XGBoost Fails With AssertionError When Specifying Custom Fold Column

[exalate-issue-sync]

When attempting to run an XGBoost model, both through AutoML and independently, while specifying a custom fold column the build process fails with an AssertionError. Testing the same custom fold column on other algorithms (i.e. GBM) does not result in this error.

Error:
{code:java}

OSError Traceback (most recent call last)
in
1 from h2o.estimators import H2OXGBoostEstimator
2 xg_model = H2OXGBoostEstimator(seed=1234, stopping_metric='rmse')
----> 3 xg_model.train(x=features, y='reactivity', training_frame=model_train, validation_frame=model_test, weights_column=weights_column, fold_column=fold_column)
/opt/conda/lib/python3.7/site-packages/h2o/estimators/estimator_base.py in train(self, x, y, training_frame, offset_column, fold_column, weights_column, validation_frame, max_runtime_secs, ignored_columns, model_id, verbose)
113 validation_frame=validation_frame, max_runtime_secs=max_runtime_secs,
114 ignored_columns=ignored_columns, model_id=model_id, verbose=verbose)
--> 115 self._train(parms, verbose=verbose)
116
117 def train_segments(self, x=None, y=None, training_frame=None, offset_column=None, fold_column=None,
/opt/conda/lib/python3.7/site-packages/h2o/estimators/estimator_base.py in _train(self, parms, verbose)
205 return
206
--> 207 job.poll(poll_updates=self._print_model_scoring_history if verbose else None)
208 model_json = h2o.api("GET /%d/Models/%s" % (rest_ver, job.dest_key))["models"][0]
209 self._resolve_model(job.dest_key, model_json)
/opt/conda/lib/python3.7/site-packages/h2o/job.py in poll(self, poll_updates)
76 if (isinstance(self.job, dict)) and ("stacktrace" in list(self.job)):
77 raise EnvironmentError("Job with key {} failed with an exception: {}\nstacktrace: "
---> 78 "\n{}".format(self.job_key, self.exception, self.job["stacktrace"]))
79 else:
80 raise EnvironmentError("Job with key %s failed with an exception: %s" % (self.job_key, self.exception))
OSError: Job with key $03017f00000132d4ffffffff$_b410f1873cf50b6f36a9ad411a4344a5 failed with an exception: java.lang.AssertionError
stacktrace:
java.lang.AssertionError
at hex.tree.xgboost.matrix.DenseMatrixFactory$WriteDenseChunkFun.map(DenseMatrixFactory.java:187)
at water.LocalMR.compute2(LocalMR.java:84)
at water.H2O$H2OCountedCompleter.compute(H2O.java:1563)
at jsr166y.CountedCompleter.exec(CountedCompleter.java:468)
at jsr166y.ForkJoinTask.doExec(ForkJoinTask.java:263)
at jsr166y.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:974)
at jsr166y.ForkJoinPool.runWorker(ForkJoinPool.java:1477)
at jsr166y.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:104)
{code}

Dataset: [https://www.kaggle.com/c/stanford-covid-vaccine/data|https://www.kaggle.com/c/stanford-covid-vaccine/data]

Code:
{code:python}

Code used to create custom fold column keeping entire RNA sequences together to avoid leakage

folds = [k for k in range(1, 8) for i in range(15436)]
formatted_train['folds'] = folds

Convert to H2OFrame

h2f = h2o.H2OFrame(formatted_train)

Then split data and run XGBoost to see the error.

{code}

[exalate-issue-sync]

Travis Couture commented: Code used when encountering error.

[^competition-model (1).zip]

Note: Remove XGBoost from the excluded algorithms to encounter the error.

[h2o-ops]

JIRA Issue Migration Info

Jira Issue: PUBDEV-7819
Assignee: Pavel Pscheidl
Reporter: Travis Couture
State: Closed
Fix Version: 3.32.1.1
Attachments: Available (Count: 2)
Development PRs: Available

Linked PRs from JIRA

#5038

Attachments From Jira

Attachment Name: assert_err.py
Attached By: Jan Sterba
File Link:https://h2o-3-jira-github-migration.s3.amazonaws.com/PUBDEV-7819/assert_err.py

Attachment Name: competition-model (1).zip
Attached By: Travis Couture
File Link:https://h2o-3-jira-github-migration.s3.amazonaws.com/PUBDEV-7819/competition-model (1).zip