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Add sleep and nf-core/demo pipelines for sun-nomadlab #67

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merged 2 commits into from
Jul 15, 2024
Merged

Add sleep and nf-core/demo pipelines for sun-nomadlab #67

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7fe266b
add sleep and nf-core/demo pipelines for sun-nomadlab
abhi18av Jul 15, 2024
5db973c
alter the logging for a hard failure and soft failure [ci skip]
abhi18av Jul 15, 2024
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4 changes: 2 additions & 2 deletions plugins/nf-nomad/src/main/nextflow/nomad/executor/NomadTaskHandler.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -200,7 +200,7 @@ class NomadTaskHandler extends TaskHandler implements FusionAwareTask {
exitFile.text as Integer
}
catch (Exception e) {
log.debug "[NOMAD] Cannot read exit status for task: `$task.name` | ${e.message}"
log.warn "[NOMAD] Cannot read exit status for task: `$task.name` | ${e.message}"
return Integer.MAX_VALUE
}
}
Expand All @@ -217,7 +217,7 @@ class NomadTaskHandler extends TaskHandler implements FusionAwareTask {
clientName = nomadService.getClientOfJob( jobName )
log.debug "[NOMAD] determineClientNode: jobName:$jobName; clientName:$clientName"
} catch ( Exception e ){
log.warn ("[NOMAD] Unable to get the client name of job $jobName -- see the log file for details", e)
log.debug ("[NOMAD] Unable to get the client name of job $jobName -- awaiting for a client to be assigned.")
}
}

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26 changes: 19 additions & 7 deletions validation/run-all.sh
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Expand Up @@ -6,12 +6,16 @@ BUILD=0
SKIPLOCAL=0
NFAZURE=0
NFSUN=0
NFSLEEP=0
NFDEMO=0

[[ "$@" =~ '--build' ]] && BUILD=1
[[ -f $HOME/.nextflow/plugins/nf-nomad-latest/ ]] && BUILD=1
[[ "$@" =~ '--skiplocal' ]] && SKIPLOCAL=1
[[ "$@" =~ '--nfazure' ]] && NFAZURE=1
[[ "$@" =~ '--nfsun' ]] && NFSUN=1
[[ "$@" =~ '--sleep' ]] && NFSLEEP=1
[[ "$@" =~ '--demo' ]] && NFDEMO=1

if [ "$BUILD" == 1 ]; then
pushd ..
Expand Down Expand Up @@ -66,15 +70,23 @@ fi
#NOTE2: You need to have 2 secrets stored in your Nextlow: SUN_NOMADLAB_ACCESS_KEY and SUN_NOMADLAB_SECRET_KEY
if [ "$NFSUN" == 1 ]; then

nextflow run -w s3://juicefs/integration-test -c sun-nomadlab/nextflow.config hello
if [ "$NFSLEEP" == 1 ]; then
nextflow run -w s3://fusionfs/integration-test/work -c sun-nomadlab/nextflow.config abhi18av/nf-sleep --timeout 360

nextflow run bactopia/bactopia \
-w s3://juicefs/integration-test -c sun-nomadlab/nextflow.config \
-profile test,docker --outdir s3://juicefs/bactopia/outdir \
--accession SRX4563634 --coverage 100 --genome_size 2800000 \
--datasets_cache s3://juicefs/bactopia/assets
elif [ "$NFDEMO" == 1 ]; then
nextflow run nf-core/demo \
-w s3://fusionfs/integration-test/work -c sun-nomadlab/nextflow.config \
-profile test,docker --outdir s3://fusionfs/integration-test/nf-core-demo/outdir
else
nextflow run -w s3://fusionfs/integration-test/work -c sun-nomadlab/nextflow.config hello

nextflow run bactopia/bactopia \
-w s3://fusionfs/integration-test/work -c sun-nomadlab/nextflow.config \
-profile test,docker --outdir s3://fusionfs/integration-test/bactopia/outdir \
--accession SRX4563634 --coverage 100 --genome_size 2800000 \
--datasets_cache s3://fusionfs/integration-test/bactopia/assets
fi

else
echo "skip nfsun"
fi
fi
2 changes: 1 addition & 1 deletion validation/sun-nomadlab/nextflow.config
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Expand Up @@ -30,7 +30,7 @@ nomad {
}

jobs {
deleteOnCompletion = true
deleteOnCompletion = false
volumes = [
{ type "csi" name "juicefs-volume" }
]
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