Re: Stumped on pytest issue

["Dr. Thomas Orgis" <thomas.orgis%uni-hamburg.de@localhost>]

Am Sun, 24 Dec 2023 09:05:12 -0600
schrieb Jason Bacon <jtocino%gmx.com@localhost>:

> > Yeah, my scipy superlu doesn't seem to be picking up blas at all.  What 
> > scipy are you using, and on what OS?  There's no reference to superlu in 
> > the scipy pkgsrc Makefile, .

Yes, the superlu is vendored. I'm testing on Xubuntu 22.04 x86-64 right
now. I just built scipy from pkgsrc CVS.

> > 
> > NetBSD netbsd9.acadix  bacon ~ 1011: (pkgsrc): pkg_info | grep scipy
> > py311-scipy-1.11.4nb1 Scientific Algorithms Library for Python

py311-scipy-1.11.4nb1 Scientific Algorithms Library for Python

> > NetBSD netbsd9.acadix  bacon ~ 1012: (pkgsrc): ldd 
> > ~/Pkgsrc/pkg/lib/python3.11/site-packages/scipy/sparse/linalg/_dsolve/_superlu.so
> > /home/bacon/Pkgsrc/pkg/lib/python3.11/site-packages/scipy/sparse/linalg/_dsolve/_superlu.so:
> >          -lm.0 => /usr/lib/libm.so.0
> >          -lc.12 => /usr/lib/libc.so.12
> >
> > That's all: No pruning here.

Weird it is.
 
> > My superlu is the latest:

And of no relevance, as scipy doesn't try to use it externally … but your BLAS linkage in scipy is fine? E.g. for

$ ldd /data/pkg/lib/python3.11/site-packages/scipy/sparse/linalg/_isolve/_iterative.so
	linux-vdso.so.1 (0x00007ffe13776000)
	libopenblas_openmp.so.0 => /data/pkg/lib/libopenblas_openmp.so.0 (0x00007ff31a2d0000)
	libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007ff31a1ba000)
	libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007ff319f92000)
	libgfortran.so.5 => /lib/x86_64-linux-gnu/libgfortran.so.5 (0x00007ff319cb7000)
	libgomp.so.1 => /lib/x86_64-linux-gnu/libgomp.so.1 (0x00007ff319c6d000)
	/lib64/ld-linux-x86-64.so.2 (0x00007ff31c32c000)
	libquadmath.so.0 => /lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007ff319c25000)
	libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007ff319c05000)


> > This is on NetBSD.  On Darwin I get the _hmmc import error, like you, 
> > but it doesn't reference blas either:

What the … ?

> > Darwin tarpon.local  bacon ~ 1012: (pkgsrc): otool -L 
> > ~/Pkgsrc/pkg/lib/python3.11/site-packages/scipy/sparse/linalg/_dsolve/_superlu.so
> > /Users/bacon/Pkgsrc/pkg/lib/python3.11/site-packages/scipy/sparse/linalg/_dsolve/_superlu.so:
> >          /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, 
> > current version 1336.0.0)



> 
> And on Alma 8:
> 

> ~/Pkgsrc/pkg/lib/python3.11/site-packages/scipy/sparse/linalg/_dsolve/_superlu.so
>          linux-vdso.so.1 (0x00007ffd541c6000)
>          libm.so.6 => /lib64/libm.so.6 (0x00007f94f4dde000)
>          libc.so.6 => /lib64/libc.so.6 (0x00007f94f4a19000)
>          /lib64/ld-linux-x86-64.so.2 (0x00007f94f53ad000)

Is this something for upstream? 

What is your BLAS_TYPE? Did you try with default netlib or also
openblas?


Alrighty then,

Thomas

-- 
Dr. Thomas Orgis
HPC @ Universität Hamburg