On Sun, Feb 5, 2023 at 12:44 PM 'Nasser M. Abbasi' via sage-release
<sage-release@googlegroups.com> wrote:
>
>
> I agree with you. I think the best thing for me, is just to make a brand new
> Virtual box, and install a new Linux and start everything from clean system.
> It will take me 2-3 days as I have to install few things I need, Then will
> try installing sagemath again after that.
you can try to temporarily move /usr/local somewhere, and see if it
helps; no need to rebuild the whole Sage then, just rebuild
scipy:
make scipy-clean scipy-uninstall
make scipy
Then start sage
./sage
and run
sage: import scipy
there. If this works, run
make
to see if it finishes fine.
>
> Thanks for the help.
> --Nasser
>
> On Sunday, February 5, 2023 at 5:58:14 AM UTC-6 Dima Pasechnik wrote:
>>
>> I suspect you have an installation of openblas, or/and some other
>> blas/lapack, in /usr/local - and this results in scipy being unable
>> to link it correctly.
>>
>>
>> (or perhaps it's not /usr/local, but some other location known to pkg-config)
>>
>> numpy and scipy accumulated ~20 years of layer upon layer of old
>> outdated code for recognising BLAS/LAPACK libraries, it's such a
>> nightmare to debug.
>>
>>
>>
>> On Sun, Feb 5, 2023 at 10:36 AM 'Nasser M. Abbasi' via sage-release
>> <sage-r...@googlegroups.com> wrote:
>> >
>> > Here is the output for the new command you posted
>> >
>> > >ldd
>> > >local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/numpy/core/_multiarray_umath.cpython-310-x86_64-linux-gnu.so
>> > linux-vdso.so.1 (0x00007ffd883d4000)
>> > libcblas.so.3 => /usr/lib/libcblas.so.3 (0x00007f25a6532000)
>> > libopenblas.so.3 => /usr/lib/libopenblas.so.3 (0x00007f25a5260000)
>> > libm.so.6 => /usr/lib/libm.so.6 (0x00007f25a5178000)
>> > libc.so.6 => /usr/lib/libc.so.6 (0x00007f25a4f91000)
>> > /usr/lib64/ld-linux-x86-64.so.2 (0x00007f25a6a5b000)
>> > libgomp.so.1 => /usr/lib/libgomp.so.1 (0x00007f25a4f48000)
>> > libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x00007f25a4f28000)
>> > >
>> >
>> > I've also put in same folder here a file called log_folders.tar.gz which
>> > is backup of the logs/ folder in my build tree of 9.8 rc0 so it will have
>> > the logs you asked for.
>> >
>> > any other information needed please let me know.
>> > --Nasser
>> >
>> >
>> > On Sunday, February 5, 2023 at 4:17:44 AM UTC-6 Dima Pasechnik wrote:
>> >>
>> >> On Sun, Feb 5, 2023 at 9:58 AM Dima Pasechnik <dim...@gmail.com> wrote:
>> >> >
>> >> > On Sun, Feb 5, 2023 at 9:04 AM 'Nasser M. Abbasi' via sage-release
>> >> > <sage-r...@googlegroups.com> wrote:
>> >> > >
>> >> > >
>> >> > > Here is the output
>> >> > >
>> >> > > >ldd
>> >> > > >/home/me/TMP/sage-9.8.rc0/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/scipy/special/_ufuncs.cpython-310-x86_64-linux-gnu.so
>> >> > > linux-vdso.so.1 (0x00007ffc53be9000)
>> >> > > libgfortran.so.5 => /usr/lib/libgfortran.so.5 (0x00007fc232878000)
>> >> > > libm.so.6 => /usr/lib/libm.so.6 (0x00007fc232790000)
>> >> > > libmvec.so.1 => /usr/lib/libmvec.so.1 (0x00007fc232696000)
>> >> > > libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x00007fc232676000)
>> >> > > libc.so.6 => /usr/lib/libc.so.6 (0x00007fc23248f000)
>> >> > > libquadmath.so.0 => /usr/lib/../lib/libquadmath.so.0
>> >> > > (0x00007fc232444000)
>> >> > > /usr/lib64/ld-linux-x86-64.so.2 (0x00007fc232ce1000)
>> >> >
>> >> > here is how it looks on a non-broken installation.
>> >> >
>> >> > $ ldd
>> >> > local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/scipy/special/_ufuncs.cpython-310-x86_64-linux-gnu.so
>> >> > linux-vdso.so.1 (0x00007ffe6b935000)
>> >> > libopenblas.so.0 => /lib64/libopenblas.so.0 (0x00007fe561400000)
>> >> > libgfortran.so.5 => /lib64/libgfortran.so.5 (0x00007fe561000000)
>> >> > libm.so.6 => /lib64/libm.so.6 (0x00007fe563865000)
>> >> > libmvec.so.1 => /lib64/libmvec.so.1 (0x00007fe561303000)
>> >> > libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fe563845000)
>> >> > libc.so.6 => /lib64/libc.so.6 (0x00007fe560c00000)
>> >> > libquadmath.so.0 => /lib64/libquadmath.so.0 (0x00007fe560fb8000)
>> >> > /lib64/ld-linux-x86-64.so.2 (0x00007fe563ad3000)
>> >> >
>> >> > As you see, in your case libopenblas.so is not there, and you have an
>> >> > error due to this.
>> >> > Why scipy builds such a broken module, I don't know. I'd say it's a
>> >> > scipy bug.
>> >> >
>> >> > Please post logs/pkgs/numpy* and logs/pkgs/scipy*
>> >>
>> >> please also check that
>> >>
>> >> ldd
>> >> local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/numpy/core/_multiarray_umath.cpython-310-x86_64-linux-gnu.so
>> >>
>> >> has openblas in its output.
>> >>
>> >> >
>> >> >
>> >> > > >
>> >> > >
>> >> > > "You should add fpylll at the end of the line in
>> >> > >
>> >> > > build/pkgs/sagemath_doc_html/dependencies
>> >> > >
>> >> > > and run ./configure and make again"
>> >> > >
>> >> > > Ok thanks. Will give this a try.
>> >> > >
>> >> > > "sage in a different directory which is in your PATH typically breaks
>> >> > > things"
>> >> > >
>> >> > > but it is NOT in the path. This is the reason I do
>> >> > >
>> >> > > unset SAGE_ROOT
>> >> > > unset SAGE_LOCAL
>> >> > >
>> >> > > before building any new release. I make sure current installed
>> >> > > sagemath (in different folder) is not visible.
>> >> > >
>> >> > > --Nasser
>> >> > >
>> >> > > On Saturday, February 4, 2023 at 9:15:14 AM UTC-6 Dima Pasechnik
>> >> > > wrote:
>> >> > >>
>> >> > >> On Sat, Feb 4, 2023 at 1:51 PM 'Nasser M. Abbasi' via sage-release
>> >> > >> <sage-r...@googlegroups.com> wrote:
>> >> > >> >
>> >> > >> > "Was it an incremental build. If so,
>> >> > >> > make distclean
>> >> > >> > and
>> >> > >> > build again from scratch."
>> >> > >> >
>> >> > >> > It was not an incremental build. I extracted the gzip file and did
>> >> > >> > the steps I showed. So I do not need to do "make distclean" since
>> >> > >> > everything is new.
>> >> > >> >
>> >> > >> > But I repeated now everything again using "make distclean" and got
>> >> > >> > same error.
>> >> > >> >
>> >> > >> > "Probably the problem is linking with openblas. Do you have a
>> >> > >> > number of openblas versions accessible to the linker?"
>> >> > >> >
>> >> > >> > I have no idea. What command should I use to check?
>> >> > >>
>> >> > >> run
>> >> > >>
>> >> > >> ldd
>> >> > >> /home/me/TMP/sage-9.8.rc0/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/scipy/special/_ufuncs.cpython-310-x86_64-linux-gnu.so
>> >> > >>
>> >> > >> Post its output
>> >> > >> - there should be an openblas mentioned, the question is which one.
>> >> > >>
>> >> > >> As far as fpylll is concerned, you've hit the bug fixed in not yet
>> >> > >> merged
>> >> > >> https://trac.sagemath.org/ticket/34940
>> >> > >>
>> >> > >> You should add fpylll at the end of the line in
>> >> > >>
>> >> > >> build/pkgs/sagemath_doc_html/dependencies
>> >> > >>
>> >> > >> and run ./configure and make again
>> >> > >>
>> >> > >>
>> >> > >>
>> >> > >>
>> >> > >> >
>> >> > >> > I am just following the instruction to download and install
>> >> > >> > sagemath.
>> >> > >> >
>> >> > >> > I have giac and maxima and fricas and texlive already installed on
>> >> > >> > this virtual box already. I also have sagemath 9.7 installed in
>> >> > >> > different folder.
>> >> > >> >
>> >> > >> > --Nasser
>> >> > >> >
>> >> > >> >
>> >> > >> > On Saturday, February 4, 2023 at 5:27:59 AM UTC-6 Dima Pasechnik
>> >> > >> > wrote:
>> >> > >> >>
>> >> > >> >> Hello,
>> >> > >> >> Was it an incremental build. If so,
>> >> > >> >> make distclean
>> >> > >> >> and
>> >> > >> >> build again from scratch.
>> >> > >> >>
>> >> > >> >> Anyhow, if you look in your istall.log you'll see problems with a
>> >> > >> >> number of packages, e.g. fpylll, scipy.
>> >> > >> >>
>> >> > >> >> [sagemath_doc_html-none] [manifolds] ImportError:
>> >> > >> >> /home/me/TMP/sage-9.8.rc0/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/scipy/special/_ufuncs.cpython-310-x86_64-linux-gnu.so:
>> >> > >> >> undefined symbol: dstevr_
>> >> > >> >>
>> >> > >> >> Probably the problem is linking with openblas. Do you have a
>> >> > >> >> number of openblas versions accessible to the linker?
>> >> > >> >>
>> >> > >> >>
>> >> > >> >>
>> >> > >> >> By the way,
>> >> > >> >> what are you trying to achieve with exporting
>> >> > >> >> MAXIMA ?
>> >> > >> >> Sage does not support using external Maxima at the moment,
>> >> > >> >>
>> >> > >> >>
>> >> > >> >>
>> >> > >> >>
>> >> > >> >> On Sat, 4 Feb 2023, 08:12 'Nasser M. Abbasi' via sage-release,
>> >> > >> >> <sage-r...@googlegroups.com> wrote:
>> >> > >> >>>
>> >> > >> >>> I get this error on Linux virtual box running
>> >> > >> >>>
>> >> > >> >>> lsb_release -a
>> >> > >> >>> LSB Version: n/a
>> >> > >> >>> Distributor ID: ManjaroLinux
>> >> > >> >>> Description: Manjaro Linux
>> >> > >> >>> Release: 22.0.0
>> >> > >> >>> Codename: Sikaris
>> >> > >> >>>
>> >> > >> >>> After extracting the gzip file, these are the commands I did
>> >> > >> >>>
>> >> > >> >>> unset SAGE_ROOT
>> >> > >> >>> unset SAGE_LOCAL
>> >> > >> >>> export GIAC=/usr/local/bin/giac
>> >> > >> >>> export MAXIMA=/usr/local/bin/maxima
>> >> > >> >>> ./configure --with-system-python=no
>> >> > >> >>> make
>> >> > >> >>>
>> >> > >> >>> At the end I see
>> >> > >> >>>
>> >> > >> >>> -------------
>> >> > >> >>> sagemath_doc_html-none] File
>> >> > >> >>> "/home/me/TMP/sage-9.8.rc0/src/sage_docbuild/sphinxbuild.py",
>> >> > >> >>> line 263, in raise_errors
>> >> > >> >>> [sagemath_doc_html-none] raise OSError(self._error)
>> >> > >> >>> [sagemath_doc_html-none] OSError:
>> >> > >> >>> /home/me/TMP/sage-9.8.rc0/src/sage/manifolds/chart.py:docstring
>> >> > >> >>> of sage.manifolds.chart.RealChart.plot:104: WARNING: Exception
>> >> > >> >>> occurred in plotting chart-1
>> >> > >> >>> [sagemath_doc_html-none]
>> >> > >> >>> [sagemath_doc_html-none] Note: incremental documentation builds
>> >> > >> >>> sometimes cause spurious
>> >> > >> >>> [sagemath_doc_html-none] error messages. To be certain that
>> >> > >> >>> these are real errors, run
>> >> > >> >>> [sagemath_doc_html-none] "make doc-clean doc-uninstall" first
>> >> > >> >>> and try again.
>> >> > >> >>> [sagemath_doc_html-none] make[6]: *** [Makefile:28:
>> >> > >> >>> doc-inventory--reference-manifolds] Error 1
>> >> > >> >>> [sagemath_doc_html-none] make[5]: *** [Makefile:45:
>> >> > >> >>> doc-inventory-reference] Error 2
>> >> > >> >>> make[4]: *** [Makefile:3262:
>> >> > >> >>> sagemath_doc_html-SAGE_DOCS-no-deps] Error 2
>> >> > >> >>> make[3]: *** [Makefile:3262:
>> >> > >> >>> /home/me/TMP/sage-9.8.rc0/local/var/lib/sage/installed/sagemath_doc_html-none]
>> >> > >> >>> Error 2
>> >> > >> >>> make[2]: *** [Makefile:2766: all-start] Error 2
>> >> > >> >>> make[2]: Leaving directory '/home/me/TMP/sage-9.8.rc0/build/make'
>> >> > >> >>>
>> >> > >> >>> real 71m30.833s
>> >> > >> >>> user 103m7.355s
>> >> > >> >>> sys 5m48.306s
>> >> > >> >>> ***************************************************************
>> >> > >> >>> Error building Sage.
>> >> > >> >>>
>> >> > >> >>> The following package(s) may have failed to build (not
>> >> > >> >>> necessarily
>> >> > >> >>> during this run of 'make all-start'):
>> >> > >> >>>
>> >> > >> >>> It is safe to delete any log files and build directories, but
>> >> > >> >>> they
>> >> > >> >>> contain information that is helpful for debugging build problems.
>> >> > >> >>> WARNING: If you now run 'make' again, the build directory of the
>> >> > >> >>> same version of the package will, by default, be deleted. Set the
>> >> > >> >>> environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.
>> >> > >> >>> ----------------------------
>> >> > >> >>>
>> >> > >> >>> The following folder contains config.log and install.log files
>> >> > >> >>>
>> >> > >> >>> Thank you
>> >> > >> >>> --Nasser
>> >> > >> >>>
>> >> > >> >>>
>> >> > >> >>>
>> >> > >> >>>
>> >> > >> >>>
>> >> > >> >>>
>> >> > >> >>> On Friday, February 3, 2023 at 3:40:20 AM UTC-6 Dima Pasechnik
>> >> > >> >>> wrote:
>> >> > >> >>>>
>> >> > >> >>>> On Fri, Feb 3, 2023 at 7:33 AM Sébastien Labbé
>> >> > >> >>>> <sla...@gmail.com> wrote:
>> >> > >> >>>> >
>> >> > >> >>>> >
>> >> > >> >>>> >
>> >> > >> >>>> > On Thursday, February 2, 2023 at 7:37:27 PM UTC+1
>> >> > >> >>>> > matthia...@gmail.com wrote:
>> >> > >> >>>> > On Thursday, February 2, 2023 at 9:30:30 AM UTC-8 Sébastien
>> >> > >> >>>> > Labbé wrote:
>> >> > >> >>>> > ./bootstrap: 9: m4: Permission denied
>> >> > >> >>>> > make: *** [Makefile:365 : configure] Erreur 1
>> >> > >> >>>> >
>> >> > >> >>>> > Do you have "." in PATH?
>> >> > >> >>>> >
>> >> > >> >>>> >
>> >> > >> >>>> > No
>> >> > >> >>>> >
>> >> > >> >>>> > What does "which m4" say?
>> >> > >> >>>> >
>> >> > >> >>>> >
>> >> > >> >>>> > It returns nothing! Thanks for the hint. I found the problem:
>> >> > >> >>>> > when reading the sage README to install sage from scratch on
>> >> > >> >>>> > this new machine, I installed the basic stuff as follows:
>> >> > >> >>>> >
>> >> > >> >>>> > $ sudo apt install gcc gfortran g++ make m4 perl ranlib tar bc
>> >> > >> >>>> > [...]
>> >> > >> >>>> > E: Impossible de trouver le paquet ranlib
>> >> > >> >>>> >
>> >> > >> >>>> > But this returned an error on ranlib and I assumed it had
>> >> > >> >>>> > installed the other packages in the list but no, it did not
>> >> > >> >>>> > (gcc, gfortran, etc. were not installed as well).
>> >> > >> >>>> >
>> >> > >> >>>> > Is ranlib really needed for sage? Can we remove it from the
>> >> > >> >>>> > README?
>> >> > >> >>>>
>> >> > >> >>>> ranlib is a standard tool, and is used by various build
>> >> > >> >>>> systems. On
>> >> > >> >>>> Debian it's a part of binutils package.
>> >> > >> >>>>
>> >> > >> >>>> README is not platform-specific, and it does not tell you to
>> >> > >> >>>> install
>> >> > >> >>>> *package* called ranlib.
>> >> > >> >>>> However, we should add there an advice to look for what
>> >> > >> >>>> packages to install in
>> >> > >> >>>> build/pkgs/_prereq/distros/
>> >> > >> >>>> (e.g. for Debian it's in build/pkgs/_prereq/distros/debian.txt)
>> >> > >> >>>>
>> >> > >> >>>> (Once our GitHub is live in few days, it's a very quick PR to
>> >> > >> >>>> do :-))
>> >> > >> >>>>
>> >> > >> >>>>
>> >> > >> >>>>
>> >> > >> >>>> >
>> >> > >> >>>> >
>> >> > >> >>>> >
>> >> > >> >>>> > --
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>> >> > >> >>>
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