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AN-300 Fall back to large Docker image size if we can't find a real one #7673

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merged 4 commits into from
Jan 6, 2025
Merged

AN-300 Fall back to large Docker image size if we can't find a real one #7673

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8971bfe
Fall back to large Docker image size if we can't find a real one
jgainerdewar Jan 3, 2025
57a1c33
Make image size fallback detectable in logs
jgainerdewar Jan 6, 2025
cdef9f9
Revert to 10GB default boot disk size
jgainerdewar Jan 6, 2025
2577994
Changelog
jgainerdewar Jan 6, 2025
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4 changes: 2 additions & 2 deletions CHANGELOG.md
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Expand Up @@ -59,9 +59,9 @@ The index had low cardinality and workflow pickup is faster without it. Migratio

The `IX_METADATA_ENTRY_WEU_MK` index is added to `METADATA_ENTRY`. In pre-release testing, the migration proceeded at about 3 million rows per minute. Please plan downtime accordingly.

### Bug fixes and small changes
### Reduce errors from boot disk filling up on Google Lifesciences API

* Changed default boot disk size from 10GB to 20GB in PipelinesAPI and Google Batch backends
* If Cromwell can't determine the size of the user command Docker image, it will increase Lifesciences API boot disk size by 30GB rather than 0. This should reduce incidence of tasks failing due to boot disk filling up.

#### Improved `size()` function performance on arrays

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4 changes: 2 additions & 2 deletions centaur/src/main/resources/standardTestCases/docker_size_dockerhub.test
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Expand Up @@ -11,8 +11,8 @@ files {

metadata {
status: Succeeded
"outputs.docker_size_dockerhub.large_dockerhub_image_with_hash.bootDiskSize": 27
"outputs.docker_size_dockerhub.large_dockerhub_image_with_tag.bootDiskSize": 27
"outputs.docker_size_dockerhub.large_dockerhub_image_with_hash.bootDiskSize": 17
"outputs.docker_size_dockerhub.large_dockerhub_image_with_tag.bootDiskSize": 17
}

workflowType: WDL
4 changes: 2 additions & 2 deletions centaur/src/main/resources/standardTestCases/docker_size_gcr.test
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Expand Up @@ -11,8 +11,8 @@ files {

metadata {
status: Succeeded
"outputs.docker_size_gcr.large_gcr_image_with_hash.bootDiskSize": 27
"outputs.docker_size_gcr.large_gcr_image_with_tag.bootDiskSize": 27
"outputs.docker_size_gcr.large_gcr_image_with_hash.bootDiskSize": 17
"outputs.docker_size_gcr.large_gcr_image_with_tag.bootDiskSize": 17
}

workflowType: WDL
2 changes: 1 addition & 1 deletion ...batch/src/main/scala/cromwell/backend/google/batch/models/GcpBatchRuntimeAttributes.scala
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Expand Up @@ -60,7 +60,7 @@

val BootDiskSizeKey = "bootDiskSizeGb"
private val bootDiskValidationInstance = new IntRuntimeAttributesValidation(BootDiskSizeKey)
private val BootDiskDefaultValue = WomInteger(20)
private val BootDiskDefaultValue = WomInteger(10)

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val NoAddressKey = "noAddress"
private val noAddressValidationInstance = new BooleanRuntimeAttributesValidation(NoAddressKey)
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2 changes: 1 addition & 1 deletion ...c/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiRuntimeAttributes.scala
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Expand Up @@ -66,7 +66,7 @@

val BootDiskSizeKey = "bootDiskSizeGb"
private val bootDiskValidationInstance = new IntRuntimeAttributesValidation(BootDiskSizeKey)
private val BootDiskDefaultValue = WomInteger(20)
private val BootDiskDefaultValue = WomInteger(10)

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val NoAddressKey = "noAddress"
private val noAddressValidationInstance = new BooleanRuntimeAttributesValidation(NoAddressKey)
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18 changes: 11 additions & 7 deletions .../v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/LifeSciencesFactory.scala
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Expand Up @@ -154,13 +154,17 @@
*/
val adjustedBootDiskSize = {
val fromRuntimeAttributes = createPipelineParameters.runtimeAttributes.bootDiskSize
// Compute the decompressed size based on the information available
val userCommandImageSizeInBytes = createPipelineParameters.jobDescriptor.dockerSize

// Compute the decompressed size based on the information available. If we couldn't get the image size,
// default to 30GB. Defaulting to 0 can cause task to run out of disk. (more in AN-300)
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This is 30 GB extra for the image, right? Not a 30 GB disk overall.

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Correct!

val maybeUserCommandImageSizeInGB = createPipelineParameters.jobDescriptor.dockerSize
.map(_.toFullSize(DockerConfiguration.instance.sizeCompressionFactor))
.getOrElse(0L)
val userCommandImageSizeInGB =
MemorySize(userCommandImageSizeInBytes.toDouble, MemoryUnit.Bytes).to(MemoryUnit.GB).amount
val userCommandImageSizeRoundedUpInGB = userCommandImageSizeInGB.ceil.toInt
.map(s => MemorySize(s.toDouble, MemoryUnit.Bytes).to(MemoryUnit.GB))
val (userCommandImageSizeInGB, userImageLogString) = maybeUserCommandImageSizeInGB match {

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case Some(imageSize) => (imageSize, "user command image")
case None => (MemorySize(30, MemoryUnit.GB), "failed to obtain user command image size, using safe default")
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I appreciate this specific message.

}
val userCommandImageSizeRoundedUpInGB = userCommandImageSizeInGB.amount.ceil.toInt

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@jgainerdewar jgainerdewar Jan 3, 2025 •
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Slight refactor because I didn't want to write .getOrElse(30000000000L)


val totalSize = fromRuntimeAttributes +
createPipelineParameters.dockerImageCacheDiskOpt
Expand All @@ -171,7 +175,7 @@

if (totalSize != fromRuntimeAttributes) {
jobLogger.info(
s"Adjusting boot disk size to $totalSize GB: $fromRuntimeAttributes GB (runtime attributes) + $userCommandImageSizeRoundedUpInGB GB (user command image) + ${ActionUtils.cromwellImagesSizeRoundedUpInGB} GB (Cromwell support images)"
s"Adjusting boot disk size to $totalSize GB: $fromRuntimeAttributes GB (runtime attributes) + $userCommandImageSizeRoundedUpInGB GB ($userImageLogString) + ${ActionUtils.cromwellImagesSizeRoundedUpInGB} GB (Cromwell support images)"
)
}

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