Openblas: Symbol lookup error: /usr/lib/libblas.so.3: undefined symbol: gotoblas

[adonese]

I've tried the solution of issue #1033, but that didn't work. I'm using Ubuntu 16.04, I've installed OpenBLAS using apt-get.

sudo update-alternatives --set libblas.so.3 /usr/lib/openblas-base/libblas.so.3

My libblas.so.3 alternatives are,

sudo update-alternatives --list libblas.so.3
/usr/lib/atlas-base/atlas/libblas.so.3
/usr/lib/libblas/libblas.so.3
/usr/lib/openblas-base/libblas.so.3

I've also tried to install OpenBLAS from the source, it compiled well, but the problem still existed.

I get this error: <application_name>: symbol lookup error: /usr/lib/libblas.so.3: undefined symbol: gotoblas, whenever I try to run any program that uses OpenBLAS

[brada4]

Did you restore system openblas base and relinked all your programs to -lblas after your trip into source build ? What does ldd say if ran against your program?
Dooes something simple like python> import numpy.* exhibit same errors?

[martin-frbg]

Perhaps the steps outlined in https://github.com/JuliaLang/julia/issues/11913 will help ? (I never encountered this, but I now suspect that the symbol "openblas" may only be present in builds with DYNAMIC_ARCH=1 set)

[adonese]

I did from numpy import * and it doesn't raise any error.

@brada4 I'm a bit beginner here. Would you mind to show simple steps procedures?

@martin-frbg I will try those of Julia, thanks!

[adonese]

Thank you so much!

I had libopenblas.so.0 in /usr/local/lib. That causes the error. I assume that I should remove the version of OpenBLAS I built from the source, since I had one from Ubuntu PPA.

[adonese]

I was trying to install qgis. For some reason, qgis installs its own version of openblas at usr/local/lib. I had to remove libopenblas.so.0 from that location. When I installed qgis, I got the same error again. So, I removed libopenblas.so.0 from /usr/local/lib again, and did apt-get install -f. And it solves the problem. I just want to that conflict because of me, or from qgis?

[brada4]

Ubuntu provided openblas is in your alternatives list
If you built your own then it is /opt/OpenBLAS/libopenblas.so.0
apt-file can help you locate source of that file, but it did not come from either of 2 sources mentioned.

[martin-frbg]

I have now confirmed that it is (only) the multi-cputype builds of the library that contain the symbol "gotoblas", so I guess it should be possible to use your own build of OpenBLAS with the other code if you just build OpenBLAS with "make DYNAMIC_ARCH=1". (DYNAMIC_ARCH will make the library file bigger of course, but it should not hurt otherwise)

[martin-frbg]

Updated the FAQ (in the Wiki) accordingly.

[ph-preux]

Hi,
this morning I "apt-get install julia" on my Ubuntu 16.04.
It automatically installed libopenblass-base and now, when I call R, I have the exact same message as yours.
Before this update, R was working, and I was using blas through the atlas package.

Now, I've "apt-get remove libopenblas-base" and R, I mean blas, is back.

[brada4]

I cannot get to your R issue with Ubuntu R or CRAN R. What special setup you have?

[ph-preux]

I've installed R with Ubuntu packages. Regarding blas, I get it through libatlas-dev and libatlas3-base Ubuntu packages.

[ysh329]

Same issue as yours, it's okay after removing /usr/local/lib/libopenblas.so.* files, which I built previously from source.
Thanks a lot!

[brada4]

There is sane procedure in FAQ for your own build of OpenBLAS:
https://github.com/xianyi/OpenBLAS/wiki/faq#debianlts

[ysh329]

@brada4 Thanks! :laughing:

[rayanelleuch]

I got the same problem too by the following import line.

import cv2
from skimage.color import label2rgb  # error occur here

But I realised that get this problem only if I import opencv before
just inter changing lines was enough. (Not sure why)
Solution:

from skimage.color import label2rgb
import cv2

Hope it can helps someone.

[brada4]

Probably each module is linked against different blas implementation.
It is cleaner if only blas library during build/pip install is either reference blas or openblas planted as default -lblas.
Binary packages/wheels usually have static blas linked in that conflicts with other implementations loaded in same process

[sahilbandar]

Hi,
this morning I "apt-get install julia" on my Ubuntu 16.04.
It automatically installed libopenblass-base and now, when I call R, I have the exact same message as yours.
Before this update, R was working, and I was using blas through the atlas package.

Now, I've "apt-get remove libopenblas-base" and R, I mean blas, is back.

This one worked out for me..

[brada4]

Openblas package lapack has high alternative priority, if you ever fixed blas to other than openblas it gets incompatible blas. Reference lapack (liblapack-dev) will work with any blas lib.
Probably typical error messages could help consumability of faq.

[xbsd]

I was trying to install qgis. For some reason, qgis installs its own version of openblas at usr/local/lib. I had to remove libopenblas.so.0 from that location. When I installed qgis, I got the same error again. So, I removed libopenblas.so.0 from /usr/local/lib again, and did apt-get install -f. And it solves the problem. I just want to that conflict because of me, or from qgis?

This is a saviour. Thanks so much !! :)

[brada4]

You can replace "private installs" with symlink to /usr/lib/libblas.so.3, then process with update-alternatives --config libblas.so.3 , then expect all apps to use your chosen implementation.
It is just once per install...