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More robust parsing of shm-size containerOptions #5177

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merged 3 commits into from
Jul 27, 2024
Merged

More robust parsing of shm-size containerOptions #5177

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8beef54
More robust parsing of shm-size containerOptions
robsyme Jul 26, 2024
4cbbd74
Add tests (and correct existing test)
robsyme Jul 26, 2024
548d40a
Minor change [ci fast]
pditommaso Jul 27, 2024
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4 changes: 3 additions & 1 deletion plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsContainerOptionsMapper.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@ import com.amazonaws.services.batch.model.Tmpfs
import com.amazonaws.services.batch.model.Ulimit
import groovy.transform.CompileStatic
import nextflow.util.CmdLineOptionMap
import nextflow.util.MemoryUnit

/**
* Maps task container options to AWS container properties
Expand Down Expand Up @@ -106,7 +107,8 @@ class AwsContainerOptionsMapper {
// shared Memory Size
def value = findOptionWithSingleValue(options, 'shm-size')
if ( value ) {
params.setSharedMemorySize(value as Integer)
final sharedMemorySize = MemoryUnit.of(value)
params.setSharedMemorySize(sharedMemorySize.mega as Integer)
atLeastOneSet = true
}

Expand Down
20 changes: 19 additions & 1 deletion plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsContainerOptionsMapperTest.groovy
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Expand Up @@ -94,7 +94,25 @@ class AwsContainerOptionsMapperTest extends Specification {
def map = CmdLineHelper.parseGnuArgs('--shm-size 12048024')
def properties = AwsContainerOptionsMapper.createContainerProperties(map)
then:
properties.getLinuxParameters().getSharedMemorySize() == 12048024
properties.getLinuxParameters().getSharedMemorySize() == 11
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}

def 'should set shared memory size with unit in MiB'() {

when:
def map = CmdLineHelper.parseGnuArgs('--shm-size 256m')
def properties = AwsContainerOptionsMapper.createContainerProperties(map)
then:
properties.getLinuxParameters().getSharedMemorySize() == 256
}

def 'should set shared memory size with unit in GiB'() {

when:
def map = CmdLineHelper.parseGnuArgs('--shm-size 1g')
def properties = AwsContainerOptionsMapper.createContainerProperties(map)
then:
properties.getLinuxParameters().getSharedMemorySize() == 1024
}

def 'should set memory swappiness'() {
Expand Down