I am trying to install numpy into a pypy3 virtualenv, but I'm stuck with that error (at importing) :
venv_pypy/site-packages/numpy-1.16.0.dev0+1d38e41-py3.5-linux-x86_64.egg/numpy/core/_multiarray_umath.pypy3-60-x86_64-linux-gnu.so: undefined symbol: cblas_sgemm
I am on an up to date archlinux, numpy works fine with CPython, but I have a project using pandas (which depends on numpy) that I need to test on pypy.
I first tried the recommended method (pip install numpy in the venv) but didn't work. (install is fine, but still the same error at execution).
I then, I tried what is suggested https://stackoverflow.com/a/14391693/1745291 (linked from Numpy multiarray.so: undefined symbol: cblas_sgemm ), since I didn't installed ATLAS (aur package on arch I don't want to install), to try building with OpenBias. But still not working (same error, and the method could be outdated since it's from 2013)
...And finally, I tried a build with no accelerations (at least, that is claimed) following : https://docs.scipy.org/doc/numpy-1.15.0/user/building.html#disabling-atlas-and-other-accelerated-libraries
...But still the same result...
What am i doing wrong ?
You can try uninstall it from pip and install from apt (if you are using ubuntu etc.)
This approach solved my problem
pip3 uninstall numpy
sudo apt-get install python3-numpy
Related
I'm using MacOS catalina and try to install pandas by
pip3 install pandas
But while I tried to import pandas, I got this error
python3 -c "import pandas"
This is error:
RuntimeError: Polyfit sanity test emitted a warning, most likely due to using a buggy Accelerate backend. If you compiled yourself, see site.cfg.example for information. Otherwise report this to the vendor that provided NumPy.
RankWarning: Polyfit may be poorly conditioned
I've been facing the same issue. There quite a bit of info here:
https://github.com/numpy/numpy/issues/15947
As I understand, its because your python version is detecting issues with the 'buggy Accelerate backend' in NumPy (NumPy is installed with Pandas).
I was running Python 3.9.0 and I was not able to fix. However I have been able to bypass the issue by using version Python 3.8.6. I used this guide to install 3.8.6
https://opensource.com/article/19/5/python-3-default-mac
See the part about
pyenv install
which I modified to:
pyenv install 3.8.6
After I restart, the debug in visual code now shows 3.8.6. I added all required modules again inluding NumPy and its working for me.
good luck
I'm trying to follow this guide to test this new algorithm: https://github.com/lalonderodney/SegCaps
I can't do it in my PC, so i'm using another server with Putty. Now I'm connected with the other server.
First of all I installed TensorFlow as indicates in the guide with :
pip install -r requirements.txt
After I wrote this code: ./main.py segcaps.png
in which segcaps.png is the image that i want to use
Finally I wrote python main.py --data_root_dir data
that is the only required parameter with the directory containing imgs and masks folders.
Now it gives me an error:
ModuleNotFoundError: No module named 'tensorflow.python.framework'
I searched it in the directory tensorflow/python/framework and it exists.
So, i don't know how to solve it. Ideas?
If you have multiple Python versions installed, then you'll (most likely) have multiple pip versions installed too. Make sure that the pip command you use installs the package(s) into the Python version you want it to. It may so happen that the package got installed into python2 but you wanted it in python3.
Since using pip did not install the packages in python3, pip3 is most likely to the PyPI for python3. Try
pip3 install -r requirements.txt
and that should work.
In case you have an EnvironmentError you can try this (bad idea):
pip3 install -r requirements.txt --user
This solves the problem most of the times on standalone machines. I'm not sure about the server; insufficient permissions might block this.
Why is the --user flag a bad idea? Read: What is the purpose “pip install --user …”?
You can use pip show tensorflow to see if it is installed or not.
As for ModuleNotFoundError try uninstalling keras and reinstalling an earlier version by pip install keras==2.1.6
I'm trying to install pandas. When I run: pip install pandas in cmd, I get the following error message: Could not find a version that satisfies the requirement numpy==1.9.3. Not sure how to fix this.
It's likely you have a different version of numpy installed, try upgrade numpy first with:
pip install numpy==1.9.3 --upgrade
then run pip install pandas. Also check this github issue. Maybe your python version is not supported.
I Installed pillow using brew, and when I try to repeat the isntallation I see it's there:
brew install Homebrew/python/pillow
Warning: pillow-2.7.0 already installed
But when I try to load it into a script I get an error:
ImportError: No module named Image
Any suggestions?
python usually looks for Pillow under normal site package installs. Here's what I would do to get a minimal Pillow setup where python should be guaranteed to see it:
sudo easy_install pip
pip install Pillow
I think it may also be possible to just do:
sudo easy_install Pillow
but pip is a bit more user friendly if you're planning on using more python scripts that might have dependencies.
Note: another issue you might be running into is if you're trying to use the Homebrew python but are ending up using the base OSX install of it instead. Make sure which python is showing you what you expect it to be.
I installed Theano on my machine, but the nosetests break with a Numpy/Fortran related error message. For me it looks like Numpy was compiled with a different Fortran version than Theano. I already reinstalled Theano (sudo pip uninstall theano + sudo pip install --upgrade --no-deps theano) and Numpy / Scipy (apt-get install --reinstall python-numpy python-scipy), but this did not help.
What steps would you recommend?
Complete error message:
ImportError: ('/home/Nick/.theano/compiledir_Linux-2.6.35-31-generic-x86_64-with-Ubuntu-10.10-maverick--2.6.6/tmpIhWJaI/0c99c52c82f7ddc775109a06ca04b360.so: undefined symbol: _gfortran_st_write_done'
My research:
The Installing SciPy / BuildingGeneral page about the undefined symbol: _gfortran_st_write_done' error:
If you see an error message
ImportError: /usr/lib/atlas/libblas.so.3gf: undefined symbol: _gfortran_st_write_done
when building SciPy, it means that NumPy picked up the wrong Fortran compiler during build (e.g. ifort).
Recompile NumPy using:
python setup.py build --fcompiler=gnu95
or whichever is appropriate (see python setup.py build --help-fcompiler).
But:
Nick#some-serv2:/usr/local/lib/python2.6/dist-packages/numpy$ python setup.py build --help-fcompiler
This is the wrong setup.py file to run
Used software versions:
scipy 0.10.1 (scipy.test() works)
NumPy 1.6.2 (numpy.test() works)
theano 0.5.0 (several tests fails with undefined symbol: _gfortran_st_write_done')
python 2.6.6
Ubuntu 10.10
[UPDATE]
So I removed numpy and scipy from my system with apt-get remove and using find -name XXX -delete of what was left.
Than I installed numpy and scipy from the github sources with sudo python setpy.py install.
Afterwards I entered again sudo pip uninstall theano and sudo pip install --upgrade --no-deps theano.
Error persists :/
I also tried the apt-get source ... + apt-get build-dep ... approach, but for my old Ubuntu (10.10) it installs too old version of numpy and scipy for theano: ValueError: numpy >= 1.4 is required (detected 1.3.0 from /usr/local/lib/python2.6/dist-packages/numpy/__init__.pyc)
I had the same problem, and after reviewing the source code, user212658's answer seemed like it would work (I have not tried it). I then looked for a way to deploy user212658's hack without modifying the source code.
Put these lines in your theanorc file:
[blas]
ldflags = -lblas -lgfortran
This worked for me.
Have you tried to recompile NumPy from the sources?
I'm not familiar with the Ubuntu package system, so I can't check what's in your dist-packages/numpy. With a clean archive of the NumPy sources, you should have a setup.py at the same level as the directories numpy, tools and benchmarks (among others). I'm pretty sure that's the one you want to use for a python setup.py build.
[EDIT]
Now that you have recompiled numpy with the proper --fcompiler option, perhaps could you try to do the same with Theano, that is, compiling directly from sources without relying on a apt-get or even pip. You should have a better control on the build process that way, which will make debugging/trying to find a solution easier.
I had the same problem. The solution I found is to add a hack in theano/gof/cmodule.py to link against gfortran whenever 'blas' is in the libs. That fixed it.
class GCC_compiler(object):
...
#staticmethod
def compile_str(module_name, src_code, location=None,
include_dirs=None, lib_dirs=None, libs=None,
preargs=None):
...
cmd.extend(['-l%s' % l for l in libs])
if 'blas' in libs:
cmd.append('-lgfortran')
A better fix is to remove atlas and install openblas. openblas is faster then atlas. Also, openblas don't request gfortran and is the one numpy was linked with. So it will work out of the box.