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6.7 Gradient boosting and XGBoost

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Installing XGBoost on Mac

Some students reported problems with installing XGBoost on Mac.

When you run pip install xgboost and when you try to import xgboost in a script you might get an warning or error stating that libomp has not been installed and to run brew install libomp in the terminal.

Be careful: this will install a version of libomp that does not work with xgboost!

This shows in one of two ways after attempting to run xgb.DMatrix(X_train, label=y_train, feature_names=features):

  • python script: Segmentation fault: 11
  • jupyter notebook: Never finished running, and notebook is unresponsive until kernal restart. However confusingly it sometimes works

Conda

If you use anaconda or miniconda, try installing xgboost with conda.

First, uninstall xgboost with pip (if you already installed it previously with pip):

pip uninstall xgboost

Then re-install it with conda:

conda install -c conda-forge xgboost

It will also install the required version of libomp.

Without conda

If you don't use conda, you can manualy install a different version of libopm that works well with XGBoost.

The versions of libomp with this problem are 12.x.x and 13.x.x, however issue has a workaround xgboost issue #7039 installing the older libomp 11 using the terminal. In the terminal run brew list --version libomp, to determine the current version of libomp if any. Then if you have a problematic version run brew unlink libomp.

To install the old version of libomp run:

brew update
wget https://raw.githubusercontent.com/chenrui333/homebrew-core/0094d1513ce9e2e85e07443b8b5930ad298aad91/Formula/libomp.rb
brew install --build-from-source ./libomp.rb

and then run

brew list --version libomp

to check that everything worked, it should now state libomp 11.1.0, and your code should now be able to run.

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