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Posted to github@beam.apache.org by GitBox <gi...@apache.org> on 2021/11/02 20:01:17 UTC

[GitHub] [beam] msbukal opened a new pull request #15873: Remove Sharding from FhirIO.Import

msbukal opened a new pull request #15873:
URL: https://github.com/apache/beam/pull/15873


   The import operation on the FHIR API is made to handle large amounts of data, similar to a pipeline on apache beam. Starting an import operation on the FHIR API for a small amount of input is inefficient, as:
   - The operation will scale itself up to manage millions of resources of input, spinning up many operations (each for a small number of resources) incurs a lot of overhead costs in managing an operation.
   - There is a quota on the number of long-running operations on the FHIR service per project, which by default is 100. Therefore, creating 100 shards uses all this quota up in one instance of the pipeline.
   - It is possible to request increases for the quota, however limitations of the FHIR service mean that operations after a certain # will be unable to make progress until earlier operations complete.
   
   Therefore, sharding causes a severe loss of import performance and burdens the FHIR services. This change removing the sharding + GroupIntoBatches part of FhirIO.Import, relying on DoFns & bundle handling to partition import input into more reasonable, large batches of resources.
   
   Also updated comments & changed the import to move files instead of copying since we already handle re-tries resulting in missing files in the source.
   
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[GitHub] [beam] pabloem commented on pull request #15873: [BEAM-13181] Remove Sharding from FhirIO.Import

Posted by GitBox <gi...@apache.org>.
pabloem commented on pull request #15873:
URL: https://github.com/apache/beam/pull/15873#issuecomment-963538610


   thanks a lot for doing some performance tests. It would be great if a performance test could be operationalized so that we can track the performance of the IOs / templates - either in the open source repo or in your own codebase.
   either way this looks good. I'll merge this. Thanks!


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[GitHub] [beam] msbukal commented on pull request #15873: [BEAM-13181] Remove Sharding from FhirIO.Import

Posted by GitBox <gi...@apache.org>.
msbukal commented on pull request #15873:
URL: https://github.com/apache/beam/pull/15873#issuecomment-962118962


   I ran some performance tests with an import of 68 million resources.
   
   With sharding, aka before this PR:
   
   | Elapsed Time | # Import Operations | Resources Imported | Results |
   | ------------- | -------------------- | -------------------- | ------- |
   | 1h33 | 3 | 9,803,961 |  FAILED due to java.lang.IllegalStateException: Not all temporary files are present for importing |
   | 2h6 | 3 | 34,706,066 | FAILED due to java.lang.IllegalStateException: Not all temporary files are present for importing |
   | 2h37 | 16 | 67,480,522 | Finally got a successful run, only used 1 worker. |
   
   Without sharding, aka after this PR:
   
   | Elapsed Time | # Import Operations | Resources Imported | Results |
   | ------------- | -------------------- | -------------------- | ------- |
   | 1h30 | 12 | 67,480,522 | Scaled to ~6 workers. |
   | 2h17 | 4 | 67,480,522 | Force limited to 1 worker |
   
   Overall, without pre-sharding performed better on the two key points: Less operations triggered (good to avoid hitting quota), and less elapsed time.. additionally didn’t fail as constantly as with sharding which was more problematic than I expected.
   


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[GitHub] [beam] msbukal commented on pull request #15873: Remove Sharding from FhirIO.Import

Posted by GitBox <gi...@apache.org>.
msbukal commented on pull request #15873:
URL: https://github.com/apache/beam/pull/15873#issuecomment-959149883


   Run Java PreCommit


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[GitHub] [beam] msbukal commented on pull request #15873: Remove Sharding from FhirIO.Import

Posted by GitBox <gi...@apache.org>.
msbukal commented on pull request #15873:
URL: https://github.com/apache/beam/pull/15873#issuecomment-959149883






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[GitHub] [beam] pabloem commented on pull request #15873: [BEAM-13181] Remove Sharding from FhirIO.Import

Posted by GitBox <gi...@apache.org>.
pabloem commented on pull request #15873:
URL: https://github.com/apache/beam/pull/15873#issuecomment-960344499


   Run Java PostCommit


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[GitHub] [beam] msbukal commented on pull request #15873: [BEAM-13181] Remove Sharding from FhirIO.Import

Posted by GitBox <gi...@apache.org>.
msbukal commented on pull request #15873:
URL: https://github.com/apache/beam/pull/15873#issuecomment-962101811






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[GitHub] [beam] msbukal commented on pull request #15873: [BEAM-13181] Remove Sharding from FhirIO.Import

Posted by GitBox <gi...@apache.org>.
msbukal commented on pull request #15873:
URL: https://github.com/apache/beam/pull/15873#issuecomment-962101811


   Run Java PostCommit
   
   


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[GitHub] [beam] pabloem commented on pull request #15873: [BEAM-13181] Remove Sharding from FhirIO.Import

Posted by GitBox <gi...@apache.org>.
pabloem commented on pull request #15873:
URL: https://github.com/apache/beam/pull/15873#issuecomment-960344499


   Run Java PostCommit


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[GitHub] [beam] pabloem merged pull request #15873: [BEAM-13181] Remove Sharding from FhirIO.Import

Posted by GitBox <gi...@apache.org>.
pabloem merged pull request #15873:
URL: https://github.com/apache/beam/pull/15873


   


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[GitHub] [beam] msbukal commented on pull request #15873: Remove Sharding from FhirIO.Import

Posted by GitBox <gi...@apache.org>.
msbukal commented on pull request #15873:
URL: https://github.com/apache/beam/pull/15873#issuecomment-959482715


   R: @pabloem
   
   


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[GitHub] [beam] msbukal commented on pull request #15873: Remove Sharding from FhirIO.Import

Posted by GitBox <gi...@apache.org>.
msbukal commented on pull request #15873:
URL: https://github.com/apache/beam/pull/15873#issuecomment-959149883






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[GitHub] [beam] msbukal commented on pull request #15873: [BEAM-13181] Remove Sharding from FhirIO.Import

Posted by GitBox <gi...@apache.org>.
msbukal commented on pull request #15873:
URL: https://github.com/apache/beam/pull/15873#issuecomment-962101811






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