Wrong zlib library might be loaded
jdemeyer opened this issue · 12 comments
jdemeyer commented
After the zlib upgrade, I cannot no longer run Sage under plain Python:
./sage --python
Python 2.7.13 (default, May 31 2017, 17:36:06)
[GCC 4.9.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import sage.all
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/opt/sage/sage-git/local/lib/python2.7/site-packages/sage/all.py", line 98, in <module>
from sage.rings.all import *
File "/opt/sage/sage-git/local/lib/python2.7/site-packages/sage/rings/all.py", line 54, in <module>
from .number_field.all import *
File "/opt/sage/sage-git/local/lib/python2.7/site-packages/sage/rings/number_field/all.py", line 9, in <module>
from .totallyreal import enumerate_totallyreal_fields_prim
File "sage/rings/number_field/totallyreal_data.pxd", line 12, in init sage.rings.number_field.totallyreal (/opt/sage/sage-git/src/build/cythonized/sage/rings/number_field/totallyreal.c:12702)
File "sage/rings/number_field/totallyreal_data.pyx", line 41, in init sage.rings.number_field.totallyreal_data (/opt/sage/sage-git/src/build/cythonized/sage/rings/number_field/totallyreal_data.c:13440)
File "/opt/sage/sage-git/local/lib/python2.7/site-packages/sage/rings/polynomial/polynomial_ring_constructor.py", line 462, in PolynomialRing
R = _single_variate(base_ring, name, sparse, implementation)
File "/opt/sage/sage-git/local/lib/python2.7/site-packages/sage/rings/polynomial/polynomial_ring_constructor.py", line 540, in _single_variate
R = m.PolynomialRing_integral_domain(base_ring, name, sparse, implementation)
File "/opt/sage/sage-git/local/lib/python2.7/site-packages/sage/rings/polynomial/polynomial_ring.py", line 1603, in __init__
sparse=sparse, element_class=element_class, category=category)
File "/opt/sage/sage-git/local/lib/python2.7/site-packages/sage/rings/polynomial/polynomial_ring.py", line 1474, in __init__
sparse=sparse, element_class=element_class, category=category)
File "/opt/sage/sage-git/local/lib/python2.7/site-packages/sage/rings/polynomial/polynomial_ring.py", line 290, in __init__
from sage.matrix.matrix_space import MatrixSpace
File "/opt/sage/sage-git/local/lib/python2.7/site-packages/sage/matrix/matrix_space.py", line 48, in <module>
from . import matrix_modn_sparse
File "sage/matrix/matrix_integer_dense.pxd", line 10, in init sage.matrix.matrix_modn_sparse (/opt/sage/sage-git/src/build/cythonized/sage/matrix/matrix_modn_sparse.c:15164)
File "sage/matrix/matrix_mod2_dense.pxd", line 4, in init sage.matrix.matrix_integer_dense (/opt/sage/sage-git/src/build/cythonized/sage/matrix/matrix_integer_dense.c:56343)
ImportError: /lib64/libz.so.1: version `ZLIB_1.2.9' not found (required by /opt/sage/sage-git/local/lib/libpng16.so.16)
This is because there is some kind of race condition: certain system libraries (OpenSSL for example) link against /lib64/libz.so.1 while Sage components link against the Sage-built libz.
In turns out that the first libz library which is loaded "wins": that one will be used by anything linking against libz. When starting IPython, the correct libz library is loaded because some IPython component uses libz. When running plain Python, this is not the case and the wrong libz is loaded. The easiest fix is to explicitly import libz when Sage starts up.
Component: build
Author: Jeroen Demeyer
Branch/Commit: d59afe3
Reviewer: Erik Bray
Issue created by migration from https://trac.sagemath.org/ticket/23122
jdemeyer commented
Description changed:
---
+++
@@ -35,4 +35,4 @@
This is because there is some kind of race condition: certain system libraries link against `/lib64/libz.so.1` while Sage components link against the Sage-built libz.
-In turns out that the first zlib library which is loaded "wins", so we need to make sure that this is the Sage-built libz.
+In turns out that the first libz library which is loaded "wins", so we need to make sure that this is the Sage-built libz. When starting IPython, the correct libz library is loaded because some IPython component uses libz. When running plain Python, this is not the case and the wrong libz is loaded. The easiest fix is to explicitly `import libz` when Sage starts up.jdemeyer commented
Description changed:
---
+++
@@ -35,4 +35,4 @@
This is because there is some kind of race condition: certain system libraries link against `/lib64/libz.so.1` while Sage components link against the Sage-built libz.
-In turns out that the first libz library which is loaded "wins", so we need to make sure that this is the Sage-built libz. When starting IPython, the correct libz library is loaded because some IPython component uses libz. When running plain Python, this is not the case and the wrong libz is loaded. The easiest fix is to explicitly `import libz` when Sage starts up.
+In turns out that the first libz library which is loaded "wins": that one will be used by anything linking against `libz`. When starting IPython, the correct libz library is loaded because some IPython component uses libz. When running plain Python, this is not the case and the wrong libz is loaded. The easiest fix is to explicitly `import libz` when Sage starts up.vbraun commented
comment:3
Who is requiring the system libz? Maybe run with LD_DEBUG=files sage -python
jdemeyer commented
comment:4
Replying to @vbraun:
Who is requiring the system libz?
$ ldd local/lib/python2.7/lib-dynload/_ssl.so
linux-vdso.so.1 (0x00007fffaa1ff000)
libssl.so.1.0.0 => /usr/lib64/libssl.so.1.0.0 (0x00007ff017e96000)
libcrypto.so.1.0.0 => /usr/lib64/libcrypto.so.1.0.0 (0x00007ff017a52000)
libpython2.7.so.1.0 => /opt/sage/sage-git/local/lib/libpython2.7.so.1.0 (0x00007ff01762c000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007ff017410000)
libc.so.6 => /lib64/libc.so.6 (0x00007ff017076000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007ff016e72000)
libz.so.1 => /lib64/libz.so.1 (0x00007ff016c5c000)
libutil.so.1 => /lib64/libutil.so.1 (0x00007ff016a58000)
libm.so.6 => /lib64/libm.so.6 (0x00007ff016753000)
/lib64/ld-linux-x86-64.so.2 (0x00007ff01832a000)
jdemeyer commented
Description changed:
---
+++
@@ -33,6 +33,6 @@
ImportError: /lib64/libz.so.1: version `ZLIB_1.2.9' not found (required by /opt/sage/sage-git/local/lib/libpng16.so.16)
```
-This is because there is some kind of race condition: certain system libraries link against `/lib64/libz.so.1` while Sage components link against the Sage-built libz.
+This is because there is some kind of race condition: certain system libraries (OpenSSL for example) link against `/lib64/libz.so.1` while Sage components link against the Sage-built libz.
In turns out that the first libz library which is loaded "wins": that one will be used by anything linking against `libz`. When starting IPython, the correct libz library is loaded because some IPython component uses libz. When running plain Python, this is not the case and the wrong libz is loaded. The easiest fix is to explicitly `import libz` when Sage starts up.jdemeyer commented
embray commented
Reviewer: Erik Bray
embray commented
comment:7
I think this is fine. I've run into this problem before, for example, with libxml.
vbraun commented
comment:8
Hmm strange, I get
$ ldd local/lib/python2.7/lib-dynload/_ssl.so
linux-vdso.so.1 (0x00007ffd963e3000)
libssl.so.10 => /lib64/libssl.so.10 (0x00007f9162479000)
libcrypto.so.10 => /lib64/libcrypto.so.10 (0x00007f9162018000)
libpython2.7.so.1.0 => /home/vbraun/Code/sage.git/local/lib/libpython2.7.so.1.0 (0x00007f9161bfd000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f91619df000)
libc.so.6 => /lib64/libc.so.6 (0x00007f9161619000)
libgssapi_krb5.so.2 => /lib64/libgssapi_krb5.so.2 (0x00007f91613ca000)
libkrb5.so.3 => /lib64/libkrb5.so.3 (0x00007f91610e4000)
libcom_err.so.2 => /lib64/libcom_err.so.2 (0x00007f9160ee0000)
libk5crypto.so.3 => /lib64/libk5crypto.so.3 (0x00007f9160caf000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f9160aab000)
libz.so.1 => /home/vbraun/Code/sage.git/local/lib/libz.so.1 (0x00007f9160891000)
libc.so.6 => /lib/libc.so.6 (0xf71dc000)
libkrb5support.so.0 => /lib/libkrb5support.so.0 (0xf71cd000)
libkeyutils.so.1 => /lib/libkeyutils.so.1 (0xf71c6000)
libpthread.so.0 => /lib/libpthread.so.0 (0xf71a9000)
/lib/ld-linux.so.2 (0x56570000)
libselinux.so.1 => /lib/libselinux.so.1 (0xf7182000)
libpcre.so.1 => /lib/libpcre.so.1 (0xf710b000)
vbraun commented
Changed branch from u/jdemeyer/wrong_zlib_library_might_be_loaded to d59afe3