Comments (67)
xgdgsc
commented on July 18, 2024
1
I rebuilt them and uploaded to https://github.com/peterwittek/somoclu/releases/tag/1.6 because pypi doesn' t allow files with the same name get reuploaded after deletion. And I remember it may not a building problem as https://github.com/peterwittek/somoclu/tree/master/src/Python#installation documented, before you try the new built packages, you can try using Dependency Walker on site-packages\_somoclu_wrap.pyd. Usually right version (32/64bit) of vcomp90.dll, msvcp90.dll, msvcr90.dll should be put to C:\Windows\System32 or C:\Windows\SysWOW64.
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xgdgsc
commented on July 18, 2024
1
OK. Thanks for pointing this out. Closing this.
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xgdgsc
commented on July 18, 2024
1
@arhuang Can you find _somoclu_wrap.so under you site-packages directory?
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arhuang
commented on July 18, 2024
1
ok sorry, I think the somoclu_wrap.so didn't install the first time, everything works now. Thanks for your help
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xgdgsc
commented on July 18, 2024
There seems some problems with my pre-built wheel package. I will rebuild them.
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dinos66
commented on July 18, 2024
It must have been the build, cause I reinstalled it using the new 1.6 which you uploaded and it seems to be working fine.
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wooandoo
commented on July 18, 2024
Hi,
I still have the error with os x 10.10 and somoclu 1.6.1.
Do you have an idea?
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dinos66
commented on July 18, 2024
Apologies for checking but did you delete all somoclu files and reinstalled fresh?
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xgdgsc
commented on July 18, 2024
@wooandoo Which Python version? How did you install? Wheel package or running setup.py?
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wooandoo
commented on July 18, 2024
@xgdgsc I use python 3.5 in pineapple (iPython on OSX)
@dinos66 it was my first installation
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xgdgsc
commented on July 18, 2024
@wooandoo I just built a wheel package for 3.5 you can try installing it https://pypi.python.org/packages/3.5/s/somoclu/somoclu-1.6.1-cp35-cp35m-macosx_10_11_x86_64.whl#md5=e8aef774e93fe47a990798e7771173a2
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arhuang
commented on July 18, 2024
Hi, I keep getting the import error: "Warning: training function cannot be imported. Only pre-trained maps can be analyzed." so wrap_train never gets imported from .somoclu_wrap and thus global name 'wrap_train' is not defined
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xgdgsc
commented on July 18, 2024
@arhuang How did you install?
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arhuang
commented on July 18, 2024
I first did it using pip and then the 1.6 version linked above.
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xgdgsc
commented on July 18, 2024
@arhuang What' s your platform and Python version?
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arhuang
commented on July 18, 2024
osx 10.11 python 2.7
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xgdgsc
commented on July 18, 2024
@arhuang Are you using the python installed by homebrew or system python? I tested the wheel package with the python installed by homebrew and it worked fine.
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arhuang
commented on July 18, 2024
I am using python installed by homebrew, is that wheel package the one installed with pip?
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xgdgsc
commented on July 18, 2024
@arhuang It should be. You can try downloading the wheel to make sure.
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arhuang
commented on July 18, 2024
Am I missing .somoclu_wrap? I get the warning both when i import somoclu and when i use train.
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arhuang
commented on July 18, 2024
sorry where is the site-packages directory?
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arhuang
commented on July 18, 2024
I found a site packages directory in ~Library/Python/2.7/site-packages but it does not include somoclu
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arhuang
commented on July 18, 2024
I found somoclu_wrap.py in site packages but not somoclu_wrap.so
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arhuang
commented on July 18, 2024
oh wait sorry, I found somoclu_wrap.so
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KevinAyuque
commented on July 18, 2024
I'm getting the same problem "Warning: training function cannot be imported. Only pre-trained maps can be analyzed." using Python 2.7 (default and virtualenv) on OSX El Capitan. Hopefully someone can help me. I tried installing directly from pip and the wheel package with no luck.
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xgdgsc
commented on July 18, 2024
@KevinAyuque Do you mean the system python by "default"? Have you tried the brew python?
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KevinAyuque
commented on July 18, 2024
I'm using the python located on /usr/local/bin/python which I think is the homebrew python.
This are all the files I have related to somoclu:
/usr/local/lib/python2.7/site-packages/_somoclu_wrap.so
/usr/local/lib/python2.7/site-packages/somoclu-1.6.1.dist-info/DESCRIPTION.rst
/usr/local/lib/python2.7/site-packages/somoclu-1.6.1.dist-info/INSTALLER
/usr/local/lib/python2.7/site-packages/somoclu-1.6.1.dist-info/METADATA
/usr/local/lib/python2.7/site-packages/somoclu-1.6.1.dist-info/RECORD
/usr/local/lib/python2.7/site-packages/somoclu-1.6.1.dist-info/WHEEL
/usr/local/lib/python2.7/site-packages/somoclu-1.6.1.dist-info/metadata.json
/usr/local/lib/python2.7/site-packages/somoclu-1.6.1.dist-info/top_level.txt
/usr/local/lib/python2.7/site-packages/somoclu/init.py
/usr/local/lib/python2.7/site-packages/somoclu/init.pyc
/usr/local/lib/python2.7/site-packages/somoclu/somoclu_wrap.py
/usr/local/lib/python2.7/site-packages/somoclu/somoclu_wrap.pyc
/usr/local/lib/python2.7/site-packages/somoclu/train.py
/usr/local/lib/python2.7/site-packages/somoclu/train.pyc
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KevinAyuque
commented on July 18, 2024
I tried with python3 and still get the same problem.
Here is a more detailed look at the error it throws:
som.train()
File "/usr/local/lib/python3.5/site-packages/somoclu/train.py", line 181, in train
wrap_train(np.ravel(self._data), epochs, self._n_columns, self._n_rows,
NameError: name 'wrap_train' is not defined
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xgdgsc
commented on July 18, 2024
Which package did you install? The so file name is wrong. It should be:
Soul-MacBook-Pro:tests gsc$ ls /usr/local/lib/python3.5/site-packages/_somoclu*
-rwxr-xr-x 1 gsc admin 84752 Mar 23 12:58 /usr/local/lib/python3.5/site-packages/_somoclu_wrap.cpython-35m-darwin.so
Soul-MacBook-Pro:tests gsc$ ls /usr/local/lib/python2.7/site-packages/_somoclu*
-rwxr-xr-x 1 gsc admin 86476 May 10 18:57 /usr/local/lib/python2.7/site-packages/_somoclu_wrap.so
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KevinAyuque
commented on July 18, 2024
@xgdgsc I used this one (posted above) https://pypi.python.org/packages/6f/f7/03939347c04b265d07142c8566048086b9f56b780db8c04c0fdf9ed07893/somoclu-1.6.1-cp27-none-macosx_10_11_x86_64.whl#md5=50b19cf29b2e2567e21ea8135ac577e1 for the 2.7 and https://pypi.python.org/packages/3.5/s/somoclu/somoclu-1.6.1-cp35-cp35m-macosx_10_11_x86_64.whl#md5=e8aef774e93fe47a990798e7771173a2 for 3.5
I installed it using pip:
pip3 install somoclu-1.6.1-cp35-cp35m-macosx_10_11_x86_64.whl
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xgdgsc
commented on July 18, 2024
I tried with the same packages and they install fine here. You can try changing the file names. Maybe there are something wrong with your pip.
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KevinAyuque
commented on July 18, 2024
I tried reinstalling again and this are the files I get:
/usr/local/lib/python2.7/site-packages/_somoclu_wrap.so
/usr/local/lib/python2.7/site-packages/somoclu-1.6.1.dist-info/DESCRIPTION.rst
/usr/local/lib/python2.7/site-packages/somoclu-1.6.1.dist-info/INSTALLER
/usr/local/lib/python2.7/site-packages/somoclu-1.6.1.dist-info/METADATA
/usr/local/lib/python2.7/site-packages/somoclu-1.6.1.dist-info/RECORD
/usr/local/lib/python2.7/site-packages/somoclu-1.6.1.dist-info/WHEEL
/usr/local/lib/python2.7/site-packages/somoclu-1.6.1.dist-info/metadata.json
/usr/local/lib/python2.7/site-packages/somoclu-1.6.1.dist-info/top_level.txt
/usr/local/lib/python2.7/site-packages/somoclu/__init__.py
/usr/local/lib/python2.7/site-packages/somoclu/__init__.pyc
/usr/local/lib/python2.7/site-packages/somoclu/somoclu_wrap.py
/usr/local/lib/python2.7/site-packages/somoclu/somoclu_wrap.pyc
/usr/local/lib/python2.7/site-packages/somoclu/train.py
/usr/local/lib/python2.7/site-packages/somoclu/train.pyc
I also updated my pip to the latest (8.1.2) and still no luck. I'll keep trying and let you know if I find a solution. Thanks for the assistance.
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xgdgsc
commented on July 18, 2024
Have you installed libiomp?
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KevinAyuque
commented on July 18, 2024
@xgdgsc that solved it! thank you so much!
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kunal-ray
commented on July 18, 2024
I using python 2.7.10 on windows 10
I tried installing somoclu by pip as well as from https://github.com/peterwittek/somoclu/releases/tag/1.6
In both cases installation was fine but importing somoclu gives an error of training function cannot be imported.
Please help
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xgdgsc
commented on July 18, 2024
@kunal-ray Have you tried https://pypi.python.org/packages/72/39/cb5c9dc0724c285225abc539b02d0af77e6e619eb7aa73d0a4af9eab4216/somoclu-1.6.1-cp27-none-win_amd64.whl ?
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kunal-ray
commented on July 18, 2024
I just tried it, but that did not solve the problem. I am still getting the same warning of training function cannot be imported
By the way i am uninstalling previous packages by pip uninstall (installs for which the warning was there)
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xgdgsc
commented on July 18, 2024
Do you have \site-packages\_somoclu_wrap.[YOUR ARCH].pyd under your python directory? Have you tried #28 (comment) using Dependency Walker?
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kunal-ray
commented on July 18, 2024
I have _somoclu_wrap.pyd under site-packages
Dependency Walker says that the following files it could not open as the files were not found
API-MS-WIN-CORE-APIQUERY-L1-1-0.DLL
API-MS-WIN-CORE-APPCOMPAT-L1-1-1.DLL
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EXT-MS-WIN-APPCOMPAT-APPHELP-L1-1-0.DLL
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EXT-MS-WIN-NTUSER-DRAW-L1-1-2.DLL
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EXT-MS-WIN-NTUSER-KEYBOARD-L1-1-1.DLL
EXT-MS-WIN-NTUSER-KEYBOARD-L1-2-0.DLL
EXT-MS-WIN-NTUSER-MENU-L1-1-2.DLL
EXT-MS-WIN-NTUSER-MESSAGE-L1-1-1.DLL
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EXT-MS-WIN-NTUSER-WINDOWSTATION-L1-1-1.DLL
EXT-MS-WIN-OLE32-BINDCTX-L1-1-0.DLL
EXT-MS-WIN-OLE32-IE-EXT-L1-1-0.DLL
EXT-MS-WIN-OLE32-OLEAUTOMATION-L1-1-0.DLL
EXT-MS-WIN-PROFILE-EXTENDER-L1-1-0.DLL
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EXT-MS-WIN-PROFILE-USERENV-L1-1-0.DLL
EXT-MS-WIN-PROFILE-USERENV-L1-1-1.DLL
EXT-MS-WIN-RPC-SSL-L1-1-0.DLL
EXT-MS-WIN-RTCORE-GDI-DEVCAPS-L1-1-0.DLL
EXT-MS-WIN-RTCORE-GDI-OBJECT-L1-1-0.DLL
EXT-MS-WIN-RTCORE-GDI-RGN-L1-1-0.DLL
EXT-MS-WIN-RTCORE-GDI-RGN-L1-1-1.DLL
EXT-MS-WIN-RTCORE-MINUSER-PRIVATE-EXT-L1-1-0.DLL
EXT-MS-WIN-RTCORE-NTUSER-CURSOR-L1-1-0.DLL
EXT-MS-WIN-RTCORE-NTUSER-DC-ACCESS-L1-1-0.DLL
EXT-MS-WIN-RTCORE-NTUSER-IAM-L1-1-0.DLL
EXT-MS-WIN-RTCORE-NTUSER-INTEGRATION-L1-1-0.DLL
EXT-MS-WIN-RTCORE-NTUSER-SYNCH-EXT-L1-1-0.DLL
EXT-MS-WIN-RTCORE-NTUSER-SYSCOLORS-L1-1-0.DLL
EXT-MS-WIN-RTCORE-NTUSER-SYSPARAMS-L1-1-0.DLL
EXT-MS-WIN-RTCORE-NTUSER-WINDOW-EXT-L1-1-0.DLL
EXT-MS-WIN-SECUR32-TRANSLATENAME-L1-1-0.DLL
EXT-MS-WIN-SECURITY-CAPAUTHZ-L1-1-0.DLL
EXT-MS-WIN-SECURITY-CHAMBERS-L1-1-0.DLL
EXT-MS-WIN-SECURITY-CREDUI-L1-1-0.DLL
EXT-MS-WIN-SECURITY-EFS-L1-1-0.DLL
EXT-MS-WIN-SECURITY-EFSWRT-L1-1-1.DLL
EXT-MS-WIN-SESSION-USERMGR-L1-1-0.DLL
EXT-MS-WIN-SESSION-USERTOKEN-L1-1-0.DLL
EXT-MS-WIN-SESSION-WINSTA-L1-1-0.DLL
EXT-MS-WIN-SESSION-WTSAPI32-L1-1-0.DLL
EXT-MS-WIN-SETUPAPI-INF-L1-1-0.DLL
EXT-MS-WIN-SHELL-DIRECTORY-L1-1-0.DLL
EXT-MS-WIN-SHELL-PROPSYS-L1-1-0.DLL
EXT-MS-WIN-SHELL-SHELL32-L1-2-0.DLL
EXT-MS-WIN-SHELL-SHLWAPI-L1-1-0.DLL
EXT-MS-WIN-SHELL32-SHELLCOM-L1-1-0.DLL
EXT-MS-WIN-SXS-OLEAUTOMATION-L1-1-0.DLL
EXT-MS-WIN-UI-VIEWMANAGEMENT-L1-1-0.DLL
EXT-MS-WIN-USP10-L1-1-0.DLL
EXT-MS-WIN-WER-UI-L1-1-0.DLL
EXT-MS-WIN-WER-XBOX-L1-1-0.DLL
EXT-MS-WIN-WINRT-STORAGE-L1-1-0.DLL
EXT-MS-WIN-WLAN-ONEXUI-L1-1-0.DLL
IESHIMS.DLL
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xgdgsc
commented on July 18, 2024
Usually adding MSVCP90.DLL and VCOMP90.DLL would do.
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kunal-ray
commented on July 18, 2024
Where do I find them from?
I understand they should go in C:\Windows\System32 or C:\Windows\SysWOW64.
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xgdgsc
commented on July 18, 2024
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kunal-ray
commented on July 18, 2024
Warning is gone, so I hope it is fine now. Thanks
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davidlamb
commented on July 18, 2024
I'm having the same problem with installing somoclu on Windows 10 Python 2.7 (using 32 bit). It gives me the same warning and then the error name 'wrap_train' is not defined. I have installed through pip using the whl as well as the executable. I've uninstalled through pip and just deleting the folder. I've installed Visual C++ 2008 express, as well as the redistributable.
I've also tried it through winpython https://winpython.github.io/ (64 and 32 bit versions). I was surprised that didn't work and I get the same errors.
I tried anaconda and that did work. I tried copying the dll files that come with that version and paste them in the System32 folder to see if that would do it but it didn't.
Any other suggestions? Is there a way to test it with winpython?
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xgdgsc
commented on July 18, 2024
Is your Windows 10 32bit or 64bit?
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davidlamb
commented on July 18, 2024
It's a 64bit version of windows, but 32bit python. It is an installation of python that comes installed with ArcGIS software. Maybe that's the issue. I've managed to get myself setup with Anaconda, so I will use that instead. Thank you, though.
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Apoorvakuril
commented on July 18, 2024
I am using Windows 10 Python 2.7.11 (using 64 bit). It gives me the same warning and then the error name 'wrap_train' is not defined. Plz help. I installed using pip and wheel for somoclu - 1.7 and before that 1.6.1 too.
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xgdgsc
commented on July 18, 2024
@Apoorvakuril Have you tried adding some dlls as above comments said?
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bennsandoval
commented on July 18, 2024
For Mac users:
is not valid: brew install libiomp
use this instead: brew install homebrew/boneyard/libiomp
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peterwittek
commented on July 18, 2024
@bennsandoval, thanks for this. If libiomp was migrated to the boneyard, it surely isn't a future-proof solution. As far as I understand, Xcode's clang still does not support OpenMP. On Linux with clang 3.9, the code compiles with OpenMP without any issue. Do you see a better way forward? I can't test it, but would llvm work?
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bennsandoval
commented on July 18, 2024
@peterwittek I tried llvm and did not work.
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peterwittek
commented on July 18, 2024
Thanks for checking it. I just pushed commit c542db9 to update the Mac-related documentation.
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shaayaansayed
commented on July 18, 2024
Facing the same issue on linux machine with python 2.7, using the python installed by anaconda. I'm trying to use pip to install somoclu but getting the 'Warning: training function cannot be imported. Only pre-trained maps can be analyzed' error . Any idea what the issue could be?
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peterwittek
commented on July 18, 2024
You probably lack a compiler. Either install it from your distribution's repo, or install Anaconda's own by 'conda install gcc'.
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tomekzbrozek
commented on July 18, 2024
@peterwittek did you manage to fix it for Python 3.5, mac OS 64bit? I proceeded with all the tips listed above, and still get the error:
"Warning: training function cannot be imported. Only pre-trained maps can be analyzed.
If you installed Somoclu with pip on OS X, this typically means missing libiomp. Please refer to the documentation and to this issue:
#28"
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peterwittek
commented on July 18, 2024
The wheel file on PyPI was compiled with Python 3.6. Either upgrade your Python version, or go through the instructions of how to compile it from scratch.
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xgdgsc
commented on July 18, 2024
Sorry currently there is no binary for macOS on pypi now since I have no access to a mac.
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festarju
commented on July 18, 2024
Hi, @xgdgsc & @peterwittek
Thank you for your work!
I tried everything I could imagine, but I sill have problems with the import #83 :
ImportError: failed to import (/home/bdalab/anaconda3/lib/python3.6/site-packages/somoclu-1.7.4-py3.6-linux-x86_64.egg/_somoclu_wrap.cpython-36m-x86_64-linux-gnu.so: undefined symbol: _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE10_M_replaceEmmPKcm)
Warning: training function cannot be imported. Only pre-trained maps can be analyzed.
more info: https://a.pomf.space/zilkxsyxitvy.htm
Can you suggest something?
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xgdgsc
commented on July 18, 2024
This usually relates to glibc version, maybe you can try using system python.
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peterwittek
commented on July 18, 2024
That is precisely the problem. The system GCC and the one that Anaconda was compiled with are different. Either use the system Python or try the experimental conda recipe.
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festarju
commented on July 18, 2024
Thank you @xgdgsc !
I switched to system python (with some downgrading of zlib1g...) and can now compile a binary for CLI & libsomoclu.so (not the _somoclu_wrap.cpython-36m-x86_64-linux-gnu.so)
But what is the trick to get a python module (with pip install somoclu ?) that knows about envvar CUDAHOME?
In jupyter notebook, when
som = somoclu.Somoclu(n_columns, n_rows, compactsupport=False, kerneltype=1)
I get RuntimeError: Compiled without CUDA!
installed with pip:
~/.pyenv/versions/3.6.1/lib/python3.6/site-packages/somoclu-1.7.4-py3.6.egg-info$ cat installed-files.txt
../somoclu/__init__.py
../somoclu/somoclu_wrap.py
../somoclu/train.py
../somoclu/__pycache__/__init__.cpython-36.pyc
../somoclu/__pycache__/somoclu_wrap.cpython-36.pyc
../somoclu/__pycache__/train.cpython-36.pyc
../_somoclu_wrap.cpython-36m-x86_64-linux-gnu.so
dependency_links.txt
requires.txt
SOURCES.txt
PKG-INFO
top_level.txt
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xgdgsc
commented on July 18, 2024
When you run pip install somoclu or python setup.py install , you should run in an environment where variable CUDAHOME has been set.
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festarju
commented on July 18, 2024
I belive I have CUDAHOME set:
group8@bdalab-249:~/git2-somoclu$ python
Python 3.6.1 (default, Jul 30 2017, 15:00:21)
[GCC 5.4.0 20160609] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import os
>>> os.environ['CUDAHOME']
'/usr/local/cuda-8.0'
here is the log from my python ./setup.py install
https://a.pomf.space/jwvjtqncqlnw.html
BTW, this I found in setup.py and corrected:
try:
#CUDA = find_cuda()
CUDA = None
except EnvironmentError:
CUDA = None
print("Proceeding without CUDA")
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peterwittek
commented on July 18, 2024
The log looks fine to me. The CUDA compiler is verbose, but the output is a series of irrelevant warnings.
Please try the conda recipe that we are trying to put together. I just tried it, and if you set CUDAHOME, it compiles with GPU kernel and it works from Anaconda.
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Zub4ir
commented on July 18, 2024
I got this error on my fresh install of Windows 10. An easy fix is to download a "Visual C++ Redistributable for Visual Studio 2015" installer or newer. It contains the OpenMP libraries in an easy single click install.
Edit: Using Windows 10 64bit, Python 3.6.5 64bit, and SOMOCLU via pip3.
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JimmyGao0204
commented on July 18, 2024
I have got the same error as follows:
Using Windows 10 64 bit, python 3.5.2 and install somoclu via pip install somoclu.
Does anybody know how to fix this bug?Thank you very much.
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JimmyGao0204
commented on July 18, 2024
@xgdgsc I have not \site-packages_somoclu_wrap.[YOUR ARCH].pyd under my python directory. I have try to add MSVCP90.DLL and VCOMP90.DLL to C:\Windows\System32. But it didn't work. How should I fix this problem.
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Related Issues (20)
- /home/docker/R/Rsomoclu/libs/Rsomoclu.so: undefined symbol: _ZTI8Snapshot
- Licensing and GPL HOT 6
- MATLAB interfece Batch algorithm HOT 4
- (core dumped) HOT 3
- Attempting to use an MPI routine before initializing MPI HOT 4
- single dimensional clustering
- upgradation problem HOT 1
- errors importing native C library (python 3.8.6 & swig 4.0.1) HOT 4
- update official repos (pypi and conda) HOT 3
- TypeError: train expected 23 arguments, got 22 HOT 2
- Can I set the random seed? HOT 4
- Get bmu of testing data HOT 2
- Numpy requirement in setup.py HOT 5
- conda-forge PackagesNotFoundError HOT 6
- How can I assign a cluster to new data? HOT 1
- Batch mode and learning rate HOT 3
- Can't build wheel with somoclu and pip 23.1 HOT 2
- Warning: the binary library cannot be imported. You cannot train maps, but you can load and analyze ones that you have already saved. If you installed Somoclu with pip on Windows, this typically means missing DLLs. Please refer to the documentation. HOT 4
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