No luck. I am not sure what to do next.
On Saturday, February 27, 2021 at 6:22:35 PM UTC-6 brettpim wrote:
> True, and removing libopenblas did not help; I am still getting the same
> error. I put libopenblas back but not numpy and am trying again
>
>
> On Saturday, February 27, 2021 at 4:10:51 PM UTC-6 dim...@gmail.com wrote:
>
>> by right, one ought to read the last part of the output of ./configure
>> for advice on
>> packages to to install, and follow it.
>>
>> Without libopenblas-dev installed you're going to build it, and
>> everything that depends on it, from source...
>>
>> On Sat, Feb 27, 2021 at 9:45 PM brettpim <br...@math.carleton.ca> wrote:
>> >
>> > I have finally tracked down and removed all installations of numpy; I
>> also removed libopenblas. I have done make bootstrap-clean distclean;
>> ./configure; and started make again. I will report the results
>> >
>> > On Saturday, February 27, 2021 at 2:02:59 PM UTC-6 brettpim wrote:
>> >>
>> >> also my git branches I am working on would be lost if I wiped
>> everything.
>> >>
>> >> On Saturday, February 27, 2021 at 1:50:18 PM UTC-6 brettpim wrote:
>> >>>
>> >>> make bootstrap-clean distclean did not solve the problem. I have
>> considered removing python3 from my system and reinstalling it but there
>> are so many other things I have that depend on python3 and would be
>> removed. I don't want to have to reinstall such a huge list. I am not sure
>> what to do next. One thought is to delete my entire sage directory and pull
>> it afresh but I am not sure this will address the issue that blas is not
>> being found properly.
>> >>>
>> >>>
>> >>> On Saturday, February 27, 2021 at 11:18:04 AM UTC-6 brettpim wrote:
>> >>>>
>> >>>> DIma,
>> >>>>
>> >>>> I found that pip installs in /usr/local when it is run as sudo. I
>> have not found anything definitive that says it should not be run as sudo
>> but just in case I sudo pip uninstalled all the packages in /usr/local and
>> pip installed them as a user which puts them all in $HOME/.local. But even
>> after this there something is still wrong with my numpy install and I am
>> still working on.
>> >>>>
>> >>>> While I am investigating my numpy problem I will try the serious
>> clean-up you suggest. My build was an attempt at a re-build after a git
>> pull so the clean-up is justified. I will report back
>> >>>>
>> >>>> thanks
>> >>>> brett
>> >>>> On Saturday, February 27, 2021 at 2:06:03 AM UTC-6 dim...@gmail.com
>> wrote:
>> >>>>>
>> >>>>> On Sat, Feb 27, 2021 at 4:07 AM brettpim <br...@math.carleton.ca>
>> wrote:
>> >>>>> >
>> >>>>> > /usr/local/ is where pip has installed my python packages so
>> don't these files belong here?
>> >>>>> >
>> >>>>> >
>> >>>>> > On Friday, February 26, 2021 at 5:20:03 PM UTC-6 dim...@gmail.com
>> wrote:
>> >>>>> >>
>> >>>>> >> looks like you have a copy of (c)blas in /usr/local - and this
>> leads to trouble
>> >>>>>
>> >>>>> oops, sorry, it's a wrong guess, I suppose.
>> >>>>>
>> >>>>> What is the branch you are installing? master from github, which is
>> Sage 9.2 ?
>> >>>>> Or the development branch, 9.3.beta7?
>> >>>>>
>> >>>>> Was it an attempt to re-build after git pull,or a fresh install?
>> >>>>> Fresh install should work, but for an update, you might need a
>> serious clean-up:
>> >>>>>
>> >>>>> make bootstrap-clean distclean
>> >>>>>
>> >>>>> Sage has a bit fragile system of re-creating missing .pc files for
>> >>>>> (c)blas/lapack, and
>> >>>>> recent changes in the build system might have confused it (so that's
>> >>>>> why a fresh rebuild
>> >>>>> might be needed)
>> >>>>>
>> >>>>>
>> >>>>> >>
>> >>>>> >> On Fri, 26 Feb 2021, 21:57 brettpim, <br...@math.carleton.ca>
>> wrote:
>> >>>>> >>>
>> >>>>> >>>
>> >>>>> >>> I am trying to install sage from the master branch on PC
>> running Ubuntu 20.04.
>> >>>>> >>> The make is failing to build numpy-1.19.1.
>> >>>>> >>> It is complaining about not finding cblas or blas.
>> >>>>> >>>
>> >>>>> >>> In my config.log it finds openblas and so decides it will not
>> install is as SPKG
>> >>>>> >>>
>> >>>>> >>> but when I run python3:
>> >>>>> >>> >>> import numpy
>> >>>>> >>> >>> numpy.show_config()
>> >>>>> >>>
>> >>>>> >>> it reports
>> >>>>> >>>
>> >>>>> >>> blas_info:
>> >>>>> >>> libraries = ['blas', 'blas']
>> >>>>> >>> library_dirs = ['/usr/lib/x86_64-linux-gnu']
>> >>>>> >>> include_dirs = ['/usr/local/include', '/usr/include']
>> >>>>> >>> language = c
>> >>>>> >>> define_macros = [('HAVE_CBLAS', None)]
>> >>>>> >>> blas_opt_info:
>> >>>>> >>> define_macros = [('NO_ATLAS_INFO', 1), ('HAVE_CBLAS', None)]
>> >>>>> >>> libraries = ['blas', 'blas']
>> >>>>> >>> library_dirs = ['/usr/lib/x86_64-linux-gnu']
>> >>>>> >>> include_dirs = ['/usr/local/include', '/usr/include']
>> >>>>> >>> language = c
>> >>>>> >>>
>> >>>>> >>> which makes me think there is something wrong with blas.
>> >>>>> >>>
>> >>>>> >>> --
>> >>>>> >>> 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 view this discussion on the web visit
>> https://groups.google.com/d/msgid/sage-devel/a8054ce0-69ee-4537-80ed-f51ced0f7c8cn%40googlegroups.com
>> .
>> >>>>> >
>> >>>>> > --
>> >>>>> > You received this message because you are subscribed to the
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>> >>>>> > To unsubscribe from this group and stop receiving emails from it,
>> send an email to sage-devel+...@googlegroups.com.
>> >>>>> > To view this discussion on the web visit
>> https://groups.google.com/d/msgid/sage-devel/4c7f11e6-246d-4f58-b6d2-dfcbaf0b284bn%40googlegroups.com
>> .
>> >
>> > --
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>>
>
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Found local metadata for numpy-1.19.1
Using cached file /home/brett/Projects/SAGE/sage/upstream/numpy-1.19.1.zip
numpy-1.19.1
====================================================
Setting up build directory for numpy-1.19.1
Finished extraction
Applying patches from ../patches...
Applying ../patches/0001-ENH-Use-AVX-512-for-np.isnan-np.infinite-np.isinf-an.patch
patching file benchmarks/benchmarks/bench_avx.py
patching file numpy/core/code_generators/generate_umath.py
patching file numpy/core/include/numpy/npy_common.h
patching file numpy/core/setup_common.py
patching file numpy/core/src/umath/loops.c.src
patching file numpy/core/src/umath/loops.h.src
patching file numpy/core/src/umath/simd.inc.src
patching file numpy/core/tests/test_umath.py
Applying ../patches/0002-BUG-Update-compiler-check-for-AVX-512F.patch
patching file numpy/core/setup_common.py
****************************************************
Host system:
Linux hamm 5.4.0-65-generic #73-Ubuntu SMP Mon Jan 18 17:25:17 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
****************************************************
C compiler: gcc
C compiler version:
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/9/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none:hsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 9.3.0-17ubuntu1~20.04' --with-bugurl=file:///usr/share/doc/gcc-9/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,gm2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-9 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-9-HskZEa/gcc-9-9.3.0/debian/tmp-nvptx/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 9.3.0 (Ubuntu 9.3.0-17ubuntu1~20.04)
****************************************************
Uninstalling 'numpy' with legacy uninstaller
Package 'numpy' is currently not installed
Traceback (most recent call last):
File "../lapack_conf.py", line 7, in <module>
pc_blas = pkgconfig.parse('cblas blas')
File "/home/brett/Projects/SAGE/sage/local/lib/python3.8/site-packages/pkgconfig/pkgconfig.py", line 248, in parse
_raise_if_not_exists(package)
File "/home/brett/Projects/SAGE/sage/local/lib/python3.8/site-packages/pkgconfig/pkgconfig.py", line 103, in _raise_if_not_exists
raise PackageNotFoundError(package)
pkgconfig.pkgconfig.PackageNotFoundError: cblas not found
real 0m0.043s
user 0m0.035s
sys 0m0.009s
************************************************************************
Error installing package numpy-1.19.1
************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the log file
/home/brett/Projects/SAGE/sage/logs/pkgs/numpy-1.19.1.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/home/brett/Projects/SAGE/sage/local/var/tmp/sage/build/numpy-1.19.1 and type 'make' or whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:
(cd '/home/brett/Projects/SAGE/sage/local/var/tmp/sage/build/numpy-1.19.1' && '/home/brett/Projects/SAGE/sage/sage' --buildsh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************
