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htInEdin
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Joined: 06 Jan 2022
Posts: 6
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 Posted: Thu Jan 06, 2022 6:31 pm Post subject: scipy.test() fails importing from scipy.stats |
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I just did a complete install of numpy and scipy (after a successful world update). Running scipy.test() fails, and indeed any attempt to import scipy.stats fails:
| Code: | :> python3
Python 3.9.9 (main, Jan 5 2022, 08:31:50)
[GCC 10.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy.stats
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/lustre/home/dc007/hst/gentoo/usr/lib/python3.9/site-packages/scipy/stats/__init__.py", line 441, in <module>
from .stats import *
File "/lustre/home/dc007/hst/gentoo/usr/lib/python3.9/site-packages/scipy/stats/stats.py", line 43, in <module>
from . import distributions
File "/lustre/home/dc007/hst/gentoo/usr/lib/python3.9/site-packages/scipy/stats/distributions.py", line 10, in <module>
from . import _continuous_distns
File "/lustre/home/dc007/hst/gentoo/usr/lib/python3.9/site-packages/scipy/stats/_continuous_distns.py", line 22, in <module>
from . import _stats
File "_stats.pyx", line 1, in init scipy.stats._stats
ImportError: /lustre/home/dc007/hst/gentoo/usr/lib/python3.9/site-packages/scipy/special/cython_special.cpython-39-x86_64-linux-gnu.so: undefined symbol: _gfortran_stop_numeric
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Couldn't find anything that looks relevant in Bugzilla, but before submitting a bug I thought I'd check here. Is it possible that something is wrong with my setup such that the right fortran library is not being found? As far as I can see that symbol is defined in libgfortran.so...
Thanks
ht
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Naib
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| Posted: Thu Jan 06, 2022 6:46 pm Post subject: |
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| Code: | py
Python 3.9.9 (main, Nov 21 2021, 11:47:16)
[Clang 13.0.0 ] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy.stats
>>> |
either python or scipy needs to be rebuilt (or both), you have an abi mismatch somewhere
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htInEdin
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Joined: 06 Jan 2022
Posts: 6
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| Posted: Thu Jan 06, 2022 10:38 pm Post subject: |
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| Naib wrote: | | Code: | py
Python 3.9.9 (main, Nov 21 2021, 11:47:16)
[Clang 13.0.0 ] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy.stats
>>> |
either python or scipy needs to be rebuilt (or both), you have an abi mismatch somewhere |
Thanks, but no joy. That is, I
- Resynced
- emerge --depclean
- Did a world update
- emerge @preserved-rebuild
- emerge =dev-lang/python-3.9.9
- emerge dev-python/scipy
Same problem.
I noticed one difference, however.
Your python shows "[Clang 13.0.0]"
My python (now) shows "[GCC 11.2.1 20211127]"
Could that be related to the problem? If so, how did you install your python?
Thanks,
ht
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Naib
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| Posted: Thu Jan 06, 2022 11:18 pm Post subject: |
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you might need to rebuild lapack as this is the fortran part that scipy uses. That should bring all ABI in alignment.
As to myself using clang... im just messing around with a clang built system ( 99% of all packages use clang for me) so you using gcc and myself using clang won't be why ( I am a heavy scipy user so used it when I used gcc). HOWEVER... I have rebuilt my entire world a few times while I was converting over and thus all ABI's were 100% aligned. I could have done that with gcc
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htInEdin
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Joined: 06 Jan 2022
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| Posted: Fri Jan 07, 2022 2:01 pm Post subject: |
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| Naib wrote: | | you might need to rebuild lapack as this is the fortran part that scipy uses. That should bring all ABI in alignment. |
Still no joy.
I have checked that the missing binding (of _gfortran_stop_numeric) is present in .../gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/11.2.1/libgfortran.so, and that
gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/11.2.1 is present in /etc/ld.so.conf.d/05gcc-x86_64-pc-linux-gnu.conf
So I don't understand how the error is happening:
| Code: | | ImportError: /lustre/home/dc007/hst/gentoo/usr/lib/python3.9/site-packages/scipy/special/cython_special.cpython-39-x86_64-linux-gnu.so: undefined symbol: _gfortran_stop_numeric |
Just to avoid obvious things, can you just tell me your python, scipy, openblas and lapack versions?
Can anyone report on a successful python-3.9.9 scipy-1.7.3 numpy-1.22.0 lapack-3.10.0 openblas-0.3.19 install?
Thanks for any suggestions, I'm struggling here...
ht
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sam_
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Joined: 14 Aug 2020
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| Posted: Fri Jan 07, 2022 2:51 pm Post subject: |
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| Can you rebuild numpy (latest revision)? It's possibly related to bug 830630. |
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Naib
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| Posted: Fri Jan 07, 2022 3:53 pm Post subject: |
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| htInEdin wrote: | | Naib wrote: | | you might need to rebuild lapack as this is the fortran part that scipy uses. That should bring all ABI in alignment. |
Still no joy.
I have checked that the missing binding (of _gfortran_stop_numeric) is present in .../gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/11.2.1/libgfortran.so, and that
gentoo/usr/lib/gcc/x86_64-pc-linux-gnu/11.2.1 is present in /etc/ld.so.conf.d/05gcc-x86_64-pc-linux-gnu.conf
So I don't understand how the error is happening:
| Code: | | ImportError: /lustre/home/dc007/hst/gentoo/usr/lib/python3.9/site-packages/scipy/special/cython_special.cpython-39-x86_64-linux-gnu.so: undefined symbol: _gfortran_stop_numeric |
Just to avoid obvious things, can you just tell me your python, scipy, openblas and lapack versions?
Can anyone report on a successful python-3.9.9 scipy-1.7.3 numpy-1.22.0 lapack-3.10.0 openblas-0.3.19 install?
Thanks for any suggestions, I'm struggling here...
ht |
| Code: |
merge -pv python:3.9 scipy numpy lapack openblas
These are the packages that would be merged, in order:
Calculating dependencies... done!
[ebuild R ] dev-lang/python-3.9.9:3.9::gentoo USE="gdbm lto ncurses pgo readline sqlite ssl tk xml -bluetooth -build -examples -hardened -test -verify-sig -wininst" 0 KiB
[ebuild N ] sci-libs/openblas-0.3.19::gentoo USE="eselect-ldso openmp -dynamic -index-64bit -pthread -relapack -test" 12,409 KiB
[ebuild R ] sci-libs/lapack-3.10.0::gentoo USE="eselect-ldso -deprecated -doc -lapacke -test" 0 KiB
[ebuild U ] dev-python/numpy-1.22.0-r1::gentoo [1.22.0::gentoo] USE="lapack -doc -test" PYTHON_TARGETS="python3_9 -python3_8 -python3_10" 0 KiB
[ebuild R ] dev-python/scipy-1.7.3::gentoo USE="pythran -doc -sparse -test" PYTHON_TARGETS="python3_9 -python3_8 -python3_10" 0 KiB
Total: 5 packages (1 upgrade, 1 new, 3 reinstalls), Size of downloads: 12,409 KiB
[jrb:~] $ eselect blas list
Available BLAS/CBLAS (lib) candidates:
(none found)
Available BLAS/CBLAS (lib64) candidates:
[1] reference * |
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#define HelloWorld int
#define Int main()
#define Return printf
#define Print return
#include <stdio>
HelloWorld Int {
Return("Hello, world!\n");
Print 0; |
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htInEdin
n00b
Joined: 06 Jan 2022
Posts: 6
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| Posted: Fri Jan 07, 2022 6:37 pm Post subject: |
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| Naib wrote: |
| Code: |
merge -pv python:3.9 scipy numpy lapack openblas
These are the packages that would be merged, in order:
Calculating dependencies... done!
[ebuild R ] dev-lang/python-3.9.9:3.9::gentoo USE="gdbm lto ncurses pgo readline sqlite ssl tk xml -bluetooth -build -examples -hardened -test -verify-sig -wininst" 0 KiB
[ebuild N ] sci-libs/openblas-0.3.19::gentoo USE="eselect-ldso openmp -dynamic -index-64bit -pthread -relapack -test" 12,409 KiB
[ebuild R ] sci-libs/lapack-3.10.0::gentoo USE="eselect-ldso -deprecated -doc -lapacke -test" 0 KiB
[ebuild U ] dev-python/numpy-1.22.0-r1::gentoo [1.22.0::gentoo] USE="lapack -doc -test" PYTHON_TARGETS="python3_9 -python3_8 -python3_10" 0 KiB
[ebuild R ] dev-python/scipy-1.7.3::gentoo USE="pythran -doc -sparse -test" PYTHON_TARGETS="python3_9 -python3_8 -python3_10" 0 KiB
Total: 5 packages (1 upgrade, 1 new, 3 reinstalls), Size of downloads: 12,409 KiB
[jrb:~] $ eselect blas list
Available BLAS/CBLAS (lib) candidates:
(none found)
Available BLAS/CBLAS (lib64) candidates:
[1] reference * |
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Bingo! Rebuilding in that order fixed it. Hope this helps someone else in the same situation as me...
Thanks very much,
ht
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