Simulation State Machine Tests

docker/build/Dockerfile-sched-dev

@@ -68,7 +68,10 @@ ENV softwareVersion=SOFTWARE-VERSION-NOT-SET \
 	maxOdeJobsPerUser="max-ode-jobs-per-user-not-set" \
 	vcell_ssh_cmd_cmdtimeout="cmdSrvcSshCmdTimeoutMS-not-set" \
     vcell_ssh_cmd_restoretimeout="cmdSrvcSshCmdRestoreTimeoutFactor-not-set" \
-	maxPdeJobsPerUser="max-pde-jobs-per-user-not-set"
+	maxPdeJobsPerUser="max-pde-jobs-per-user-not-set" \
+	htcMinMemoryMB="htc-min-memory-not-set" \
+	htcMaxMemoryMB="htc-max-memory-not-set" \
+	htcPowerUserMemoryFloorMB="htc-power-user-memory-floor-not-set"
 
 ENV dbpswdfile=/run/secrets/dbpswd \
     jmspswdfile=/run/secrets/jmspswd \
@@ -119,4 +122,7 @@ ENTRYPOINT java \
 	-Dvcell.server.maxPdeJobsPerUser=${maxPdeJobsPerUser} \
 	-Dvcell.ssh.cmd.cmdtimeout=${vcell_ssh_cmd_cmdtimeout} \
 	-Dvcell.ssh.cmd.restoretimeout=${vcell_ssh_cmd_restoretimeout} \
-	-cp "./lib/*" cbit.vcell.message.server.dispatcher.SimulationDispatcher
+	-Dvcell.htc.memory.min.mb=${htcMinMemoryMB} \
+	-Dvcell.htc.memory.max.mb=${htcMaxMemoryMB} \
+	-Dvcell.htc.memory.pu.floor.mb=${htcPowerUserMemoryFloorMB} \
+	-cp "./lib/*" cbit.vcell.message.server.dispatcher.SimulationDispatcherMain

vcell-core/src/main/java/cbit/rmi/event/WorkerEvent.java

@@ -19,6 +19,8 @@
 import cbit.vcell.solver.VCSimulationIdentifier;
 import cbit.vcell.solver.server.SimulationMessage;
 
+import java.util.ArrayList;
+
 /**
  * Insert the type's description here.
  * Creation date: (2/5/2004 12:35:20 PM)
@@ -36,6 +38,10 @@ public class WorkerEvent extends MessageEvent {
 	public static final int JOB_WORKER_EXIT_NORMAL = 1015;
 	public static final int JOB_WORKER_EXIT_ERROR = 1016;
 
+	public static final ArrayList<Integer> ALL_JOB_EVENTS = new ArrayList<>(){{add(JOB_ACCEPTED);
+	add(JOB_STARTING); add(JOB_DATA); add(JOB_PROGRESS); add(JOB_FAILURE); add(JOB_COMPLETED); add(JOB_WORKER_ALIVE);
+	add(JOB_WORKER_EXIT_NORMAL); add(JOB_WORKER_EXIT_ERROR);}};
+
 	private VCSimulationIdentifier vcSimulationIdentifier = null;
 	private int jobIndex = -1;
 	private String hostName = null;

vcell-core/src/main/java/cbit/vcell/resource/PropertyLoader.java

@@ -80,6 +80,9 @@ public static void setConfigProvider(VCellConfigProvider configProvider) {
 	public static final String htcPbsHome		 			= record("vcell.htc.pbs.home",ValueType.GEN);
 	public static final String htcSgeHome		 			= record("vcell.htc.sge.home",ValueType.GEN);
 	public static final String htcNodeList                   = record("vcell.htc.nodelist",ValueType.GEN);
+	public static final String htcMinMemoryMB				= record("vcell.htc.memory.min.mb", ValueType.INT); // minimum memory request in MB, currently 4g
+	public static final String htcMaxMemoryMB				= record("vcell.htc.memory.max.mb", ValueType.INT); // maximum memory request in MB
+	public static final String htcPowerUserMemoryFloorMB	= record("vcell.htc.memory.pu.floor.mb", ValueType.INT); // MIN memory allowed if declared to be a power user, currently 50g (Previously Existing Value)
 	public static final String slurm_cmd_sbatch				= record("vcell.slurm.cmd.sbatch",ValueType.GEN);
 	public static final String slurm_cmd_scancel				= record("vcell.slurm.cmd.scancel",ValueType.GEN);
 	public static final String slurm_cmd_sacct				= record("vcell.slurm.cmd.sacct",ValueType.GEN);

vcell-core/src/main/java/org/vcell/util/document/User.java

@@ -20,11 +20,17 @@
  * This type was created in VisualAge.
  */
 @SuppressWarnings("serial")
-public class User implements java.io.Serializable, Matchable, Immutable {
+public class User implements java.io.Serializable, Matchable, Immutable, Comparable {
 	private final static String PREVIOUS_DATABASE_VALUE_ADMIN = "special0";
 	private final static String PREVIOUS_DATABASE_VALUE_POWERUSER = "special1";
 	private final static String PREVIOUS_DATABASE_VALUE_PUBLICATION = "publication";
 
+	@Override
+	public int compareTo(Object o) {
+		User user = (User) o;
+		return this.getID().compareTo(user.key);
+	}
+
 	public enum SPECIAL_CLAIM {
 		admins/*special0*/,
 		powerUsers/*special1*/,

vcell-rest/src/main/java/org/vcell/restq/Simulations/SimulationExecutionStatusRecord.java → vcell-rest/src/main/java/org/vcell/restq/Simulations/DTO/SimulationExecutionStatus.java

@@ -1,11 +1,10 @@
-package org.vcell.restq.Simulations;
+package org.vcell.restq.Simulations.DTO;
 
 import cbit.vcell.server.HtcJobID;
-import cbit.vcell.server.SimulationExecutionStatus;
 
 import java.time.Instant;
 
-public record SimulationExecutionStatusRecord(
+public record SimulationExecutionStatus(
         Instant fieldStartDate,
         Instant fieldLatestUpdateDate,
         Instant fieldEndDate,
@@ -14,9 +13,9 @@ public record SimulationExecutionStatusRecord(
         HtcJobID fieldHtcJobID
 ) {
 
-    public static SimulationExecutionStatusRecord fromSimulationExecutionStatus(SimulationExecutionStatus status) {
+    public static SimulationExecutionStatus fromSimulationExecutionStatus(cbit.vcell.server.SimulationExecutionStatus status) {
         if (status == null) {return null;}
-        return new SimulationExecutionStatusRecord(
+        return new SimulationExecutionStatus(
                 status.getStartDate() != null ? status.getStartDate().toInstant(): null,
                 status.getLatestUpdateDate() != null ? status.getLatestUpdateDate().toInstant() : null,
                 status.getEndDate() != null ? status.getEndDate().toInstant(): null,

vcell-rest/src/main/java/org/vcell/restq/Simulations/DTO/SimulationJobStatus.java

@@ -0,0 +1,37 @@
+package org.vcell.restq.Simulations.DTO;
+
+import cbit.vcell.solver.VCSimulationIdentifier;
+import cbit.vcell.solver.server.SimulationMessage;
+
+import java.time.Instant;
+
+public record SimulationJobStatus(
+        Instant fieldTimeDataStamp,
+        VCSimulationIdentifier fieldVCSimID,
+        Instant fieldSubmitDate,
+        cbit.vcell.server.SimulationJobStatus.SchedulerStatus fieldSchedulerStatus,
+        SimulationMessage fieldSimulationMessage,
+        int fieldTaskID,
+        String fieldServerID,
+        int fieldJobIndex,
+        SimulationExecutionStatus fieldSimulationExecutionStatus,
+        SimulationQueueEntryStatus fieldSimulationQueueEntryStatus
+) {
+
+    public static SimulationJobStatus fromSimulationJobStatus(cbit.vcell.server.SimulationJobStatus s) {
+        if (s == null) {return null;}
+        return new SimulationJobStatus(
+                s.getTimeDateStamp() != null ? s.getTimeDateStamp().toInstant(): null,
+                s.getVCSimulationIdentifier(),
+                s.getSubmitDate() != null ? s.getSubmitDate().toInstant(): null,
+                s.getSchedulerStatus(),
+                s.getSimulationMessage(),
+                s.getTaskID(),
+                s.getServerID() != null ? s.getServerID().toString() : null,
+                s.getJobIndex(),
+                SimulationExecutionStatus.fromSimulationExecutionStatus(s.getSimulationExecutionStatus()),
+                SimulationQueueEntryStatus.fromStatusRecord(s.getSimulationQueueEntryStatus())
+        );
+    }
+
+}

vcell-rest/src/main/java/org/vcell/restq/Simulations/SimulationQueueEntryStatusRecord.java → vcell-rest/src/main/java/org/vcell/restq/Simulations/DTO/SimulationQueueEntryStatus.java

@@ -1,19 +1,18 @@
-package org.vcell.restq.Simulations;
+package org.vcell.restq.Simulations.DTO;
 
 import cbit.vcell.server.SimulationJobStatus;
-import cbit.vcell.server.SimulationQueueEntryStatus;
 
 import java.time.Instant;
 
-public record SimulationQueueEntryStatusRecord(
+public record SimulationQueueEntryStatus(
         int fieldQueuePriority,
         Instant fieldQueueDate,
         SimulationJobStatus.SimulationQueueID fieldQueueID
 ) {
 
-    public static SimulationQueueEntryStatusRecord fromStatusRecord(SimulationQueueEntryStatus simulationQueueEntryStatus) {
+    public static SimulationQueueEntryStatus fromStatusRecord(cbit.vcell.server.SimulationQueueEntryStatus simulationQueueEntryStatus) {
         if (simulationQueueEntryStatus == null) {return null;}
-        return new SimulationQueueEntryStatusRecord(
+        return new SimulationQueueEntryStatus(
                 simulationQueueEntryStatus.getQueuePriority(),
                 simulationQueueEntryStatus.getQueueDate().toInstant(),
                 simulationQueueEntryStatus.getQueueID()

vcell-rest/src/main/java/org/vcell/restq/Simulations/SimulationStatusPersistentRecord.java → vcell-rest/src/main/java/org/vcell/restq/Simulations/DTO/SimulationStatus.java

@@ -1,10 +1,8 @@
-package org.vcell.restq.Simulations;
+package org.vcell.restq.Simulations.DTO;
 
 import cbit.vcell.server.SimulationStatusPersistent;
 
-import java.util.HashMap;
-
-public record SimulationStatusPersistentRecord(
+public record SimulationStatus(
         Status status,
         String details,
         boolean hasData
@@ -46,9 +44,9 @@ public static Status statusFromString(String statusString){
         }
     }
 
-    public static SimulationStatusPersistentRecord fromSimulationStatusPersistent(SimulationStatusPersistent s) {
+    public static SimulationStatus fromSimulationStatusPersistent(SimulationStatusPersistent s) {
         if (s == null) return null;
-        return new SimulationStatusPersistentRecord(
+        return new SimulationStatus(
                 Status.statusFromString(s.getStatusString()),
                 s.getDetails(),
                 s.getHasData()

vcell-rest/src/main/java/org/vcell/restq/Simulations/DTO/StatusMessage.java

@@ -0,0 +1,16 @@
+package org.vcell.restq.Simulations.DTO;
+
+import java.util.ArrayList;
+
+public record StatusMessage(SimulationJobStatus jobStatus, String userName, Double progress, Double timepoint) {
+
+
+    public static ArrayList<StatusMessage> convertServerStatusMessages(ArrayList<cbit.vcell.message.messages.StatusMessage> statusMessages){
+        ArrayList<StatusMessage> dtoStatusMessage = new ArrayList<>();
+        for (cbit.vcell.message.messages.StatusMessage statusMessage: statusMessages){
+            dtoStatusMessage.add(new StatusMessage(SimulationJobStatus.fromSimulationJobStatus(statusMessage.getJobStatus()), statusMessage.getUserName(),
+                    statusMessage.getProgress(), statusMessage.getTimePoint()));
+        }
+        return dtoStatusMessage;
+    }
+}