Sage Crash Report

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Mathieu Dutour

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Jan 24, 2021, 11:22:20 AMJan 24
to sage-s...@googlegroups.com
Sage_crash_report.txt

Dima Pasechnik

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Jan 24, 2021, 1:16:24 PMJan 24
to sage-support
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 <mathieu...@gmail.com> wrote:
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Mike Lee

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Mar 23, 2021, 6:27:02 PMMar 23
to sage-support
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 (0x00007ffde17a7000)
liblinbox.so.0 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../liblinbox.so.0 (0x00007fa325ba0000)
libfflas.so.1 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libfflas.so.1 (0x00007fa325ad4000)
libblas.so.3 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libblas.so.3 (0x00007fa323ae3000)
libgivaro.so.9 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libgivaro.so.9 (0x00007fa323a88000)
libflint.so.14 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libflint.so.14 (0x00007fa32320d000)
libntl.so.43 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libntl.so.43 (0x00007fa322fca000)
libgmp.so.10 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libgmp.so.10 (0x00007fa322f24000)
libstdc++.so.6 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libstdc++.so.6 (0x00007fa322daf000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fa3229fb000)
libgcc_s.so.1 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libgcc_s.so.1 (0x00007fa3229e7000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fa3225f6000)
libffpack.so.1 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libffpack.so.1 (0x00007fa3224e3000)
libgmpxx.so.4 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libgmpxx.so.4 (0x00007fa3224da000)
libmpfr.so.6 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libmpfr.so.6 (0x00007fa32245b000)
libiml.so.0 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libiml.so.0 (0x00007fa322436000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fa322217000)
libgfortran.so.5 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libgfortran.so.5 (0x00007fa322075000)
/lib64/ld-linux-x86-64.so.2 (0x00007fa325aa8000)
libgf2x.so.3 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libgf2x.so.3 (0x00007fa322062000)
libquadmath.so.0 => /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libquadmath.so.0 (0x00007fa322028000)

Mike

Sage_crash_report.txt

Dima Pasechnik

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Mar 24, 2021, 5:41:48 AMMar 24
to sage-support, Isuru Fernando
On Tue, Mar 23, 2021 at 10:27 PM Mike Lee <syml...@gmail.com> 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<char,
std::char_traits<char>, std::allocator<char> >[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.
> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/3af54436-2cb1-4a8f-ac5e-ef109602fa0en%40googlegroups.com.

Mike Lee

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Mar 24, 2021, 8:42:29 AMMar 24
to sage-s...@googlegroups.com, Isuru Fernando
I believe the following line in the output of the nm command you suggested is the corresponding symbol?

0000000000017da0 T Givaro::Integer::operator std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >() const

I've also attached the full output of the nm command as a txt file below in case it's helpful!

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output.txt

Mike Lee

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Mar 24, 2021, 10:07:20 AMMar 24
to sage-s...@googlegroups.com, Isuru Fernando
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!
conda_update_givaro.txt

Isuru Fernando

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Mar 24, 2021, 12:55:05 PMMar 24
to Mike Lee, sage-s...@googlegroups.com
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.
(You could also try doing `conda install "givaro=4.1.1=h192cbe9_1"` to get the older link.)

Isuru

Mariusz Sokolowski

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Mar 24, 2021, 3:21:20 PMMar 24
to sage-support
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

Mike Lee

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Mar 24, 2021, 3:54:49 PMMar 24
to sage-s...@googlegroups.com, Isuru Fernando
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. 

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