upgrade to postgres 12 with jit off

[denis-yuen]

companion for #4388

comparable performance to postgres 11 if we turn off jit
background at https://severalnines.com/database-blog/overview-just-time-compilation-jit-postgresql or hhttps://dba.stackexchange.com/questions/257759/recursive-cte-based-on-function-values-significantly-slower-on-postgres-12-than/258493#258493
guessing this might be a testing only issue since llvm should be available in the docker image, but we are inserting and dropping data rapidly which may be throwing off the query planner

[codecov]

Codecov Report

Merging #4390 (b68f28d) into develop (6f701da) will not change coverage.
The diff coverage is n/a.

@@            Coverage Diff             @@
##             develop    #4390   +/-   ##
==========================================
  Coverage      69.23%   69.23%           
  Complexity      3694     3694           
==========================================
  Files            267      267           
  Lines          15205    15205           
  Branches        1653     1653           
==========================================
  Hits           10527    10527           
  Misses          3909     3909           
  Partials         769      769           

Flag	Coverage Δ
integrationtests	57.61% <ø> (ø)
languageparsingtests	0.57% <ø> (ø)
toolintegrationtests	30.22% <ø> (ø)
workflowintegrationtests	42.55% <ø> (ø)

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[denis-yuen]

[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 846.903 s - in io.dockstore.webservice.WebhookIT
[INFO] testGithubDirDockstoreYml(io.dockstore.webservice.WebhookIT)  Time elapsed: 26.859 s
[INFO] testTestParameterPaths(io.dockstore.webservice.WebhookIT)  Time elapsed: 24.65 s
[INFO] testDescriptorChange(io.dockstore.webservice.WebhookIT)  Time elapsed: 61.915 s
[INFO] testTools(io.dockstore.webservice.WebhookIT)  Time elapsed: 69.005 s
[INFO] testGitHubReleaseNoWorkflowOnDockstore(io.dockstore.webservice.WebhookIT)  Time elapsed: 128.18 s
[INFO] testWorkflowMigration(io.dockstore.webservice.WebhookIT)  Time elapsed: 89.227 s
[INFO] testGitHubReleaseNoWorkflowOnDockstoreNoUser(io.dockstore.webservice.WebhookIT)  Time elapsed: 25.132 s
[INFO] testDockstoreYmlFilters(io.dockstore.webservice.WebhookIT)  Time elapsed: 129.888 s
[INFO] testDockstoreYmlAuthors(io.dockstore.webservice.WebhookIT)  Time elapsed: 86.305 s
[INFO] testInvalidDockstoreYmlFiles(io.dockstore.webservice.WebhookIT)  Time elapsed: 48.153 s
[INFO] testManualRefreshWorkflowWithGitHubApp(io.dockstore.webservice.WebhookIT)  Time elapsed: 30.555 s
[INFO] testDockstoreYmlPublish(io.dockstore.webservice.WebhookIT)  Time elapsed: 36.618 s
[INFO] testDeleteDefaultWorkflowVersion(io.dockstore.webservice.WebhookIT)  Time elapsed: 78.215 s

No good

[denis-yuen]

[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 885.169 s - in io.dockstore.webservice.WebhookIT
[INFO] testGithubDirDockstoreYml(io.dockstore.webservice.WebhookIT)  Time elapsed: 28.049 s
[INFO] testTestParameterPaths(io.dockstore.webservice.WebhookIT)  Time elapsed: 25.924 s
[INFO] testDescriptorChange(io.dockstore.webservice.WebhookIT)  Time elapsed: 63.284 s
[INFO] testTools(io.dockstore.webservice.WebhookIT)  Time elapsed: 69.913 s
[INFO] testGitHubReleaseNoWorkflowOnDockstore(io.dockstore.webservice.WebhookIT)  Time elapsed: 171.052 s
[INFO] testWorkflowMigration(io.dockstore.webservice.WebhookIT)  Time elapsed: 109.252 s
[INFO] testGitHubReleaseNoWorkflowOnDockstoreNoUser(io.dockstore.webservice.WebhookIT)  Time elapsed: 26.693 s
[INFO] testDockstoreYmlFilters(io.dockstore.webservice.WebhookIT)  Time elapsed: 123.056 s
[INFO] testDockstoreYmlAuthors(io.dockstore.webservice.WebhookIT)  Time elapsed: 77.394 s
[INFO] testInvalidDockstoreYmlFiles(io.dockstore.webservice.WebhookIT)  Time elapsed: 43.372 s
[INFO] testManualRefreshWorkflowWithGitHubApp(io.dockstore.webservice.WebhookIT)  Time elapsed: 27.933 s
[INFO] testDockstoreYmlPublish(io.dockstore.webservice.WebhookIT)  Time elapsed: 34.45 s
[INFO] testDeleteDefaultWorkflowVersion(io.dockstore.webservice.WebhookIT)  Time elapsed: 72.553 s

nope, 12.0 is slow too

[denis-yuen]

Notes on factors to rule out via local testing:

• update to dropwizard 4.0.24 and associated updates to hibernate 5.5.3 and liquibase 3.10.3
• probably not liquibase-core update to 4.4.3
• might be this https://dba.stackexchange.com/questions/257759/recursive-cte-based-on-function-values-significantly-slower-on-postgres-12-than/258493#258493 at least it sped up tests by a lot for me locally, not sure what the Docker situation is

[sonarcloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
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[coverbeck]

Are you closing this PR in favor of the 13.x one?

[coverbeck]

Add command here as well?

[denis-yuen]

Are you closing this PR in favor of the 13.x one?

No, the performance is slightly different and just in case of other issues we discover, I think I'll squash this one before the postgres 13 one so we can pick and choose whether to revert to 12 or 11 "next" time.

Add command here as well?

Undecided, I think I'll create a ticket to investigate when we get the performance testing back up. We're second guessing the query planner here and while that pays off in our tests, I'm not sure that is the case for "real".

https://ucsc-cgl.atlassian.net/browse/SEAB-3226

[coverbeck]

FYI, I made this comment on https://ucsc-cgl.atlassian.net/browse/SEAB-3226, but I believe JIT is off by default in RDS.