Merge pull request #166 from TheRoddyWMS/slurm-fix-eligible-and-start…

…-time-for-jobs-that-never-started Slurm fix eligible and start time for jobs that never started
TheRoddyWMS · Jul 5, 2023 · e5c3b5d · e5c3b5d
2 parents 87f1b5b + f456e98
commit e5c3b5d
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Showing 4 changed files with 178 additions and 10 deletions.
diff --git a/README.md b/README.md
@@ -89,6 +89,11 @@ To start the integration tests, please fill in host and user settings (password
 
 # Change Logs
 
+* 0.1.4
+  - patch: Changed the conversion of EpochSeconds to ZonedDateTime for the value "0".
+    * For eligibleTime it is set to null
+    * For startTime it is set to endTime
+
 * 0.1.3
   - patch: Added getter for JobState enum.
   - patch: Fix SLURM API.

diff --git a/src/main/groovy/de/dkfz/roddy/execution/jobs/cluster/slurm/SlurmJobManager.groovy b/src/main/groovy/de/dkfz/roddy/execution/jobs/cluster/slurm/SlurmJobManager.groovy
@@ -160,7 +160,7 @@ class SlurmJobManager extends GridEngineBasedJobManager {
         if (!supplement) {
             return primary
         }
-        primary.properties.findAll { k, v->
+        primary.properties.findAll { k, v ->
             if (!v && supplement."${k}") {
                 primary."${k}" = supplement."${k}"
             }
@@ -337,9 +337,15 @@ class SlurmJobManager extends GridEngineBasedJobManager {
 
         /** Timestamps */
         jobInfo.submitTime = parseTimeOfEpochSecond(jsonEntry["time"]["submission"] as String)
-        jobInfo.eligibleTime = parseTimeOfEpochSecond(jsonEntry["time"]["eligible"] as String)
-        jobInfo.startTime = parseTimeOfEpochSecond(jsonEntry["time"]["start"] as String)
+        String eligibleTime = jsonEntry["time"]["eligible"] as String
+        jobInfo.eligibleTime = eligibleTime != "0" ? parseTimeOfEpochSecond(eligibleTime) : null // convert "0" to null
         jobInfo.endTime = parseTimeOfEpochSecond(jsonEntry["time"]["end"] as String)
+        /**
+         * When startTime is "0", endTime should be used. Otherwise parseTimeOfEpochSecond will return 1970.
+         * Null here is not an option with how this value is currently used.
+         **/
+        String startTime = jsonEntry["time"]["start"] as String
+        jobInfo.startTime = startTime != "0" ? parseTimeOfEpochSecond(startTime) : jobInfo.endTime
 
 
         return jobInfo

diff --git a/src/test/groovy/de/dkfz/roddy/execution/jobs/cluster/slurm/SlurmJobManagerSpec.groovy b/src/test/groovy/de/dkfz/roddy/execution/jobs/cluster/slurm/SlurmJobManagerSpec.groovy
@@ -44,9 +44,9 @@ class SlurmJobManagerSpec extends Specification {
         jobInfo.logFile == new File("/path/to/outputFile")
         jobInfo.user == "user(192456)"
         jobInfo.submissionHost == "compute038"
-        jobInfo.executionHosts ==  ["compute038"]
-        jobInfo.errorLogFile ==  new File("/path/to/errorFile")
-        jobInfo.execHome ==  "/home/user"
+        jobInfo.executionHosts == ["compute038"]
+        jobInfo.errorLogFile == new File("/path/to/errorFile")
+        jobInfo.execHome == "/home/user"
 
         /** Status info */
         jobInfo.jobState == JobState.RUNNING
@@ -59,12 +59,12 @@ class SlurmJobManagerSpec extends Specification {
         jobInfo.askedResources.cores == 76
         jobInfo.askedResources.nodes == 1
         jobInfo.askedResources.walltime == Duration.parse("PT20H")
-        jobInfo.askedResources.queue  == "compute"
+        jobInfo.askedResources.queue == "compute"
         jobInfo.usedResources.mem == new BufferValue(300, BufferUnit.G, BufferUnit.K)
         jobInfo.usedResources.cores == 76
         jobInfo.usedResources.nodes == 1
         jobInfo.usedResources.walltime == Duration.parse("PT3H21M58S")
-        jobInfo.usedResources.queue  == "compute"
+        jobInfo.usedResources.queue == "compute"
         jobInfo.submitTime.toString().startsWith("2023-06-20T07:07:33")
         jobInfo.eligibleTime.toString().startsWith("2023-06-20T07:07:33")
         jobInfo.startTime.toString().startsWith("2023-06-20T07:07:34")
@@ -93,12 +93,12 @@ class SlurmJobManagerSpec extends Specification {
         jobInfo.askedResources.cores == 1
         jobInfo.askedResources.nodes == 1
         jobInfo.askedResources.walltime == Duration.parse("PT5H")
-        jobInfo.askedResources.queue  == "compute"
+        jobInfo.askedResources.queue == "compute"
         jobInfo.usedResources.mem == new BufferValue(7168, BufferUnit.M, BufferUnit.K)
         jobInfo.usedResources.cores == 1
         jobInfo.usedResources.nodes == 1
         jobInfo.usedResources.walltime == Duration.parse("PT3M58S")
-        jobInfo.usedResources.queue  == "compute"
+        jobInfo.usedResources.queue == "compute"
         jobInfo.runTime == Duration.parse("PT3M58S")
 
         /** Directories and files */
@@ -119,6 +119,17 @@ class SlurmJobManagerSpec extends Specification {
         jobInfo.executionHosts == ["compute015"]
     }
 
+    def "test processSacctOutputFromJson with sacct_not_started.json"() {
+        when:
+        GenericJobInfo jobInfo = jobManager.processSacctOutputFromJson(getResourceFile("sacct_not_started.json").text)
+
+        then:
+        jobInfo.submitTime.toInstant().toEpochMilli() / 1000 == 1688463559
+        !jobInfo.eligibleTime
+        jobInfo.endTime.toInstant().toEpochMilli() / 1000 == 1688498739
+        jobInfo.startTime == jobInfo.endTime
+    }
+
     def "test fillFromSupplement"() {
         given:
         GenericJobInfo primary = new GenericJobInfo("jobName", new File("command"), new BEJobID("1"), [:], [])

diff --git a/src/test/resources/de/dkfz/roddy/execution/jobs/cluster/slurm/sacct_not_started.json b/src/test/resources/de/dkfz/roddy/execution/jobs/cluster/slurm/sacct_not_started.json
@@ -0,0 +1,146 @@
+{
+  "meta": {
+    "plugin": {
+      "type": "openapi\/dbv0.0.37",
+      "name": "Slurm OpenAPI DB v0.0.37"
+    },
+    "Slurm": {
+      "version": {
+        "major": 22,
+        "micro": 2,
+        "minor": 5
+      },
+      "release": "22.05.2"
+    }
+  },
+  "errors": [
+  ],
+  "jobs": [
+    {
+      "account": "users",
+      "comment": {
+        "administrator": null,
+        "job": null,
+        "system": null
+      },
+      "allocation_nodes": 0,
+      "array": {
+        "job_id": 0,
+        "limits": {
+          "max": {
+            "running": {
+              "tasks": 0
+            }
+          }
+        },
+        "task": null,
+        "task_id": null
+      },
+      "association": {
+        "account": "users",
+        "cluster": "slurm-cluster",
+        "partition": null,
+        "user": "user"
+      },
+      "cluster": "slurm-cluster",
+      "constraints": "",
+      "derived_exit_code": {
+        "status": "SUCCESS",
+        "return_code": 0
+      },
+      "time": {
+        "elapsed": 0,
+        "eligible": 0,
+        "end": 1688498739,
+        "start": 0,
+        "submission": 1688463559,
+        "suspended": 0,
+        "system": {
+          "seconds": 0,
+          "microseconds": 0
+        },
+        "limit": 7200,
+        "total": {
+          "seconds": 0,
+          "microseconds": 0
+        },
+        "user": {
+          "seconds": 0,
+          "microseconds": 0
+        }
+      },
+      "exit_code": {
+        "status": "SUCCESS",
+        "return_code": 0
+      },
+      "flags": [
+      ],
+      "group": "users",
+      "het": {
+        "job_id": 0,
+        "job_offset": null
+      },
+      "job_id": 275097,
+      "name": "jobName",
+      "mcs": {
+        "label": ""
+      },
+      "nodes": "None assigned",
+      "partition": "devel",
+      "priority": 1116,
+      "qos": "normal",
+      "required": {
+        "CPUs": 6,
+        "memory": 102400
+      },
+      "kill_request_user": "user",
+      "reservation": {
+        "id": 0,
+        "name": 0
+      },
+      "state": {
+        "current": "CANCELLED",
+        "reason": "Dependency"
+      },
+      "steps": [
+      ],
+      "tres": {
+        "allocated": [
+        ],
+        "requested": [
+          {
+            "type": "cpu",
+            "name": null,
+            "id": 1,
+            "count": 6
+          },
+          {
+            "type": "mem",
+            "name": null,
+            "id": 2,
+            "count": 102400
+          },
+          {
+            "type": "node",
+            "name": null,
+            "id": 4,
+            "count": 1
+          },
+          {
+            "type": "billing",
+            "name": null,
+            "id": 5,
+            "count": 31
+          }
+        ]
+      },
+      "user": "user",
+      "wckey": {
+        "wckey": "",
+        "flags": [
+        ]
+      },
+      "working_directory": "\/path\/to\/file"
+    }
+  ]
+}