Re: [sage-support] Sage Crash Report
Thank you Dima and Isuru, creating a new conda environment worked! (I'm guessing you updated the givaro dependency for the conda install) And it looks like manually specifying an older version of givaro will also work, based on Mariusz's report. On Wed, Mar 24, 2021 at 3:21 PM Mariusz Sokolowski wrote: > hey, > > I had similar/same(?) problem as Mike and installing older version of > givaro (conda install "givaro=4.1.1=h192cbe9_1") fixed it. > > -M > > On Wednesday, March 24, 2021 at 12:55:05 PM UTC-4 isu...@gmail.com wrote: > >> Mike, >> >> Can you try creating a new conda environment? This is an issue with the >> latest givaro build we had and we marked it as broken. >> Details at https://github.com/conda-forge/givaro-feedstock/issues/13 >> >> (You could also try doing `conda install "givaro=4.1.1=h192cbe9_1"` to >> get the older link.) >> >> Isuru >> >> On Wed, Mar 24, 2021 at 9:07 AM Mike Lee wrote: >> >>> Not sure if this is relevant, but I get the following messages when I >>> try running 'conda update givaro' in my sage conda environment (attached). >>> I apologize for multiple messages! >>> >>> On Wed, Mar 24, 2021 at 8:42 AM Mike Lee wrote: >>> >>>> I believe the following line in the output of the nm command you >>>> suggested is the corresponding symbol? >>>> >>>> 00017da0 T Givaro::Integer::operator >>>> std::__cxx11::basic_string, >>>> std::allocator >() const >>>> >>>> I've also attached the full output of the nm command as a txt file >>>> below in case it's helpful! >>>> >>>> On Wed, Mar 24, 2021 at 5:41 AM Dima Pasechnik >>>> wrote: >>>> >>>>> On Tue, Mar 23, 2021 at 10:27 PM Mike Lee wrote: >>>>> > >>>>> > Hi, >>>>> > >>>>> > I'm facing a similar issue when I tried to install Sage through >>>>> conda (I followed the 'Setting Up' directions in >>>>> https://wiki.sagemath.org/Conda). I get the following error in my >>>>> Sage_crash_report.txt (attached) >>>>> > >>>>> > 'ImportError: >>>>> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/ >>>>> matrix_modn_sparse.cpython-39-x86_64-linux-gnu.so: undefined symbol: >>>>> _ZNK6Givaro7IntegercvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEB5cxx11Ev' >>>>> >>>>> this is, demangled: >>>>> >>>>> $ c++filt >>>>> _ZNK6Givaro7IntegercvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEB5cxx11Ev >>>>> Givaro::Integer::operator std::__cxx11::basic_string>>>> std::char_traits, std::allocator >[abi:cxx11]() const >>>>> >>>>> Can you find this in the output of >>>>> >>>>> $ nm -D --demangle >>>>> /home/msl/software/miniconda3/envs/sage/lib/libgivaro.so.9 >>>>> >>>>> Perhaps, wrong C++ standard version chosen somewhere? >>>>> >>>>> Maybe Isuru knows what's wrong there. >>>>> >>>>> > >>>>> > What could I do to fix this issue? Thank you in advance for the help! >>>>> > >>>>> > By the way, when I run 'ldd >>>>> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/ >>>>> matrix_modn_sparse.cpython-39-x86_64-linux-gnu.so ' I get the >>>>> following output: >>>>> > >>>>> > linux-vdso.so.1 (0x7ffde17a7000) >>>>> > liblinbox.so.0 => >>>>> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../liblinbox.so.0 >>>>> (0x7fa325ba) >>>>> > libfflas.so.1 => >>>>> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libfflas.so.1 >>>>> (0x7fa325ad4000) >>>>> > libblas.so.3 => >>>>> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libblas.so.3 >>>>> (0x7fa323ae3000) >>>>> > libgivaro.so.9 => >>>>> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libgivaro.so.9 >>>>> (0x7fa323a88000) >>>>> > libflint.so.14 => >>>>> /home/msl/softw
Re: [sage-support] Sage Crash Report
Not sure if this is relevant, but I get the following messages when I try running 'conda update givaro' in my sage conda environment (attached). I apologize for multiple messages! On Wed, Mar 24, 2021 at 8:42 AM Mike Lee wrote: > I believe the following line in the output of the nm command you > suggested is the corresponding symbol? > > 00017da0 T Givaro::Integer::operator > std::__cxx11::basic_string, > std::allocator >() const > > I've also attached the full output of the nm command as a txt file below > in case it's helpful! > > On Wed, Mar 24, 2021 at 5:41 AM Dima Pasechnik wrote: > >> On Tue, Mar 23, 2021 at 10:27 PM Mike Lee wrote: >> > >> > Hi, >> > >> > I'm facing a similar issue when I tried to install Sage through conda >> (I followed the 'Setting Up' directions in >> https://wiki.sagemath.org/Conda). I get the following error in my >> Sage_crash_report.txt (attached) >> > >> > 'ImportError: >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/ >> matrix_modn_sparse.cpython-39-x86_64-linux-gnu.so: undefined symbol: >> _ZNK6Givaro7IntegercvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEB5cxx11Ev' >> >> this is, demangled: >> >> $ c++filt >> _ZNK6Givaro7IntegercvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEB5cxx11Ev >> Givaro::Integer::operator std::__cxx11::basic_string> std::char_traits, std::allocator >[abi:cxx11]() const >> >> Can you find this in the output of >> >> $ nm -D --demangle >> /home/msl/software/miniconda3/envs/sage/lib/libgivaro.so.9 >> >> Perhaps, wrong C++ standard version chosen somewhere? >> >> Maybe Isuru knows what's wrong there. >> >> > >> > What could I do to fix this issue? Thank you in advance for the help! >> > >> > By the way, when I run 'ldd >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/ >> matrix_modn_sparse.cpython-39-x86_64-linux-gnu.so ' I get the following >> output: >> > >> > linux-vdso.so.1 (0x7ffde17a7000) >> > liblinbox.so.0 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../liblinbox.so.0 >> (0x7fa325ba) >> > libfflas.so.1 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libfflas.so.1 >> (0x7fa325ad4000) >> > libblas.so.3 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libblas.so.3 >> (0x7fa323ae3000) >> > libgivaro.so.9 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libgivaro.so.9 >> (0x7fa323a88000) >> > libflint.so.14 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libflint.so.14 >> (0x7fa32320d000) >> > libntl.so.43 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libntl.so.43 >> (0x7fa322fca000) >> > libgmp.so.10 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libgmp.so.10 >> (0x7fa322f24000) >> > libstdc++.so.6 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libstdc++.so.6 >> (0x7fa322daf000) >> > libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x7fa3229fb000) >> > libgcc_s.so.1 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libgcc_s.so.1 >> (0x7fa3229e7000) >> > libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x7fa3225f6000) >> > libffpack.so.1 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libffpack.so.1 >> (0x7fa3224e3000) >> > libgmpxx.so.4 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libgmpxx.so.4 >> (0x7fa3224da000) >> > libmpfr.so.6 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libmpfr.so.6 >> (0x7fa32245b000) >> > libiml.so.0 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libiml.so.0 >> (0x7fa322436000) >> > libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 >> (0x7fa322217000) >> > libgfortran.so.5 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/si
Re: [sage-support] Sage Crash Report
I believe the following line in the output of the nm command you suggested is the corresponding symbol? 00017da0 T Givaro::Integer::operator std::__cxx11::basic_string, std::allocator >() const I've also attached the full output of the nm command as a txt file below in case it's helpful! On Wed, Mar 24, 2021 at 5:41 AM Dima Pasechnik wrote: > On Tue, Mar 23, 2021 at 10:27 PM Mike Lee wrote: > > > > Hi, > > > > I'm facing a similar issue when I tried to install Sage through conda (I > followed the 'Setting Up' directions in https://wiki.sagemath.org/Conda). > I get the following error in my Sage_crash_report.txt (attached) > > > > 'ImportError: > /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/ > matrix_modn_sparse.cpython-39-x86_64-linux-gnu.so: undefined symbol: > _ZNK6Givaro7IntegercvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEB5cxx11Ev' > > this is, demangled: > > $ c++filt > _ZNK6Givaro7IntegercvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEB5cxx11Ev > Givaro::Integer::operator std::__cxx11::basic_string std::char_traits, std::allocator >[abi:cxx11]() const > > Can you find this in the output of > > $ nm -D --demangle > /home/msl/software/miniconda3/envs/sage/lib/libgivaro.so.9 > > Perhaps, wrong C++ standard version chosen somewhere? > > Maybe Isuru knows what's wrong there. > > > > > What could I do to fix this issue? Thank you in advance for the help! > > > > By the way, when I run 'ldd > /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/ > matrix_modn_sparse.cpython-39-x86_64-linux-gnu.so ' I get the following > output: > > > > linux-vdso.so.1 (0x7ffde17a7000) > > liblinbox.so.0 => > /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../liblinbox.so.0 > (0x7fa325ba) > > libfflas.so.1 => > /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libfflas.so.1 > (0x7fa325ad4000) > > libblas.so.3 => > /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libblas.so.3 > (0x7fa323ae3000) > > libgivaro.so.9 => > /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libgivaro.so.9 > (0x7fa323a88000) > > libflint.so.14 => > /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libflint.so.14 > (0x7fa32320d000) > > libntl.so.43 => > /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libntl.so.43 > (0x7fa322fca000) > > libgmp.so.10 => > /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libgmp.so.10 > (0x7fa322f24000) > > libstdc++.so.6 => > /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libstdc++.so.6 > (0x7fa322daf000) > > libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x7fa3229fb000) > > libgcc_s.so.1 => > /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libgcc_s.so.1 > (0x7fa3229e7000) > > libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x7fa3225f6000) > > libffpack.so.1 => > /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libffpack.so.1 > (0x7fa3224e3000) > > libgmpxx.so.4 => > /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libgmpxx.so.4 > (0x7fa3224da000) > > libmpfr.so.6 => > /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libmpfr.so.6 > (0x7fa32245b000) > > libiml.so.0 => > /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libiml.so.0 > (0x7fa322436000) > > libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 > (0x7fa322217000) > > libgfortran.so.5 => > /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libgfortran.so.5 > (0x7fa322075000) > > /lib64/ld-linux-x86-64.so.2 (0x7fa325aa8000) > > libgf2x.so.3 => > /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libgf2x.so.3 > (0x7fa322062000) > > libquadmath.so.0 => > /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libquadmath.so.0 > (0x7fa322028000) > > > > Mike > > > > On Sunday, January 24, 2021 at 1:16:24 PM UTC-5 dim...@gmail.com wrote: > >> > >>
Re: [sage-support] Sage Crash Report
Hi, I'm facing a similar issue when I tried to install Sage through conda (I followed the 'Setting Up' directions in https://wiki.sagemath.org/Conda). I get the following error in my Sage_crash_report.txt (attached) 'ImportError: /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/matrix_modn_sparse.cpython-39-x86_64-linux-gnu.so: undefined symbol: _ZNK6Givaro7IntegercvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEB5cxx11Ev' What could I do to fix this issue? Thank you in advance for the help! By the way, when I run 'ldd /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/matrix_modn_sparse.cpython-39-x86_64-linux-gnu.so ' I get the following output: linux-vdso.so.1 (0x7ffde17a7000) liblinbox.so.0 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../liblinbox.so.0 (0x7fa325ba) libfflas.so.1 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libfflas.so.1 (0x7fa325ad4000) libblas.so.3 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libblas.so.3 (0x7fa323ae3000) libgivaro.so.9 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libgivaro.so.9 (0x7fa323a88000) libflint.so.14 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libflint.so.14 (0x7fa32320d000) libntl.so.43 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libntl.so.43 (0x7fa322fca000) libgmp.so.10 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libgmp.so.10 (0x7fa322f24000) libstdc++.so.6 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libstdc++.so.6 (0x7fa322daf000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x7fa3229fb000) libgcc_s.so.1 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libgcc_s.so.1 (0x7fa3229e7000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x7fa3225f6000) libffpack.so.1 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libffpack.so.1 (0x7fa3224e3000) libgmpxx.so.4 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libgmpxx.so.4 (0x7fa3224da000) libmpfr.so.6 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libmpfr.so.6 (0x7fa32245b000) libiml.so.0 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libiml.so.0 (0x7fa322436000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x7fa322217000) libgfortran.so.5 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libgfortran.so.5 (0x7fa322075000) /lib64/ld-linux-x86-64.so.2 (0x7fa325aa8000) libgf2x.so.3 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libgf2x.so.3 (0x7fa322062000) libquadmath.so.0 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libquadmath.so.0 (0x7fa322028000) Mike On Sunday, January 24, 2021 at 1:16:24 PM UTC-5 dim...@gmail.com wrote: > at the bottom of the log you see > > ImportError: > /home/mathieu/opt/SageMath/local/lib/python3.8/site-packages/sage/matrix/ > matrix_modn_sparse.cpython-38-x86_64-linux-gnu.so: > undefined symbol: > > _ZNK6Givaro7IntegercvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEB5cxx11Ev > > > which is an indication that something went wrong with linking givaro. > E.g. you might be linking to a system-wide > installed givaro, but it's expected to be the one built by Sage - > whether the latter is the case can be found out in the top-level > config.log. > > What is the output of > > ldd > /home/mathieu/opt/SageMath/local/lib/python3.8/site-packages/sage/matrix/ > matrix_modn_sparse.cpython-38-x86_64-linux-gnu.so > > ? > > > On Sun, Jan 24, 2021 at 4:22 PM Mathieu Dutour > wrote: > > > > > > -- > > 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...@googlegroups.com. > > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-support/CADm_teOrk03gf8bzyUxtvt9m16wEAP3%2BOsfkzxbjSjz4VN9bKw%40mail.gmail.com > . > -- 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
