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Bug #8191

closed

[Crunch] Tool fails and srun reports error: Abandoning IO 60 secs after job shutdown initiated

Added by Bryan Cosca over 8 years ago. Updated over 4 years ago.

Status:
Closed
Priority:
Normal
Assigned To:
-
Category:
-
Target version:
-
Story points:
-

Description

It looks like a job prematurely finished and no output was recorded because of this error.

2016-01-11_22:17:38 wx7k5-8i9sb-3m1ey3oj3sibv7l 48530 1 stderr 00:07:30.881\011\011\011X:85419918
2016-01-11_22:17:38 wx7k5-8i9sb-3m1ey3oj3sibv7l 48530 1 stderr ERROR: ALT field does not match
2016-01-11_22:17:38 wx7k5-8i9sb-3m1ey3oj3sibv7l 48530 1 stderr \011VCF entry dbsnp_138\011X\01185470602\011rs201008478\011TC\011T\011.\011.\011CAF=[0.9553,0.04474];COMMON=1;INT;KGPROD;KGPhase1;KGPilot123;RS=201008478;RSPOS=85470603;SAO=0;SSR=0;VC=DIV;VP=0x05000008000110001c000200;WGT=1;dbSNPBuildID=137
2016-01-11_22:17:38 wx7k5-8i9sb-3m1ey3oj3sibv7l 48530 1 stderr srun: error: Abandoning IO 60 secs after job shutdown initiated
2016-01-11_22:17:38 wx7k5-8i9sb-3m1ey3oj3sibv7l 48530 1 child 50302 on compute2.1 exit 1 success=
2016-01-11_22:17:38 wx7k5-8i9sb-3m1ey3oj3sibv7l 48530 1 ERROR: Task process exited 1, but never updated its task record to indicate success and record its output.
2016-01-11_22:17:39 wx7k5-8i9sb-3m1ey3oj3sibv7l 48530 1 failure (#1, permanent) after 1009 seconds

https://workbench.wx7k5.arvadosapi.com/collections/d0cd77591c4db547ce1f9daf62341eaf+91/wx7k5-8i9sb-3m1ey3oj3sibv7l.log.txt

Related issues

Related to Arvados - Bug #8284: [Crunch] Task killed even though it is still runningResolvedTom Clegg01/23/2016Actions
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