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Changed the SmithWaterman implementation to default to FASTEST_AVAILABLE #8485

Merged
merged 1 commit into from
Aug 21, 2023
Merged

Changed the SmithWaterman implementation to default to FASTEST_AVAILABLE #8485

merged 1 commit into from
Aug 21, 2023

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jonn-smith
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@droazen @jamesemery @lbergelson Is there a reason not to change this?

@jonn-smith
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jonn-smith commented Aug 18, 2023 •
edited
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For some performance comparisons with a small dataset:

Smith-Waterman runtime without AVX: 256.88s
Smith-Waterman runtime with AVX: 34.09s (7.5x faster 😱)

It's not surprising, but it is a huge difference.

@jonn-smith
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#carrot(HaplotypeCaller CARROT Regression Tests, VariantCallingCarrotOrchestrated.gatk_docker, )

@droazen
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droazen commented Aug 18, 2023

@jonn-smith Can you run the Carrot HaplotypeCaller tests on this branch? Agree that it might finally be time to make this the default, if we can convince ourselves that the accelerated implementation is stable.

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🥕CARROT🥕 run started

Test: HaplotypeCaller CARROT Regression Tests | Status: building

Run: HaplotypeCaller CARROT Regression Tests_run_2023-08-18 19:32:11.841209749 UTC

Full details 
 
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@CarrotBroadBot
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🥕CARROT🥕 run finished

Test: HaplotypeCaller CARROT Regression Tests | Status: succeeded

Run: HaplotypeCaller CARROT Regression Tests_run_2023-08-18 19:32:11.841209749 UTC

Results
Results
CHM controlHCprocesshours 89.85896666666667
CHM controlHCsystemhours 0.20056666666666664
CHM controlHCwallclockhours 63.561513888888875
CHM controlHCwallclockmax 3.142697222222222
CHM controlMonitoringLogs View in the GCS Console
CHM controlindelF1Score 0.8724
CHM controlindelPrecision 0.8814
CHM controlsnpF1Score 0.9784
CHM controlsnpPrecision 0.9706
CHM controlsnpRecall 0.9863
CHM controlsummary View in the GCS Console
CHM evalHCprocesshours 78.10857222222224
CHM evalHCsystemhours 0.28728055555555554
CHM evalHCwallclockhours 52.84132777777778
CHM evalHCwallclockmax 2.9151722222222225
CHM evalMonitoringLogs View in the GCS Console
CHM evalindelF1Score 0.8724
CHM evalindelPrecision 0.8814
CHM evalsnpF1Score 0.9784
CHM evalsnpPrecision 0.9706
CHM evalsnpRecall 0.9863
CHM evalsummary View in the GCS Console
EXOME1 controlindelF1Score 0.727
EXOME1 controlindelPrecision 0.632
EXOME1 controlsnpF1Score 0.9878
EXOME1 controlsnpPrecision 0.9815
EXOME1 controlsnpRecall 0.9941
EXOME1 controlsummary View in the GCS Console
EXOME1 evalindelF1Score 0.727
EXOME1 evalindelPrecision 0.632
EXOME1 evalsnpF1Score 0.9878
EXOME1 evalsnpPrecision 0.9815
EXOME1 evalsnpRecall 0.9941
EXOME1 evalsummary View in the GCS Console
NIST controlHCprocesshours 108.55041388888888
NIST controlHCsystemhours 0.2213388888888889
NIST controlHCwallclockhours 78.14672499999998
NIST controlHCwallclockmax 4.031741666666667
NIST controlMonitoringLogs View in the GCS Console
NIST controlindelF1Score 0.9902
NIST controlindelPrecision 0.9903
NIST controlsnpF1Score 0.9899
NIST controlsnpPrecision 0.9887
NIST controlsnpRecall 0.9911
NIST controlsummary View in the GCS Console
NIST evalHCprocesshours 93.23600000000005
NIST evalHCsystemhours 0.2127972222222222
NIST evalHCwallclockhours 62.422702777777786
NIST evalHCwallclockmax 3.1571083333333334
NIST evalMonitoringLogs View in the GCS Console
NIST evalindelF1Score 0.9902
NIST evalindelPrecision 0.9903
NIST evalsnpF1Score 0.9899
NIST evalsnpPrecision 0.9887
NIST evalsnpRecall 0.9911
NIST evalsummary View in the GCS Console
ROC_Plots_Reported View in the GCS Console
Full details 
 
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    "VariantCallingCarrotOrchestrated.use_gatk3_haplotype_caller": true
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  "test_options": {
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    "BenchmarkVCFsHeadToHeadOrchestrated.refIndex": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta.fai",
    "BenchmarkVCFsHeadToHeadOrchestrated.reference": "gs://dsp-methods-carrot-data/test_data/haplotypecaller_tests/Homo_sapiens_assembly38.fasta",
    "BenchmarkVCFsHeadToHeadOrchestrated.referenceVersion": "HG38",
    "BenchmarkVCFsHeadToHeadOrchestrated.stratIntervals": [
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    "BenchmarkVCFsHeadToHeadOrchestrated.stratLabels": [
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    ]
  },
  "eval_options": {
    "read_from_cache": false
  },
  "test_cromwell_job_id": "36c1f67a-93a8-45b4-857a-ae22db7ac9e7",
  "eval_cromwell_job_id": "81dbf637-d90c-4111-93b9-9cec426c5a39",
  "created_at": "2023-08-18T19:32:11.841274",
  "created_by": null,
  "finished_at": "2023-08-19T05:42:56.447",
  "results": {
    "CHM controlHCprocesshours": "89.85896666666667",
    "CHM controlHCsystemhours": "0.20056666666666664",
    "CHM controlHCwallclockhours": "63.561513888888875",
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    "CHM controlindelF1Score": "0.8724",
    "CHM controlindelPrecision": "0.8814",
    "CHM controlsnpF1Score": "0.9784",
    "CHM controlsnpPrecision": "0.9706",
    "CHM controlsnpRecall": "0.9863",
    "CHM controlsummary": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/81dbf637-d90c-4111-93b9-9cec426c5a39/call-CHMSampleHeadToHead/BenchmarkComparison/3609bc35-c943-4006-8b6f-9d71e6c68ef5/call-BenchmarkVCFControlSample/Benchmark/96b872e8-26c0-4406-a7d0-addf04f4ad0e/call-CombineSummaries/summary.csv",
    "CHM evalHCprocesshours": "78.10857222222224",
    "CHM evalHCsystemhours": "0.28728055555555554",
    "CHM evalHCwallclockhours": "52.84132777777778",
    "CHM evalHCwallclockmax": "2.9151722222222225",
    "CHM evalMonitoringLogs": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/81dbf637-d90c-4111-93b9-9cec426c5a39/call-CHMSampleHeadToHead/BenchmarkComparison/3609bc35-c943-4006-8b6f-9d71e6c68ef5/call-EVALRuntimeTask/monitoring.pdf",
    "CHM evalindelF1Score": "0.8724",
    "CHM evalindelPrecision": "0.8814",
    "CHM evalsnpF1Score": "0.9784",
    "CHM evalsnpPrecision": "0.9706",
    "CHM evalsnpRecall": "0.9863",
    "CHM evalsummary": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/81dbf637-d90c-4111-93b9-9cec426c5a39/call-CHMSampleHeadToHead/BenchmarkComparison/3609bc35-c943-4006-8b6f-9d71e6c68ef5/call-BenchmarkVCFTestSample/Benchmark/a2486748-6d71-463f-bf78-84627e64f2d1/call-CombineSummaries/summary.csv",
    "EXOME1 controlindelF1Score": "0.727",
    "EXOME1 controlindelPrecision": "0.632",
    "EXOME1 controlsnpF1Score": "0.9878",
    "EXOME1 controlsnpPrecision": "0.9815",
    "EXOME1 controlsnpRecall": "0.9941",
    "EXOME1 controlsummary": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/81dbf637-d90c-4111-93b9-9cec426c5a39/call-EXOME1SampleHeadToHead/BenchmarkComparison/a8851b03-1abb-4622-b481-5425ce01418b/call-BenchmarkVCFControlSample/Benchmark/7730c81c-23aa-4802-9fc0-34528b6158d4/call-CombineSummaries/summary.csv",
    "EXOME1 evalindelF1Score": "0.727",
    "EXOME1 evalindelPrecision": "0.632",
    "EXOME1 evalsnpF1Score": "0.9878",
    "EXOME1 evalsnpPrecision": "0.9815",
    "EXOME1 evalsnpRecall": "0.9941",
    "EXOME1 evalsummary": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/81dbf637-d90c-4111-93b9-9cec426c5a39/call-EXOME1SampleHeadToHead/BenchmarkComparison/a8851b03-1abb-4622-b481-5425ce01418b/call-BenchmarkVCFTestSample/Benchmark/7d946274-eb9e-4be8-b04f-c1b3399d4068/call-CombineSummaries/summary.csv",
    "NIST controlHCprocesshours": "108.55041388888888",
    "NIST controlHCsystemhours": "0.2213388888888889",
    "NIST controlHCwallclockhours": "78.14672499999998",
    "NIST controlHCwallclockmax": "4.031741666666667",
    "NIST controlMonitoringLogs": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/81dbf637-d90c-4111-93b9-9cec426c5a39/call-NISTSampleHeadToHead/BenchmarkComparison/3238c3ac-5e7c-4130-bb68-26871868b49e/call-CONTROLRuntimeTask/monitoring.pdf",
    "NIST controlindelF1Score": "0.9902",
    "NIST controlindelPrecision": "0.9903",
    "NIST controlsnpF1Score": "0.9899",
    "NIST controlsnpPrecision": "0.9887",
    "NIST controlsnpRecall": "0.9911",
    "NIST controlsummary": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/81dbf637-d90c-4111-93b9-9cec426c5a39/call-NISTSampleHeadToHead/BenchmarkComparison/3238c3ac-5e7c-4130-bb68-26871868b49e/call-BenchmarkVCFControlSample/Benchmark/4121c5eb-9771-43ee-84f1-262115dcf151/call-CombineSummaries/summary.csv",
    "NIST evalHCprocesshours": "93.23600000000005",
    "NIST evalHCsystemhours": "0.2127972222222222",
    "NIST evalHCwallclockhours": "62.422702777777786",
    "NIST evalHCwallclockmax": "3.1571083333333334",
    "NIST evalMonitoringLogs": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/81dbf637-d90c-4111-93b9-9cec426c5a39/call-NISTSampleHeadToHead/BenchmarkComparison/3238c3ac-5e7c-4130-bb68-26871868b49e/call-EVALRuntimeTask/monitoring.pdf",
    "NIST evalindelF1Score": "0.9902",
    "NIST evalindelPrecision": "0.9903",
    "NIST evalsnpF1Score": "0.9899",
    "NIST evalsnpPrecision": "0.9887",
    "NIST evalsnpRecall": "0.9911",
    "NIST evalsummary": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/81dbf637-d90c-4111-93b9-9cec426c5a39/call-NISTSampleHeadToHead/BenchmarkComparison/3238c3ac-5e7c-4130-bb68-26871868b49e/call-BenchmarkVCFTestSample/Benchmark/499d7c71-c488-4bfb-9802-34f6c5696c8d/call-CombineSummaries/summary.csv",
    "ROC_Plots_Reported": "gs://dsde-methods-carrot-prod-cromwell/BenchmarkVCFsHeadToHeadOrchestrated/81dbf637-d90c-4111-93b9-9cec426c5a39/call-CreateHTMLReport/report.html"
  },
  "errors": null
}

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🥕CARROT🥕 report map stub finished

for test HaplotypeCaller CARROT Regression Tests (run: fca2c322-83ec-454a-a917-deb026411e19)

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populated_notebook View in the GCS Console
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@droazen droazen merged commit 98b3b4f into master Aug 21, 2023
@droazen droazen deleted the jts_smithwaterman_fastest_available_default_fix branch August 21, 2023 18:33
rickymagner pushed a commit that referenced this pull request Nov 28, 2023
@jonn-smith @rickymagner
Changed the SmithWaterman implementation to default to FASTEST_AVAILA…
acc0437 
…BLE (#8485)
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@droazen droazen droazen approved these changes

@lbergelson lbergelson Awaiting requested review from lbergelson

@jamesemery jamesemery Awaiting requested review from jamesemery

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