Setting up Python interface for openEMS and CSXCAD #167
Replies: 2 comments 7 replies
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First of all, please never post text as screenshot when you're reporting an issue for any software project. Screenshots cannot be edited or searched like text, so they're wastes of everyone's time. For short error messages like these, it only takes a few seconds to copy the entire console output as text and press the "code" formatting button. For long error messages, use attachments.
This has just been fixed several days ago. The patch can be applied manually from here: thliebig/openEMS@bf30b7d - but it's not enough to solve your problem because there's also a CSXCAD problem.
I'm the author of the documentation, but I don't understand why this happens, It worked on my machine. What macOS version are you using? Anyway, it sounds like a problem related to compiler search path. For now, try copying all CC @aWZHY0yQH81uOYvH: Please take a look when you have time. |
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I am seeing this problem too. The C++ files generated during the cythonizing process have include paths like (again I'm on an Intel Mac so my brew prefix is The resulting compilation command is as follows: The include search paths do not include If you attempt to build using the system-provided python, it works. Notice the use of To fix this, either you need to build with the system-supplied version of python (by explicitly specifying diff --git a/python/setup.py b/python/setup.py
index c8c6c05..994360e 100644
--- a/python/setup.py
+++ b/python/setup.py
@@ -5,6 +5,7 @@ import os
extensions = [
Extension("*", [os.path.join(os.path.dirname(__file__), "CSXCAD","*.pyx")],
+ include_dirs = ["/usr/local/include"],
language="c++", # generate C++ code
libraries = ['CSXCAD',]),
]A better permanent solution to this would be to figure out a cross-platform way of finding the default system include paths and specifying them as above, modifying the flags provided to clang (perhaps by replacing |
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I have opened issues regarding this. The problem is present in openEMS as well. |
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Excellent troubleshooting, thank you.
Yes. I just remembered seeing the same problem as well with Homebrew's Python, but I thought that it was a non-default environment anyway so supporting it was not strictly necessary, so I simply uninstalled Homebrew's Python in favor of macOS's built-in one and didn't continue investigating. If I recall correctly, if openEMS is the only thing you've installed, Homebrew won't pull its own Python as a dependency, so everything worked. But naturally this is not a typical setup and we really need to solve the real underlying problem. |
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Got the same
I think that it's because I have conda in the middle but not sure Have a mac M1 and Sequoia 15.1 |
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Is CSXCAD in your /usr/local/include/? Otherwise you'll need to add the path your headers are located or copy them there. Also I highly recommend a docker image for this, the dependencies were a big issue for me. |
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Thanks for the quick reply, but I finally use a macport install. Not an experienced user at all on openEMS so haven't been able to check if it works correctly, but it seems to be okay. |
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Can you leave a short description of what you did in case future Mac users stumble over here? |
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Just for reference, not long ago someone was having similar issues and the PR with the |
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Hello, I am very new to openEMS and I have been having troubles setting up the python interface for CSXCAD and openEMS. I followed the instructions given on the website for setting this up. However when I am trying to use pip to install the required python libraries it is throwing a /usr/local/clang exited with code 1 for the CSXCAD python interface. It also says,
/Users/adityamalhotra/Library/Caches/Homebrew/openems--git/CSXCAD/python/CSXCAD/CSPrimitives.cpp:1222:10: fatal error: 'CSXCAD/ParameterObjects.h' file not found
#include "CSXCAD/ParameterObjects.h"
I checked and the ParameterObjects.h file is not present inside the CSXCAD directory anywhere. It also says "python setup.py bdist_wheel did not run successfully".
When trying to setup the python interface for openEMS, the error thrown is "Error compiling cython file". It also says "python setup.py egg_info did not run successfully". For this the file that is being compiled is trying to cimport cython.numeric. However it is throwing the error cython.numeric is not a valid cython.* module.
I have already installed the required python libraries but it has not worked.
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