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Pull request overview
Adds additional guidance to the Seqera/Azure Batch infrastructure notes, focusing on node allocation behavior and troubleshooting pipeline launch issues from Seqera Platform.
Changes:
- Document Azure Batch “spreading vs packing” behavior with a reference link.
- Add troubleshooting notes for connection issues (with screenshots) and guidance on handling mixed VM size requirements via autopools.
- Add a new screenshot asset for the Compute Environment configuration UI.
Reviewed changes
Copilot reviewed 1 out of 3 changed files in this pull request and generated 4 comments.
| File | Description |
|---|---|
seqera/setup_infrastructure.md |
Adds new operational notes (node packing/spreading) and a troubleshooting section (timeouts, screenshots, VM sizing/autopool pointers). |
seqera/assets/seqera_compute_env_0.png |
Adds a screenshot referenced by the new troubleshooting section. |
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| If you encounter connection issues when launching pipelines from Seqera using | ||
| Azure Batch compute environment, try to increase the timeout settings in the | ||
| Compute Environment configuration on Seqera Platform to around 8-16 hours. | ||
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| ``` | ||
| NXF_OPTS="-Dsun.net.client.defaultConnectTimeout=30000 -Dsun.net.client.defaultReadTimeout=60000" | ||
| ``` |
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The text says to increase timeouts to ~8–16 hours, but the shown NXF_OPTS values (30000/60000) are only 30s/60s (and are typically interpreted as milliseconds). Please align the stated duration with the actual values and/or explicitly state the units.
| ``` | ||
| NXF_OPTS="-Dsun.net.client.defaultConnectTimeout=30000 -Dsun.net.client.defaultReadTimeout=60000" | ||
| ``` | ||
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| Here are some example screenshots for setting it as global Environment variables | ||
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| So you will need to set the `NXF_OPTS` environment variable in the Compute Environment | ||
| configuration on Seqera Platform to | ||
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| ``` | ||
| -Dsun.net.client.defaultConnectTimeout=30000 -Dsun.net.client.defaultReadTimeout=60000 | ||
| ``` |
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The two code blocks for NXF_OPTS are inconsistent (one includes NXF_OPTS="...", the other only the JVM args). Please clarify what exactly should be entered in the Seqera UI field(s) and keep a single, unambiguous example.
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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