Centos 7.3: 'import sage.all' fails with 'ImportError: /lib64/libz.so.1: version `ZLIB_1.2.9' not found (required by /sage-9.8/local/lib/libpng16.so.16)' #35636
Description
Is there an existing issue for this?
- I have searched the existing issues for a bug report that matches the one I want to file, without success.
Did you read the documentation and troubleshoot guide?
- I have read the documentation and troubleshoot guide
Environment
- **OS**: CentOS Linux release 7.3.1611 (Core)
- **Sage Version**: 9.8 (similar behaviour was observed with Sage 9.5 and Sage 9.6)Steps To Reproduce
from a clean Sage 9.8 source directory
./configure
make build
./sage
sage: import sage.all
Config log
Package logs
No package failed to install.
Additional Information
The error is visible when trying to run ./sage:
$ ./sage
┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 9.8, Release Date: 2023-02-11 │
│ Using Python 3.9.13. Type "help()" for help. │
└────────────────────────────────────────────────────────────────────┘
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Warning: sage.all is not available; this is a limited REPL. ┃
┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛
sage: import sage.all
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
Cell In [1], line 1
----> 1 import sage.all
File /sage-9.8/src/sage/all.py:168
166 from sage.modules.all import *
167 from sage.monoids.all import *
--> 168 from sage.algebras.all import *
169 from sage.modular.all import *
170 from sage.sat.all import *
File /sage-9.8/src/sage/algebras/all.py:21
5 #*****************************************************************************
6 # Copyright (C) 2005 William Stein <wstein@gmail.com>
7 #
(...)
17 # http://www.gnu.org/licenses/
18 #*****************************************************************************
19 from sage.misc.lazy_import import lazy_import
---> 21 import sage.algebras.catalog as algebras
23 from .quatalg.all import *
24 from .steenrod.all import *
File /sage-9.8/src/sage/algebras/catalog.py:84
1 r"""
2 Catalog of Algebras
3
(...)
80 <sage.algebras.yokonuma_hecke_algebra.YokonumaHeckeAlgebra>`
81 """
83 from sage.algebras.free_algebra import FreeAlgebra as Free
---> 84 from sage.algebras.quatalg.quaternion_algebra import QuaternionAlgebra as Quaternion
85 from sage.algebras.steenrod.steenrod_algebra import SteenrodAlgebra as Steenrod
86 from sage.algebras.finite_dimensional_algebras.finite_dimensional_algebra import FiniteDimensionalAlgebra as FiniteDimensional
File /sage-9.8/src/sage/algebras/quatalg/quaternion_algebra.py:68
61 from operator import itemgetter
63 from .quaternion_algebra_element import (
64 QuaternionAlgebraElement_abstract,
65 QuaternionAlgebraElement_generic,
66 QuaternionAlgebraElement_rational_field,
67 QuaternionAlgebraElement_number_field)
---> 68 from . import quaternion_algebra_cython
70 from sage.modular.modsym.p1list import P1List
72 from sage.misc.cachefunc import cached_method
File /sage-9.8/src/sage/algebras/quatalg/quaternion_algebra_cython.pyx:1, in init sage.algebras.quatalg.quaternion_algebra_cython()
----> 1 # distutils: language = c++
2 # distutils: libraries = gmp m NTL_LIBRARIES
3 # distutils: extra_compile_args = NTL_CFLAGS
File /sage-9.8/src/sage/matrix/matrix_integer_dense.pyx:1, in init sage.matrix.matrix_integer_dense()
----> 1 # -*- coding: utf-8 -*-
2 # distutils: extra_compile_args = NTL_CFLAGS M4RI_CFLAGS
3 # distutils: libraries = iml NTL_LIBRARIES gmp m CBLAS_LIBRARIES
ImportError: /lib64/libz.so.1: version `ZLIB_1.2.9' not found (required by /sage-9.8/local/lib/libpng16.so.16)From what I understand from config.log, sage needed to install libz because the one on the machine was not new enough (it did not have function inflateValidate as required by build/pkgs/zlib/spkg-configure.m4):
$ nm -gD /lib64/libz.so | grep -i inflateV
#no output
It also needed to install libpng (even if it is available on the machine).
The error looks very similar to #31670, but the issue seems to indicate that it was fixed in 9.5.beta8. I try the same steps with sage 9.5 and sage 9.6 and it failed for both (the error message is the same but the failure happens directly when ./sage is run, without the need to do import all)
Here are some extract of objdump of the different libraries:
$ objdump -x local/lib/libpng16.so
...
Dynamic Section:
NEEDED libz.so.1
NEEDED libm.so.6
NEEDED libc.so.6
SONAME libpng16.so.16
RPATH /sage-9.8/local/lib
...
Version definitions:
1 0x01 0x08cf6c26 libpng16.so.16
2 0x00 0x052a4c70 PNG16_0
Version References:
required from libm.so.6:
0x09691a75 0x00 06 GLIBC_2.2.5
required from libz.so.1:
0x0827e5c9 0x00 05 ZLIB_1.2.9
0x07e5ce34 0x00 04 ZLIB_1.2.3.4
required from libc.so.6:
0x06969194 0x00 07 GLIBC_2.14
0x09691a75 0x00 03 GLIBC_2.2.5
...
$ objdump -x local/lib/libz.so
...
Dynamic Section:
NEEDED libc.so.6
SONAME libz.so.1
RPATH /sage-9.8/local/lib
...
Version definitions:
1 0x01 0x09d5f4e1 libz.so.1
2 0x00 0x0827e5c0 ZLIB_1.2.0
3 0x00 0x07e5cb32 ZLIB_1.2.0.2
ZLIB_1.2.0
4 0x00 0x07e5cb38 ZLIB_1.2.0.8
ZLIB_1.2.0.2
5 0x00 0x0827e5c2 ZLIB_1.2.2
ZLIB_1.2.0.8
6 0x00 0x07e5cd33 ZLIB_1.2.2.3
ZLIB_1.2.2
7 0x00 0x07e5cd34 ZLIB_1.2.2.4
ZLIB_1.2.2.3
8 0x00 0x07e5ce33 ZLIB_1.2.3.3
ZLIB_1.2.2.4
9 0x00 0x07e5ce34 ZLIB_1.2.3.4
ZLIB_1.2.3.3
10 0x00 0x07e5ce35 ZLIB_1.2.3.5
ZLIB_1.2.3.4
11 0x00 0x07e5d031 ZLIB_1.2.5.1
ZLIB_1.2.3.5
12 0x00 0x07e5d032 ZLIB_1.2.5.2
ZLIB_1.2.5.1
13 0x00 0x07e5c231 ZLIB_1.2.7.1
ZLIB_1.2.5.2
14 0x00 0x0827e5c9 ZLIB_1.2.9
ZLIB_1.2.7.1
...
$ objdump -x /lib64/libz.so
...
Dynamic Section:
NEEDED libc.so.6
SONAME libz.so.1
...
Version definitions:
1 0x01 0x09d5f4e1 libz.so.1
2 0x00 0x0827e5c0 ZLIB_1.2.0
3 0x00 0x07e5cb32 ZLIB_1.2.0.2
ZLIB_1.2.0
4 0x00 0x07e5cb38 ZLIB_1.2.0.8
ZLIB_1.2.0.2
5 0x00 0x0827e5c2 ZLIB_1.2.2
ZLIB_1.2.0.8
6 0x00 0x07e5cd33 ZLIB_1.2.2.3
ZLIB_1.2.2
7 0x00 0x07e5cd34 ZLIB_1.2.2.4
ZLIB_1.2.2.3
8 0x00 0x07e5ce33 ZLIB_1.2.3.3
ZLIB_1.2.2.4
9 0x00 0x07e5ce34 ZLIB_1.2.3.4
ZLIB_1.2.3.3
10 0x00 0x07e5ce35 ZLIB_1.2.3.5
ZLIB_1.2.3.4
11 0x00 0x07e5d031 ZLIB_1.2.5.1
ZLIB_1.2.3.5
12 0x00 0x07e5d032 ZLIB_1.2.5.2
ZLIB_1.2.5.1
...
$ ldd local/lib/libpng16.so
linux-vdso.so.1 => (0x00007ffff83b3000)
libz.so.1 => /sage-9.8/local/lib/libz.so.1 (0x00007fd4f9234000)
libm.so.6 => /lib64/libm.so.6 (0x00007fd4f8f1a000)
libc.so.6 => /lib64/libc.so.6 (0x00007fd4f8b59000)
/lib64/ld-linux-x86-64.so.2 (0x00007fd4f967f000)