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[GH-38] Track job with tags #39

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merged 1 commit into from
Jul 13, 2023
Merged

[GH-38] Track job with tags #39

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5 changes: 3 additions & 2 deletions plugins/nf-float/src/main/com/memverge/nextflow/CmdResult.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -94,8 +94,9 @@ class CmdResult {
for (i in obj) {
def id = i.id as String
def status = i.status as String
def taskID = i.name as String
if (id && status) {
def tags = i.customTags as Map
String taskID = tags ? tags[FloatConf.NF_JOB_ID] : ""
if (id && status && taskID) {
ret[id] = new JobStatus(taskID, status)
}
}
Expand Down
1 change: 1 addition & 0 deletions plugins/nf-float/src/main/com/memverge/nextflow/FloatConf.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@ class FloatConf {
static String MMC_USERNAME = "MMC_USERNAME"
static String MMC_PASSWORD = "MMC_PASSWORD"
static String ADDR_SEP = ","
static String NF_JOB_ID = "nf-job-id"

/** credentials for op center */
String username
Expand Down
5 changes: 3 additions & 2 deletions plugins/nf-float/src/main/com/memverge/nextflow/FloatGridExecutor.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -200,6 +200,7 @@ class FloatGridExecutor extends AbstractGridExecutor {
@Override
List<String> getSubmitCommandLine(TaskRun task, Path scriptFile) {
validateTaskConf(task.config)
String tag = "${FloatConf.NF_JOB_ID}:${floatJobs.getJobName(task.id)}"
def cmd = getSubmitCmdPrefix()
cmd << 'sbatch'
cmd << '--dataVolume'
Expand All @@ -212,8 +213,8 @@ class FloatGridExecutor extends AbstractGridExecutor {
cmd << getMem(task)
cmd << '--job'
cmd << scriptFile.toString()
cmd << '--name'
cmd << floatJobs.getJobName(task.id)
cmd << '--customTag'
cmd << tag
cmd.addAll(getExtra(task))
log.info "[float] submit job: ${toCmdString(cmd)}"
return cmd
Expand Down
2 changes: 1 addition & 1 deletion plugins/nf-float/src/main/com/memverge/nextflow/FloatJobs.groovy
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Expand Up @@ -42,7 +42,7 @@ class FloatJobs {
job2oc = new ConcurrentHashMap<>()
task2workDir = new ConcurrentHashMap<>()
ocs = ocAddresses
def charset = (('A'..'Z')+('0'..'9')).join('')
def charset = (('a'..'z')+('0'..'9')).join('')
taskPrefix = RandomStringUtils.random(
6, charset.toCharArray())
}
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16 changes: 12 additions & 4 deletions plugins/nf-float/src/test/com/memverge/nextflow/CmdResultTest.groovy
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Expand Up @@ -116,15 +116,23 @@ class CmdResultTest extends Specification {
"name": "cactus-c5d.large",
"user": "admin",
"imageID": "docker.io/memverge/cactus:latest",
"status": "FailToExecute"
"status": "FailToExecute",
"customTags": {
"nf-job-id": "job-a",
"a": "apple"
}
},
{
"id": "u5x3sSLe0p3OznGavmYu3",
"name": "cactus-t3a.medium",
"workingHost": "3.143.251.235 (2Core4GB/Spot)",
"user": "admin",
"imageID": "docker.io/memverge/cactus:latest",
"status": "Executing"
"status": "Executing",
"customTags": {
"b": "banana",
"nf-job-id": "job-b"
}
}
]"""
def stMap = res.getQStatus()
Expand All @@ -133,9 +141,9 @@ class CmdResultTest extends Specification {

then:
st1.status == 'FailToExecute'
st1.taskID == 'cactus-c5d.large'
st1.taskID == 'job-a'
st2.status == 'Executing'
st2.taskID == 'cactus-t3a.medium'
st2.taskID == 'job-b'
}

def "get queue empty"() {
Expand Down
8 changes: 4 additions & 4 deletions plugins/nf-float/src/test/com/memverge/nextflow/FloatGridExecutorMultiOCTest.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -69,11 +69,11 @@ class FloatGridExecutorMultiOCTest extends Specification {
cmd1.join(' ') == "float -a fb -u admin -p password sbatch " +
"--dataVolume ${dataVol} --image ${image} " +
"--cpu ${cpu} --mem ${mem} --job ${script}" +
" --name tJob-${taskID}"
" --customTag nf-job-id:tJob-${taskID}"
cmd2.join(' ') == "float -a fa -u admin -p password sbatch " +
"--dataVolume ${dataVol} --image ${image} " +
"--cpu ${cpu} --mem ${mem} --job ${script}" +
" --name tJob-${taskID}"
" --customTag nf-job-id:tJob-${taskID}"
}

def "get queue status commands"() {
Expand Down Expand Up @@ -116,10 +116,10 @@ class FloatGridExecutorMultiOCTest extends Specification {
cmd1.join(' ') == "float -a fb -u admin -p password sbatch " +
"--dataVolume ${dataVol} --image ${image} " +
"--cpu ${cpu} --mem ${mem} --job ${script}" +
" --name tJob-${taskID}"
" --customTag nf-job-id:tJob-${taskID}"
cmd2.join(' ') == "float -a fa -u admin -p password sbatch " +
"--dataVolume ${dataVol} --image ${image} " +
"--cpu ${cpu} --mem ${mem} --job ${script}" +
" --name tJob-${taskID}"
" --customTag nf-job-id:tJob-${taskID}"
}
}
78 changes: 54 additions & 24 deletions plugins/nf-float/src/test/com/memverge/nextflow/FloatGridExecutorTest.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@ class FloatGridExecutorTest extends Specification {
}

def jobID(TaskId id) {
return "$tJob-$id"
return "${FloatConf.NF_JOB_ID}:$tJob-$id"
}

def "get the prefix of kill command"() {
Expand Down Expand Up @@ -133,7 +133,7 @@ class FloatGridExecutorTest extends Specification {
'--cpu', cpu.toString(),
'--mem', mem.toString(),
'--job', script,
'--name', jobID(taskID)].join(' ')
'--customTag', jobID(taskID)].join(' ')
}

def "add default local mount point"() {
Expand All @@ -160,7 +160,7 @@ class FloatGridExecutorTest extends Specification {
'--cpu', cpu.toString(),
'--mem', mem.toString(),
'--job', script,
'--name', jobID(taskID)].join(' ')
'--customTag', jobID(taskID)].join(' ')
}

def "use cpus, memory and container"() {
Expand All @@ -187,7 +187,7 @@ class FloatGridExecutorTest extends Specification {
'--cpu', '8',
'--mem', '16',
'--job', script,
'--name', jobID(taskID)].join(' ')
'--customTag', jobID(taskID)].join(' ')
}

def "add common extras"() {
Expand Down Expand Up @@ -216,7 +216,7 @@ class FloatGridExecutorTest extends Specification {
'--cpu', '2',
'--mem', '4',
'--job', script,
'--name', jobID(taskID),
'--customTag', jobID(taskID),
'-t', 'small', '-f'].join(" ")
}

Expand All @@ -242,7 +242,7 @@ class FloatGridExecutorTest extends Specification {
'--cpu', '2',
'--mem', '4',
'--job', script,
'--name', jobID(taskID),
'--customTag', jobID(taskID),
'-f', '-t', 'small'].join(' ')
}

Expand All @@ -259,7 +259,7 @@ class FloatGridExecutorTest extends Specification {

when:
task.config = [nfs : nfs,
extra: '--name hello',] as TaskConfig
extra: '--customTag hello',] as TaskConfig
task.id = taskID
def cmd = exec.getSubmitCommandLine(task, Paths.get(script))

Expand All @@ -273,9 +273,9 @@ class FloatGridExecutorTest extends Specification {
'--cpu', '2',
'--mem', '4',
'--job', script,
'--name', jobID(taskID),
'--customTag', jobID(taskID),
'-t', 'small', '-f',
'--name', 'hello'].join(' ')
'--customTag', 'hello'].join(' ')
}

def "config level cpu and memory"() {
Expand Down Expand Up @@ -307,7 +307,7 @@ class FloatGridExecutorTest extends Specification {
'--cpu', cpu.toString(),
'--mem', mem.toString(),
'--job', script,
'--name', jobID(taskID)].join(' ')
'--customTag', jobID(taskID)].join(' ')
}

def "use default cpu, memory and image"() {
Expand Down Expand Up @@ -337,7 +337,7 @@ class FloatGridExecutorTest extends Specification {
'--cpu', '2',
'--mem', '4',
'--job', script,
'--name', jobID(taskID)].join(' ')
'--customTag', jobID(taskID)].join(' ')
}

def "use default nfs and work dir"() {
Expand Down Expand Up @@ -367,7 +367,7 @@ class FloatGridExecutorTest extends Specification {
'--cpu', cpu.toString(),
'--mem', mem.toString(),
'--job', script,
'--name', jobID(taskID)].join(' ')
'--customTag', jobID(taskID)].join(' ')
}

def "parse data volume"() {
Expand Down Expand Up @@ -399,7 +399,7 @@ class FloatGridExecutorTest extends Specification {
'--cpu', cpu.toString(),
'--mem', mem.toString(),
'--job', script,
'--name', jobID(taskID),
'--customTag', jobID(taskID),
'-M', 'cpu.upperBoundDuration=5s',
'--dataVolume', '"[size=50]":/BWA_BASE'].join(' ')
}
Expand All @@ -414,70 +414,100 @@ class FloatGridExecutorTest extends Specification {
"name": "tJob-0",
"user": "admin",
"imageID": "docker.io/memverge/cactus:latest",
"status": "Submitted"
"status": "Submitted",
"customTags": {
"nf-job-id": "tJob-0"
}
},
{
"id": "task1",
"name": "tJob-1",
"user": "admin",
"imageID": "docker.io/memverge/cactus:latest",
"status": "Initializing"
"status": "Initializing",
"customTags": {
"nf-job-id": "tJob-1"
}
},
{
"id": "task2",
"name": "tJob-2",
"user": "admin",
"imageID": "docker.io/memverge/cactus:latest",
"status": "Executing"
"status": "Executing",
"customTags": {
"nf-job-id": "tJob-2"
}
},
{
"id": "task3",
"name": "tJob-3",
"user": "admin",
"imageID": "docker.io/memverge/cactus:latest",
"status": "Floating"
"status": "Floating",
"customTags": {
"nf-job-id": "tJob-3"
}
},
{
"id": "task4",
"name": "tJob-4",
"user": "admin",
"imageID": "docker.io/memverge/cactus:latest",
"status": "Completed"
"status": "Completed",
"customTags": {
"nf-job-id": "tJob-4"
}
},
{
"id": "task5",
"name": "tJob-5",
"user": "admin",
"imageID": "docker.io/memverge/cactus:latest",
"status": "Cancelled"
"status": "Cancelled",
"customTags": {
"nf-job-id": "tJob-5"
}
},
{
"id": "task6",
"name": "tJob-6",
"user": "admin",
"imageID": "docker.io/memverge/cactus:latest",
"status": "FailToComplete"
"status": "FailToComplete",
"customTags": {
"nf-job-id": "tJob-6"
}
},
{
"id": "task7",
"name": "tJob-7",
"user": "admin",
"imageID": "docker.io/memverge/cactus:latest",
"status": "FailToExecute"
"status": "FailToExecute",
"customTags": {
"nf-job-id": "tJob-7"
}
},
{
"id": "task8",
"name": "tJob-8",
"user": "admin",
"imageID": "docker.io/memverge/cactus:latest",
"status": "Completed"
"status": "Completed",
"customTags": {
"nf-job-id": "tJob-8"
}
},
{
"id": "task9",
"name": "tJob-9",
"user": "admin",
"imageID": "docker.io/memverge/cactus:latest",
"status": "Starting"
"status": "Starting",
"customTags": {
"nf-job-id": "tJob-9"
}
}
]
""".stripIndent()
Expand Down Expand Up @@ -555,7 +585,7 @@ class FloatGridExecutorTest extends Specification {
'--cpu', cpu.toString(),
'--mem', mem.toString(),
'--job', script,
'--name', jobID(taskID)].join(' ')
'--customTag', jobID(taskID)].join(' ')

cleanup:
setEnv('MMC_ADDRESS', '')
Expand Down