make ptest
reported "all tests passed!"
thank you for your help getting this working.
brett
On Tuesday, March 2, 2021 at 4:17:14 AM UTC-6 dim...@gmail.com wrote:
> On Tue, 2 Mar 2021, 03:11 brettpim, <br...@math.carleton.ca> wrote:
>
>> I ran
>>
>> make toolchain
>>
>> and then
>>
>> make
>>
>> This was successful. I note in the log section on numpy that it is using
>> a non-optimized netlib Blas.
>>
>
> OK, great.
>
>>
>> What exactly does "make toolchain" do and not do? Is there anything
>> likely not to work with the sage that successfully built?
>>
>
> in particular "make toolchain" readies
> pkg-config .pc files for blas, lapack, etc.
>
> (on a modern Linux system with most recommended packages installed it does
> not do much more)
>
> numpy has a very old and a bit insane way to check for its dependencies
> (basically, compilers and (c)blas/lapack)
> So somehow it manages to get itself confused on your machine, when we
> build it as Sage package.
> Your logs say
>
> 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
>
> which indicate that said pkg-config files are not present (at least one
> for cblas). They are recreated by the "make toolchain",
> so that's why it all works after this. Your config.log indicates that
> cblas capabilities are available in your openblas,
> so it boils down to .pc file not bein set up.
>
> The reason you see netlib Blas is due to your openblas not recognised to
> have lapack capabilities,
> as far as I can see from your config.log.
> Maybe an Ubuntu "feature", as it's perfectly possible to have
> openblas-optimised lapack included in libopenblas, maybe Ubuntu, unlike
> e.g. Debian, does not do it.
>
> Maybe it's a bug in our tests, which are admittedly a hack, introduced in
> https://trac.sagemath.org/ticket/29361
> This hack is something that should go once we al last deside that we
> should not bother with packaging compilers
> in Sage (FFS, this moment cannot be too soon, it should have happen years
> ago!), as this hack is meant to cover the case of no Fortran compiler
> available on the system (but I start ranting here, sorry :-)).
>
>
> To test is your Sage is OK, you can run
>
> make ptest
>
> to run the standard Sage tests, to see if nothing is broken (takes 2-3
> hours on a modern PC)
>
> Cheers
> Dima
>
>
>> thanks
>> brett
>> On Saturday, February 27, 2021 at 8:04:18 PM UTC-6 dim...@gmail.com
>> wrote:
>>
>>> this seems to be the error here:
>>> https://trac.sagemath.org/ticket/31135
>>>
>>> I wonder if you can run
>>>
>>> make toolchain
>>>
>>> and only then run
>>>
>>> make
>>>
>>> On Sun, Feb 28, 2021 at 1:26 AM brettpim <br...@math.carleton.ca>
>>> wrote:
>>> >
>>> > 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.
>>> >>> >>>>> >>>
>>> >>> >>>>> >>> --
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>>>
>>> >>> >>>>> >
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