But why not ATLAS? Should I look at the numpy makefile?
On Sun, Mar 3, 2019, 15:37 François Bissey <frp.bis...@gmail.com> wrote:
> Ok. Well it is finding openblas
>
> customize UnixCCompiler
> FOUND:
> libraries = ['openblas', 'blas']
> library_dirs = ['/usr/local/src/Misc/sage-8.6/local/lib', '/usr/lib64']
> language = c
> define_macros = [('HAVE_CBLAS', None)]
> include_dirs = ['/usr/local/include', '/usr/include',
> '/usr/local/src/Misc/sage-8.6/local/include']
>
> FOUND:
> libraries = ['openblas', 'blas']
> library_dirs = ['/usr/local/src/Misc/sage-8.6/local/lib', '/usr/lib64']
> define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)]
> language = c
> include_dirs = ['/usr/local/include', '/usr/include',
> '/usr/local/src/Misc/sage-8.6/local/include']
>
> F2PY Version 2
> lapack_opt_info:
> lapack_mkl_info:
> Disabled lapack_mkl_info: (MKLROOT is None)
> Disabled lapack_mkl_info: (MKLROOT is None)
> customize UnixCCompiler
> libraries mkl_rt not found in []
> NOT AVAILABLE
>
> openblas_lapack_info:
> customize UnixCCompiler
> Disabled openblas_lapack_info: (OPENBLAS is None)
> customize UnixCCompiler
> libraries openblas not found in []
> NOT AVAILABLE
>
> openblas_clapack_info:
> customize UnixCCompiler
> Disabled openblas_clapack_info: (OPENBLAS is None)
> customize UnixCCompiler
> libraries openblas,lapack not found in []
> NOT AVAILABLE
>
> atlas_3_10_threads_info:
> Disabled atlas_3_10_threads_info: (PTATLAS is None)
> <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
> NOT AVAILABLE
>
> atlas_3_10_info:
> Disabled atlas_3_10_info: (ATLAS is None)
> <class 'numpy.distutils.system_info.atlas_3_10_info'>
> NOT AVAILABLE
>
> atlas_threads_info:
> Disabled atlas_threads_info: (PTATLAS is None)
> <class 'numpy.distutils.system_info.atlas_threads_info'>
> NOT AVAILABLE
>
> atlas_info:
> Disabled atlas_info: (ATLAS is None)
> <class 'numpy.distutils.system_info.atlas_info'>
> NOT AVAILABLE
>
> lapack_info:
> customize UnixCCompiler
> customize UnixCCompiler
> FOUND:
> libraries = ['openblas', 'lapack']
> library_dirs = ['/usr/local/src/Misc/sage-8.6/local/lib', '/usr/lib64']
> language = f77
>
> FOUND:
> libraries = ['openblas', 'lapack', 'openblas', 'blas']
> library_dirs = ['/usr/local/src/Misc/sage-8.6/local/lib', '/usr/lib64']
> define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)]
> language = c
> include_dirs = ['/usr/local/include', '/usr/include',
> '/usr/local/src/Misc/sage-8.6/local/include']
>
> /usr/local/src/Misc/sage-8.6/local/lib/python2.7/distutils/dist.py:267:
> UserWarning: Unknown distribution option: 'define_macros'
> warnings.warn(msg)
>
> Is it supposed to find something else?
>
> > On 4/03/2019, at 10:33, Ike Stoddard <isaac.a.stodd...@gmail.com> wrote:
> >
> > Numpy log and sagelib log were attached to original note.
> >
> > On Sun, Mar 3, 2019 at 15:32 François Bissey <frp.bis...@gmail.com>
> wrote:
> > I need more info for a diagnostic. Logs and more logs.
> >
> > > On 4/03/2019, at 10:09, Ike Stoddard <isaac.a.stodd...@gmail.com>
> wrote:
> > >
> > > Relevantly, numpy build process does not find my ATLAS. It seems to
> check ATLAS instead of SAGE_ATLAS_LIB.
> > > Shell coding error? Or is ATLAS supposed to be set to SAGE_ATLAS_LIB
> at some point?
> > >
> > >
> > > On Sunday, March 3, 2019 at 2:17:24 AM UTC-6, François Bissey wrote:
> > > You suffer from a classic case of gcc/gfortran upgrade. I have been
> fielding bugs
> > > for the same kind of errors in Gentoo for a number of months now.
> > > up to gcc-6, gfortran provided its runtime with libgfortran.so.3.
> > > But gcc-7 broke the compatibility and provided libgfortran.so.4.
> > > And gcc-8 broke the compatibility again providing libgfortran.so.5.
> > > After upgrading gcc/gfortran from one of the version above to another
> > > you need to rebuild all packages linking to libgfortran. That means
> > > anything that uses lapack and in particular numpy when compiled with
> > > lapack bindings like in sage.
> > >
> > > > On 3/03/2019, at 19:16, Ike Stoddard <isaac.a....@gmail.com> wrote:
> > > >
> > > > Linux xxxxxxx 4.20.12-arch1-1-ARCH #1 SMP PREEMPT Sat Feb 23
> 15:11:34 UTC 2019 x86_64 GNU/Linux
> > > >
> > > > Building from source; make fails at sagelib, but implies "numpy" is
> at fault:
> > > > [sagelib-8.6] ImportError:
> > > > [sagelib-8.6] Importing the multiarray numpy extension module
> failed. Most
> > > > [sagelib-8.6] likely you are trying to import a failed build of
> numpy.
> > > > [sagelib-8.6] If you're working with a numpy git repo, try `git
> clean -xdf` (removes all
> > > > [sagelib-8.6] files not under version control). Otherwise reinstall
> numpy.
> > > > [sagelib-8.6]
> > > > [sagelib-8.6] Original error was: libgfortran.so.3: cannot open
> shared object file: No such file or directory
> > > >
> .....................................................^^^^^^^^^^^^^^^^I
> cannot see where this originates?
> > > > [sagelib-8.6]
> > > > [sagelib-8.6]
> ************************************************************************
> > > > [sagelib-8.6] Error building the Sage library
> > > > [sagelib-8.6]
> ************************************************************************
> > > > [sagelib-8.6] Please email sage-devel (
> http://groups.google.com/group/sage-devel)
> > > > [sagelib-8.6] explaining the problem and including the relevant part
> of the log file
> > > > [sagelib-8.6]
> /usr/local/src/Misc/sage-8.6/logs/pkgs/sagelib-8.6.log
> > > >
> > > > Now I have already got python2-numpy and python-numpy installed
> (Arch Linux, via pacman [canonical installer])
> > > > warning: python2-numpy-1.16.1-1 is up to date -- reinstalling
> > > > warning: python-numpy-1.16.1-1 is up to date -- reinstalling
> > > >
> > > > yet it builds its own "upstream" numpy that is not the latest:
> > > > ./logs/pkgs/numpy-1.15.4.p0.log
> > > >
> > > > I cannot at this point find where to substitute installed numpy. I
> have already redirected ATLAS and gcc:
> > > > declare -x SAGE_ATLAS_LIB="/usr/local/atlas/lib"
> > > > declare -x SAGE_INSTALL_GCC="no"
> > > >
> > > > 1) Why does this not find my numpy?
> > > > 2) Is there another environment variable to set for that? I cannot
> find it.
> > > >
> > > > Logs for numpy and sagelib are attached. Pointing me to the correct
> diagnostic lines in my logs will help.
> > > >
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> > > > <sagelib-8.6.log><numpy-1.15.4.p0.log>
> > >
> > >
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