AlexsLemonade / AlexsLemonade/OpenScPCA-nf

Update launch script to set higher JVM memory usage.

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R
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Description

Related to https://github.com/AlexsLemonade/OpenScPCA-infra/issues/106#issuecomment-2644109508

If we decrease the size of the nextflow runner instances (and even if we do not), we will want to be sure that we provide enough RAM to the JVM that Nextflow runs on. The following additional setting will set the max to 75% of the available RAM, which should be a reasonable setting as the runner is pretty much never doing anything else.

```
export NXF_JVM_ARGS="-XX:InitialRAMPercentage=25 -XX:MaxRAMPercentage=75"
```

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Research direction

Start with the launch script used for Nextflow runner instances and verify how JVM environment variables are currently configured. Set NXF_JVM_ARGS to the requested InitialRAMPercentage and MaxRAMPercentage values, then confirm the runner receives the setting and uses 75% maximum available RAM.

Written by the indexing model from the issue text.

Assessment

Tech stack
java
Domain
devops
Issue type
Feature
Difficulty
2/5
Estimated time
1-3 hours
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
55/100

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