numpy.dtype Size Changed Binary Incompatibility Error

Problem Statement

When calling Python modules from MATLAB or other execution contexts, you may encounter the following error:

ValueError: numpy.dtype size changed, may indicate binary incompatibility. 
Expected 96 from C header, got 88 from PyObject

This error typically occurs when:

• Using Python 3.9 or later
• Upgraded to NumPy 2.0.0 recently
• Working with libraries that depend on NumPy's C API extensions (spaCy, Pandas, scikit-learn, etc.)
• Running in environments that cache imported modules (MATLAB, Jupyter, Google Colab)

The core issue is binary incompatibility between NumPy 2.0.0 and older versions. NumPy 2.0 introduced breaking changes to its internal C data structures that break backward compatibility with packages built against earlier versions.

Recommended Solution

Downgrade NumPy to 1.26.x

Install a compatible NumPy version:

pip install numpy==1.26.4

Pin the requirement in your project to prevent upgrades:

# requirements.txt
numpy==1.26.4
spacy>=3.0  # your other dependencies

Full Reinstallation Process

1. Uninstall existing incompatible version:

pip uninstall -y numpy

2. Install compatible version:

pip install numpy==1.26.4

3. Force-reinstall dependent packages:

pip install --force-reinstall pandas spacy

4. Restart your execution environment (CRITICAL)
   • MATLAB: Close and reopen session
   • Google Colab: Runtime → Restart Runtime
   • Local scripts: Close/reopen terminals

Environment-Specific Notes

MATLAB Users

Must restart MATLAB completely after NumPy downgrade:

% After reinstalling NumPy in Python
exit;  % Close MATLAB
% Then restart MATLAB session

Google Colab Users

Always restart runtime after downgrading dependencies:

# After !pip install numpy==1.26.4
# Use Runtime → Restart Runtime menu
# DO NOT attempt to continue without restart

Alternative Solutions

Upgrade to pandas 2.2.0+ (requires NumPy 2.0+)

If feasible in your environment:

pip install pandas>=2.2.0

Complete Package Reinstallation

For stubborn cases, remove all NumPy files:

site_packages=$(python -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())")
rm -rf "$site_packages"/numpy*
pip install numpy==1.26.4

Explanation of the Error

Technical Cause

The error indicates a size mismatch in NumPy's internal dtype structure:

• Version 1.x used 96-byte dtype structure
• Version 2.x uses 88-byte structure
• C extensions built with 1.x headers fail when loaded with 2.x runtime

Why Downgrade Works

Most scientific Python packages (as of mid-2024):

• Declare loose NumPy dependencies (numpy>=1.21.0)
• Are pre-built against NumPy 1.x C API
• Break when NumPy 2.x loads due to ABI changes
• Require explicit upgrades to support NumPy 2.x

Compatibility Timeline

Package	Min Version for NumPy 2.x	Release Date
pandas	2.2.0+	Feb 2025
scikit-learn	Not yet compatible	Future
spaCy/thinc	Not yet compatible	Future

Long-Term Solution

WARNING

Do NOT upgrade to NumPy 2.x until ALL dependencies:

1. Explicitly announce 2.x support
2. Release new compatible binaries
3. Pin compatible versions in requirements

As dependencies evolve:

# Future update command
pip install pandas>=2.2.0 numpy>=2.0.0

Summary of Fixes

Method	Command	Environment Restart	Long-Term Stability
RECOMMENDED SOLUTION	pip install numpy==1.26.4	Required	High
pandas upgrade (NuPy 2.x compatible)	pip install pandas>=2.2.0	Required	Medium
Nuclear reinstall	rm -rf numpy* && pip install numpy==1.26.4	Required	High

Always verify fix after restart:

import numpy
print(numpy.__version__)  # Should show 1.26.X