Cant compile on Arch, Linux Kernel: 5.10.9

My issue is about … Compilation

Reproducing code example:

Sample code to reproduce the problem

Error message:

 Warning: Unused variable 't5' declared at (1) [-Wunused-variable]                                                   
  gfortran:f77: scipy/sparse/linalg/eigen/arpack/ARPACK/UTIL/ivout.f                                                  
  gfortran:f77: scipy/sparse/linalg/eigen/arpack/ARPACK/SRC/zsortc.f                                                  
  gfortran:f77: scipy/sparse/linalg/eigen/arpack/ARPACK/SRC/ssgets.f                                                  
  gfortran:f77: scipy/sparse/linalg/eigen/arpack/ARPACK/UTIL/second_NONE.f                                            
  scipy/sparse/linalg/eigen/arpack/ARPACK/UTIL/second_NONE.f:17:27:                                                   
                                                                                                                      
     17 |       REAL               T1                                                                                 
        |                           1                                                                                 
  Warning: Unused variable 't1' declared at (1) [-Wunused-variable]                                                   
  scipy/sparse/linalg/eigen/arpack/ARPACK/UTIL/second_NONE.f:20:36:                                                   
                                                                                                                      
     20 |       REAL               TARRAY( 2 )                                                                        
        |                                    1                                                                        
  Warning: Unused variable 'tarray' declared at (1) [-Wunused-variable]                                               
  gfortran:f77: scipy/sparse/linalg/eigen/arpack/ARPACK/SRC/zstatn.f                                                  
  stat.h:8:27:                                                                                                        
                                                                                                                      
  Warning: Unused variable 't2' declared at (1) [-Wunused-variable]                                                   
  stat.h:8:31:                                                                                                        
                                                                                                                      
  Warning: Unused variable 't3' declared at (1) [-Wunused-variable]                                                   
  stat.h:8:35:                                                                                                        
                                                                                                                      
  Warning: Unused variable 't4' declared at (1) [-Wunused-variable]                                                   
  stat.h:8:39:                                                                                                        
                                                                                                                      
  Warning: Unused variable 't5' declared at (1) [-Wunused-variable]                                                   
  stat.h:8:19:                                                                                                        
                                                                                                                      
  Warning: Unused variable 't0' declared at (1) [-Wunused-variable]                                                   
  stat.h:8:23:                                                                                                        
                                                                                                                      
  Warning: Unused variable 't1' declared at (1) [-Wunused-variable]                                                   
  stat.h:8:27:                                                                                                        
                                                                                                                      
  Warning: Unused variable 't2' declared at (1) [-Wunused-variable]                                                   
  stat.h:8:31:                                                                                                        
                                                                                                                      
  Warning: Unused variable 't3' declared at (1) [-Wunused-variable]                                                   
  stat.h:8:35:                                                                                                        
                                                                                                                      
  Warning: Unused variable 't4' declared at (1) [-Wunused-variable]                                                   
  stat.h:8:39:                                                                                                        
                                                                                                                      
  Warning: Unused variable 't5' declared at (1) [-Wunused-variable]                                                   
  gfortran:f77: scipy/sparse/linalg/eigen/arpack/ARPACK/UTIL/smout.f                                                  
  gfortran:f77: scipy/sparse/linalg/eigen/arpack/ARPACK/UTIL/zmout.f                                                  
  gfortran:f77: scipy/sparse/linalg/eigen/arpack/ARPACK/SRC/ssortc.f                                                  
  gfortran:f77: scipy/sparse/linalg/eigen/arpack/ARPACK/UTIL/cvout.f                                                  
  gfortran:f77: scipy/sparse/linalg/eigen/arpack/ARPACK/SRC/ssortr.f                                                  
  gfortran:f77: scipy/sparse/linalg/eigen/arpack/ARPACK/UTIL/dmout.f                                                  
  gfortran:f77: scipy/sparse/linalg/eigen/arpack/ARPACK/SRC/sstatn.f                                                  
  stat.h:8:19:                                                                                                        
                                                                                                                      
  Warning: Unused variable 't0' declared at (1) [-Wunused-variable]                                                   
  stat.h:8:23:                                                                                                        
                                                                                                                      
  Warning: Unused variable 't1' declared at (1) [-Wunused-variable]                                                   
  stat.h:8:27:                                                                                                        
                                                                                                                      
  Warning: Unused variable 't2' declared at (1) [-Wunused-variable]                                                   
  stat.h:8:31:                                                                                                        
                                                                                                                      
  Warning: Unused variable 't3' declared at (1) [-Wunused-variable]                                                   
  stat.h:8:35:                                                                                                        
                                                                                                                      
  Warning: Unused variable 't4' declared at (1) [-Wunused-variable]                                                   
  stat.h:8:39:                                                                                                        
                                                                                                                      
  Warning: Unused variable 't5' declared at (1) [-Wunused-variable]                                                   
  gfortran:f77: scipy/sparse/linalg/eigen/arpack/ARPACK/UTIL/zvout.f                                                  
  gfortran:f77: scipy/sparse/linalg/eigen/arpack/ARPACK/UTIL/svout.f                                                  
  gfortran:f77: /tmp/pip-install-4uapy4_0/scipy_97aa613b030e42cfbd8f9aa0faa42b13/scipy/_build_utils/src/wrap_dummy_g77_abi.f                                                                                                                
  gfortran:f77: scipy/sparse/linalg/eigen/arpack/ARPACK/UTIL/dvout.f                                                  
  gfortran:f77: scipy/sparse/linalg/eigen/arpack/ARPACK/UTIL/icnteq.f                                                 
  gfortran:f77: scipy/sparse/linalg/eigen/arpack/ARPACK/UTIL/icopy.f                                                  
  error: Command "/usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops -Iscipy/sparse/linalg/eigen/arpack/ARPACK/SRC -I/tmp/pip-build-env-a4lh84sk/overlay/lib/python3.9/site-packages/numpy/core/include -c -c scipy/sparse/linalg/eigen/arpack/ARPACK/SRC/dsaitr.f -o build/temp.linux-x86_64-3.9/scipy/sparse/linalg/eigen/arpack/ARPACK/SRC/dsaitr.o" failed with exit status 1 
  ...

[andyfaff]

I started archlinux:latest from docker, with image ID a8a9773ce02f, created 6 days ago. I assume this is a fairly recent version.

• I installed base-devel, gcc-fortran, python3 via pacman.
• then setup a venv, python3 -m venv myenv, and activated that env.

python3 -m pip install numpy cython pybind11 scipy pytest

worked without issue, and I could import scipy. It used the scipy-1.6.0-cp39-cp39-manylinux1_x86_64.whl wheel.

So I then tried to build scipy (from scipy/master)

• install lapack via pacman
• python3 setup.py build in the scipy source directory. This completed ok (took a long time on docker).
• python3 -m pip install . in the scipy source directory. This also appeared to work (I didn’t clean the source directory between the last step and this one), although I didn’t start an interpreter to check anything.
• python3 runtests.py completes the entire test suite without issue.

I note that your h5py build failed. From your build output your BLAS libraries seem to be provided by mkl_rt. This might be where the difficult is, perhaps you need to use the ifort compiler rather than gfortran. It may help if you create a specific site.cfg file to specifically use lapack (as installed by pacman), rather than mkl. I’m not an expert at this, but it might look something like:

[lapack]
library_dirs = /usr/lib
include_dirs = /usr/include

[rgommers]

Nice detailed checks @andyfaff, thanks. I’m on Arch Linux as well, and things work fine (also with MKL, if you specify paths correctly or use conda). So I’ll close this.