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From the error message, it seems the issue is related to timeout while fetching the data from the source, i.e. Dynamics 365 datastore.
Kindly try to increase the resources available to the Spark cluster, such as the number of cores or memory and see if it helps.
Note: SHIR is not supported in Dataflow. Kindly use AutoResolve IR.
Hope it helps. Kindly let me know if the above suggestion helped. Thanks