[BUG] The pass "eliminate_shape_op" causes output mismatch

[BUG] The pass "eliminate_shape_op" causes output mismatch

Issue
Running the single pass eliminate_shape_op with onnxoptimizer 0.4.2 changes numerical outputs.

Environment

• Ubuntu 20.04
• Python 3.10
• onnx==1.19.0
• onnxruntime==1.23.2
• onnxoptimizer==0.4.2(latest)

Repro steps (run from this folder)
eliminate_shape_op_repro.tar.gz

1. Create a Python environment (Python 3.10) and install dependencies:

python3 -m venv .venv
source .venv/bin/activate
pip install -U pip
pip install -r requirements.txt

2. Optimize a case with only eliminate_shape_op (writes model.opt.onnx next to model.onnx):

• python optimize_model.py --case ./case_03140_seed45116679

3. Differential test original and optimized models with the same oracle inputs (ORT graph optimization disabled; NaN pairs treated as equal):

• python diff_test.py --case ./case_03140_seed45116679

Expected
eliminate_shape_op should be semantics-preserving. Applying this pass alone should not change any output values.

Differential Test Output Details

1. case_03140_seed45116679 — mismatch; output[14] max_abs=4.022e+04 max_rel=4.022e+12, output[15] max_abs=5.190e+02 max_rel=5.120e+10; overall mismatch.
2. case_00324_seed22816775 — mismatch; output[3] max_abs=5.022e+18 max_rel=1.000e+00; overall mismatch.
3. case_03181_seed45441358 — mismatch; output[11] max_abs=3.352e+00 max_rel=6.005e-01, output[12] max_abs=5.664e+00 max_rel=4.489e+00; overall mismatch.

Case: case_03140_seed45116679 (ORT graph optimizations disabled)
	output[14]: max_abs=4.022e+04, max_rel=4.022e+12, shape=(1, 21, 24)
	output[15]: max_abs=5.190e+02, max_rel=5.120e+10, shape=(32, 21, 24)
Overall: max_abs=4.022e+04, max_rel=4.022e+12


Case: case_00324_seed22816775 (ORT graph optimizations disabled)
	output[3]: max_abs=5.022e+18, max_rel=1.000e+00, shape=(51, 1, 1, 1)
Overall: max_abs=5.022e+18, max_rel=1.000e+00


Case: case_03181_seed45441358 (ORT graph optimizations disabled)
	output[11]: max_abs=3.352e+00, max_rel=6.005e-01, shape=(1, 135, 17)
	output[12]: max_abs=5.664e+00, max_rel=4.489e+00, shape=(57, 45, 17)
Overall: max_abs=5.664e+00, max_rel=4.489e+00

Attachments

• requirements.txt
• optimize_model.py
• diff_test.py (runs original and optimized with same oracle inputs; ORT graph optimizations disabled; NaN pairs treated equal)
• run_optimized_model.py (executes optimized model with oracle inputs)
• case_03140_seed45116679/, case_00324_seed22816775/, case_03181_seed45441358/ (original models, optimized models, and oracle inputs)

Start by following the attached requirements.txt setup and run optimize_model.py followed by diff_test.py for the three listed cases, with ORT graph optimizations disabled. Then trace the eliminate_shape_op pass implementation against the original and optimized models. Done means applying only this pass produces matching outputs for the provided differential tests.