Created
April 14, 2020 05:49
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optgbm_multinode_rdb_error.log
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| [I 2020-04-14 14:44:15,580] Using an existing study with name 'digits_optgbm' instead of creating a new one. | |
| [I 2020-04-14 14:44:15,596] Searching the best hyperparameters... | |
| [LightGBM] [Warning] feature_fraction is set=0.1, colsample_bytree=1.0 will be ignored. Current value: feature_fraction=0.1 | |
| [LightGBM] [Warning] bagging_freq is set=10, subsample_freq=0 will be ignored. Current value: bagging_freq=10 | |
| [LightGBM] [Warning] lambda_l1 is set=6.0670460192270264e-05, reg_alpha=0.0 will be ignored. Current value: lambda_l1=6.0670460192270264e-05 | |
| [LightGBM] [Warning] lambda_l2 is set=0.06434253899747878, reg_lambda=0.0 will be ignored. Current value: lambda_l2=0.06434253899747878 | |
| [LightGBM] [Warning] bagging_fraction is set=0.7, subsample=1.0 will be ignored. Current value: bagging_fraction=0.7 | |
| [LightGBM] [Warning] min_data_in_leaf is set=64, min_child_samples=20 will be ignored. Current value: min_data_in_leaf=64 | |
| [W 2020-04-14 14:44:17,804] Setting status of trial#7 as TrialState.FAIL because of the following error: DataError('(pymysql.err.DataError) (1406, "Data too long for column \'value_json\' at row 1")') | |
| Traceback (most recent call last): | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1244, in _execute_context | |
| cursor, statement, parameters, context | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 552, in do_execute | |
| cursor.execute(statement, parameters) | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/cursors.py", line 170, in execute | |
| result = self._query(query) | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/cursors.py", line 328, in _query | |
| conn.query(q) | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/connections.py", line 517, in query | |
| self._affected_rows = self._read_query_result(unbuffered=unbuffered) | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/connections.py", line 732, in _read_query_result | |
| result.read() | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/connections.py", line 1075, in read | |
| first_packet = self.connection._read_packet() | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/connections.py", line 684, in _read_packet | |
| packet.check_error() | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/protocol.py", line 220, in check_error | |
| err.raise_mysql_exception(self._data) | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/err.py", line 109, in raise_mysql_exception | |
| raise errorclass(errno, errval) | |
| pymysql.err.DataError: (1406, "Data too long for column 'value_json' at row 1") | |
| The above exception was the direct cause of the following exception: | |
| Traceback (most recent call last): | |
| File "/home/smly/gitws/optuna/optuna/study.py", line 677, in _run_trial | |
| result = func(trial) | |
| File "/home/smly/gitws/optuna/optuna/integration/lightgbm_tuner/sklearn.py", line 318, in __call__ | |
| trial.study.set_user_attr("representations", representations) | |
| File "/home/smly/gitws/optuna/optuna/study.py", line 389, in set_user_attr | |
| self._storage.set_study_user_attr(self._study_id, key, value) | |
| File "/home/smly/gitws/optuna/optuna/storages/rdb/storage.py", line 226, in set_study_user_attr | |
| self._commit_with_integrity_check(session) | |
| File "/home/smly/gitws/optuna/optuna/storages/rdb/storage.py", line 875, in _commit_with_integrity_check | |
| session.commit() | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 1026, in commit | |
| self.transaction.commit() | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 493, in commit | |
| self._prepare_impl() | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 472, in _prepare_impl | |
| self.session.flush() | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2451, in flush | |
| self._flush(objects) | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2589, in _flush | |
| transaction.rollback(_capture_exception=True) | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/util/langhelpers.py", line 68, in __exit__ | |
| compat.reraise(exc_type, exc_value, exc_tb) | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 129, in reraise | |
| raise value | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2549, in _flush | |
| flush_context.execute() | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/unitofwork.py", line 422, in execute | |
| rec.execute(self) | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/unitofwork.py", line 589, in execute | |
| uow, | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/persistence.py", line 245, in save_obj | |
| insert, | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/persistence.py", line 1120, in _emit_insert_statements | |
| statement, params | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 988, in execute | |
| return meth(self, multiparams, params) | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/sql/elements.py", line 287, in _execute_on_connection | |
| return connection._execute_clauseelement(self, multiparams, params) | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1107, in _execute_clauseelement | |
| distilled_params, | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1248, in _execute_context | |
| e, statement, parameters, cursor, context | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1466, in _handle_dbapi_exception | |
| util.raise_from_cause(sqlalchemy_exception, exc_info) | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 383, in raise_from_cause | |
| reraise(type(exception), exception, tb=exc_tb, cause=cause) | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 128, in reraise | |
| raise value.with_traceback(tb) | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1244, in _execute_context | |
| cursor, statement, parameters, context | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 552, in do_execute | |
| cursor.execute(statement, parameters) | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/cursors.py", line 170, in execute | |
| result = self._query(query) | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/cursors.py", line 328, in _query | |
| conn.query(q) | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/connections.py", line 517, in query | |
| self._affected_rows = self._read_query_result(unbuffered=unbuffered) | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/connections.py", line 732, in _read_query_result | |
| result.read() | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/connections.py", line 1075, in read | |
| first_packet = self.connection._read_packet() | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/connections.py", line 684, in _read_packet | |
| packet.check_error() | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/protocol.py", line 220, in check_error | |
| err.raise_mysql_exception(self._data) | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/err.py", line 109, in raise_mysql_exception | |
| raise errorclass(errno, errval) | |
| sqlalchemy.exc.DataError: (pymysql.err.DataError) (1406, "Data too long for column 'value_json' at row 1") | |
| [SQL: INSERT INTO study_user_attributes (study_id, `key`, value_json) VALUES (%(study_id)s, %(key)s, %(value_json)s)] | |
| [parameters: {'study_id': 5, 'key': 'representations', 'value_json': '["tree\\nversion=v2\\nnum_class=10\\nnum_tree_per_iteration=10\\nlabel_index=0\\nmax_feature_idx=63\\nobjective=multiclass num_class:10\\nfeature_nam ... (4070901 characters truncated) ... t_filename: ]\\n[machines: ]\\n[gpu_platform_id: -1]\\n[gpu_device_id: -1]\\n[gpu_use_dp: 0]\\n\\nend of parameters\\n\\npandas_categorical:null\\n"]'}] | |
| (Background on this error at: http://sqlalche.me/e/9h9h) | |
| Traceback (most recent call last): | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1244, in _execute_context | |
| cursor, statement, parameters, context | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 552, in do_execute | |
| cursor.execute(statement, parameters) | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/cursors.py", line 170, in execute | |
| result = self._query(query) | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/cursors.py", line 328, in _query | |
| conn.query(q) | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/connections.py", line 517, in query | |
| self._affected_rows = self._read_query_result(unbuffered=unbuffered) | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/connections.py", line 732, in _read_query_result | |
| result.read() | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/connections.py", line 1075, in read | |
| first_packet = self.connection._read_packet() | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/connections.py", line 684, in _read_packet | |
| packet.check_error() | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/protocol.py", line 220, in check_error | |
| err.raise_mysql_exception(self._data) | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/err.py", line 109, in raise_mysql_exception | |
| raise errorclass(errno, errval) | |
| pymysql.err.DataError: (1406, "Data too long for column 'value_json' at row 1") | |
| The above exception was the direct cause of the following exception: | |
| Traceback (most recent call last): | |
| File "/home/smly/gitws/optuna/optuna/study.py", line 677, in _run_trial | |
| result = func(trial) | |
| File "/home/smly/gitws/optuna/optuna/integration/lightgbm_tuner/sklearn.py", line 318, in __call__ | |
| trial.study.set_user_attr("representations", representations) | |
| File "/home/smly/gitws/optuna/optuna/study.py", line 389, in set_user_attr | |
| self._storage.set_study_user_attr(self._study_id, key, value) | |
| File "/home/smly/gitws/optuna/optuna/storages/rdb/storage.py", line 226, in set_study_user_attr | |
| self._commit_with_integrity_check(session) | |
| File "/home/smly/gitws/optuna/optuna/storages/rdb/storage.py", line 875, in _commit_with_integrity_check | |
| session.commit() | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 1026, in commit | |
| self.transaction.commit() | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 493, in commit | |
| self._prepare_impl() | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 472, in _prepare_impl | |
| self.session.flush() | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2451, in flush | |
| self._flush(objects) | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2589, in _flush | |
| transaction.rollback(_capture_exception=True) | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/util/langhelpers.py", line 68, in __exit__ | |
| compat.reraise(exc_type, exc_value, exc_tb) | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 129, in reraise | |
| raise value | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2549, in _flush | |
| flush_context.execute() | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/unitofwork.py", line 422, in execute | |
| rec.execute(self) | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/unitofwork.py", line 589, in execute | |
| uow, | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/persistence.py", line 245, in save_obj | |
| insert, | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/persistence.py", line 1120, in _emit_insert_statements | |
| statement, params | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 988, in execute | |
| return meth(self, multiparams, params) | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/sql/elements.py", line 287, in _execute_on_connection | |
| return connection._execute_clauseelement(self, multiparams, params) | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1107, in _execute_clauseelement | |
| distilled_params, | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1248, in _execute_context | |
| e, statement, parameters, cursor, context | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1466, in _handle_dbapi_exception | |
| util.raise_from_cause(sqlalchemy_exception, exc_info) | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 383, in raise_from_cause | |
| reraise(type(exception), exception, tb=exc_tb, cause=cause) | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 128, in reraise | |
| raise value.with_traceback(tb) | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1244, in _execute_context | |
| cursor, statement, parameters, context | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 552, in do_execute | |
| cursor.execute(statement, parameters) | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/cursors.py", line 170, in execute | |
| result = self._query(query) | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/cursors.py", line 328, in _query | |
| conn.query(q) | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/connections.py", line 517, in query | |
| self._affected_rows = self._read_query_result(unbuffered=unbuffered) | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/connections.py", line 732, in _read_query_result | |
| result.read() | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/connections.py", line 1075, in read | |
| first_packet = self.connection._read_packet() | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/connections.py", line 684, in _read_packet | |
| packet.check_error() | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/protocol.py", line 220, in check_error | |
| err.raise_mysql_exception(self._data) | |
| File "/home/smly/a/lib/python3.7/site-packages/pymysql/err.py", line 109, in raise_mysql_exception | |
| raise errorclass(errno, errval) | |
| sqlalchemy.exc.DataError: (pymysql.err.DataError) (1406, "Data too long for column 'value_json' at row 1") | |
| [SQL: INSERT INTO study_user_attributes (study_id, `key`, value_json) VALUES (%(study_id)s, %(key)s, %(value_json)s)] | |
| [parameters: {'study_id': 5, 'key': 'representations', 'value_json': '["tree\\nversion=v2\\nnum_class=10\\nnum_tree_per_iteration=10\\nlabel_index=0\\nmax_feature_idx=63\\nobjective=multiclass num_class:10\\nfeature_nam ... (4070901 characters truncated) ... t_filename: ]\\n[machines: ]\\n[gpu_platform_id: -1]\\n[gpu_device_id: -1]\\n[gpu_use_dp: 0]\\n\\nend of parameters\\n\\npandas_categorical:null\\n"]'}] | |
| (Background on this error at: http://sqlalche.me/e/9h9h) | |
| During handling of the above exception, another exception occurred: | |
| Traceback (most recent call last): | |
| File "opt1.py", line 23, in <module> | |
| main() | |
| File "opt1.py", line 19, in main | |
| clf.fit(X, y, early_stopping_rounds=None) | |
| File "/home/smly/gitws/optuna/optuna/integration/lightgbm_tuner/sklearn.py", line 1013, in fit | |
| **fit_params | |
| File "/home/smly/gitws/optuna/optuna/integration/lightgbm_tuner/sklearn.py", line 712, in fit | |
| self.study_.optimize(objective, catch=(), n_trials=self.n_trials, timeout=self.timeout) | |
| File "/home/smly/gitws/optuna/optuna/study.py", line 331, in optimize | |
| func, n_trials, timeout, catch, callbacks, gc_after_trial, None | |
| File "/home/smly/gitws/optuna/optuna/study.py", line 626, in _optimize_sequential | |
| self._run_trial_and_callbacks(func, catch, callbacks, gc_after_trial) | |
| File "/home/smly/gitws/optuna/optuna/study.py", line 656, in _run_trial_and_callbacks | |
| trial = self._run_trial(func, catch, gc_after_trial) | |
| File "/home/smly/gitws/optuna/optuna/study.py", line 699, in _run_trial | |
| self._storage.set_trial_system_attr(trial_id, "fail_reason", message) | |
| File "/home/smly/gitws/optuna/optuna/storages/rdb/storage.py", line 642, in set_trial_system_attr | |
| self._set_trial_system_attr_without_commit(session, trial_id, key, value) | |
| File "/home/smly/gitws/optuna/optuna/storages/rdb/storage.py", line 649, in _set_trial_system_attr_without_commit | |
| trial = models.TrialModel.find_or_raise_by_id(trial_id, session) | |
| File "/home/smly/gitws/optuna/optuna/storages/rdb/models.py", line 220, in find_or_raise_by_id | |
| trial = cls.find_by_id(trial_id, session) | |
| File "/home/smly/gitws/optuna/optuna/storages/rdb/models.py", line 182, in find_by_id | |
| return query.one_or_none() | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3244, in one_or_none | |
| ret = list(self) | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3317, in __iter__ | |
| return self._execute_and_instances(context) | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3339, in _execute_and_instances | |
| querycontext, self._connection_from_session, close_with_result=True | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3354, in _get_bind_args | |
| mapper=self._bind_mapper(), clause=querycontext.statement, **kw | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3332, in _connection_from_session | |
| conn = self.session.connection(**kw) | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 1123, in connection | |
| execution_options=execution_options, | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 1129, in _connection_for_bind | |
| engine, execution_options | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 407, in _connection_for_bind | |
| self._assert_active() | |
| File "/home/smly/a/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 294, in _assert_active | |
| % self._rollback_exception | |
| sqlalchemy.exc.InvalidRequestError: This Session's transaction has been rolled back due to a previous exception during flush. To begin a new transaction with this Session, first issue Session.rollback(). Original exception was: (pymysql.err.DataError) (1406, "Data too long for column 'value_json' at row 1") | |
| [SQL: INSERT INTO study_user_attributes (study_id, `key`, value_json) VALUES (%(study_id)s, %(key)s, %(value_json)s)] | |
| [parameters: {'study_id': 5, 'key': 'representations', 'value_json': '["tree\\nversion=v2\\nnum_class=10\\nnum_tree_per_iteration=10\\nlabel_index=0\\nmax_feature_idx=63\\nobjective=multiclass num_class:10\\nfeature_nam ... (4070901 characters truncated) ... t_filename: ]\\n[machines: ]\\n[gpu_platform_id: -1]\\n[gpu_device_id: -1]\\n[gpu_use_dp: 0]\\n\\nend of parameters\\n\\npandas_categorical:null\\n"]'}] | |
| (Background on this error at: http://sqlalche.me/e/9h9h) |
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| CREATE DATABASE optuna_db; | |
| CREATE USER 'optuna_user'@'localhost' IDENTIFIED BY 'p4rW!w8@AUfJ5TkA'; | |
| GRANT CREATE,INSERT,UPDATE,SELECT ON optuna_db.* TO 'optuna_user'@'localhost'; |
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| import optuna | |
| import optuna.integration.lightgbm as lgb | |
| from sklearn.datasets import load_digits | |
| def main(): | |
| X, y = load_digits(return_X_y=True) | |
| study = optuna.create_study( | |
| direction="minimize", | |
| study_name="digits_optgbm", | |
| storage=( | |
| "mysql+pymysql://optuna_user:" | |
| "p4rW%21w8%40AUfJ5TkA@localhost/optuna_db"), | |
| load_if_exists=True, | |
| ) | |
| clf = lgb.LGBMClassifier(n_estimators=100, random_state=0, study=study) | |
| clf.fit(X, y, early_stopping_rounds=None) | |
| if __name__ == "__main__": | |
| main() |
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