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Add multiple enhancements. #64

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merged 3 commits into from
Sep 8, 2023
Merged

Add multiple enhancements. #64

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7bc44f3
Add cpu/memory factor
jealous Sep 2, 2023
dbf06b5
Do not update the job status when it's finished
jealous Sep 2, 2023
2b117c4
Handle quoted params in extra.
jealous Sep 8, 2023
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11 changes: 10 additions & 1 deletion 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 @@ -37,6 +37,7 @@ class FloatConf {
static final String NF_RUN_NAME = 'nextflow-io-run-name'
static final String NF_SESSION_ID = 'nextflow-io-session-id'
static final String NF_TASK_NAME = 'nextflow-io-task-name'
static final String NF_INPUT_SIZE = 'nextflow-io-input-size'

/** credentials for op center */
String username
Expand All @@ -54,6 +55,8 @@ class FloatConf {
String commonExtra

float timeFactor = 1
float cpuFactor = 1
float memoryFactory = 1

/**
* Create a FloatConf instance and initialize the content from the
Expand Down Expand Up @@ -146,6 +149,12 @@ class FloatConf {
if (floatNode.timeFactor) {
this.timeFactor = floatNode.timeFactor as Float
}
if (floatNode.cpuFactor) {
this.cpuFactor = floatNode.cpuFactor as Float
}
if (floatNode.memoryFactor) {
this.memoryFactory = floatNode.memoryFactor as Float
}
this.commonExtra = floatNode.commonExtra

if (floatNode.cpu)
Expand All @@ -162,7 +171,7 @@ class FloatConf {
warnDeprecated("float.container", "process.container")
}

private String collapseMapToString(Map map) {
private static String collapseMapToString(Map map) {
final collapsedStr = map
.toConfigObject()
.flatten()
Expand Down
68 changes: 58 additions & 10 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 @@ -28,6 +28,8 @@ import nextflow.util.ServiceName

import java.nio.file.Path
import java.nio.file.StandardCopyOption
import java.util.regex.Matcher
import java.util.regex.Pattern
import java.util.stream.Collectors

/**
Expand Down Expand Up @@ -122,14 +124,17 @@ class FloatGridExecutor extends AbstractGridExecutor {
log.info "[float] sync the float binary, $res"
}

private static String getMemory(TaskRun task) {
private String getMemory(TaskRun task) {
final mem = task.config.getMemory()
final giga = mem?.toGiga()
Long giga = mem?.toGiga()
if (!giga) {
log.debug "memory $mem is too small. " +
"will use default $DFT_MEM_GB"
giga = DFT_MEM_GB
}
return giga ? giga.toString() : DFT_MEM_GB
giga = (long) ((float) (giga) * floatConf.memoryFactory)
giga = Math.max(giga, DFT_MEM_GB)
return giga.toString()
}

private Collection<String> getExtra(TaskRun task) {
Expand All @@ -139,10 +144,33 @@ class FloatGridExecutor extends AbstractGridExecutor {
if (common) {
extra = common.trim() + " " + extra.trim()
}
def ret = extra.split('\\s+')
def ret = splitWithQuotes(extra)
return ret.findAll { it.length() > 0 }
}

private static List<String> splitWithQuotes(String input) {
List<String> ret = new ArrayList<String>()
int start = 0
boolean inQuotes = false
for (int i = 0; i < input.size(); i++) {
if (input[i] == '"') {
inQuotes = !inQuotes
}
if ((input[i] == '\t' || input[i] == ' ') && !inQuotes) {
String token = input.substring(start, i).trim()
if (token.size() > 0) {
ret.add(token)
}
start = i
}
}
String token = input.substring(start).trim()
if (token.size() > 0) {
ret.add(token)
}
return ret
}

private List<String> getCmdPrefixForJob(String floatJobID) {
final oc = floatJobs.getOc(floatJobID)
return floatConf.getCliPrefix(oc)
Expand All @@ -164,6 +192,7 @@ class FloatGridExecutor extends AbstractGridExecutor {

if (res.succeeded) {
job = FloatJob.parse(res.out)
job = floatJobs.updateJob(job)
}
} catch (Exception e) {
log.warn "[float] failed to retrieve job status $nfJobID, float: ${job.floatJobID}", e
Expand Down Expand Up @@ -236,6 +265,14 @@ class FloatGridExecutor extends AbstractGridExecutor {
return ret
}

private static long getInputFileSize(TaskRun task) {
long ret = 0
for (def src : task.getInputFilesMap().values()) {
ret += src.size()
}
return ret
}

private Map<String, String> getEnv(FloatTaskHandler handler) {
return isFusionEnabled()
? handler.fusionLauncher().fusionEnv()
Expand All @@ -247,6 +284,7 @@ class FloatGridExecutor extends AbstractGridExecutor {
result[FloatConf.NF_JOB_ID] = floatJobs.getNfJobID(task.id)
result[FloatConf.NF_SESSION_ID] = "uuid-${session.uniqueId}".toString()
result[FloatConf.NF_TASK_NAME] = task.name
result[FloatConf.NF_INPUT_SIZE] = getInputFileSize(task).toString()
if (task.processor.name) {
result[FloatConf.NF_PROCESS_NAME] = task.processor.name
}
Expand Down Expand Up @@ -274,6 +312,12 @@ class FloatGridExecutor extends AbstractGridExecutor {
return value
}

private Integer getCpu(TaskRun task) {
int cpu = task.config.getCpus()
int ret = (int) (((float) cpu) * floatConf.cpuFactor)
return Math.max(ret, 1)
}

List<String> getSubmitCommandLine(FloatTaskHandler handler, Path scriptFile) {
final task = handler.task

Expand All @@ -289,7 +333,7 @@ class FloatGridExecutor extends AbstractGridExecutor {
cmd << 'submit'
getMountVols(task).forEach { cmd << '--dataVolume' << it }
cmd << '--image' << task.getContainer()
cmd << '--cpu' << task.config.getCpus().toString()
cmd << '--cpu' << getCpu(task).toString()
cmd << '--mem' << getMemory(task)
cmd << '--job' << getScriptFilePath(handler, scriptFile)
getEnv(handler).each { key, val ->
Expand Down Expand Up @@ -322,6 +366,9 @@ class FloatGridExecutor extends AbstractGridExecutor {
if (floatConf.extraOptions) {
cmd << '--extraOptions' << floatConf.extraOptions
}
if (task.config.getAttempt() > 1) {
cmd << '--vmPolicy' << '[onDemand=true]'
}
cmd.addAll(getExtra(task))
log.info "[float] submit job: ${toLogStr(cmd)}"
return cmd
Expand Down Expand Up @@ -511,15 +558,16 @@ class FloatGridExecutor extends AbstractGridExecutor {
if (!job) {
return FloatStatus.UNKNOWN
}
log.debug "[float] task id: ${task.id}, nf-job-id: $job.nfJobID, " +
log.info "[float] task id: ${task.id}, nf-job-id: $job.nfJobID, " +
"float-job-id: $job.floatJobID, float status: $job.status"
if (job.finished) {
floatJobs.refreshWorkDir(job.nfJobID)
task.exitStatus = job.rcCode
}
return job.status
}

Integer getJobRC(TaskId id) {
def job = getJob(id)
return job.rcCode
}

static private Map<FloatStatus, QueueStatus> STATUS_MAP = new HashMap<>()

static {
Expand Down
6 changes: 3 additions & 3 deletions plugins/nf-float/src/main/com/memverge/nextflow/FloatJob.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -126,8 +126,8 @@ class FloatJob {
return status ? status.isFinished() : false
}

static Map<String, FloatJob> parseJobMap(String input) {
Map<String, FloatJob> ret = new HashMap<>()
static List<FloatJob> parseJobMap(String input) {
List<FloatJob> ret = []
try {
def parser = new JsonSlurper()
def obj = parser.parseText(input)
Expand All @@ -142,7 +142,7 @@ class FloatJob {
job.floatJobID = floatJobID
job.status = FloatStatus.of(status)
job.rc = i.rc as String
ret[nfJobID] = job
ret.add(job)
}
}
} catch (Exception e) {
Expand Down
49 changes: 15 additions & 34 deletions plugins/nf-float/src/main/com/memverge/nextflow/FloatJobs.groovy
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Expand Up @@ -15,14 +15,12 @@
*/
package com.memverge.nextflow

import groovy.transform.WithReadLock
import groovy.transform.WithWriteLock

import groovy.util.logging.Slf4j
import nextflow.file.FileHelper
import nextflow.processor.TaskId
import org.apache.commons.lang.RandomStringUtils

import java.nio.file.NoSuchFileException
import java.nio.file.Path
import java.util.concurrent.ConcurrentHashMap

Expand Down Expand Up @@ -59,7 +57,6 @@ class FloatJobs {
return floatJobID2oc.getOrDefault(floatJobID, ocs[0])
}

@WithReadLock
Map<String, FloatJob> getNfJobID2job() {
return nfJobID2FloatJob
}
Expand All @@ -73,12 +70,18 @@ class FloatJobs {
return updateOcStatus(ocs[0], text)
}

FloatStatus getJobStatus(String nfJobID) {
FloatJob job = nfJobID2FloatJob.get(nfJobID)
if (job == null) {
return FloatStatus.UNKNOWN
FloatJob updateJob(FloatJob job) {
FloatJob existingJob = nfJobID2job.get(job.nfJobID)
if (existingJob != null && existingJob.finished) {
// job already finished, no need to update
job = existingJob
} else {
nfJobID2job.put(job.nfJobID, job)
}
if (job.finished) {
refreshWorkDir(job.nfJobID)
}
return job.status
return job
}

def refreshWorkDir(String nfJobID) {
Expand All @@ -89,37 +92,15 @@ class FloatJobs {
}
}

@WithWriteLock
def updateOcStatus(String oc, String text) {
def stMap = FloatJob.parseJobMap(text)
stMap.each { nfJobID, job ->
def jobs = FloatJob.parseJobMap(text)
jobs.each {job ->
if (!job.nfJobID || !job.status) {
return
}
floatJobID2oc.put(job.floatJobID, oc)
def currentSt = getJobStatus(nfJobID)
def workDir = nfJobID2workDir.get(job.nfJobID)
if (workDir && job.finished) {
refreshWorkDir(job.nfJobID)
def files = ['.command.out', '.command.err', '.exitcode']
if (!currentSt.finished && job.finished) {
for (filename in files) {
def name = workDir.resolve(filename)
try {
!FileHelper.checkIfExists(name, [checkIfExists: true])
} catch (NoSuchFileException ex) {
log.info "[float] job $nfJobID completed " +
"but file not found: ${ex.message}"
job.status = currentSt
return
}
}
log.debug "[float] found $files in: $workDir"
}
}

updateJob(job)
}
nfJobID2FloatJob += stMap
log.debug "[float] update op-center $oc job status"
return nfJobID2FloatJob
}
Expand Down
6 changes: 4 additions & 2 deletions plugins/nf-float/src/main/com/memverge/nextflow/FloatTaskHandler.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -74,16 +74,18 @@ class FloatTaskHandler extends GridTaskHandler {
final FloatStatus st = floatExecutor.getJobStatus(task)
if (st.finished) {
status = COMPLETED
task.exitStatus = readExitStatus()
if (task.exitStatus == null) {
task.exitStatus = readExitStatus()
task.exitStatus = floatExecutor.getJobRC(task.id)
}
// both exit status and job rc code are empty
if (task.exitStatus == null) {
if (st.isError()) {
task.exitStatus = 1
} else {
task.exitStatus = 0
}
log.info "both .exitcode and rc are empty for ${task.id}," +
"set exit to ${task.exitStatus}"
}
task.stdout = outputFile
task.stderr = errorFile
Expand Down
7 changes: 4 additions & 3 deletions plugins/nf-float/src/test/com/memverge/nextflow/FloatBaseTest.groovy
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Expand Up @@ -110,8 +110,9 @@ class FloatBaseTest extends BaseTest {
'--mem', param.memory ?: mem.toString(),
'--job', script,
'--customTag', jobID(taskID),
'--customTag', "nextflow-io-session-id:uuid-$uuid",
'--customTag', "nextflow-io-task-name:foo-$taskIndex",
'--customTag', 'nextflow-io-run-name:test-run']
'--customTag', "${FloatConf.NF_SESSION_ID}:uuid-$uuid",
'--customTag', "${FloatConf.NF_TASK_NAME}:foo-$taskIndex",
'--customTag', "${FloatConf.NF_INPUT_SIZE}:0",
'--customTag', "${FloatConf.NF_RUN_NAME}:test-run"]
}
}
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