TYPE=Debug -DENABLE_ICECC=0'
make
make install
sudo ldconfig
The first problem here was that after it was compiled, and the installation began, and it wanted to install the shiboken python module, this happend:
-- Installing: .../lib/python2.7/site-packages/shiboken.so
-- Removed runtime path from .../lib/python2.7/site-packages/shiboken.so
Then I found somewhere that I should add this parameter to cmake:
-DCMAKE_SKIP_RPATH:BOOL=YES
Now the installation was successful, but when I tried to import shiboken in python, this happened:
import shiboken
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: libshiboken.so: cannot open shared object file: No such file or directory
Google revealed that the issue is caused because $LD_LIBRARY_PATH does not contain the path where those libs are located. First of all ubuntu 12 (and I think 10 and 11 also) does not use the $LD_LIBRARY_PATH environment variable anymore, so it was not even set.
So even the path was incorrect because I tried to join that unset variable with a path:
export LD_LIBRARY_PATH=$PYSIDESANDBOXPATH/lib:$LD_LIBRARY_PATH
So it treated it as two regular strings and just joined them together. The snippet below shows how to join them safely to avoid causing such troubles. But that didn't solve the problem either. as running ldconfig still didn't update anything, so the importing in python failed again.
The final solution found with google too :) was creating a new file in /etc/ld.so.conf.d/ and put there the contents of $LD_LIBRARY_PATH, and run ldconfig after that. So here is the final install script which worked as expected:
#!/usr/bin/env bash
export PYSIDESANDBOXPATH=/path/to/my/virtualenv
export PATH="$PYSIDESANDBOXPATH/bin${PATH:+:$PATH}"
export PYTHONPATH="$PYSIDESANDBOXPATH/lib/python2.7/site-packages${PYTHONPATH:+:$PYTHONPATH}"
export LD_LIBRARY_PATH="$PYSIDESANDBOXPATH/lib${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH}"
export PKG_CONFIG_PATH="$PYSIDESANDBOXPATH/lib/pkgconfig${PKG_CONFIG_PATH:+:$PKG_CONFIG_PATH}"
mkdir build
cd build
cmake .. -DCMAKE_INSTALL_PREFIX=$PYSIDESANDBOXPATH -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_BUILD_TYPE=Debug -DENABLE_ICECC=0
make
make install
sudo sh -c "echo $LD_LIBRARY_PATH > /etc/ld.so.conf.d/shiboken.conf"
sudo ldconfig
That's all, it cost me several hours to figure out, hope this will save someone else :)
Here's how I compile shiboken.pyd on Windows from source code, tested with PySide-1.1.2 + Qt4.8.4 + msvc2010.
First, manually download shiboken-1.1.2.tar.bz2, extract it. Then compile it this way (you might need to set up virtualenv):
python setup.py build --openssl=C:\dev\OpenSSL\1.0.0j\bin --qmake=C:\Qt\4.8.4\bin\qmake.exe
After it finished, I got shiboken.pyd at:
PySide-1.1.2\pyside_install\py2.7-qt4.8.4-32bit-release\lib\site-packages\shiboken.pyd
P.S.
However, shiboken.pyd was missing in "PySide-1.1.2\build\lib", where files would be installed to site-packages. This explains why I coundn't get shiboken.pyd by compiling PySide from PIP using:
pip install PySide --install-option="--openssl=C:\dev\OpenSSL\1.0.0j\bin" --install-option="--qmake=C:\Qt\4.8.4\bin\qmake.exe"
btw, on Mac OS X, if you install PySide using macports, "import shiboken" will also fail, because it is installed into the wrong location ("/opt/local/lib/python2.7/site-packages" instead of "/opt/local/Library/Frameworks/Python.framework/Version/2.7/lib/python2.7/site-packages"). Add "/opt/local/lib/python2.7/site-packages" to PYTHONPATH will solve the issue.
There are definitely bugs in the pyside-setup scripts. Hope Digia could send somebody to fix PySide before the project goes dead.

ImportError: No module named Foundation

I am trying to follow the instructions for the accepted answer to "PyObjC development with Xcode 3.2". I will repost them here since I don't have enough rep to comment on the actual question:
Here's what I have done to get PyObjC working in Snow Leopard:
Using the Finder, I went to Go > Connect to Server... and connected to http://svn.red-bean.com/pyobjc/trunk/pyobjc/pyobjc-xcode/ as a guest.
I then made a folder called Xcode on my local system at ~Library/Application Support/Developer/Shared/Xcode/. (You may already have this folder, but I hadn't customized anything for myself yet).
I copied the File Templates folder from the red-bean server into my new Xcode folder.
Copied the Project Templates folder to some other place, for example, the Desktop.
Using the Terminal, navigated to the temporary Project Templates folder on my Desktop and ran this command to "build" the template.:
$ cd ~/Desktop/Project\ Templates/
$ ./project-tool.py -k -v --template ~/Desktop/Project\ Templates/Cocoa-Python\ Application/CocoaApp.xcodeproj/TemplateInfo.plist Cocoa-Python\ Application ~/Library/Application\ Support/Developer/Shared/Xcode/Project\ Templates/Cocoa-Python\ Application
When I try to run the line that starts with ./project-tool.py, I get the following error in Terminal:
Traceback (most recent call last):
File "./project-tool.py", line 22, in <module>
from Foundation import NSDictionary
ImportError: No module named Foundation
I am running Snow Leopard and have installed Xcode 3.2.1 and have read that this module should already be installed and working. I've read that you can test if the PyObjC modules are working by running >>> import objc in the Python command-line. When I run this, I get:
>>> import objc
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: No module named objc
Could anyone help me dispel this error? It seems like I should be able to do all of this automatically with my Snow Leopard installation, but I can't.
I had the same problem. Mine was caused I think by using homebrew to install my own Python to tinker with.
Because I was worried about mixing python versions, rather than creating the link as described above, I installed a new pyobjc using:
$ pip install pyobjc
For interest, from (http://pythonhosted.org/pyobjc/)
The PyObjC project aims to provide a bridge between the Python and Objective-C programming languages.
Okay, it turned out that, amending mjv's answer, I was able to get it working by typing
export PYTHONPATH="/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/PyObjC/"
before executing the ./project-tool.py line. I still find it ridiculous that I had to do this and if anyone can see why, I would be delighted to know.
Doing this also got the
>>> import objc
line working.
It's because PyObjC is there :
/System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/PyObjC
Edit :
I found how to make "import objc" work, just :
export PYTHONPATH="/System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/"
It will add all the directories to the python path (sys.path)
for python 2.7
export PYTHONPATH="/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/"
One of two things:
Either the Fundation module doesn't exists
Or Python interpretor doesn't know when to find this file
Python looks for modules in the PythonPath
See this SO question for more details on how Python Path is created etc.
Run python -v to trace import statements, this work for interactive mode too.
I could access a Python installation with Foundation on my OSX by running /usr/bin/python file-to-run.py
remove your python or remove site-packages/Foundation | site-packages/foundation
pip3 install pyobjc
the name Foundation is in conflict with https://pypi.org/project/foundation/
I found the foundation folder in /usr/local/lib/python3.9/site-packages/ next to the AppKit folder. After renaming it to Foundation (with uppercase F), the import worked. The Filesystem is not case-sensitive but it seems some part of the import implementation is.
Saw it mentioned in another comment and I too ran into this problem due to installing Python via homebrew. My pyobjc installation wound up going to the Python homebrew installation, yet my pythonpath was linked to the Python that comes bundled with macOS, so there was this big disconnect and I had no luck getting pythonpath re-routed in .zshrc or .zprofile.
In the end, these steps resolved the issue:
brew uninstall python
pip3 install -U pyobjc

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