On Mon, Mar 4, 2019 at 11:34 AM Ike Stoddard <isaac.a.stodd...@gmail.com> wrote: > > But why not ATLAS? Should I look at the numpy makefile?
I have reported this before as https://trac.sagemath.org/ticket/20507 > 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. >> > > > >> > > > -- >> > > > You received this message because you are subscribed to the Google >> > > > Groups "sage-devel" group. >> > > > To unsubscribe from this group and stop receiving emails from it, send >> > > > an email to sage-devel+...@googlegroups.com. >> > > > To post to this group, send email to sage-...@googlegroups.com. >> > > > Visit this group at https://groups.google.com/group/sage-devel. >> > > > For more options, visit https://groups.google.com/d/optout. >> > > > <sagelib-8.6.log><numpy-1.15.4.p0.log> >> > > >> > > >> > > -- >> > > You received this message because you are subscribed to the Google >> > > Groups "sage-devel" group. >> > > To unsubscribe from this group and stop receiving emails from it, send >> > > an email to sage-devel+unsubscr...@googlegroups.com. >> > > To post to this group, send email to sage-devel@googlegroups.com. >> > > Visit this group at https://groups.google.com/group/sage-devel. >> > > For more options, visit https://groups.google.com/d/optout. >> > >> > -- >> > You received this message because you are subscribed to the Google Groups >> > "sage-devel" group. >> > To unsubscribe from this group and stop receiving emails from it, send an >> > email to sage-devel+unsubscr...@googlegroups.com. >> > To post to this group, send email to sage-devel@googlegroups.com. >> > Visit this group at https://groups.google.com/group/sage-devel. >> > For more options, visit https://groups.google.com/d/optout. >> > >> > -- >> > You received this message because you are subscribed to the Google Groups >> > "sage-devel" group. >> > To unsubscribe from this group and stop receiving emails from it, send an >> > email to sage-devel+unsubscr...@googlegroups.com. >> > To post to this group, send email to sage-devel@googlegroups.com. >> > Visit this group at https://groups.google.com/group/sage-devel. >> > For more options, visit https://groups.google.com/d/optout. >> >> -- >> You received this message because you are subscribed to the Google Groups >> "sage-devel" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to sage-devel+unsubscr...@googlegroups.com. >> To post to this group, send email to sage-devel@googlegroups.com. >> Visit this group at https://groups.google.com/group/sage-devel. >> For more options, visit https://groups.google.com/d/optout. > > -- > You received this message because you are subscribed to the Google Groups > "sage-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-devel+unsubscr...@googlegroups.com. > To post to this group, send email to sage-devel@googlegroups.com. > Visit this group at https://groups.google.com/group/sage-devel. > For more options, visit https://groups.google.com/d/optout. -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
