pywraplp broken on Linux void musl

[voidbert]

What version of OR-Tools and what language are you using?
Version: 9.14 (ortools-9.14.6206-cp313-cp313-musllinux_1_2_x86_64.whl)
Language: Python

Which solver are you using (e.g. CP-SAT, Routing Solver, GLOP, BOP, Gurobi)
N/A

What operating system (Linux, Windows, ...) and version?
Void Linux x86_64-musl

What did you do?
Steps to reproduce the behavior:

1. pip install --ortools==9.14.6206
2. python
3. >>> from ortools.linear_solver import pywraplp

What did you expect to see

Successful module importation

What did you see instead?

The following protobuf error:

WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
E0000 00:00:1752892068.348568   24377 descriptor_database.cc:595] Invalid file descriptor data passed to EncodedDescriptorDatabase::Add().
F0000 00:00:1752892068.348612   24377 descriptor.cc:2519] Check failed: GeneratedDatabase()->Add(encoded_file_descriptor, size)
*** Check failure stack trace: ***
Aborted

Anything else we should know about your project / environment

• The problem doesn't occur when ortools==9.12.4544 is used
• The problem doesn't occur on a glibc Void Linux chroot (ortools-9.14.6206-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl)

[lperron]

looks like you have an incompatible protobuf version installed.
Can you check the python and the c++ version installed ?

[voidbert]

Python 3.13.5, libprotobuf 25.2 (Python package: protobuf 6.31.1), libstdc++ 14.2.1+20250405_2

Yes, the system's libprotobuf is from early 2024. I realized that, on the glibc chroot, it was not installed system-wide, so maybe pip installed it from PyPI? The versions of Python's protobuf package are the same on both musl and glibc.

[Mizux]

Dev Note

Alpine Linux

% docker run --rm --init -it alpine:edge
$ apk add python3 py3-pip
$ python -m pip install --user --break-system-packages "ortools==9.14.*"
$ python -c "from ortools.linear_solver import pywraplp"
WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
E0000 00:00:1753079504.798693      42 descriptor_database.cc:595] Invalid file descriptor data passed to EncodedDescriptorDatabase::Add().
F0000 00:00:1753079504.798756      42 descriptor.cc:2519] Check failed: GeneratedDatabase()->Add(encoded_file_descriptor, size) 
*** Check failure stack trace: ***
Aborted (core dumped)

After investigation

$ apk add binutils
$ objdump -p ~/.local/lib/python3.12/site-packages/ortools/.libs/libortools.so.9
$ ldd ~/.local/lib/python3.12/site-packages/ortools/.libs/libortools.so.9

Pypa MuslLinux

FYI we have used the pypa provided musl image to built it:

or-tools/tools/docker/python/amd64/musllinux.Dockerfile

Line 1 in 0d60e8a

FROM quay.io/pypa/musllinux_1_2_x86_64:latest AS env

Same error inside quay.io/pypa/musllinux_1_2_x86_64:latest ...

% docker run --rm --init -it quay.io/pypa/musllinux_1_2_x86_64:latest 
$ python --version
Python 3.12.11
$ apk add py3-pip
$ python -m pip install --user --break-system-packages "ortools==9.14.*"
$ python -c "from ortools.linear_solver import pywraplp"
WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
E0000 00:00:1753080273.303628      24 descriptor_database.cc:595] Invalid file descriptor data passed to EncodedDescriptorDatabase::Add().
F0000 00:00:1753080273.303712      24 descriptor.cc:2519] Check failed: GeneratedDatabase()->Add(encoded_file_descriptor, size) 
*** Check failure stack trace: ***

Rebuild (WiP)

Try to rebuild a musllinux package using branch v99bugfix HEAD

% cd tools/docker
% make python_amd64_musllinux_export
...

note: to save time I've only build the cp312-cp312 package (default python use by pypa vm)

diff --git a/tools/docker/Makefile b/tools/docker/Makefile
index 70c88c92db..8dafa7fd78 100644
--- a/tools/docker/Makefile
+++ b/tools/docker/Makefile
@@ -204,7 +204,8 @@ cache/python: | cache
        -mkdir $@
 
 ## MANYLINUX ##
-PYTHON_VERSIONS := 39 310 311 312 313
+PYTHON_VERSIONS := 312
+# 39 310 311 312 313
 
 export/python/manylinux: | export/python
        -mkdir -p $@

% docker run --rm --init -it -v $(pwd)/export/python:/plop quay.io/pypa/musllinux_1_2_x86_64:latest 
$ apk add py3-pip
$ cd /plop
$ pip install --user --break-system-packages ortools-9.14.6232-cp312-cp312-musllinux_1_2_x86_64.whl 
$ python -c "from ortools.linear_solver import pywraplp"
WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
E0000 00:00:1753086623.426216      22 descriptor_database.cc:595] Invalid file descriptor data passed to EncodedDescriptorDatabase::Add().
F0000 00:00:1753086623.426283      22 descriptor.cc:2519] Check failed: GeneratedDatabase()->Add(encoded_file_descriptor, size) 
*** Check failure stack trace: ***

On the contrary this work:

% docker run --rm --init -it -v $(pwd)/export/python:/plop quay.io/pypa/musllinux_1_2_x86_64:latest 
$ apk add py3-pip
$ cd /plop
$ pip install --user --break-system-packages ortools-9.14.6232-cp312-cp312-linux_x86_64.whl 
$ python -c "from ortools.linear_solver import pywraplp"
# no error....

Pretty sure the auditwheel repair ,which transform ortools-9.14.6232-cp312-cp312-linux_x86_64.whl into the
ortools-9.14.6232-cp312-cp312-musllinux_1_2_x86_64.whl messup the wheel

or-tools/tools/docker/python/build-musllinux.sh

Lines 141 to 147 in 0d60e8a

	# Check all generated wheel packages
	pushd "${BUILD_DIR}/python/dist"
	for FILE in *.whl; do
	# if no files found do nothing
	[[ -e "$FILE" ]] || continue
	auditwheel show "$FILE" || true
	auditwheel -v repair --plat "musllinux_1_2_$PLATFORM" "$FILE" -w "$export_root"

EDIT: also work on alpine:edge

%docker run --rm --init -it -v $(pwd)/export/python:/plop alpine:edge                              
$ apk add py3-pip
$ python -m pip install --user --break-system-package /plop/ortools-9.14.6232-cp312-cp312-linux_x86_64.whl
$  python -c "from ortools.linear_solver import pywraplp"

[Mizux]

A potential fix would be to upload the not repaired wheel but hack the metadata by hand...
need to diff both wheels and see what's change...