DataBiosphere / leonardo

Notebook service
BSD 3-Clause "New" or "Revised" License
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[IA-5028] Increase default docker shared memory size #4725

Closed LizBaldo closed 1 month ago

LizBaldo commented 1 month ago

Jira ticket: https://broadworkbench.atlassian.net/browse/IA-5028

Summary of changes

What

Why

What to test

Tested on my BEE for both a GCE (jupyter and RStudio) runtime with and without GPU, as well as for a dataproc cluster, and can see the amount of memory matching what is requested in the docker composes:

Screenshot 2024-07-29 at 5 01 58 PM

Who tested and where

codecov[bot] commented 1 month ago

Codecov Report

Attention: Patch coverage is 68.00000% with 8 lines in your changes missing coverage. Please review.

Project coverage is 73.90%. Comparing base (e5e1cb9) to head (56c6a77). Report is 1 commits behind head on develop.

Files Patch % Lines
...titute/dsde/workbench/leonardo/runtimeModels.scala 0.00% 6 Missing :warning:
.../workbench/leonardo/util/DataprocInterpreter.scala 90.00% 1 Missing :warning:
.../dsde/workbench/leonardo/util/GceInterpreter.scala 80.00% 1 Missing :warning:
Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/DataBiosphere/leonardo/pull/4725/graphs/tree.svg?width=650&height=150&src=pr&token=NZGL9e1XHh&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=DataBiosphere)](https://app.codecov.io/gh/DataBiosphere/leonardo/pull/4725?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=DataBiosphere) ```diff @@ Coverage Diff @@ ## develop #4725 +/- ## =========================================== - Coverage 73.90% 73.90% -0.01% =========================================== Files 161 161 Lines 15047 15054 +7 Branches 1222 1222 =========================================== + Hits 11121 11125 +4 - Misses 3926 3929 +3 ``` | [Files](https://app.codecov.io/gh/DataBiosphere/leonardo/pull/4725?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=DataBiosphere) | Coverage Δ | | |---|---|---| | [...titute/dsde/workbench/leonardo/config/Config.scala](https://app.codecov.io/gh/DataBiosphere/leonardo/pull/4725?src=pr&el=tree&filepath=http%2Fsrc%2Fmain%2Fscala%2Forg%2Fbroadinstitute%2Fdsde%2Fworkbench%2Fleonardo%2Fconfig%2FConfig.scala&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=DataBiosphere#diff-aHR0cC9zcmMvbWFpbi9zY2FsYS9vcmcvYnJvYWRpbnN0aXR1dGUvZHNkZS93b3JrYmVuY2gvbGVvbmFyZG8vY29uZmlnL0NvbmZpZy5zY2FsYQ==) | `97.79% <100.00%> (ø)` | | | [...orkbench/leonardo/util/RuntimeTemplateValues.scala](https://app.codecov.io/gh/DataBiosphere/leonardo/pull/4725?src=pr&el=tree&filepath=http%2Fsrc%2Fmain%2Fscala%2Forg%2Fbroadinstitute%2Fdsde%2Fworkbench%2Fleonardo%2Futil%2FRuntimeTemplateValues.scala&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=DataBiosphere#diff-aHR0cC9zcmMvbWFpbi9zY2FsYS9vcmcvYnJvYWRpbnN0aXR1dGUvZHNkZS93b3JrYmVuY2gvbGVvbmFyZG8vdXRpbC9SdW50aW1lVGVtcGxhdGVWYWx1ZXMuc2NhbGE=) | `97.93% <100.00%> (+0.02%)` | :arrow_up: | | [.../workbench/leonardo/util/DataprocInterpreter.scala](https://app.codecov.io/gh/DataBiosphere/leonardo/pull/4725?src=pr&el=tree&filepath=http%2Fsrc%2Fmain%2Fscala%2Forg%2Fbroadinstitute%2Fdsde%2Fworkbench%2Fleonardo%2Futil%2FDataprocInterpreter.scala&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=DataBiosphere#diff-aHR0cC9zcmMvbWFpbi9zY2FsYS9vcmcvYnJvYWRpbnN0aXR1dGUvZHNkZS93b3JrYmVuY2gvbGVvbmFyZG8vdXRpbC9EYXRhcHJvY0ludGVycHJldGVyLnNjYWxh) | `63.71% <90.00%> (+0.22%)` | :arrow_up: | | [.../dsde/workbench/leonardo/util/GceInterpreter.scala](https://app.codecov.io/gh/DataBiosphere/leonardo/pull/4725?src=pr&el=tree&filepath=http%2Fsrc%2Fmain%2Fscala%2Forg%2Fbroadinstitute%2Fdsde%2Fworkbench%2Fleonardo%2Futil%2FGceInterpreter.scala&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=DataBiosphere#diff-aHR0cC9zcmMvbWFpbi9zY2FsYS9vcmcvYnJvYWRpbnN0aXR1dGUvZHNkZS93b3JrYmVuY2gvbGVvbmFyZG8vdXRpbC9HY2VJbnRlcnByZXRlci5zY2FsYQ==) | `67.00% <80.00%> (+0.16%)` | :arrow_up: | | [...titute/dsde/workbench/leonardo/runtimeModels.scala](https://app.codecov.io/gh/DataBiosphere/leonardo/pull/4725?src=pr&el=tree&filepath=core%2Fsrc%2Fmain%2Fscala%2Forg%2Fbroadinstitute%2Fdsde%2Fworkbench%2Fleonardo%2FruntimeModels.scala&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=DataBiosphere#diff-Y29yZS9zcmMvbWFpbi9zY2FsYS9vcmcvYnJvYWRpbnN0aXR1dGUvZHNkZS93b3JrYmVuY2gvbGVvbmFyZG8vcnVudGltZU1vZGVscy5zY2FsYQ==) | `10.79% <0.00%> (-0.24%)` | :arrow_down: | ------ [Continue to review full report in Codecov by Sentry](https://app.codecov.io/gh/DataBiosphere/leonardo/pull/4725?dropdown=coverage&src=pr&el=continue&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=DataBiosphere). > **Legend** - [Click here to learn more](https://docs.codecov.io/docs/codecov-delta?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=DataBiosphere) > `Δ = absolute (impact)`, `ø = not affected`, `? = missing data` > Powered by [Codecov](https://app.codecov.io/gh/DataBiosphere/leonardo/pull/4725?dropdown=coverage&src=pr&el=footer&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=DataBiosphere). Last update [821005b...56c6a77](https://app.codecov.io/gh/DataBiosphere/leonardo/pull/4725?dropdown=coverage&src=pr&el=lastupdated&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=DataBiosphere). Read the [comment docs](https://docs.codecov.io/docs/pull-request-comments?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=DataBiosphere).
LizBaldo commented 1 month ago

@jdcanas I made the changes and moved the logic so it an be unit testable. However I can't merge it because the integration tests can't run due to a path being deleted ls: cannot access '/home/runner/work/terra-github-workflows/terra-github-workflows/leonardo/test-reports': No such file or directory

I am not going to be around next week, neither will Lucy, so would you be able to:

Many thanks 🙏