Vs 1561 Merging in new monitoring script #9089
Open
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
mcovarr
approved these changes
Feb 5, 2025
Comment on lines
+242
to
+252
| function getGATKheapDump() { | ||
| # Get the PID of the Java process running gatk.jar | ||
| GATK_PID=$(jps -l | grep 'gatk.jar' | awk '{print $1}') | ||
| if [[ -z "$GATK_PID" ]]; then | ||
| echo "GATK process not found in list of running java processes." | ||
| jps -l | ||
| else | ||
| # We have the GATK PID, now get the heap dump | ||
| jmap -histo $GATK_PID | head -n 50 | ||
| fi | ||
| } |
There was a problem hiding this comment.
This is gonna be a bad time on non-GATK images... perhaps document this at the top or name the script more explicitly or something?
There was a problem hiding this comment.
ooh or maybe have the script accept optional args that allows this to be unified with the baseline script
bash ~{monitoring_script} --monitor-gatk --sampling-rate-seconds 1800 > monitoring.log &
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
I needed to create a new new version of the cromwell monitoring script to grab specific heap data for identifying where our memory is being used during a previously problematic shard during our AoU extract. It has been uploaded to gs://gvs_quickstart_storage/cromwell_monitoring_script_with_heap.sh
If you want to generate these high-level gatk histograms for extract, just replace the definition of
File monitoring_scriptin the ExtractTask within GvsExtractCallset.wdl to point to the new one.Here's a successful AoU extract using the new monitoring script:
https://app.terra.bio/#workspaces/allofus-drc-wgs-dev/GVS%20AoU%20WGS%20Echo%20Callset%20v2/job_history/aa5bb1e4-b860-48f3-9c8c-53dd5e6ec206