libopenblas problem after updating to Ubuntu 20

Hey Jérôme,

Can you verify that you installed libopenblas-dev and libsuitesparse-dev with apt-get?

Cheers,

Robert

It looks like yes (and, if not, there would be something missing in the packaging procedure, no ?)

jerome.duriez@XX:~$ apt policy libopenblas-dev libsuitesparse-dev
libopenblas-dev:
  Installed: 0.3.8+ds-1ubuntu0.20.04.1
  Candidate: 0.3.8+ds-1ubuntu0.20.04.1
  Version table:
 *** 0.3.8+ds-1ubuntu0.20.04.1 500
        500 http://archive.ubuntu.com/ubuntu focal-updates/universe amd64 Packages
        100 /var/lib/dpkg/status
     0.3.8+ds-1 500
        500 http://archive.ubuntu.com/ubuntu focal/universe amd64 Packages
libsuitesparse-dev:
  Installed: 1:5.7.1+dfsg-2
  Candidate: 1:5.7.1+dfsg-2
  Version table:
 *** 1:5.7.1+dfsg-2 500
        500 http://archive.ubuntu.com/ubuntu focal/main amd64 Packages
        100 /var/lib/dpkg/status

For verification, what is the output of the commands

ls -l /usr/lib/x86_64-linux-gnu/openblas*/libopenblas.*
dpkg -l | grep openblas

jerome.duriez@XX:~$ ls -l /usr/lib/x86_64-linux-gnu/openblas*/libopenblas.*
lrwxrwxrwx 1 root root 21 juin 2 2020 /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.a -> libopenblasp-r0.3.8.a
lrwxrwxrwx 1 root root 22 juin 2 2020 /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so -> libopenblasp-r0.3.8.so
lrwxrwxrwx 1 root root 22 juin 2 2020 /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 -> libopenblasp-r0.3.8.so

jerome.duriez@XX:~$ dpkg -l | grep openblas
ii libopenblas-dev:amd64 0.3.8+ds-1ubuntu0.20.04.1 amd64 Optimized BLAS (linear algebra) library (dev, meta)
ii libopenblas-pthread-dev:amd64 0.3.8+ds-1ubuntu0.20.04.1 amd64 Optimized BLAS (linear algebra) library (dev, pthread)
ii libopenblas0:amd64 0.3.8+ds-1ubuntu0.20.04.1 amd64 Optimized BLAS (linear algebra) library (meta)
ii libopenblas0-pthread:amd64 0.3.8+ds-1ubuntu0.20.04.1 amd64 Optimized BLAS (linear algebra) library (shared lib, pthread)

Note also a plain /usr/lib/x86_64-linux-gnu/libopenblas.so:

jerome.duriez@XX:~$ locate *openblas* | grep libopenblas.so
/etc/alternatives/libopenblas.so-x86_64-linux-gnu
/etc/alternatives/libopenblas.so.0-x86_64-linux-gnu
/usr/lib/x86_64-linux-gnu/libopenblas.so
/usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so
/usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0
/var/lib/dpkg/alternatives/libopenblas.so-x86_64-linux-gnu
/var/lib/dpkg/alternatives/libopenblas.so.0-x86_64-linux-gnu

What is the output of

ls -l /usr/lib/x86_64-linux-gnu/libopenblas.so
ldd /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0

There should also be a
/usr/lib/x86_64-linux-gnu/libopenblas.so.0

Try
sudo apt install --reinstall libopenblas0-pthread

It is very strange. Could you please check, whether maybe LD_LIBRARY_PATH is set in your environment?

echo $LD_LIBRARY_PATH

And please check, how libyade is linked:

ldd /usr/lib/x86_64-linux-gnu/yade/libyade.so | grep -i openblas

>>> libopenblas.so.0 => /lib/x86_64-linux-gnu/libopenblas.so.0 (0x00007f409ddb0000)

I have just installed yade in Ubuntu 20.04 docker-container and it works as it should. Please also show all your environmental variables:

env

Regarding #5
*************

jerome.duriez@XX:~$ ls -l /usr/lib/x86_64-linux-gnu/libopenblas.so
lrwxrwxrwx 1 root root 49 sept. 6 15:04 /usr/lib/x86_64-linux-gnu/libopenblas.so -> /etc/alternatives/libopenblas.so-x86_64-linux-gnu
jerome.duriez@XX~$ ldd /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0
 linux-vdso.so.1 (0x00007ffe9d9e0000)
 libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f796a435000)
 libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f796a412000)
 libgfortran.so.5 => /usr/lib/x86_64-linux-gnu/libgfortran.so.5 (0x00007f796a14a000)
 libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f7969f58000)
 /lib64/ld-linux-x86-64.so.2 (0x00007f796c759000)
 libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007f7969f0e000)
 libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f7969ef3000)

Regarding #6
*************

I do not have the .so.0 there:
jerome.duriez@XX:~$ ls /usr/lib/x86_64-linux-gnu/libopenblas.so.0
ls: cannot access '/usr/lib/x86_64-linux-gnu/libopenblas.so.0': No such file or directory

(will try the reinstall just after)

Regarding #7
*************

THAT *PATH variable is not set:
jerome.duriez@XX:~$ echo $LD_LIBRARY_PATH
# empty line returned, comment is mine

And indeed a problem in libyade linkage:
jerome.duriez@XX:~$ ldd /usr/lib/x86_64-linux-gnu/yade/libyade.so | grep -i openblas
 libopenblas.so.0 => not found

(Note that things work on other Ubuntu 20 machines here, so it is probably just a config problem on that one but help is much appreciated, thank you)

sudo apt install --reinstall libopenblas0-pthread did the trick !

I got back /usr/lib/x86_64-linux-gnu/libopenblas.so.0, and the expected ldd output of #7 (note that $LD_LIBRARY_PATH is still empty / not defined though)

yade* packages now start correctly, thanks everyone for fixing my machine.
(Do not hesitate to tell me if you know where this could come from..)

OK, I am glad that the problem is fixed. But I do not really know, why it libopenblas0 package was not installed on your system.

From here [1]: libyade strictly depends on libopenblas0, so it HAS to be installed by the package manager.
From here [2] libopenblas0 can be provided by libopenblas0-pthread, libopenblas0-openmp or libopenblas0-serial and all of them are providing libopenblas0.so....

No idea, what was wrong there.

[1] https://packages.debian.org/unstable/libyade
[2] https://packages.debian.org/sid/libopenblas0

Anton