Re: Stumped on pytest issue

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

Am Sat, 23 Dec 2023 08:29:24 -0600
schrieb Jason Bacon <jtocino%gmx.com@localhost>:

> /home/bacon/Pkgsrc/pkg/lib/python3.11/site-packages/scipy/sparse/linalg/_dsolve/_superlu.so:
> Undefined PLT symbol "dnrm2_" (symnum = 2)

Your scipy superlu misses a BLAS symbol from libblas.so / libopenblas.so.

Did you build it with old superlu that provided 

$ readelf -d -s /data/pkg/lib/libopenblas_openmp.so |grep -w dnrm2_
  5951: 0000000000138cd0   101 FUNC    GLOBAL DEFAULT   12 dnrm2_
 18042: 0000000000138cd0   101 FUNC    GLOBAL DEFAULT   12 dnrm2_
$ ldd /data/pkg/lib/python3.11/site-packages/scipy/sparse/linalg/_dsolve/_superlu.so |grep blas
	libopenblas_openmp.so.0 => /data/pkg/lib/libopenblas_openmp.so.0 (0x00007f5dcc5b8000)

It occurs to me that this probably includes an vendored copy of superlu
and is not linking to math/superlu. Might consider changing that in
scipy. Anyhow, my scipy doesn't have that problem …

Trying to reproduce … is this a step further or one behind?


=================================================================================================================================== ERRORS ====================================================================================================================================
________________________________________________________________________________________________________________________ ERROR collecting test session ________________________________________________________________________________________________________________________
/data/pkg/lib/python3.11/site-packages/_pytest/config/__init__.py:641: in _importconftest
    mod = import_path(conftestpath, mode=importmode, root=rootpath)
/data/pkg/lib/python3.11/site-packages/_pytest/pathlib.py:567: in import_path
    importlib.import_module(module_name)
/data/pkg/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1204: in _gcd_import
    ???
<frozen importlib._bootstrap>:1176: in _find_and_load
    ???
<frozen importlib._bootstrap>:1126: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:241: in _call_with_frames_removed
    ???
<frozen importlib._bootstrap>:1204: in _gcd_import
    ???
<frozen importlib._bootstrap>:1176: in _find_and_load
    ???
<frozen importlib._bootstrap>:1147: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:690: in _load_unlocked
    ???
<frozen importlib._bootstrap_external>:940: in exec_module
    ???
<frozen importlib._bootstrap>:241: in _call_with_frames_removed
    ???
lib/hmmlearn/tests/__init__.py:9: in <module>
    from hmmlearn.base import DECODER_ALGORITHMS
lib/hmmlearn/base.py:12: in <module>
    from . import _hmmc, _kl_divergence as _kl, _utils
E   ImportError: cannot import name '_hmmc' from 'hmmlearn' (/data/projekte/pkgsrc/work/wip/py-hmmlearn/work/hmmlearn-0.3.0/lib/hmmlearn/__init__.py)
=========================================================================================================================== short test summary info ===========================================================================================================================
ERROR  - ImportError: cannot import name '_hmmc' from 'hmmlearn' (/data/projekte/pkgsrc/work/wip/py-hmmlearn/work/hmmlearn-0.3.0/lib/hmmlearn/__init__.py)
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
============================================================================================================================== 1 error in 1.04s ===============================================================================================================================
*** Error code 2

Stop.


-- 
Dr. Thomas Orgis
HPC @ Universität Hamburg