reduce .gitignore

.gitignore

@@ -1,2 +1 @@
 cleanup-volume-claim.sh
-build.sh

k8s-dvfs/src/main/groovy/recreationaltech/plugin/K8sExecutor.groovy

@@ -17,6 +17,7 @@
 package recreationaltech.plugin
 
 import groovy.transform.CompileDynamic
+import recreationaltech.plugin.strategies.K8sDVFSFrequencyBandsSchedulingStrategy
 import recreationaltech.plugin.strategies.K8sDVFSSchedulingStrategy
 import recreationaltech.plugin.strategies.K8sHashSchedulingStrategy
 
@@ -137,12 +138,11 @@ class K8sExecutor extends Executor implements ExtensionPoint {
                 ips[i] = client.getNodeExternalIp(nodes[i])
                 log.info "[K8s] node ${nodes[i]} -> ${ips[i]}"
             }
-            strategy = new K8sDVFSSchedulingStrategy(this.runtimeEstimator,
+            strategy = new K8sDVFSFrequencyBandsSchedulingStrategy(this.runtimeEstimator,
                     new K8sDVFSClient(nodes, ips),
                     () -> getClient(),
                     k8sConfig.runtimeComparisonEpsilon,
                     k8sConfig.dvfsSchedulingNumTopRuntimes)
-            strategy.fullSpeedMode = false
         } else {
             log.error "[K8s] invalid scheduling strategy $k8sConfig.schedulingStrategy, falling back on \"Hash\""
             strategy = new K8sHashSchedulingStrategy()

sarek/.gitignore

@@ -0,0 +1 @@
+*.fastq.gz

sarek/clean.sh

@@ -0,0 +1,3 @@
+#!/bin/sh
+
+rm -rf out work .nextflow .nextflow.log .nextflow.log.* measurements

sarek/nextflow-k8s.config

@@ -0,0 +1,24 @@
+workDir = '/workspace'
+
+process {
+	executor = 'k8s'
+	//container = 'ubuntu:22.04'
+
+	pod = [
+		imagePullPolicy: 'IfNotPresent'
+	]
+}
+
+k8s {
+	namespace = 'trogantk'
+
+	storageClaimName = 'cephfs-trogantk'
+	storageMountPath = '/workspace'
+	launchDir = '/workspace/launch'
+	projectDir = '/workspace/projects'
+	cleanup = true
+
+	pod = [
+		nodeSelector: [usedby: 'trogantk']
+	]
+}

sarek/nextflow.config

@@ -0,0 +1,41 @@
+plugins {
+	id 'k8s-dvfs@0.1.0'
+}
+
+workDir = '/workspace'
+
+process {
+	executor = 'k8s-dvfs'
+	//container = 'ubuntu:22.04'
+
+	pod = [
+		imagePullPolicy: 'IfNotPresent'
+	]
+}
+
+k8s {
+	namespace = 'trogantk'
+
+	storageClaimName = 'cephfs-trogantk'
+	storageMountPath = '/workspace'
+	launchDir = '/workspace/launch'
+	projectDir = '/workspace/projects'
+	cleanup = true
+
+	imagePullPolicy = 'IfNotPresent'
+	schedulerInterval = '1m'
+	recordTaskRuntimes = false
+	schedulingStrategy = 'DVFS'
+	runtimeComparisonEpsilon = '10s'
+	dvfsSchedulingNumTopRuntimes = 3
+	nodeLabel = 'usedby=trogantk'
+
+	nodeInit {
+		enabled = true
+		image = 'gitea.kleine.eulenhexe.de/kevin/ma/dvfs-agent:0.2.0'
+		command = ['/usr/local/bin/agent']
+		wait = 'Running'
+		cleanup = true
+	}
+	
+}

sarek/run-k8s.sh

@@ -0,0 +1,30 @@
+#!/bin/bash
+
+if [ "$#" -ne 2 ]; then
+  echo "Usage: $0 <size: 1 or 3> <logfile-outname>"
+  exit
+fi
+SIZE=$1
+LOGOUT=$2
+
+TESTDATA_ARCHIVE=/root/sarek-testdata.tar.gz
+
+MYDIR=$(pwd)
+
+mkdir -p /workspace/sarek
+mkdir -p /workspace/launch/work
+cp nextflow-k8s.config /workspace/sarek/nextflow-k8s.config
+cp runtimes.csv /workspace/launch/work/runtimes.csv
+cp samplesheet${SIZE}.csv /workspace/launch/samplesheet.csv
+cp samplesheet${SIZE}.csv /workspace/sarek/samplesheet.csv
+
+cd /workspace/launch
+tar xzf ${TESTDATA_ARCHIVE}
+
+cd /workspace/sarek
+time nextflow run -c nextflow-k8s.config  nf-core/sarek -r 3.9.0 -profile docker --genome GRCm38 --input samplesheet.csv --outdir out --skip_tools multiqc
+rm -rf out
+cp .nextflow.log /${LOGOUT}
+
+cd ${MYDIR}
+rm -rf /workspace/*

sarek/run.sh

@@ -0,0 +1,30 @@
+#!/bin/bash
+
+if [ "$#" -ne 2 ]; then
+  echo "Usage: $0 <size: 1 or 3> <logfile-outname>"
+  exit
+fi
+SIZE=$1
+LOGOUT=$2
+
+TESTDATA_ARCHIVE=/root/sarek-testdata.tar.gz
+
+MYDIR=$(pwd)
+
+mkdir -p /workspace/sarek
+mkdir -p /workspace/launch/work
+cp nextflow.config /workspace/sarek/nextflow.config
+cp runtimes.csv /workspace/launch/work/runtimes.csv
+cp samplesheet${SIZE}.csv /workspace/launch/samplesheet.csv
+cp samplesheet${SIZE}.csv /workspace/sarek/samplesheet.csv
+
+cd /workspace/launch
+tar xzf ${TESTDATA_ARCHIVE}
+
+cd /workspace/sarek
+time nextflow run -c nextflow.config  nf-core/sarek -r 3.9.0 -profile docker --genome GRCm38 --input samplesheet.csv --outdir out --skip_tools multiqc
+rm -rf out
+cp .nextflow.log /${LOGOUT}
+
+cd ${MYDIR}
+rm -rf /workspace/*

sarek/samplesheet1.csv

@@ -0,0 +1,2 @@
+patient,sample,lane,fastq_1,fastq_2
+ID1,S1,L001,SRR27016609_1.fastq.gz,SRR27016609_2.fastq.gz

sarek/samplesheet3.csv

@@ -0,0 +1,4 @@
+patient,sample,lane,fastq_1,fastq_2
+ID1,S1,L001,SRR27016609_1.fastq.gz,SRR27016609_2.fastq.gz
+ID1,S2,L001,SRR27016607_1.fastq.gz,SRR27016607_2.fastq.gz
+ID1,S3,L001,SRR27016605_1.fastq.gz,SRR27016605_2.fastq.gz