Installing lapack for numpy
Question:
Running Ubuntu 11.10 + python2.7…built numpy from source and installed it, but when I go to install it, I get
ImportError: /usr/lib/liblapack.so.3gf: undefined symbol: ATL_chemv
when it tries to import lapack_lite from numpy.linalg. I tried to rebuild lapack from scratch, but it seems to just make
/usr/local/lib/libblas.a
/usr/local/lib/liblapack.a
/usr/local/lib/libtmglib.a
and the .so file. Where does the .so.3gf come from, and how do I fix it?
Answers:
According to some bugreports I see around, you may have more than one provider of BLAS/ATLAS/LAPACK installed, like ATLAS and OpenBLAS/GotoBLAS, that conflict with each other. Have a look on this:
$ ls -l /etc/alternatives/*.so.3gf
and check that all them correspond to the same package (eg. they all point into /usr/lib/atlas-base/)
Try checking the LD_LIBRARY_PATH. You might point in there to another version of that library that does not support the symbol the numpy call needs. I had the same situation on my Mac.
But be careful, the problem might not be visible directly, because one library could link to the next using the LD_LIBRARY_PATH.
You can check if you see a difference in the following command with and without the LD_LIBRARY_PATH set (to remove temporarily for the active shell: unset LD_LIBRARY_PATH):
ldd /usr/lib/liblapack.so.3gf
In my case, libraries provided by the ISIS software system clashed with the onboard libraries that numpy requires.
I was having the same problem and removing the package libopenblas-base did the trick:
sudo apt-get remove libopenblas-base
As already explained by others, several packages provide incompatible versions of liblapack.so.3gf.
This issue arises when you have libopenblas-base and libatlas3-base installed, but don’t have liblapack3 installed. This combination of packages installs conflicting versions of libblas.so (from OpenBLAS) and liblapack.so (from ATLAS).
Solution 1 (my favorite): You can keep both OpenBLAS and ATLAS on your machine if you also install liblapack3.
sudo apt-get install liblapack3
Solution 2: Uninstall ATLAS (this will actually install liblapack3 for you automatically because of some deb package shenanigans)
sudo apt-get uninstall libatlas3-base
Solution 3: Uninstall OpenBLAS
sudo apt-get uninstall libopenblas-base
Bad configuration
$ dpkg -l | grep 'openblas|atlas|lapack'
ii libatlas3-base 3.10.1-4 amd64 Automatically Tuned Linear Algebra Software, generic shared
ii libopenblas-base 0.2.8-6ubuntu1 amd64 Optimized BLAS (linear algebra) library based on GotoBLAS2
$ update-alternatives --get-selections | grep 'blas|lapack'
libblas.so.3 auto /usr/lib/openblas-base/libblas.so.3
liblapack.so.3 auto /usr/lib/atlas-base/atlas/liblapack.so.3
$ python -c 'import numpy'
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/usr/lib/python2.7/dist-packages/numpy/__init__.py", line 153, in <module>
from . import add_newdocs
File "/usr/lib/python2.7/dist-packages/numpy/add_newdocs.py", line 13, in <module>
from numpy.lib import add_newdoc
File "/usr/lib/python2.7/dist-packages/numpy/lib/__init__.py", line 18, in <module>
from .polynomial import *
File "/usr/lib/python2.7/dist-packages/numpy/lib/polynomial.py", line 19, in <module>
from numpy.linalg import eigvals, lstsq, inv
File "/usr/lib/python2.7/dist-packages/numpy/linalg/__init__.py", line 50, in <module>
from .linalg import *
File "/usr/lib/python2.7/dist-packages/numpy/linalg/linalg.py", line 29, in <module>
from numpy.linalg import lapack_lite, _umath_linalg
ImportError: /usr/lib/liblapack.so.3: undefined symbol: ATL_chemv
Solution 1
$ dpkg -l | grep 'openblas|atlas|lapack'
ii libatlas3-base 3.10.1-4 amd64 Automatically Tuned Linear Algebra Software, generic shared
ii liblapack3 3.5.0-2ubuntu1 amd64 Library of linear algebra routines 3 - shared version
ii libopenblas-base 0.2.8-6ubuntu1 amd64 Optimized BLAS (linear algebra) library based on GotoBLAS2
$ update-alternatives --get-selections | grep 'blas|lapack'
libblas.so.3 auto /usr/lib/openblas-base/libblas.so.3
liblapack.so.3 auto /usr/lib/lapack/liblapack.so.3
$ python -c 'import numpy'
Solution 2
$ dpkg -l | grep 'openblas|atlas|lapack'
ii liblapack3 3.5.0-2ubuntu1 amd64 Library of linear algebra routines 3 - shared version
ii libopenblas-base 0.2.8-6ubuntu1 amd64 Optimized BLAS (linear algebra) library based on GotoBLAS2
$ update-alternatives --get-selections | grep 'blas|lapack'
libblas.so.3 auto /usr/lib/openblas-base/libblas.so.3
liblapack.so.3 auto /usr/lib/lapack/liblapack.so.3
$ python -c 'import numpy'
Solution 3
$ dpkg -l | grep 'openblas|atlas|lapack'
ii libatlas3-base 3.10.1-4 amd64 Automatically Tuned Linear Algebra Software, generic shared
$ update-alternatives --get-selections | grep 'blas|lapack'
libblas.so.3 auto /usr/lib/atlas-base/atlas/libblas.so.3
liblapack.so.3 auto /usr/lib/atlas-base/atlas/liblapack.so.3
$ python -c 'import numpy'
Running Ubuntu 11.10 + python2.7…built numpy from source and installed it, but when I go to install it, I get
ImportError: /usr/lib/liblapack.so.3gf: undefined symbol: ATL_chemv
when it tries to import lapack_lite from numpy.linalg. I tried to rebuild lapack from scratch, but it seems to just make
/usr/local/lib/libblas.a
/usr/local/lib/liblapack.a
/usr/local/lib/libtmglib.a
and the .so file. Where does the .so.3gf come from, and how do I fix it?
According to some bugreports I see around, you may have more than one provider of BLAS/ATLAS/LAPACK installed, like ATLAS and OpenBLAS/GotoBLAS, that conflict with each other. Have a look on this:
$ ls -l /etc/alternatives/*.so.3gf
and check that all them correspond to the same package (eg. they all point into /usr/lib/atlas-base/)
Try checking the LD_LIBRARY_PATH. You might point in there to another version of that library that does not support the symbol the numpy call needs. I had the same situation on my Mac.
But be careful, the problem might not be visible directly, because one library could link to the next using the LD_LIBRARY_PATH.
You can check if you see a difference in the following command with and without the LD_LIBRARY_PATH set (to remove temporarily for the active shell: unset LD_LIBRARY_PATH):
ldd /usr/lib/liblapack.so.3gf
In my case, libraries provided by the ISIS software system clashed with the onboard libraries that numpy requires.
I was having the same problem and removing the package libopenblas-base did the trick:
sudo apt-get remove libopenblas-base
As already explained by others, several packages provide incompatible versions of liblapack.so.3gf.
This issue arises when you have libopenblas-base and libatlas3-base installed, but don’t have liblapack3 installed. This combination of packages installs conflicting versions of libblas.so (from OpenBLAS) and liblapack.so (from ATLAS).
Solution 1 (my favorite): You can keep both OpenBLAS and ATLAS on your machine if you also install liblapack3.
sudo apt-get install liblapack3
Solution 2: Uninstall ATLAS (this will actually install liblapack3 for you automatically because of some deb package shenanigans)
sudo apt-get uninstall libatlas3-base
Solution 3: Uninstall OpenBLAS
sudo apt-get uninstall libopenblas-base
Bad configuration
$ dpkg -l | grep 'openblas|atlas|lapack'
ii libatlas3-base 3.10.1-4 amd64 Automatically Tuned Linear Algebra Software, generic shared
ii libopenblas-base 0.2.8-6ubuntu1 amd64 Optimized BLAS (linear algebra) library based on GotoBLAS2
$ update-alternatives --get-selections | grep 'blas|lapack'
libblas.so.3 auto /usr/lib/openblas-base/libblas.so.3
liblapack.so.3 auto /usr/lib/atlas-base/atlas/liblapack.so.3
$ python -c 'import numpy'
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/usr/lib/python2.7/dist-packages/numpy/__init__.py", line 153, in <module>
from . import add_newdocs
File "/usr/lib/python2.7/dist-packages/numpy/add_newdocs.py", line 13, in <module>
from numpy.lib import add_newdoc
File "/usr/lib/python2.7/dist-packages/numpy/lib/__init__.py", line 18, in <module>
from .polynomial import *
File "/usr/lib/python2.7/dist-packages/numpy/lib/polynomial.py", line 19, in <module>
from numpy.linalg import eigvals, lstsq, inv
File "/usr/lib/python2.7/dist-packages/numpy/linalg/__init__.py", line 50, in <module>
from .linalg import *
File "/usr/lib/python2.7/dist-packages/numpy/linalg/linalg.py", line 29, in <module>
from numpy.linalg import lapack_lite, _umath_linalg
ImportError: /usr/lib/liblapack.so.3: undefined symbol: ATL_chemv
Solution 1
$ dpkg -l | grep 'openblas|atlas|lapack'
ii libatlas3-base 3.10.1-4 amd64 Automatically Tuned Linear Algebra Software, generic shared
ii liblapack3 3.5.0-2ubuntu1 amd64 Library of linear algebra routines 3 - shared version
ii libopenblas-base 0.2.8-6ubuntu1 amd64 Optimized BLAS (linear algebra) library based on GotoBLAS2
$ update-alternatives --get-selections | grep 'blas|lapack'
libblas.so.3 auto /usr/lib/openblas-base/libblas.so.3
liblapack.so.3 auto /usr/lib/lapack/liblapack.so.3
$ python -c 'import numpy'
Solution 2
$ dpkg -l | grep 'openblas|atlas|lapack'
ii liblapack3 3.5.0-2ubuntu1 amd64 Library of linear algebra routines 3 - shared version
ii libopenblas-base 0.2.8-6ubuntu1 amd64 Optimized BLAS (linear algebra) library based on GotoBLAS2
$ update-alternatives --get-selections | grep 'blas|lapack'
libblas.so.3 auto /usr/lib/openblas-base/libblas.so.3
liblapack.so.3 auto /usr/lib/lapack/liblapack.so.3
$ python -c 'import numpy'
Solution 3
$ dpkg -l | grep 'openblas|atlas|lapack'
ii libatlas3-base 3.10.1-4 amd64 Automatically Tuned Linear Algebra Software, generic shared
$ update-alternatives --get-selections | grep 'blas|lapack'
libblas.so.3 auto /usr/lib/atlas-base/atlas/libblas.so.3
liblapack.so.3 auto /usr/lib/atlas-base/atlas/liblapack.so.3
$ python -c 'import numpy'