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.
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 outdated code for recognising BLAS/LAPACK libraries, it's such a 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 :-)) > >> > >> >>>> > >> > >> >>>> > >> > >> >>>> > >> > >> >>>> > > >> > >> >>>> > > >> > >> >>>> > > >> > >> >>>> > -- > >> > >> >>>> > You received this message because you are subscribed to the > Google Groups "sage-release" group. > >> > >> >>>> > To unsubscribe from this group and stop receiving emails > from it, send an email to sage-release...@googlegroups.com. > >> > >> >>>> > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-release/d6aecaee-279a-45f8-a645-36483d72a382n%40googlegroups.com > . > >> > >> >>> > >> > >> >>> -- > >> > >> >>> You received this message because you are subscribed to the > Google Groups "sage-release" group. > >> > >> >>> To unsubscribe from this group and stop receiving emails from > it, send an email to sage-release...@googlegroups.com. > >> > >> >>> > >> > >> >>> To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-release/4a516a44-b761-4f02-ac10-e121cadc54d3n%40googlegroups.com > . > >> > >> > > >> > >> > -- > >> > >> > You received this message because you are subscribed to the > Google Groups "sage-release" group. > >> > >> > To unsubscribe from this group and stop receiving emails from > it, send an email to sage-release...@googlegroups.com. > >> > >> > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-release/4d86cb2d-8c03-4101-904e-21a1a1ce8b93n%40googlegroups.com > . > >> > > > >> > > -- > >> > > You received this message because you are subscribed to the Google > Groups "sage-release" group. > >> > > To unsubscribe from this group and stop receiving emails from it, > send an email to sage-release...@googlegroups.com. > >> > > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-release/2660c6b9-57cd-4d75-b0f8-97636bbfaf71n%40googlegroups.com > . > > > > -- > > You received this message because you are subscribed to the Google > Groups "sage-release" group. > > To unsubscribe from this group and stop receiving emails from it, send > an email to sage-release...@googlegroups.com. > > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-release/f362b0db-0f36-4c03-9949-473954352652n%40googlegroups.com > . > -- You received this message because you are subscribed to the Google Groups "sage-release" group. 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