RuntimeError: /usr/lib/libopenblas.so: undefined symbol: LAPACKE_dgesvd

[mrkn]

When I use Ubuntu Xenial, Numo::Linalg.svd raises RuntimeError because it cannot resolve the symbol LAPACKE_dgesvd.

As I investigated libopenblas.so, I found that the library has dgesvd_ but not LAPACKE_dgesvd.

$ objdump -T /usr/lib/libopenblas.so | grep svd
0000000001aacb90 g    DF .text  0000000000008b48  Base        sgesvd_
000000000198ad60 g    DF .text  00000000000008e8  Base        dggsvd3_
0000000001ad0f50 g    DF .text  00000000000008e4  Base        sggsvd3_
000000000181fa30 g    DF .text  0000000000001e62  Base        cgesvdx_
0000000001939190 g    DF .text  0000000000001fe3  Base        dbdsvdx_
0000000001a7f960 g    DF .text  0000000000001f82  Base        sbdsvdx_
0000000001c11780 g    DF .text  00000000000007a5  Base        zggsvd_
0000000001beddd0 g    DF .text  00000000000088a4  Base        zgesvd_
000000000183a240 g    DF .text  0000000000000794  Base        cggsvd_
0000000001816f90 g    DF .text  0000000000008a94  Base        cgesvd_
0000000001bf6680 g    DF .text  0000000000001ee2  Base        zgesvdx_
000000000196f1d0 g    DF .text  0000000000001da5  Base        dgesvdx_
0000000001ab56e0 g    DF .text  0000000000001da5  Base        sgesvdx_
000000000198a5e0 g    DF .text  0000000000000775  Base        dggsvd_
000000000183a9e0 g    DF .text  0000000000000947  Base        cggsvd3_
00000000019667f0 g    DF .text  00000000000089dd  Base        dgesvd_
0000000001c11f30 g    DF .text  0000000000000953  Base        zggsvd3_
0000000001ad07d0 g    DF .text  0000000000000774  Base        sggsvd_

[masa16]

If libopenblas.so does not include LAPACKE API, it needs to load liblapacke.so. The following is not tested on Ubuntu but probably works.

Fiddle.dlopen("/usr/lib/libopenblas.so")
Numo::Linalg::Lapack.dlopen("/usr/lib/liblapacke.so")

[giuse]

Can confirm it works on Ubuntu 16.04, though the second file has an extra '.3' in the name:

Fiddle.dlopen("/usr/lib/libopenblas.so")
Numo::Linalg::Lapack.dlopen("/usr/lib/liblapacke.so.3")

Any chance to make this the default when using OpenBLAS?

[masa16]

Does this short name cause an error on Ubuntu?

Numo::Linalg::Lapack.dlopen("liblapacke.so")

[giuse]

I confirm the short name causes an error on Ubuntu. Full trace:

giuse@free:~$ rvm gemset create test_numo_linalg
ruby-2.4.2 - #gemset created /home/giuse/.rvm/gems/ruby-2.4.2@test_numo_linalg
ruby-2.4.2 - #generating test_numo_linalg wrappers.......
giuse@free:~$ rvm gemset use test_numo_linalg
Using ruby-2.4.2 with gemset test_numo_linalg
giuse@free:~$ gem install numo-linalg
Fetching: numo-narray-0.9.1.1.gem (100%)
Building native extensions.  This could take a while...
Successfully installed numo-narray-0.9.1.1
Fetching: numo-linalg-0.1.1.gem (100%)
Building native extensions.  This could take a while...
Successfully installed numo-linalg-0.1.1
2 gems installed
giuse@free:~$ irb
2.4.2 :001 > require 'numo/narray'
 => true 
2.4.2 :002 > require 'numo/linalg'
 => true 
2.4.2 :003 > Fiddle.dlopen("/usr/lib/libopenblas.so")
 => #<Fiddle::Handle:0x00000000024c95d0> 
2.4.2 :004 > Numo::Linalg::Lapack.dlopen("liblapacke.so")
RuntimeError: liblapacke.so: cannot open shared object file: No such file or directory
  from (irb):4:in `dlopen'
  from (irb):4
  from /home/giuse/.rvm/rubies/ruby-2.4.2/bin/irb:11:in `<main>'
2.4.2 :005 > Numo::Linalg::Lapack.dlopen("liblapacke.so.3")
 => nil 

Should I try with your commit 3c94713 ?

[masa16]

numo-linalg 0.1.2 will work with version suffix.

[masa16]

I have also checked loading openblas without configuration on MSYS2. I have not checked it on Mac.

[giuse]

I am currently working to get Travis CI to pass. I noticed this line when it installs libopenblas-base which may be pertinent to this issue:

update-alternatives: using /usr/lib/openblas-base/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode

[giuse]

I confirm numo-linalg 0.1.2 fixes this for me.

([...] stands for matrix content truncated. Notice no explicit call to Fiddle::dlopen nor Numo::Linalg::Lapack::dlopen)

2.4.2 :001 > require 'numo/narray'
 => true 
2.4.2 :002 > require 'numo/linalg'
 => true 
2.4.2 :003 > a = Numo::DFloat.new(3,3).seq
 => Numo::DFloat#shape=[3,3] [[0, 1, 2], [3, 4, 5], [6, 7, 8]] 
2.4.2 :004 > Numo::Linalg::Lapack.call(:geev, a, jobvl: false, jobvr: true)
 => [Numo::DFloat#shape=[3] [...], Numo::DFloat#shape=[3] [...], nil, Numo::DFloat#shape=[3,3] [...], 0] 
2.4.2 :005 > Numo::Linalg.eig a
 => [Numo::DComplex#shape=[3] [...], nil, Numo::DComplex#shape=[3,3] [...]] 
2.4.2 :006 > Numo::Linalg.svd a
 => [Numo::DFloat#shape=[3] [...], Numo::DFloat#shape=[3,3] [...], Numo::DFloat#shape=[3,3] [...]]

Does that work for you @mrkn -san? Can we close this issue?

[giuse]

UPDATE: it seems Travis CI is having the same issue as @mrkn -san. You can see the full log on my Travis, errors 5 through 11. To see the complete config used, click on "view config" (here for convenience).

[masa16]

The error is because "liblapacke" package is not installed. Please add it to config file.

[giuse]

Great! It works! Thank you so much Tanaka-san! Installation on Travis is now working. I need to find out why some of my tests are red although they are all green on my machine, but oh well, I will fix that. For me the issue can be closed. Thanks for your time and support!