On Fri, 5 Mar 2021, 16:30 Dima Pasechnik, <dimp...@gmail.com> wrote: > > > On Fri, 5 Mar 2021, 16:17 'Hackenberg, Klaus' via sage-support, < > sage-support@googlegroups.com> wrote: > >> High, >> >> adding /usr/local/Gcc/lib64 to $LD_LIBRARY_PATH helps compiling >> gfan-0.6.2.p1. >> >> Next problem is with r-3.6.3: >> The bzip2 from RHEL6 seem to be to old: >> >> [root@dlp762 Sage]# bzip2 --version >> bzip2, a block-sorting file compressor. Version 1.0.5, 10-Dec-2007. >> >> Is there any option to use another version (built within sage)? >> > > make bzip2 >
this will build sage's version of bzip2 Then run make again, to build r, etc > > > >> I include the error log. >> >> Regards, Klaus Hackenberg >> >> -- >> Klaus Hackenberg >> IT-Systeme und Software-Integration >> IT.SERVICES >> Ruhr-Universität Bochum | 44780 Bochum >> fon: +49 234 32 23485 >> http://www.it-services.rub.de/ >> >> >> -----Ursprüngliche Nachricht----- >> Von: sage-support@googlegroups.com <sage-support@googlegroups.com> Im >> Auftrag von Dima Pasechnik >> Gesendet: Freitag, 5. März 2021 15:58 >> An: sage-support <sage-support@googlegroups.com> >> Betreff: Re: [sage-support] problem compiling sage 9.2 on RHEL 6 >> >> On Fri, Mar 5, 2021 at 2:30 PM 'Hackenberg, Klaus' via sage-support < >> sage-support@googlegroups.com> wrote: >> > >> > High, >> > >> > I find the following >> > >> > [lsf@dlp762 Sage]$ echo $PATH >> > /usr/local/Gcc/bin:/usr/lib64/qt-3.3/bin:/usr/local/sbin:/usr/local/bi >> > n:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin >> > [lsf@dlp762 Sage]$ >> > [lsf@dlp762 Sage]$ g++ -v >> > Using built-in specs. >> > COLLECT_GCC=g++ >> > COLLECT_LTO_WRAPPER=/net/dlp762/share/application-software/Gcc/bin/../ >> > libexec/gcc/x86_64-pc-linux-gnu/9.2.0/lto-wrapper >> > Target: x86_64-pc-linux-gnu >> > Configured with: ../gcc-9.2.0/configure --disable-multilib >> > --exec-prefix=/usr/local/Gcc --prefix=/usr/local/Gcc Thread model: >> > posix gcc version 9.2.0 (GCC) >> > [lsf@dlp762 Sage]$ >> > [lsf@dlp762 Sage]$ find /usr/local/Gcc/ -name libstdc++.so.6 >> > /usr/local/Gcc/lib64/libstdc++.so.6 >> > /usr/local/Gcc/gcc-build/stage1-x86_64-pc-linux-gnu/libstdc++-v3/src/. >> > libs/libstdc++.so.6 >> > /usr/local/Gcc/gcc-build/x86_64-pc-linux-gnu/libstdc++-v3/src/.libs/li >> > bstdc++.so.6 >> > /usr/local/Gcc/gcc-build/prev-x86_64-pc-linux-gnu/libstdc++-v3/src/.li >> > bs/libstdc++.so.6 >> > [lsf@dlp762 Sage]$ >> >> try >> >> export LD_LIBRARY_PATH=/usr/local/Gcc/lib64:$LD_LIBRARY_PATH >> >> and then run make >> >> >> >> >> > >> > Regards, Klaus Hackenberg >> > >> > -- >> > Klaus Hackenberg >> > IT-Systeme und Software-Integration >> > IT.SERVICES >> > Ruhr-Universität Bochum | 44780 Bochum >> > fon: +49 234 32 23485 >> > http://www.it-services.rub.de/ >> > >> > >> > -----Ursprüngliche Nachricht----- >> > Von: sage-support@googlegroups.com <sage-support@googlegroups.com> Im >> > Auftrag von Dima Pasechnik >> > Gesendet: Freitag, 5. März 2021 15:08 >> > An: sage-support <sage-support@googlegroups.com> >> > Betreff: Re: [sage-support] problem compiling sage 9.2 on RHEL 6 >> > >> > On Fri, Mar 5, 2021 at 12:55 PM 'Hackenberg, Klaus' via sage-support < >> sage-support@googlegroups.com> wrote: >> > > >> > > High, >> > > >> > > when using "./configure --with-mp=gmp" things look much better. >> > > >> > > But now I get an error for gfan-0.6.2.p1. >> > > I include the error log. >> > it says >> > >> > ./gfan: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found >> > (required by ./gfan) >> > ./gfan: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found >> > (required by ./gfan) >> > ./gfan: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.26' not found >> > (required by ./gfan) >> > ./gfan: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found >> > (required by ./gfan) >> > ./gfan: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.22' not found >> > (required by ./gfan) >> > ./gfan: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found >> > (required by ./gfan) >> > >> > Something is not quite right with your C++ toolchain. As your gcc/g++ >> > data says --prefix=/usr/local/Gcc one would expect libstdc++.so.6 to >> > be in /usr/local/Gcc, and not in /usr/lib64/ (where you probably have >> > old RHEL 6 gcc/g++ things) >> > >> > No idea what exactly. What is the output of >> > >> > g++ -v >> > >> > Do you have libstdc++.so.6 in /usr/local/ at all? >> > >> > >> > >> > > >> > > Regards, Klaus Hackenberg >> > > >> > > -- >> > > Klaus Hackenberg >> > > IT-Systeme und Software-Integration >> > > IT.SERVICES >> > > Ruhr-Universität Bochum | 44780 Bochum >> > > fon: +49 234 32 23485 >> > > http://www.it-services.rub.de/ >> > > >> > > >> > > -----Ursprüngliche Nachricht----- >> > > Von: sage-support@googlegroups.com <sage-support@googlegroups.com> >> > > Im Auftrag von Dima Pasechnik >> > > Gesendet: Freitag, 5. März 2021 12:45 >> > > An: sage-support <sage-support@googlegroups.com> >> > > Betreff: Re: [sage-support] problem compiling sage 9.2 on RHEL 6 >> > > >> > > On Fri, Mar 5, 2021 at 11:24 AM 'Hackenberg, Klaus' via sage-support < >> sage-support@googlegroups.com> wrote: >> > > > >> > > > High, >> > > > >> > > > I did the following >> > > > >> > > > [lsf@dlp762 Sage]$ cd sage-9.2 >> > > > [lsf@dlp762 sage-9.2]$ ./configure --with-gmp=gmp > >> > > > /tmp/configure.log 2>&1 >> > > >> > > and so you once again mixed up --with-gmp= and --with-mp= >> > > >> > > It should be --with-mp=gmp >> > > >> > > >> > > > [lsf@dlp762 sage-9.2]$ make mpir-clean > /tmp/mpir.clean.log 2>&1 >> > > > >> > > > and include the logs. >> > > > >> > > > Regards, Klaus Hackenberg >> > > > >> > > > -- >> > > > Klaus Hackenberg >> > > > IT-Systeme und Software-Integration IT.SERVICES Ruhr-Universität >> > > > Bochum | 44780 Bochum >> > > > fon: +49 234 32 23485 >> > > > http://www.it-services.rub.de/ >> > > > >> > > > >> > > > -----Ursprüngliche Nachricht----- >> > > > Von: sage-support@googlegroups.com <sage-support@googlegroups.com> >> > > > Im Auftrag von Dima Pasechnik >> > > > Gesendet: Freitag, 5. März 2021 11:31 >> > > > An: sage-support <sage-support@googlegroups.com> >> > > > Betreff: Re: [sage-support] problem compiling sage 9.2 on RHEL 6 >> > > > >> > > > On Fri, Mar 5, 2021 at 10:02 AM 'Hackenberg, Klaus' via >> sage-support <sage-support@googlegroups.com> wrote: >> > > > > >> > > > > High, >> > > > > >> > > > > I installed python 3.9.2 in /usr/local/Python and added it to >> > > > > PATH variable >> > > > > >> > > > > [lsf@dlp762 root]$ echo $PATH >> > > > > /usr/local/Python/bin:/usr/lib64/qt-3.3/bin:/usr/local/sbin:/usr >> > > > > /l oc al /bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin >> > > > > [lsf@dlp762 root]$ python --version Python 3.9.2 >> > > > > >> > > > > Now symmetrica-3.0.1. compiles successfull. >> > > > > But ppl-1.2 no longer compiles !!! >> > > > > So I seem to be in a deadlock . >> > > > > >> > > > It's the same misconfiguration of mp/gmp stuff as before. >> > > > Without knowning what exactly you did after changing PATH, it's >> hard to tell. >> > > > >> > > > please post the top level config.log (the one in the same >> > > > directory as the main ./configure script) >> > > > - the ppl problems come from the top level misconfiguration. >> > > > >> > > > >> > > > >> > > > > I include ppl error logs. >> > > > > >> > > > > Regards, Klaus Hackenberg >> > > > > >> > > > > -- >> > > > > Klaus Hackenberg >> > > > > IT-Systeme und Software-Integration IT.SERVICES Ruhr-Universität >> > > > > Bochum | 44780 Bochum >> > > > > fon: +49 234 32 23485 >> > > > > http://www.it-services.rub.de/ >> > > > > >> > > > > >> > > > > -----Ursprüngliche Nachricht----- >> > > > > Von: sage-support@googlegroups.com >> > > > > <sage-support@googlegroups.com> Im Auftrag von Dima Pasechnik >> > > > > Gesendet: Donnerstag, 4. März 2021 18:53 >> > > > > An: sage-support <sage-support@googlegroups.com> >> > > > > Betreff: Re: [sage-support] problem compiling sage 9.2 on RHEL 6 >> > > > > >> > > > > On Thu, Mar 4, 2021 at 5:08 PM 'Hackenberg, Klaus' via >> sage-support <sage-support@googlegroups.com> wrote: >> > > > > > >> > > > > > High, >> > > > > > >> > > > > > >> > > > > > >> > > > > > on my RHEL6 server I see >> > > > > > >> > > > > > >> > > > > > >> > > > > > [root@dlp762 Sage]# python --version >> > > > > > >> > > > > > Python 2.6.6 >> > > > > > >> > > > > > >> > > > > > >> > > > > > But the server has installed xz packages >> > > > > > >> > > > > > >> > > > > > >> > > > > > [root@dlp762 Sage]# rpm -qa --last|grep xz >> > > > > > >> > > > > > xz-devel-4.999.9-0.5.beta.20091007git.el6.x86_64 Tue Jun 18 >> > > > > > 11:06:45 >> > > > > > 2019 >> > > > > > >> > > > > > xz-lzma-compat-4.999.9-0.5.beta.20091007git.el6.x86_64 Fri Sep >> > > > > > 18 >> > > > > > 09:39:37 2015 >> > > > > > >> > > > > > xz-4.999.9-0.5.beta.20091007git.el6.x86_64 Fri Sep 18 >> 09:39:26 2015 >> > > > > > >> > > > > > xz-libs-4.999.9-0.5.beta.20091007git.el6.x86_64 Fri Sep 18 >> > > > > > 09:39:03 >> > > > > > 2015 >> > > > > > >> > > > > > >> > > > > > >> > > > > > Is it possible to use the buildin xz ? >> > > > > >> > > > > Do you have xz application installed and accepted by Sage (it >> > > > > should be visible in config.log)? If so, something is breaking >> > > > > in >> > > > > https://github.com/sagemath/sage/blob/master/build/sage_bootstra >> > > > > p/ >> > > > > un >> > > > > co >> > > > > mpress/tar_file.py#L161 >> > > > > >> > > > > Mind you, python 2.6.6 has been released about 12 years ago, not >> > > > > sure this code, from 2016, was ever tested on 2.6.6 (perhaps on >> > > > > less buggy >> > > > > 2.6.7...) >> > > > > >> > > > > You may try installing pyenv with newer python and run Sage >> > > > > installation from there. See >> > > > > https://gist.github.com/ysaotome/7956676 >> > > > > (you ought to replace 2.7.6 with 3.9.1 there, to escape the >> > > > > Python2 hell completely) >> > > > > >> > > > > >> > > > > > >> > > > > > >> > > > > > >> > > > > > Regards, Klaus Hackenberg >> > > > > > >> > > > > > >> > > > > > >> > > > > > -- >> > > > > > >> > > > > > Klaus Hackenberg >> > > > > > >> > > > > > IT-Systeme und Software-Integration >> > > > > > >> > > > > > IT.SERVICES >> > > > > > >> > > > > > Ruhr-Universität Bochum | 44780 Bochum >> > > > > > >> > > > > > fon: +49 234 32 23485 >> > > > > > >> > > > > > http://www.it-services.rub.de/ >> > > > > > >> > > > > > >> > > > > > >> > > > > > Von: sage-support@googlegroups.com >> > > > > > <sage-support@googlegroups.com> Im Auftrag von Dima Pasechnik >> > > > > > Gesendet: Donnerstag, 4. März 2021 17:18 >> > > > > > An: sage-support <sage-support@googlegroups.com> >> > > > > > Betreff: Re: [sage-support] problem compiling sage 9.2 on RHEL >> > > > > > 6 >> > > > > > >> > > > > > >> > > > > > >> > > > > > your system python cannot uncompress .xz files... :( >> > > > > > >> > > > > > >> > > > > > >> > > > > > how old is it? >> > > > > > >> > > > > > >> > > > > > >> > > > > > can you install systemwide python2 to be python 2.7? >> > > > > > >> > > > > > >> > > > > > >> > > > > > On Thu, 4 Mar 2021, 16:04 'Hackenberg, Klaus' via sage-support, >> <sage-support@googlegroups.com> wrote: >> > > > > > >> > > > > > High, >> > > > > > >> > > > > > I startet in a fresh directory sage-9.2 (from sage-9.2.tag.gz) >> > > > > > using the command " make mpir-clean" and got >> > > > > > >> > > > > > ============================================================== >> > > > > > == >> > > > > > == >> > > > > > == >> > > > > > == >> > > > > > === >> > > > > > [lsf@dlp762 sage-9.2]$ make mpir-clean make >> > > > > > build/make/Makefile --stop >> > > > > > make[1]: Entering directory >> `/net/dlp762/share/application-software/Sage/sage-9.2' >> > > > > > rm -f config.log >> > > > > > mkdir -p logs/pkgs >> > > > > > ln -s logs/pkgs/config.log config.log >> > > > > > ************************************************************** >> > > > > > ** >> > > > > > ** >> > > > > > ** >> > > > > > ** >> > > > > > ****** >> > > > > > error: Sage source tree is unconfigured. Please run >> "./configure" first. >> > > > > > note: Type "./configure --help" to see the available >> configuration options. >> > > > > > ************************************************************** >> > > > > > ** >> > > > > > ** >> > > > > > ** >> > > > > > ** >> > > > > > ****** >> > > > > > make[1]: *** [build/make/Makefile] Error 1 >> > > > > > make[1]: Leaving directory >> `/net/dlp762/share/application-software/Sage/sage-9.2' >> > > > > > make: *** [mpir-clean] Error 2 >> > > > > > [lsf@dlp762 sage-9.2]$ >> > > > > > ============================================================== >> > > > > > == >> > > > > > == >> > > > > > == >> > > > > > == >> > > > > > === >> > > > > > >> > > > > > I then used >> > > > > > >> > > > > > ./configure --with-mp=gmp >> > > > > > make mpir-clean >> > > > > > make -j4 >> > > > > > >> > > > > > and ppl-1.2 compiled ! >> > > > > > >> > > > > > But now I get a new error with symmetrica-3.0.1. >> > > > > > I attach the error log file >> > > > > > >> > > > > > Regards, Klaus Hackenberg >> > > > > > >> > > > > > -- >> > > > > > Klaus Hackenberg >> > > > > > IT-Systeme und Software-Integration IT.SERVICES >> > > > > > Ruhr-Universität Bochum | 44780 Bochum >> > > > > > fon: +49 234 32 23485 >> > > > > > http://www.it-services.rub.de/ >> > > > > > >> > > > > > >> > > > > > -----Ursprüngliche Nachricht----- >> > > > > > Von: sage-support@googlegroups.com >> > > > > > <sage-support@googlegroups.com> Im Auftrag von Dima Pasechnik >> > > > > > Gesendet: Donnerstag, 4. März 2021 15:57 >> > > > > > An: sage-support <sage-support@googlegroups.com> >> > > > > > Betreff: Re: [sage-support] problem compiling sage 9.2 on RHEL >> > > > > > 6 >> > > > > > >> > > > > > Please post the top-level config.log, then we'll see more >> details about GMP. >> > > > > > >> > > > > > In Sage 9.2, if you do ./configure without arguments, Sage is >> building a GMP-compatible MPIR, not "real" GMP. >> > > > > > (Perhaps MPIR is broken now beyond repair, and shoud not be >> > > > > > used on RHEL 6,I don't know) We're changing with in the coming >> > > > > > 9.3, see >> > > > > > https://trac.sagemath.org/ticket/30752 >> > > > > > Meanwhile please do >> > > > > > >> > > > > > make mpir-clean >> > > > > > ./configure --with-mp=gmp >> > > > > > make -j4 >> > > > > > >> > > > > > >> > > > > > On Thu, Mar 4, 2021 at 2:06 PM 'Hackenberg, Klaus' via >> sage-support <sage-support@googlegroups.com> wrote: >> > > > > > > >> > > > > > > High, >> > > > > > > >> > > > > > > I startet in a fresh directory sage-9.2 (from >> sage-9.2.tag.gz) >> > > > > > > using the commands >> > > > > > > >> > > > > > > ./configure >> > > > > > > make -j4 >> > > > > > > >> > > > > > > and ran into the same error. >> > > > > > > >> > > > > > > gmp binaries are build automatically >> > > > > > > >> > > > > > > ls -lrt sage-9.2/local/lib/*gmp* -rwxr-xr-x 1 lsf lsf >> > > > > > > 3342817 Mar 4 12:35 sage-9.2/local/lib/libgmp.so.23.0.3 >> > > > > > > lrwxrwxrwx 1 lsf lsf 16 Mar 4 12:35 >> sage-9.2/local/lib/libgmp.so.23 -> libgmp.so.23.0.3 >> > > > > > > lrwxrwxrwx 1 lsf lsf 16 Mar 4 12:35 >> sage-9.2/local/lib/libgmp.so -> libgmp.so.23.0.3 >> > > > > > > -rwxr-xr-x 1 lsf lsf 318950 Mar 4 12:36 >> sage-9.2/local/lib/libgmpxx.so.8.4.3 >> > > > > > > lrwxrwxrwx 1 lsf lsf 17 Mar 4 12:36 >> sage-9.2/local/lib/libgmpxx.so.8 -> libgmpxx.so.8.4.3 >> > > > > > > lrwxrwxrwx 1 lsf lsf 17 Mar 4 12:36 >> sage-9.2/local/lib/libgmpxx.so -> libgmpxx.so.8.4.3 >> > > > > > > -rw-r--r-- 1 lsf lsf 6804714 Mar 4 12:36 >> > > > > > > sage-9.2/local/lib/libgmp.a >> > > > > > > -rw-r--r-- 1 lsf lsf 796188 Mar 4 12:36 >> > > > > > > sage-9.2/local/lib/libgmpxx.a -rwxr-xr-x 1 lsf lsf 955210 >> Mar 4 12:43 sage-9.2/local/lib/libcddgmp.so.0.0.0 >> > > > > > > lrwxrwxrwx 1 lsf lsf 18 Mar 4 12:43 >> sage-9.2/local/lib/libcddgmp.so.0 -> libcddgmp.so.0.0.0 >> > > > > > > lrwxrwxrwx 1 lsf lsf 18 Mar 4 12:43 >> sage-9.2/local/lib/libcddgmp.so -> libcddgmp.so.0.0.0 >> > > > > > > -rw-r--r-- 1 lsf lsf 1532644 Mar 4 12:43 >> > > > > > > sage-9.2/local/lib/libcddgmp.a >> > > > > > > >> > > > > > > I attach the error log file. >> > > > > > > >> > > > > > > Regards, Klaus Hackenberg >> > > > > > > >> > > > > > > -- >> > > > > > > Klaus Hackenberg >> > > > > > > IT-Systeme und Software-Integration IT.SERVICES >> > > > > > > Ruhr-Universität Bochum | 44780 Bochum >> > > > > > > fon: +49 234 32 23485 >> > > > > > > http://www.it-services.rub.de/ >> > > > > > > >> > > > > > > >> > > > > > > -----Ursprüngliche Nachricht----- >> > > > > > > Von: sage-support@googlegroups.com >> > > > > > > <sage-support@googlegroups.com> Im Auftrag von Dima >> > > > > > > Pasechnik >> > > > > > > Gesendet: Mittwoch, 3. März 2021 18:28 >> > > > > > > An: sage-support <sage-support@googlegroups.com> >> > > > > > > Betreff: Re: [sage-support] problem compiling sage 9.2 on >> > > > > > > RHEL >> > > > > > > 6 >> > > > > > > >> > > > > > > On Wed, Mar 3, 2021 at 5:15 PM 'Klaus Hackenberg' via >> sage-support <sage-support@googlegroups.com> wrote: >> > > > > > > > >> > > > > > > > High, >> > > > > > > > I tried to compile sage 9.2 on a server running RHEL 6. >> > > > > > > > I use gcc 9.2.0 to compile and the following commands >> > > > > > > > >> > > > > > > > ./configure --with-gmp=gmp >> > > > > > > might be in error. >> > > > > > > >> > > > > > > What did you mean to achieve by '--with-gmp=gmp' ? By default >> Sage will look for a systemwide GMP installation and try to use it (else it >> will build its own) But Sage needs GMP version 6.1, at least. Most probably >> what you have on the 10-years old RHEL 6 is still GMP version 4, so it >> won't fly. >> > > > > > > >> > > > > > > You probably want to force building GMP rather than much >> iffier MPIR, so you'd probably need '--with-mp=gmp' in this case. >> > > > > > > >> > > > > > > >> > > > > > > >> > > > > > > > make -j4 >> > > > > > > > >> > > > > > > > ppl-1.2 fails to compile whith the attached error log file. >> > > > > > > > Do you have any idea what's going wrong and how to fix it? >> > > > > > > > Regards, Klaus Hackenberg >> > > > > > > > >> > > > > > > > -- >> > > > > > > > You received this message because you are subscribed to the >> Google Groups "sage-support" group. >> > > > > > > > To unsubscribe from this group and stop receiving emails >> from it, send an email to sage-support+unsubscr...@googlegroups.com. >> > > > > > > > To view this discussion on the web visit >> 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