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Passing exact memory to executors in GiB #1696

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merged 2 commits into from
Aug 5, 2020
Merged

Passing exact memory to executors in GiB #1696

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141ab82
Make the toGiga conversion in the module, using a double instead of a…
lvarin Aug 5, 2020
7489152
Symplify flow control. Following the advice of Paolo Di Tommaso
lvarin Aug 5, 2020
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7 changes: 6 additions & 1 deletion modules/nf-ga4gh/src/main/nextflow/ga4gh/tes/executor/TesTaskHandler.groovy
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Expand Up @@ -38,6 +38,7 @@ import nextflow.processor.TaskConfig
import nextflow.processor.TaskHandler
import nextflow.processor.TaskRun
import nextflow.processor.TaskStatus
import nextflow.util.MemoryUnit
/**
* Handle execution phases for a task executed by a TES executor
*
Expand Down Expand Up @@ -204,14 +205,18 @@ class TesTaskHandler extends TaskHandler {
private TesResources getResources(TaskConfig cfg) {
def res = new TesResources()
res.cpuCores(cfg.getCpus())
.ramGb(cfg.getMemory()?.toGiga()) // @TODO only works for >= 1.GB
.ramGb(toGiga(cfg.getMemory()))
.diskGb(cfg.getDisk()?.toGiga())
log.trace("[TES] Adding resource request: $res")
// @TODO preemptible
// @TODO zones
return res
}

private Double toGiga(MemoryUnit size) {
// 1073741824 = 1GB
return size != null ? ((double)size.bytes)/1073741824 : null
}

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private TesInput inItem( Path realPath, String fileName = null) {
def result = new TesInput()
Expand Down