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Posted to issues@beam.apache.org by "Beam JIRA Bot (Jira)" <ji...@apache.org> on 2021/10/24 17:25:01 UTC
[jira] [Updated] (BEAM-11956) 504 Deadline Exceeded code for very
large datasets in Python
[ https://issues.apache.org/jira/browse/BEAM-11956?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]
Beam JIRA Bot updated BEAM-11956:
---------------------------------
Labels: stale-assigned (was: )
> 504 Deadline Exceeded code for very large datasets in Python
> ------------------------------------------------------------
>
> Key: BEAM-11956
> URL: https://issues.apache.org/jira/browse/BEAM-11956
> Project: Beam
> Issue Type: Bug
> Components: io-py-gcp
> Environment: Python 3.8, Apache Beam SDK 2.28, Google Dataflow
> Reporter: Sebastian Montero
> Assignee: Sebastian Montero
> Priority: P3
> Labels: stale-assigned
> Time Spent: 40m
> Remaining Estimate: 0h
>
> I am building an application in Apache Beam and Python that runs in Google DataFlow. I am using the {{ReadFromSpanner}} method in {{apache_beam.io.gcp.experimental.spannerio}}. This works for most of my Spanner tables but the really large ones that are >16m rows tend to fail due to the following error:
> Traceback (most recent call last):
> File "/usr/local/lib/python3.8/site-packages/dataflow_worker/batchworker.py", line 649, in do_work
> work_executor.execute()
> File "/usr/local/lib/python3.8/site-packages/dataflow_worker/executor.py", line 179, in execute
> op.start()
> File "dataflow_worker/shuffle_operations.py", line 63, in dataflow_worker.shuffle_operations.GroupedShuffleReadOperation.start
> File "dataflow_worker/shuffle_operations.py", line 64, in dataflow_worker.shuffle_operations.GroupedShuffleReadOperation.start
> File "dataflow_worker/shuffle_operations.py", line 79, in dataflow_worker.shuffle_operations.GroupedShuffleReadOperation.start
> File "dataflow_worker/shuffle_operations.py", line 80, in dataflow_worker.shuffle_operations.GroupedShuffleReadOperation.start
> File "dataflow_worker/shuffle_operations.py", line 84, in dataflow_worker.shuffle_operations.GroupedShuffleReadOperation.start
> File "apache_beam/runners/worker/operations.py", line 359, in apache_beam.runners.worker.operations.Operation.output
> File "apache_beam/runners/worker/operations.py", line 221, in apache_beam.runners.worker.operations.SingletonConsumerSet.receive
> File "dataflow_worker/shuffle_operations.py", line 261, in dataflow_worker.shuffle_operations.BatchGroupAlsoByWindowsOperation.process
> File "dataflow_worker/shuffle_operations.py", line 268, in dataflow_worker.shuffle_operations.BatchGroupAlsoByWindowsOperation.process
> File "apache_beam/runners/worker/operations.py", line 359, in apache_beam.runners.worker.operations.Operation.output
> File "apache_beam/runners/worker/operations.py", line 221, in apache_beam.runners.worker.operations.SingletonConsumerSet.receive
> File "apache_beam/runners/worker/operations.py", line 718, in apache_beam.runners.worker.operations.DoOperation.process
> File "apache_beam/runners/worker/operations.py", line 719, in apache_beam.runners.worker.operations.DoOperation.process
> File "apache_beam/runners/common.py", line 1241, in apache_beam.runners.common.DoFnRunner.process
> File "apache_beam/runners/common.py", line 1306, in apache_beam.runners.common.DoFnRunner._reraise_augmented
> File "apache_beam/runners/common.py", line 1239, in apache_beam.runners.common.DoFnRunner.process
> File "apache_beam/runners/common.py", line 587, in apache_beam.runners.common.SimpleInvoker.invoke_process
> File "apache_beam/runners/common.py", line 1401, in apache_beam.runners.common._OutputProcessor.process_outputs
> File "apache_beam/runners/worker/operations.py", line 221, in apache_beam.runners.worker.operations.SingletonConsumerSet.receive
> File "apache_beam/runners/worker/operations.py", line 718, in apache_beam.runners.worker.operations.DoOperation.process
> File "apache_beam/runners/worker/operations.py", line 719, in apache_beam.runners.worker.operations.DoOperation.process
> File "apache_beam/runners/common.py", line 1241, in apache_beam.runners.common.DoFnRunner.process
> File "apache_beam/runners/common.py", line 1306, in apache_beam.runners.common.DoFnRunner._reraise_augmented
> File "apache_beam/runners/common.py", line 1239, in apache_beam.runners.common.DoFnRunner.process
> File "apache_beam/runners/common.py", line 587, in apache_beam.runners.common.SimpleInvoker.invoke_process
> File "apache_beam/runners/common.py", line 1401, in apache_beam.runners.common._OutputProcessor.process_outputs
> File "apache_beam/runners/worker/operations.py", line 221, in apache_beam.runners.worker.operations.SingletonConsumerSet.receive
> File "apache_beam/runners/worker/operations.py", line 718, in apache_beam.runners.worker.operations.DoOperation.process
> File "apache_beam/runners/worker/operations.py", line 719, in apache_beam.runners.worker.operations.DoOperation.process
> File "apache_beam/runners/common.py", line 1241, in apache_beam.runners.common.DoFnRunner.process
> File "apache_beam/runners/common.py", line 1321, in apache_beam.runners.common.DoFnRunner._reraise_augmented
> File "/usr/local/lib/python3.8/site-packages/future/utils/__init__.py", line 446, in raise_with_traceback
> raise exc.with_traceback(traceback)
> File "apache_beam/runners/common.py", line 1239, in apache_beam.runners.common.DoFnRunner.process
> File "apache_beam/runners/common.py", line 587, in apache_beam.runners.common.SimpleInvoker.invoke_process
> File "apache_beam/runners/common.py", line 1374, in apache_beam.runners.common._OutputProcessor.process_outputs
> File "/usr/local/lib/python3.8/site-packages/apache_beam/io/gcp/experimental/spannerio.py", line 550, in process
> for row in read_action(element['partitions']):
> File "/usr/local/lib/python3.8/site-packages/google/cloud/spanner_v1/streamed.py", line 143, in __iter__
> self._consume_next()
> File "/usr/local/lib/python3.8/site-packages/google/cloud/spanner_v1/streamed.py", line 116, in _consume_next
> response = six.next(self._response_iterator)
> File "/usr/local/lib/python3.8/site-packages/google/cloud/spanner_v1/snapshot.py", line 45, in _restart_on_unavailable
> for item in iterator:
> File "/usr/local/lib/python3.8/site-packages/google/api_core/grpc_helpers.py", line 116, in next
> six.raise_from(exceptions.from_grpc_error(exc), exc)
> File "<string>", line 3, in raise_from
> google.api_core.exceptions.DeadlineExceeded: 504 Deadline Exceeded [while running 'Read from Spanner/Read From Partitions']
> From my understanding this error comes from the {{ReadFromSpanner}} operation as it's workers have timed out.
> To solve this I have tried the following:
> * Changed the {{num_workers}} and {{disk_size_gb}} and added the {{--experiments=shuffle_mode=service}} flag as suggested in [Google's Common error guidance|https://cloud.google.com/dataflow/docs/guides/common-errors#tsg-rpc-timeout]
> * Changed the Machine Type from {{n1-standard-1}} to {{n1-standard-2}} from [here|https://cloud.google.com/compute/docs/machine-types#n1_machine_types]
> My latest code is attached below. I am including {{Transformation}} for simple data wrangling in the rows.
> """Set pipeline arguments."""
> options = PipelineOptions(
> region=RUNNER_REGION,
> project=RUNNER_PROJECT_ID,
> runner=RUNNER,
> temp_location=TEMP_LOCATION,
> job_name=JOB_NAME,
> service_account_email=SA_EMAIL,
> setup_file=SETUP_FILE_PATH,
> disk_size_gb=500,
> num_workers=10,
> machine_type="n1-standard-2",
> save_main_session=True)
> """Build and run the pipeline."""
> with beam.Pipeline(options=options) as p:
> (p
> | "Read from Spanner" >> ReadFromSpanner(SPANNER_PROJECT_ID, SPANNER_INSTANCE_ID, SPANNER_DB, sql=QUERY)
> | "Transform elements into dictionary" >> beam.ParDo(Transformation)
> | "Write new records to BQ" >> WriteToBigQuery(
> BIGQUERY_TABLE,
> schema=SCHEMA,
> write_disposition=beam.io.BigQueryDisposition.WRITE_APPEND,
> create_disposition=beam.io.BigQueryDisposition.CREATE_IF_NEEDED)
> )
> A *potential solution* is to edit the timeout control; I have seen this being available in Java but not in Python. How can I edit timeout control in Python or is there any other solution to this issue?
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