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[GH-38] Track job with tags
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For now, we use the name of the job to track the ownership of the
job. But many user want to give their own job names.

It's better to use the tag to track the source of the job. And user
could always add more tags for their own usage.

Add `nf-job-id` tag to track the nf task info.
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@jealous
jealous committed Jul 13, 2023
1 parent de44ee2 commit 0acbb84
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Showing 7 changed files with 77 additions and 36 deletions.
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)
}
}
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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
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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
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2 changes: 1 addition & 1 deletion plugins/nf-float/src/main/com/memverge/nextflow/FloatJobs.groovy
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Original file line number Diff line number Diff line change
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"() {
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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}"
}
}
76 changes: 53 additions & 23 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()
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