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Add .command.log redirection in K8s container command when Fusion is not enabled#6455

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pditommaso merged 2 commits intomasterfrom
fix-k8s-command-log-not-saved
Oct 21, 2025
Merged

Add .command.log redirection in K8s container command when Fusion is not enabled#6455
pditommaso merged 2 commits intomasterfrom
fix-k8s-command-log-not-saved

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@jorgee jorgee commented Oct 7, 2025

When using k8s without Fusion the .command.log file is only saved if a task fails. However, Platform tries to get .command.log for all tasks executed. So for non-failed tasks it is unable to find the log file.

This PR changes the container command to include the redirection of .command.run outputs to .command.log when Fusion is not enabled. It replaces #6451 because getting .command.log from the pod logs for all tasks overload the Kubernetes API with large number of tasks.

See also #2782

Tested with local K3d cluster:

$ nextflow kuberun -head-image jorgeejarquea/nextflow:25.08.0-edge-2765d4a69 hello -v nextflow-pvc:/mnt/data/launch
Pod started: focused-noyce
N E X T F L O W  ~  version 25.08.0-edge
Pulling nextflow-io/hello ...
 downloaded from https://github.com/nextflow-io/hello.git
Launching `https://github.com/nextflow-io/hello` [focused-noyce] DSL2 - revision: 2ce0b0e294 [master]
[33/9aad8c] Submitted process > sayHello (2)
[31/17e511] Submitted process > sayHello (3)
[23/a4f15c] Submitted process > sayHello (1)
[4a/9738de] Submitted process > sayHello (4)
Ciao world!

Hello world!

Bonjour world!

Hola world!


/tmp/k3d-storage/jorgee/work/33/9aad8c9e9711ce00bd30f7a383f3ce$ ls -lart
total 28
drwxr-xr-x 3 root root 4096 oct  7 15:45 ..
-rw-r--r-- 1 root root 3163 oct  7 15:45 .command.run
-rw-r--r-- 1 root root   35 oct  7 15:45 .command.sh
-rw-r--r-- 1 root root    0 oct  7 15:46 .command.begin
-rw-r--r-- 1 root root    0 oct  7 15:46 .command.err
-rw-r--r-- 1 root root   12 oct  7 15:46 .command.out
-rw-r--r-- 1 root root   12 oct  7 15:46 .command.log
-rw-r--r-- 1 root root    1 oct  7 15:46 .exitcode
drwxr-xr-x 2 root root 4096 oct  7 15:46 .

@jorgee
redirect .command.run output to .command.log when fusion is not enabled
2765d4a 
Signed-off-by: jorgee <jorge.ejarque@seqera.io>
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@jorgee jorgee mentioned this pull request Oct 7, 2025
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@jorgee jorgee changed the title Add .command.log redirection in K8s continer command when no Fusion Add .command.log redirection in K8s container command when no Fusion Oct 7, 2025
@jorgee jorgee changed the title Add .command.log redirection in K8s container command when no Fusion Add .command.log redirection in K8s container command when Fusion is not enabled Oct 7, 2025
pditommaso
pditommaso requested changes Oct 14, 2025
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It would better still trying to fetch the logs via the API in case of failure

@jorgee
revert savePodLogOnError remove
1fed07f 
Signed-off-by: jorgee <jorge.ejarque@seqera.io>
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jorgee commented Oct 14, 2025

I have reverted the savePodLogsOnError part.

@jorgee jorgee requested a review from pditommaso October 14, 2025 18:05
@bentsherman bentsherman added this to the 25.10 milestone Oct 16, 2025
@pditommaso pditommaso merged commit e6eed79 into master Oct 21, 2025
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@pditommaso pditommaso deleted the fix-k8s-command-log-not-saved branch October 21, 2025 14:21
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