[ARROW-5886] [Python][Packaging] Manylinux1/2010 compliance issue with libz

• Type: Bug
• Status: Resolved
• Priority: Major
• Resolution: Fixed
• Affects Version/s: 0.14.0
• Fix Version/s: 0.14.1, 0.15.0
• Component/s: Packaging, Python
• Labels: pull-request-available
• External issue URL: https://github.com/apache/arrow/issues/22301
• Assignee: Krisztian Szucs
• Reporter: Krisztian Szucs
• Created: 09/Jul/19 14:30
• Updated: 11/Jan/23 07:43
• Resolved: 12/Jul/19 18:09

Description

So we statically link liblz4 in the manylinux1 wheels

# ldd pyarrow-manylinux1/libarrow.so.14 | grep z
        libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007fc28cef4000)

but dynamically in the manylinux2010 wheels

# ldd pyarrow-manylinux2010/libarrow.so.14 | grep z
        liblz4.so.1 => not found  (already deleted to reproduce the issue)
        libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f56f7440000)

this what this PR resolves.

What I'm finding strange, that auditwheel seems to bundle libz for manylinux1:

# ls -lah pyarrow-manylinux1/*z*so.*
-rwxr-xr-x 1 root root 115K Jun 29 00:14 pyarrow-manylinux1/libz-7f57503f.so.1.2.11

while ldd still uses the system libz:

# ldd pyarrow-manylinux1/libarrow.so.14 | grep z
        libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f91fcf3f000)

For manylinux2010 we also have liblz4:

#  ls -lah pyarrow-manylinux2010/*z*so.*
-rwxr-xr-x 1 root root 191K Jun 28 23:38 pyarrow-manylinux2010/liblz4-8cb8bdde.so.1.8.3
-rwxr-xr-x 1 root root 115K Jun 28 23:38 pyarrow-manylinux2010/libz-c69b9943.so.1.2.11

and ldd similarly tries to load the system libs:

# ldd pyarrow-manylinux2010/libarrow.so.14 | grep z
        liblz4.so.1 => not found
        libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007fd72764e000)

Inspecting manylinux1 with `LD_DEBUG=files,libs ldd libarrow.so.14` it seems like to search the right path, but cannot find the hashed version of libz `libz-7f57503f.so.1.2.11`

       463:     file=libz.so.1 [0];  needed by ./libarrow.so.14 [0]
       463:     find library=libz.so.1 [0]; searching
       463:      search path=/tmp/pyarrow-manylinux1/.          (RPATH from file ./libarrow.so.14)
       463:       trying file=/tmp/pyarrow-manylinux1/./libz.so.1
       463:      search cache=/etc/ld.so.cache
       463:       trying file=/lib/x86_64-linux-gnu/libz.so.1

There is no `libz.so.1` just `libz-7f57503f.so.1.2.11`.

Similarly for manylinux2010 and libz:

       470:     file=libz.so.1 [0];  needed by ./libarrow.so.14 [0]
       470:     find library=libz.so.1 [0]; searching
       470:      search path=/tmp/pyarrow-manylinux2010/.               (RPATH from file ./libarrow.so.14)
       470:       trying file=/tmp/pyarrow-manylinux2010/./libz.so.1
       470:      search cache=/etc/ld.so.cache
       470:       trying file=/lib/x86_64-linux-gnu/libz.so.1

for liblz4 (again, I've deleted the system one):

       470:     file=liblz4.so.1 [0];  needed by ./libarrow.so.14 [0]
       470:     find library=liblz4.so.1 [0]; searching
       470:      search path=/tmp/pyarrow-manylinux2010/.               (RPATH from file ./libarrow.so.14)
       470:       trying file=/tmp/pyarrow-manylinux2010/./liblz4.so.1
       470:      search cache=/etc/ld.so.cache
       470:      search path=/lib/x86_64-linux-gnu/tls/x86_64:/lib/x86_64-linux-gnu/tls:/lib/x86_64-linux-gnu/x86_64:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu/tls/x86_64:/usr/lib/x86_64-linux-gnu/tls:/usr/lib/x86_64-linux-gnu/x86_6$
:/usr/lib/x86_64-linux-gnu:/lib/tls/x86_64:/lib/tls:/lib/x86_64:/lib:/usr/lib/tls/x86_64:/usr/lib/tls:/usr/lib/x86_64:/usr/lib          (system search path)

There are no `libz.so.1` nor `liblz4.so.1`, just `libz-c69b9943.so.1.2.11` and `liblz4-8cb8bdde.so.1.8.3`

According to https://www.python.org/dev/peps/pep-0571/ `liblz4` nor `libz` are part of the whitelist, and while these are bundled with the wheel, seemingly cannot be found - perhaps because of the hash in the library name?

I've tried to inspect the wheels with `auditwheel show` with version `2` and `1.10`, both says the following:

# auditwheel show pyarrow-0.14.0-cp37-cp37m-manylinux2010_x86_64.whl

pyarrow-0.14.0-cp37-cp37m-manylinux2010_x86_64.whl is consistent with
the following platform tag: "linux_x86_64".

The wheel references external versioned symbols in these system-
provided shared libraries: libgcc_s.so.1 with versions {'GCC_3.3',
'GCC_3.4', 'GCC_3.0'}, libpthread.so.0 with versions {'GLIBC_2.3.3',
'GLIBC_2.12', 'GLIBC_2.2.5', 'GLIBC_2.3.2'}, libc.so.6 with versions
{'GLIBC_2.4', 'GLIBC_2.6', 'GLIBC_2.2.5', 'GLIBC_2.7', 'GLIBC_2.3.4',
'GLIBC_2.3.2', 'GLIBC_2.3'}, libstdc++.so.6 with versions
{'CXXABI_1.3', 'GLIBCXX_3.4.10', 'GLIBCXX_3.4.9', 'GLIBCXX_3.4.11',
'GLIBCXX_3.4.5', 'GLIBCXX_3.4', 'CXXABI_1.3.2', 'CXXABI_1.3.3'},
librt.so.1 with versions {'GLIBC_2.2.5'}, libm.so.6 with versions
{'GLIBC_2.2.5'}, libdl.so.2 with versions {'GLIBC_2.2.5'}, libz.so.1
with versions {'ZLIB_1.2.0'}

This constrains the platform tag to "manylinux2010_x86_64". In order
to achieve a more compatible tag, you would need to recompile a new
wheel from source on a system with earlier versions of these
libraries, such as a recent manylinux image.

# auditwheel show pyarrow-0.14.0-cp37-cp37m-manylinux1_x86_64.whl

pyarrow-0.14.0-cp37-cp37m-manylinux1_x86_64.whl is consistent with the
following platform tag: "linux_x86_64".

The wheel references external versioned symbols in these system-
provided shared libraries: libgcc_s.so.1 with versions {'GCC_3.4',
'GCC_3.0', 'GCC_3.3'}, libc.so.6 with versions {'GLIBC_2.3',
'GLIBC_2.2.5', 'GLIBC_2.3.4', 'GLIBC_2.4', 'GLIBC_2.3.2'},
libstdc++.so.6 with versions {'CXXABI_1.3', 'GLIBCXX_3.4.5',
'GLIBCXX_3.4'}, librt.so.1 with versions {'GLIBC_2.2.5'}, libm.so.6
with versions {'GLIBC_2.2.5'}, libpthread.so.0 with versions
{'GLIBC_2.3.3', 'GLIBC_2.3.2', 'GLIBC_2.2.5'}, libdl.so.2 with
versions {'GLIBC_2.2.5'}, libz.so.1 with versions {'ZLIB_1.2.0'}

The following external shared libraries are required by the wheel:
{
    "libc.so.6": "/lib/x86_64-linux-gnu/libc-2.24.so",
    "libcrypt.so.1": "/lib/x86_64-linux-gnu/libcrypt-2.24.so",
    "libdl.so.2": "/lib/x86_64-linux-gnu/libdl-2.24.so",
    "libgcc_s.so.1": "/lib/x86_64-linux-gnu/libgcc_s.so.1",
    "libm.so.6": "/lib/x86_64-linux-gnu/libm-2.24.so",
    "libnsl.so.1": "/lib/x86_64-linux-gnu/libnsl-2.24.so",
    "libpthread.so.0": "/lib/x86_64-linux-gnu/libpthread-2.24.so",
    "librt.so.1": "/lib/x86_64-linux-gnu/librt-2.24.so",
    "libstdc++.so.6": "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.22",
    "libutil.so.1": "/lib/x86_64-linux-gnu/libutil-2.24.so",
    "libz.so.1": "/lib/x86_64-linux-gnu/libz.so.1.2.8"
}

In order to achieve the tag platform tag "manylinux2010_x86_64" the
following shared library dependencies will need to be eliminated:

libz.so.1

In order to achieve the tag platform tag "manylinux1_x86_64" the
following shared library dependencies will need to be eliminated:

libz.so.1

I think there are more todo left with the wheels. IMO the manylinux1 wheels are not compliant because of `libz` and the manylinux2010 wheels are not compliant because of both `libz` and `liblz4` (but incorrectly reported by auditwheel?).

We also need to ensure to run auditwheel show on the produced wheels in the manylinux-test script https://github.com/apache/arrow/blob/master/dev/tasks/python-wheels/manylinux-test.sh

Issue Links

• links to: GitHub Pull Request #4834