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Alternative silo limit #1025

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merged 9 commits into from
Feb 13, 2024
Merged

Alternative silo limit #1025

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f3b0bdc
add 1 hour limit for SILO import
theosanderson Feb 13, 2024
4d4f10f
make configurable
theosanderson Feb 13, 2024
885839c
Make deadline configurable at instance-level
corneliusroemer Feb 13, 2024
ed37e50
Only let jobs start within 60s of when it should have started
corneliusroemer Feb 13, 2024
8902e62
Don't restart failed jobs, it's ok if they fail, there'll be a new on…
corneliusroemer Feb 13, 2024
02c6121
Maybe some keys were in wrong place?
corneliusroemer Feb 13, 2024
e9634c0
Now this should work...
corneliusroemer Feb 13, 2024
160ab44
Finally I hope...
corneliusroemer Feb 13, 2024
e5070e5
Implement @theosanderson's original idea of central long limit
corneliusroemer Feb 13, 2024
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6 changes: 4 additions & 2 deletions kubernetes/loculus/templates/lapis-silo-import-cronjob.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
{{- $keycloakTokenUrl := "http://loculus-keycloak-service:8083/realms/loculusRealm/protocol/openid-connect/token" }}


{{- range $key, $_ := $.Values.instances }}
{{- range $key, $value := $.Values.instances }}
---
apiVersion: batch/v1
kind: CronJob
Expand All @@ -13,6 +13,8 @@ spec:
concurrencyPolicy: Forbid
jobTemplate:
spec:
activeDeadlineSeconds: {{ $value.siloImportLimitSeconds }}
startingDeadlineSeconds: 60
template:
metadata:
labels:
Expand Down Expand Up @@ -73,5 +75,5 @@ spec:
- name: lapis-silo-input-data-cache
persistentVolumeClaim:
claimName: lapis-silo-input-data-cache-{{ $key }}
restartPolicy: OnFailure
restartPolicy: Never
{{- end }}
2 changes: 2 additions & 0 deletions kubernetes/loculus/values.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@ disableBackend: false
disablePreprocessing: false
instances:
dummy-organism:
siloImportLimitSeconds: 100
schema:
instanceName: "Test Dummy Organism"
metadata:
Expand Down Expand Up @@ -76,6 +77,7 @@ instances:
- name: "S"
sequence: "MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT*"
mpox:
siloImportLimitSeconds: 1000
schema:
instanceName: "Mpox Virus"
metadata:
Expand Down
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