I am trying to find a solution to the error:
OSError: /opt/conda/lib/python3.7/site-packages/torch_sparse/_version_cuda.so: undefined symbol: _ZN5torch3jit17parseSchemaOrNameERKSs.
arising from the statement from torch_geometric.data import Data in Kaggle notebook.
There are solutions in github and stackoverflow, but none are working.
-- "nvcc --version" shows
"nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2020 NVIDIA Corporation
Built on Wed_Jul_22_19:09:09_PDT_2020
Cuda compilation tools, release 11.0, V11.0.221
Build cuda_11.0_bu.TC445_37.28845127_0"
I tried to install torch-geometric by
!conda install pyg -c pyg -c conda-forge
!pip install pyg-lib torch-scatter torch-sparse torch-cluster torch-spline-conv torch-geometric -f https://data.pyg.org/whl/torch-1.12.0+cu113.html
from here.
The first statement took more than 1 hour so I moved to the second, which installed it. But the error didn't go.
It is running with out any error in colab.
This issue is mentionned at https://pytorch-geometric.readthedocs.io/en/latest/notes/installation.html :
undefined symbol: make_function_schema: This issue signals (1) a version conflict
between your installed PyTorch version and the ${TORCH} version
specified to install the extension packages, or (2) a version conflict
between the installed CUDA version of PyTorch and the ${CUDA} version
specified to install the extension packages. Please verify that your
PyTorch version and its CUDA version match with your installation
command:
python -c "import torch; print(torch.__version__)"
python -c "import torch; print(torch.version.cuda)"
nvcc --version
For re-installation, ensure that you do not run into any caching issues by
using the pip --force-reinstall --no-cache-dir flags. In addition, the
pip --verbose option may help to track down any issues during
installation. If you still do not find any success in installation,
please try to install the extension packages from source.
So, I would try these commands, and re-install all or part of the packages into a fresh environment.
I installed Tensorflow-macos and try to install opencv-python
but always fail in this message
ERROR: Command errored out with exit status 1: /Users/sean/Documents/sysvenv/tf24v/bin/python3 /Users/sean/Documents/sysvenv/tf24v/lib/python3.8/site-packages/pip install --ignore-installed --no-user --prefix /private/var/folders/gy/jzs3xnwd1z3203d75y_31nxc0000gn/T/pip-build-env-en64krht/overlay --no-warn-script-location -v --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- setuptools wheel scikit-build cmake pip 'numpy==1.13.3; python_version=='"'"'3.6'"'"'' 'numpy==1.14.5; python_version=='"'"'3.7'"'"'' 'numpy==1.17.3; python_version=='"'"'3.8'"'"'' 'numpy==1.19.3; python_version>='"'"'3.9'"'"'' Check the logs for full command output.
it lookalike the bumpy version problem.
But In Tensorflow-macos it it 1.8.5 and python is 3.8
Does anynoe have the same problem?
thanks
You might want to look at these suggestions:
opencv issues with M1 MAC - OpenCV imshow doesnot work
conda install opencv
I was successful in installing Python 3.9.1 for Apple Silicon and then running conda install opencv. However, the slow time to compute a few functions for the first time might suggest some components are still being translated via Rosetta. Regardless, while I did not test performance the functions I needed seemed to work.
after searching the web I have successfully installed OpenCV on my Mac M1.
Probably you don't have brew installed, so here's how you should install it:
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
brew install wget
brew install miniforge
brew install cmake, you will need cmake for building OpenCV code
Then just follow this blog: https://sayak.dev/install-opencv-m1/#Install-conda
OR, here is the YouTube video which explains the second step: https://youtu.be/x_kAkabk-5o
P.S. If mdfind cv2.cpython returning an empty string then try to delete the build folder and compile opencv again. Otherwise, you have done everything correctly.
In order to install matplotlib in Debian 9 should I issue
sudo apt-get install python3-matplotlib
or
pip3 install matplotlib?
What is the preferred way? Let me add more detail.
'man pip3' says
pip is a Python package installer, recommended for installing Python
packages which are not available in the Debian archive.
matplotlib confirms this
To install Matplotlib at the system-level, we recommend that you use
your distribution's package manager. This will guarantee that
Matplotlib's dependencies will be installed as well.
According to this I shall run apt-get. However, I had a similar case with numpy. 'import numpy' worked after 'pip3 install numpy'.
Using
Debian GNU/Linux 9.6 (stretch)
$ python3 -V
Python 3.5.3
The key quote from man pip3 is:
recommended for installing Python packages which are not available in the Debian archive.
You can check whether a package is available in the Debian archive by issuing an apt search command, eg.
apt search matplotlib
If your system already has all the necessary dependencies then installing a package with pip will work (as you experienced with pip install numpy).
If you do not have the necessary dependencies your distribution’s package manager will install them automatically. However, this is not true of pip: you would need to resolve any dependency issues manually. In the case of matplotlib, you can find a list of the dependencies you'd need to install manually here.
Essentially, using your system package manager to install a package takes away the extra work of ensuring you have all the necessary dependencies for that package.
pip comes into its own if you desire to work with virtual environments.
abigail#abilina:~/Downloads$ sudo dpkg -i cuda-repo-ubuntu1604_8.0.61-1_amd64.deb
Selecting previously unselected package cuda-repo-ubuntu1604.
(Reading database ... 205999 files and directories currently installed.)
Preparing to unpack cuda-repo-ubuntu1604_8.0.61-1_amd64.deb ...
Unpacking cuda-repo-ubuntu1604 (8.0.61-1) ...
Setting up cuda-repo-ubuntu1604 (8.0.61-1) ...
Warning: The postinst maintainerscript of the package cuda-repo-ubuntu1604
Warning: seems to use apt-key (provided by apt) without depending on gnupg or gnupg2.
Warning: This will BREAK in the future and should be fixed by the package maintainer(s).
Note: Check first if apt-key functionality is needed at all - it probably isn't!
Warning: apt-key should not be used in scripts (called from postinst maintainerscript of the package cuda-repo-ubuntu1604)
OK
abigail#abilina:~/Downloads$ sudo apt-get install cuda
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
cuda : Depends: cuda-8-0 (>= 8.0.61) but it is not going to be installed
E: Unable to correct problems, you have held broken packages.
My ubuntu version is 17.04. Does this mean my Linux currently can't install CUDA? I want to install TensorFlow with GPU support.
Per suggestion:
abigail#abilina:~/Downloads$ sudo apt-get -f install
Reading package lists... Done
Building dependency tree
Reading state information... Done
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
https://launchpad.net/ubuntu/zesty/amd64/nvidia-cuda-toolkit
above is the correct one.
apt-get install nvidia-cuda-toolkit
but remember the cuda installed through apt were installed in different location. manually create ln -s at /usr/local/cuda for include,lib64,and bin
I have successfully installed CUDA 8.0 + the latest patch from NVIDIA on Ubuntu 17.04:
Download the .run file from https://developer.nvidia.com/cuda-downloads, choosing Ubuntu 16.04 (Base Installer)
You will not be able to install it by just running, because it is looking for a file called InstallUtils.pm which is not present in Ubuntu 17.04, but curiously, is present in the .run file - so: unpack the .run file using ./cuda*.run --tar mxvf
copy InstallUtils.pm (should be in the /bin path) to /usr/lib/x86_64-linux-gnu/perl-base
Run the installer (You may want to say no to the driver install step to keep the one you install through apt - I'm using 381.22, because 375.26, which is provided by the .run file does not support my 1080ti)
gcc 6 is incompatible with CUDA, but this is easily remedied for compiling the sample files: just add export EXTRA_NVCCFLAGS="-Xcompiler -std=c++98" to your bashrc file, and comment out
from one of the headers (I think it was host_config.h, but you'll see it once you try to compile) - comment out these lines:
#if __GNUC__ > 5 || (__GNUC__ == 5 && __GNUC_MINOR__ > 3)
#error -- unsupported GNU version! gcc versions later than 5.3 are not supported!
This is all from memory, so hopefully it's accurate enough.
I managed to find this solution thanks to these useful posts:
https://devtalk.nvidia.com/default/topic/983777/can-t-locate-installutils-pm-in-inc/
https://devtalk.nvidia.com/default/topic/949770/cuda-8-0rc-supporting-gcc6-/
For ubuntu 17.04, I had to use cuda 9.0 (deb version)
https://developer.nvidia.com/cuda-release-candidate-download
I couldn't get it to work otherwise. Cuda 8.0 needs gcc 5.3.1 but cuda 9.0 is compatible with gcc 6.3.0 which is installed on ubuntu 17.04 automatically.
More precisely, this is what I did:
On Ubuntu 17.04, install CUDA 9.0 — you can currently download the beta version
https://developer.nvidia.com/cuda-release-candidate-download
I downloaded the .deb file and haven’t had any problems — follow the steps they recommend when you download cuda 9.0
sudo dpkg -i cuda-repo-ubuntu1704-9-0-local-rc_9.0.103-1_amd64.deb
sudo apt-key add /var/cuda-repo-9.0-local-rc/7fa2af80.pub
sudo apt-get update
sudo apt-get install cuda
Then follow the post installation steps from the nvidia instructions (i.e., setting PATH and LD_LIBRARY_PATH)
http://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html#post-installation-actions)
export PATH=/usr/local/cuda-9.0/bin${PATH:+:${PATH}}
export LD_LIBRARY_PATH=/usr/local/cuda-9.0/lib64 ${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}
Cuda 9 is compatible with gcc 6.3.0 (which comes with 17.04). I used arch=sm_52 and sometimes for my make files have to go ‘make clean’.
Installing Cuda 9.0 was the simplest solution in my case.
Alternatively, if you'd prefer cuda 8, you can download the deb file and then use the command
dpkg-deb -x cuda_8.*.deb /usr/local/cuda-8.0
to extract the contents from the deb file and have them placed in the desired directory.
Source: http://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html#advanced-setup)
I tried to install matplotlib on my MacBook Air, but it always gives me this error message:
Processing matplotlib-1.1.1_notests.tar.gz
Running matplotlib-1.1.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-3jFpXK/matplotlib-1.1.1/egg-dist-tmp-jC7QY3
basedirlist is: []
============================================================================
BUILDING MATPLOTLIB
matplotlib: 1.1.1
python: 2.7.2 (default, Jun 20 2012, 16:23:33) [GCC 4.2.1
Compatible Apple Clang 4.0
(tags/Apple/clang-418.0.60)]
platform: darwin
REQUIRED DEPENDENCIES
numpy: 1.6.1
freetype2: found, but unknown version (no pkg-config)
* WARNING: Could not find 'freetype2' headers in any
* of '.', './freetype2'.
OPTIONAL BACKEND DEPENDENCIES
libpng: found, but unknown version (no pkg-config)
* Could not find 'libpng' headers in any of '.'
Tkinter: Tkinter: version not identified, Tk: 8.5, Tcl: 8.5
Gtk+: no
* Building for Gtk+ requires pygtk; you must be able
* to "import gtk" in your build/install environment
Mac OS X native: yes
Qt: no
Qt4: no
PySide: no
Cairo: no
OPTIONAL DATE/TIMEZONE DEPENDENCIES
datetime: present, version unknown
dateutil: 1.5
pytz: matplotlib will provide
adding pytz
OPTIONAL USETEX DEPENDENCIES
dvipng: 1.14
ghostscript: 9.05
latex: 3.1415926
[Edit setup.cfg to suppress the above messages]
pymods ['pylab']
packages ['matplotlib', 'matplotlib.backends', 'matplotlib.backends.qt4_editor', 'matplotlib.projections', 'matplotlib.testing', 'matplotlib.testing.jpl_units', 'matplotlib.tests', 'mpl_toolkits', 'mpl_toolkits.mplot3d', 'mpl_toolkits.axes_grid', 'mpl_toolkits.axes_grid1', 'mpl_toolkits.axisartist', 'matplotlib.sphinxext', 'matplotlib.tri', 'matplotlib.delaunay', 'pytz']
warning: no files found matching 'KNOWN_BUGS'
warning: no files found matching 'INTERACTIVE'
warning: no files found matching 'MANIFEST'
warning: no files found matching '__init__.py'
warning: no files found matching 'examples/data/*'
warning: no files found matching 'lib/mpl_toolkits'
warning: no files found matching 'LICENSE*' under directory 'license'
clang: warning: argument unused during compilation: '-mno-fused-madd'
In file included from src/ft2font.cpp:3:
src/ft2font.h:16:10: fatal error: 'ft2build.h' file not found
**#include <ft2build.h>
^
1 error generated.
error: Setup script exited with error: command 'clang' failed with exit status 1**
I tried to install freetype and libpng using homebrew but it doesn't work. How can I get ft2build.h?
The following worked for matplotlib installation after installing python according to instructions from thegreenroom. Those instructions didn't work for me after I installed Python. I followed the instructions from Scipy.org to install numpy and scipy. Then I did (adapted from above answer):
brew install freetype
brew install libpng
However I got the same error message whether I installed with pip install matplotlib or trying to install from source, doing
python setup.py build
python setup.py install
in the matplotlib directory I cloned via git clone https://github.com/matplotlib/matplotlib.git.
The error persisted until I ran
brew link freetype
Then from the cloned matplotlib directory I ran
python setup.py build
python setup.py install
And the installation succeeded.
This may help folks looking for a non-homebrew solution.
My goal: use pip install to build matplotlib for a non-system python 2.7.3 build.
Using latest X-Code and X-Code command line tools as of Feb 2013, no matter what gymnastics I tried, I always received C++ ostream related template errors when compiling ft2build with gcc.
I was able to get a pip install to work with the following env vars:
export CC=clang
export CXX=clang++
export LDFLAGS="-L/usr/X11/lib"
export CFLAGS="-I/usr/X11/include -I/usr/X11/include/freetype2"
I simply forced clang and added my xquartz paths. No extra pkg-config or libpng builds, no sudo-ed symlinks.
I think the other answers are on the right track, but I encountered this same problem and can attest that:
brew install pkg-config
brew install freetype
pip install matplotlib
would yield the same result. Typically on an Ubuntu box my next response would have been
sudo apt-get install libfreetype-dev
or some variation of that to install the header. However, I could find no such homebrew package. Furthermore, I was able to locate the header file in question in a pretty normal location on my system:
zoidberg:~ matt$ locate ft2build.h
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/usr/X11/include/ft2build.h
/usr/X11/include/ft2build.h
So I suspect there's either a problem with my system paths or with the homebrew packaged matplotlib. Since I'm lazy, I just tried installing the matplotlib package head from github:
pip install git+git://github.com/matplotlib/matplotlib.git#egg=matplotlib-dev
and it worked for me.
Here's the brew + pip recipe I used from a cold start. If you already have python and gfortran and such, jump in at the point where you need. The crucial steps appear to be brew install freetype and brew install libpng prior to doing pip install matplotlib
$ ruby -e "$(curl -fsSkL raw.github.com/mxcl/homebrew/go)"
$ brew doctor
$ brew install python
$ export PATH=/usr/local/bin:/usr/local/share/python:$PATH
$ easy_install pip
$ brew install gfortran
$ pip install numpy
$ pip install scipy
$ brew install pkg-config
$ brew install freetype
$ brew install libpng
$ pip install matplotlib
$ python
>>> import numpy
>>> import scipy
>>> import matplotlib
Note the 'no pkg-config' notices. You should have pkg-config on your search path, and it presumably needs to be the homebrew version so that it knows where the homebrew versions of the libraries are.
You need freetype:
brew install freetype
See the following:
http://comments.gmane.org/gmane.comp.python.matplotlib.general/31394
I also use mac air with OS X ver 10.8.2.
Using following commands can get rid of this failure:
brew install freetype
brew install libpng
pip install matplotlib
That's all. There may be some warning in the installing process, but that does not affect.
Use following python code to test:
import matplotlib.pyplot as plt
plt.plot([1,2,3,4])
plt.ylabel('some numbers')
plt.show()
which is referred from the url: http://matplotlib.org/users/pyplot_tutorial.html.
I have found installing these pacakges via homebrew to be the most reliable method
# if you haven't installed python via brew already:
brew install python
# sets up python as default python instead of system python
brew link python
# Add more brew formulae so we can install our py libs with brew
brew tap samueljohn/python
brew tap homebrew/science
# install numpy,scipy,matplotlib and dependencies ( gfortran, etc.. )
brew install numpy
brew install scipy
brew insatll matplotlib
I am using MacOs 10.8 too, and I encountered the same problem regarding not finding ft2build.h header when I tried to install matplotlib, what I l did to resolve the reported issue is :
1) replacing "ft2build.h" in the following call within the file "setupext.py" :
return self._check_for_pkg_config('freetype2',
'ft2build.h',
min_version='2.4',
version=version)
by the complete path to the ft2build.h header, in my case :
return self._check_for_pkg_config('freetype2',
'/usr/local/Cellar/freetype/2.5.2/include/freetype2/ft2build.h',
min_version='2.4',
version=version)
I think, but have not tested, that the problem is solved in an upstream commit of matplotlib. Here is my reasons why:
Discussion:
https://github.com/vbraun/sage/commit/5d17ca989eb58559af8f43b43e368c378c1bf6bb
Fix:
https://github.com/vbraun/sage/blob/5d17ca989eb58559af8f43b43e368c378c1bf6bb/build/pkgs/matplotlib/patches/pkg-config.patch
I fixed the problem with Cyris's answer thought.
I also had a similar issue, and fixed it in a reasonably straightforward way using homebrew.
You don't have to link the freetype libraries for this reason. The main problem is, after you install freetype using homebrew, you are told to add
-I/usr/local/opt/freetype/include
to your CPPFLAGS. However, this alone is not sufficient, and you also have to add the the freetype2 subfolder as well.
So in order to install matplotlib, do this:
brew install freetype
brew install libpng
LDFLAGS="-L/usr/local/opt/freetype/lib -L/usr/local/opt/libpng/lib" CPPFLAGS="-I/usr/local/opt/freetype/include -I/usr/local/opt/libpng/include -I/usr/local/opt/freetype/include/freetype2" pip install matplotlib