Cmake issue
SehongOh opened this issue · comments
Hello,
I was trying to install BanditPAM and following the steps that you offer.
When I tried to install Carma, I typed "cmake --build . --config Release --target install".
But, I got this error "make: *** No rule to make target `install'. Stop.".
Could you let me know how to fix it?
Thanks
Hi, thanks for filing an issue.
That's strange you're encountering a bug -- I'm able to install carma successfully on my M1 Mac. From /BanditPAM/headers/carma:
mkdir build && cd build && cmake -DCARMA_INSTALL_LIB=ON .. && sudo cmake --build . --config Release --target install
-- The CXX compiler identification is AppleClang 14.0.0.14000029
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Setting build type to 'Release' as none was specified.
-- carma: enable arma no debug: OFF
-- carma: enable extra debug: OFF
-- carma: enable soft steal: OFF
-- carma: enable hard steal: OFF
-- carma: don't require owndata: OFF
-- carma: don't require f-contiguous: OFF
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/motiwari/Desktop/BanditPAM/headers/carma/build
Password:
Install the project...
-- Install configuration: "Release"
-- Installing: /usr/local/share/carma/cmake/carmaCarmaTargets.cmake
-- Installing: /usr/local/share/carma/cmake/carmaHeaderTargets.cmake
-- Installing: /usr/local/share/carma/cmake/carmaConfig.cmake
-- Installing: /usr/local/share/carma/cmake/carmaConfigVersion.cmake
-- Installing: /usr/local/share/carma/cmake/carmaDependencyTargets.cmake
-- Installing: /usr/local/include/carma/carma
-- Up-to-date: /usr/local/include/carma/carma_bits
-- Installing: /usr/local/include/carma/carma_bits/typecheck.h
-- Installing: /usr/local/include/carma/carma_bits/cnalloc.h
-- Installing: /usr/local/include/carma/carma_bits/numpytoarma.h
-- Installing: /usr/local/include/carma/carma_bits/armatonumpy.h
-- Installing: /usr/local/include/carma/carma_bits/debug.h
-- Installing: /usr/local/include/carma/carma_bits/converters.h
-- Installing: /usr/local/include/carma/carma_bits/config.h
-- Installing: /usr/local/include/carma/carma_bits/exceptions.h
-- Installing: /usr/local/include/carma/carma_bits/numpyapi.h
-- Installing: /usr/local/include/carma/carma_bits/arraystore.h
-- Installing: /usr/local/include/carma/carma_bits/nparray.h
-- Installing: /usr/local/include/carma/carma_bits/cnumpy.h
-- Installing: /usr/local/include/carma/carma_bits/generated_config.h
One of the things I notice is that you're trying to run cmake from outside of a build directory, which is not recommended.
Could you provide more details? What commands did you run when you cloned the repo locally? What OS are you on? And is there a reason you're trying to install from source, instead of installing the pip package from PyPI?
Thank you for answering.
I am using Mac OS with M1
Do you mean that I can just use BanditPAM by installing it with "pip install BanditPAM"?
I installed it but when I run the example code, the error occurs.
Traceback (most recent call last):
File "/Users/ohsehong/Documents/Research/Kmedoids/BanditPAM/Kmedoids.py", line 1, in
from banditpam import KMedoids
ImportError: dlopen(/opt/homebrew/lib/python3.11/site-packages/banditpam.cpython-311-darwin.so, 0x0002): symbol not found in flat namespace (_omp_get_max_threads)
The below is my problem when I install Carma
Ah ok -- the error about symbol not found in flat namespace is a known issue that I haven't been able to reproduce or figure out, despite significant trying. In your case, it makes sense to install from source.
Could you ensure your carma git submodule is at commit 75057dd? What happens what you type git status from inside BanditPAM/headers/carma? Also, did you run git submodule update --init --recursive from BanditPAM first?
Sorry, I don't understand what you mean. What is the meaning of "git submodule is at commit 75057dd ?
This is also an error when I tried to install it on my Windows.
Do I need to install the below things before running "pip install banditpam"?
A C++ compiler; we recommend LLVM's clang: via the LLVM installation instructions
OpenMP: if using LLVM's clang, then OpenMP is already enabled
CMake: via the CMake installation instructions
Armadillo: via the Armadillo installation instructions
CARMA: via the instructions in the quickstart
How did you download the BanditPAM source code? It looks like you may have downloaded a zip file of the source -- instead, could you run git clone https://github.com/motiwari/BanditPAM.git ? This will properly preserve the .git folder of the repository and allow you to run git submodule update --init --recursive.
When you downloaded the source code as a zip, it doesn't preserve the .git folder, which is why your git submodule update --init --recursive command is failing and carma isn't being initialized correctly.
Unfortunately we don't support Windows builds right now; we're working on it, but it will be some time until we can ship a Windows build.
Sorry for keep asking.
I am still not able to make it.
Do you have any suggestions for me?
Not a problem, I'm happy to help! And this may help us debug the issue you're having with pip install banditpam about some symbols not being found.
It looks like you're making progress. Now, the carma installation is failing because it can't find OpenMP, although your second screenshot suggests it's installed. Could you try updating libomp via `brew?
If the issue still persists, you may need to try this, this, this, or updating cmake.
E.g. cmake -DCARMA_INSTALL_LIB=ON -DOpenMP_libomp_LIBRARY -DCMAKE_SHARED_LINKER_FLAGS ..
My libomp and cmake are updated version.
I will keep doing to solve it with the links. But with the command that you gave me did not work.
Hello, I was not able to make it. I tried to install the package with my friend's Mac, but the same error happened.
But, I can use it on Colab.
Thanks for the response; I'm sorry I couldn't help more. I'm glad you found a workaround.