Examples with HtcJobID cbit.vcell.server.HtcJobID used on opensource projects

Example 1 with HtcJobID

use of cbit.vcell.server.HtcJobID in project vcell by virtualcell.

the class SimulationJobStatusEvent method toJsonRep.

public SimulationJobStatusEventRepresentation toJsonRep() {
    String vcellServerID = this.jobStatus.getServerID().toString();
    Date timeDateStamp = this.jobStatus.getTimeDateStamp();
    String simulationKey = this.jobStatus.getVCSimulationIdentifier().getSimulationKey().toString();
    int taskID = this.jobStatus.getTaskID();
    int jobIndex = this.jobStatus.getJobIndex();
    Date submitDate = this.jobStatus.getSubmitDate();
    String owner_userid = this.username;
    String onwer_userkey = this.jobStatus.getVCSimulationIdentifier().getOwner().getID().toString();
    SimulationJobStatusRepresentation.SchedulerStatus schedulerStatus = SimulationJobStatusRepresentation.SchedulerStatus.valueOf(this.jobStatus.getSchedulerStatus().name());
    SimulationJobStatusRepresentation.DetailedState detailedState = SimulationJobStatusRepresentation.DetailedState.valueOf(this.jobStatus.getSimulationMessage().getDetailedState().name());
    String detailedStateMessage = this.jobStatus.getSimulationMessage().getDisplayMessage();
    Long htcJobNumber = null;
    String htcComputeServer = null;
    SimulationJobStatusRepresentation.BatchSystemType htcBatchSystemType = null;
    Date simexe_startDate = null;
    Date simexe_latestUpdateDate = null;
    Date simexe_endDate = null;
    String computeHost = null;
    Boolean hasData = null;
    SimulationExecutionStatus simExeStatus = this.jobStatus.getSimulationExecutionStatus();
    if (simExeStatus != null) {
        HtcJobID htcJobID = simExeStatus.getHtcJobID();
        if (htcJobID != null) {
            htcJobNumber = htcJobID.getJobNumber();
            htcComputeServer = htcJobID.getServer();
            htcBatchSystemType = SimulationJobStatusRepresentation.BatchSystemType.valueOf(htcJobID.getBatchSystemType().name());
        }
        simexe_startDate = simExeStatus.getStartDate();
        simexe_latestUpdateDate = simExeStatus.getLatestUpdateDate();
        simexe_endDate = simExeStatus.getEndDate();
        computeHost = simExeStatus.getComputeHost();
        hasData = simExeStatus.hasData();
    }
    Integer queuePriority = null;
    Date queueDate = null;
    SimulationJobStatusRepresentation.SimulationQueueID queueId = null;
    SimulationQueueEntryStatus simQueueStatus = this.jobStatus.getSimulationQueueEntryStatus();
    if (simQueueStatus != null) {
        queuePriority = simQueueStatus.getQueuePriority();
        queueDate = simQueueStatus.getQueueDate();
        queueId = SimulationJobStatusRepresentation.SimulationQueueID.valueOf(simQueueStatus.getQueueID().name());
    }
    SimulationJobStatusRepresentation jobStatus = new SimulationJobStatusRepresentation(vcellServerID, timeDateStamp, simulationKey, taskID, jobIndex, submitDate, owner_userid, onwer_userkey, schedulerStatus, detailedState, detailedStateMessage, htcJobNumber, htcComputeServer, htcBatchSystemType, queuePriority, queueDate, queueId, simexe_startDate, simexe_latestUpdateDate, simexe_endDate, computeHost, hasData);
    SimulationJobStatusEventRepresentation eventRep = new SimulationJobStatusEventRepresentation(jobStatus, progress, timePoint, username);
    return eventRep;
}

Example 2 with HtcJobID

use of cbit.vcell.server.HtcJobID in project vcell by virtualcell.

the class HtcProxyTest method test_isMyJob.

@Test
public void test_isMyJob() {
    System.setProperty(PropertyLoader.vcellServerIDProperty, "ALPHA");
    Assert.assertTrue(HtcProxy.isMyJob(new HtcJobInfo(new HtcJobID("1200725", BatchSystemType.SLURM), true, "V_ALPHA_115785823_0_0", null, null)));
    Assert.assertFalse(HtcProxy.isMyJob(new HtcJobInfo(new HtcJobID("1200725", BatchSystemType.SLURM), true, "V_BETA_115785823_0_0", null, null)));
    System.setProperty(PropertyLoader.vcellServerIDProperty, "BETA");
    Assert.assertTrue(HtcProxy.isMyJob(new HtcJobInfo(new HtcJobID("1200725", BatchSystemType.SLURM), true, "V_BETA_115785823_0_0", null, null)));
}

Example 3 with HtcJobID

use of cbit.vcell.server.HtcJobID in project vcell by virtualcell.

the class SlurmProxyTest method testSLURM.

// @Before
// public void setEnv() {
// //System.setProperty(PropertyLoader.htcSlurmHome,"/opt/slurm/");
// System.setProperty( PropertyLoader.htcLogDirExternal,"/home/htcLogs");
// System.setProperty( PropertyLoader.MPI_HOME_EXTERNAL,"/opt/mpich/");
// }
// 
// private void write(String name, String text) {
// try {
// File f = new File(name);
// HtcProxy.writeUnixStyleTextFile(f, text);
// } catch (IOException e) {
// e.printStackTrace();
// }
// }
// 
// private void addExit(Container ctn) {
// final String eToken = "yada-yada";
// ExecutableCommand exitC = new ExecutableCommand(null,"echo",eToken);
// exitC.setExitCodeToken(eToken);
// ctn.add(exitC);
// 
// }
// 
// @Test
// public void tryIt( ) {
// Container ctn = new ExecutableCommand.Container();
// ExecutableCommand listdog = new ExecutableCommand(null,"ls");
// listdog.addArgument("dog");
// ctn.add(listdog);
// ctn.add(new ExecutableCommand(null,"wc","dog"));
// SlurmProxy spProxy = new SlurmProxy(null, "gerard");
// String text = spProxy.generateScript("Q_3", ctn, 1, 10.0, null);
// write("out.sh",text);
// }
// 
// @Test
// public void tryItWithExit( ) {
// Container ctn = new ExecutableCommand.Container();
// ctn.add(new ExecutableCommand(null,"ls","dog"));
// ctn.add(new ExecutableCommand(null,"wc","dog"));
// addExit(ctn);
// 
// SlurmProxy spProxy = new SlurmProxy(null, "gerard");
// String text = spProxy.generateScript("Q_3", ctn, 1, 10.0, null);
// write("outexit.sh",text);
// }
// 
// @Test(expected=UnsupportedOperationException.class)
// public void tryParallelBad( ) {
// Container ctn = new ExecutableCommand.Container();
// ctn.add(new ExecutableCommand(null,true,true,"wc","dog"));
// SlurmProxy spProxy = new SlurmProxy(null, "gerard");
// spProxy.generateScript("Q_3", ctn, 1, 10.0, null);
// }
// 
// @Test
// public void tryParallel( ) {
// Container ctn = new ExecutableCommand.Container();
// ctn.add(new ExecutableCommand(null,"ls","dog"));
// ctn.add(new ExecutableCommand(null,true,true,"wc","dog"));
// SlurmProxy spProxy = new SlurmProxy(null, "gerard");
// String text = spProxy.generateScript("Q_3", ctn, 4, 10.0, null);
// write("par.sh",text);
// }
// @Test
// public void tryParallelExit( ) {
// Container ctn = new ExecutableCommand.Container();
// addExit(ctn);
// ctn.add(new ExecutableCommand(null,"ls","dog"));
// ctn.add(new ExecutableCommand(null,true,true,"wc","dog"));
// SlurmProxy spProxy = new SlurmProxy(null, "gerard");
// String text = spProxy.generateScript("Q_3", ctn, 4, 10.0, null);
// write("parexit.sh",text);
// }
@Test
public void testSLURM() throws IOException, ExecutableException {
    System.setProperty(PropertyLoader.vcellServerIDProperty, "Test2");
    System.setProperty(PropertyLoader.htcLogDirExternal, "/Volumes/vcell/htclogs");
    VCMongoMessage.enabled = false;
    CommandServiceSshNative cmd = null;
    try {
        // for (int i=0;i<10000;i++) {
        cmd = new CommandServiceSshNative("vcell-service.cam.uchc.edu", "vcell", new File("/Users/schaff/.ssh/schaff_rsa"));
        SlurmProxy slurmProxy = new SlurmProxy(cmd, "vcell");
        Map<HtcJobID, JobInfoAndStatus> runningJobs = slurmProxy.getRunningJobs();
        for (HtcJobID job : runningJobs.keySet()) {
            HtcJobStatus jobStatus = runningJobs.get(job).status;
            System.out.println("job " + job.toString() + ", status=" + jobStatus.toString());
        }
        System.out.println("\n\n\n");
        Thread.sleep(100);
    // }
    } catch (Exception e) {
        e.printStackTrace();
    } finally {
        if (cmd != null) {
            cmd.close();
        }
    }
}

Example 4 with HtcJobID

use of cbit.vcell.server.HtcJobID in project vcell by virtualcell.

the class JobIdTest method sysDiff.

private void sysDiff(BatchSystemType bt) {
    long n = r.nextLong();
    HtcJobID x = gen(n, bt, null);
    HtcJobID y = gen(n + 1, bt, null);
    assertFalse(x.equals(y));
    assertFalse(x.compareEqual(y));
    String serverx = randomServer();
    String servery = randomServer();
    x = gen(n, bt, serverx);
    y = gen(n + 1, bt, servery);
    assertFalse(x.equals(y));
    assertFalse(x.compareEqual(y));
}

Example 5 with HtcJobID

use of cbit.vcell.server.HtcJobID in project vcell by virtualcell.

the class SimulationStateMachine method onWorkerEvent.

public synchronized void onWorkerEvent(WorkerEvent workerEvent, SimulationDatabase simulationDatabase, VCMessageSession session) throws DataAccessException, VCMessagingException, SQLException {
    updateSolverProcessTimestamp();
    WorkerEventMessage workerEventMessage = new WorkerEventMessage(workerEvent);
    VCMongoMessage.sendWorkerEvent(workerEventMessage);
    // as the filter of the client
    String userName = workerEvent.getUserName();
    int workerEventTaskID = workerEvent.getTaskID();
    if (lg.isTraceEnabled())
        lg.trace("onWorkerEventMessage[" + workerEvent.getEventTypeID() + "," + workerEvent.getSimulationMessage() + "][simid=" + workerEvent.getVCSimulationDataIdentifier() + ",job=" + jobIndex + ",task=" + workerEventTaskID + "]");
    VCSimulationDataIdentifier vcSimDataID = workerEvent.getVCSimulationDataIdentifier();
    if (vcSimDataID == null) {
        VCMongoMessage.sendInfo("onWorkerEvent() ignoring WorkerEvent - no SimID in message): " + workerEvent.show());
        return;
    }
    KeyValue simKey = vcSimDataID.getSimulationKey();
    SimulationJobStatus oldSimulationJobStatus = simulationDatabase.getLatestSimulationJobStatus(simKey, jobIndex);
    if (oldSimulationJobStatus == null) {
        VCMongoMessage.sendInfo("onWorkerEvent() ignoring WorkerEvent, no current SimulationJobStatus: " + workerEvent.show());
        return;
    }
    if (oldSimulationJobStatus == null || oldSimulationJobStatus.getSchedulerStatus().isDone() || oldSimulationJobStatus.getTaskID() > workerEventTaskID) {
        VCMongoMessage.sendInfo("onWorkerEvent() ignoring outdated WorkerEvent, (currState=" + oldSimulationJobStatus.getSchedulerStatus().getDescription() + "): " + workerEvent.show());
        return;
    }
    int taskID = oldSimulationJobStatus.getTaskID();
    SchedulerStatus oldSchedulerStatus = oldSimulationJobStatus.getSchedulerStatus();
    // 
    // status information (initialized as if new record)
    // 
    Date startDate = null;
    Date lastUpdateDate = null;
    Date endDate = null;
    boolean hasData = false;
    HtcJobID htcJobID = null;
    String computeHost = null;
    VCellServerID vcServerID = VCellServerID.getSystemServerID();
    Date submitDate = null;
    Date queueDate = null;
    int queuePriority = PRIORITY_DEFAULT;
    SimulationJobStatus.SimulationQueueID simQueueID = SimulationJobStatus.SimulationQueueID.QUEUE_ID_WAITING;
    // 
    // update using previously stored status (if available).
    // 
    SimulationExecutionStatus oldSimExeStatus = oldSimulationJobStatus.getSimulationExecutionStatus();
    if (oldSimExeStatus != null && oldSimExeStatus.getStartDate() != null) {
        startDate = oldSimExeStatus.getStartDate();
    }
    if (oldSimExeStatus != null && oldSimExeStatus.getLatestUpdateDate() != null) {
        lastUpdateDate = oldSimExeStatus.getLatestUpdateDate();
    }
    if (oldSimExeStatus != null && oldSimExeStatus.getEndDate() != null) {
        endDate = oldSimExeStatus.getEndDate();
    }
    if (oldSimExeStatus != null && oldSimExeStatus.hasData()) {
        hasData = true;
    }
    if (oldSimExeStatus != null && oldSimExeStatus.getComputeHost() != null) {
        computeHost = oldSimExeStatus.getComputeHost();
    }
    if (oldSimExeStatus != null && oldSimExeStatus.getHtcJobID() != null) {
        htcJobID = oldSimExeStatus.getHtcJobID();
    }
    vcServerID = oldSimulationJobStatus.getServerID();
    submitDate = oldSimulationJobStatus.getSubmitDate();
    SimulationQueueEntryStatus oldQueueStatus = oldSimulationJobStatus.getSimulationQueueEntryStatus();
    if (oldQueueStatus != null && oldQueueStatus.getQueueDate() != null) {
        queueDate = oldQueueStatus.getQueueDate();
    }
    if (oldQueueStatus != null) {
        queuePriority = oldQueueStatus.getQueuePriority();
    }
    if (oldQueueStatus != null && oldQueueStatus.getQueueID() != null) {
        simQueueID = oldQueueStatus.getQueueID();
    }
    // 
    if (workerEvent.getHtcJobID() != null) {
        htcJobID = workerEvent.getHtcJobID();
    }
    if (workerEvent.getHostName() != null) {
        computeHost = workerEvent.getHostName();
    }
    SimulationMessage workerEventSimulationMessage = workerEvent.getSimulationMessage();
    if (workerEventSimulationMessage.getHtcJobId() != null) {
        htcJobID = workerEventSimulationMessage.getHtcJobId();
    }
    SimulationJobStatus newJobStatus = null;
    if (workerEvent.isAcceptedEvent()) {
        // 
        if (oldSchedulerStatus.isWaiting() || oldSchedulerStatus.isQueued()) {
            // new queue status
            SimulationQueueEntryStatus newQueueStatus = new SimulationQueueEntryStatus(queueDate, queuePriority, SimulationJobStatus.SimulationQueueID.QUEUE_ID_NULL);
            // new exe status
            lastUpdateDate = new Date();
            startDate = lastUpdateDate;
            endDate = null;
            SimulationExecutionStatus newExeStatus = new SimulationExecutionStatus(startDate, computeHost, lastUpdateDate, endDate, hasData, htcJobID);
            newJobStatus = new SimulationJobStatus(vcServerID, vcSimDataID.getVcSimID(), jobIndex, submitDate, SchedulerStatus.DISPATCHED, taskID, workerEventSimulationMessage, newQueueStatus, newExeStatus);
        }
    } else if (workerEvent.isStartingEvent()) {
        // only update database when the job event changes from started to running. The later progress event will not be recorded.
        if (oldSchedulerStatus.isWaiting() || oldSchedulerStatus.isQueued() || oldSchedulerStatus.isDispatched() || oldSchedulerStatus.isRunning()) {
            // new queue status
            SimulationQueueEntryStatus newQueueStatus = new SimulationQueueEntryStatus(queueDate, queuePriority, SimulationJobStatus.SimulationQueueID.QUEUE_ID_NULL);
            // new exe status
            lastUpdateDate = new Date();
            if (startDate == null) {
                startDate = lastUpdateDate;
            }
            SimulationExecutionStatus newExeStatus = new SimulationExecutionStatus(startDate, computeHost, lastUpdateDate, endDate, hasData, htcJobID);
            newJobStatus = new SimulationJobStatus(vcServerID, vcSimDataID.getVcSimID(), jobIndex, submitDate, SchedulerStatus.RUNNING, taskID, workerEventSimulationMessage, newQueueStatus, newExeStatus);
        }
    } else if (workerEvent.isNewDataEvent()) {
        if (oldSchedulerStatus.isWaiting() || oldSchedulerStatus.isQueued() || oldSchedulerStatus.isDispatched() || oldSchedulerStatus.isRunning()) {
            if (!oldSchedulerStatus.isRunning() || simQueueID != SimulationJobStatus.SimulationQueueID.QUEUE_ID_NULL || hasData == false) {
                // new queue status
                SimulationQueueEntryStatus newQueueStatus = new SimulationQueueEntryStatus(queueDate, queuePriority, SimulationJobStatus.SimulationQueueID.QUEUE_ID_NULL);
                // new exe status
                if (startDate == null) {
                    startDate = lastUpdateDate;
                }
                hasData = true;
                SimulationExecutionStatus newExeStatus = new SimulationExecutionStatus(startDate, computeHost, lastUpdateDate, endDate, hasData, htcJobID);
                newJobStatus = new SimulationJobStatus(vcServerID, vcSimDataID.getVcSimID(), jobIndex, submitDate, SchedulerStatus.RUNNING, taskID, workerEventSimulationMessage, newQueueStatus, newExeStatus);
            }
        }
    } else if (workerEvent.isProgressEvent() || workerEvent.isWorkerAliveEvent()) {
        if (oldSchedulerStatus.isWaiting() || oldSchedulerStatus.isQueued() || oldSchedulerStatus.isDispatched() || oldSchedulerStatus.isRunning()) {
            if (!oldSchedulerStatus.isRunning() || simQueueID != SimulationJobStatus.SimulationQueueID.QUEUE_ID_NULL) {
                // new queue status
                SimulationQueueEntryStatus newQueueStatus = new SimulationQueueEntryStatus(queueDate, queuePriority, SimulationJobStatus.SimulationQueueID.QUEUE_ID_NULL);
                // new exe status
                if (startDate == null) {
                    startDate = lastUpdateDate;
                }
                SimulationExecutionStatus newExeStatus = new SimulationExecutionStatus(startDate, computeHost, lastUpdateDate, endDate, hasData, htcJobID);
                newJobStatus = new SimulationJobStatus(vcServerID, vcSimDataID.getVcSimID(), jobIndex, submitDate, SchedulerStatus.RUNNING, taskID, workerEventSimulationMessage, newQueueStatus, newExeStatus);
            } else if (oldSchedulerStatus.isRunning()) {
                if (oldSimExeStatus != null) {
                    // Date latestUpdate = oldSimExeStatus.getLatestUpdateDate();
                    // if (System.currentTimeMillis() - latestUpdate.getTime() >= MessageConstants.INTERVAL_PING_SERVER_MS * 3 / 5) {
                    // new queue status
                    SimulationQueueEntryStatus newQueueStatus = new SimulationQueueEntryStatus(queueDate, queuePriority, SimulationJobStatus.SimulationQueueID.QUEUE_ID_NULL);
                    SimulationExecutionStatus newExeStatus = new SimulationExecutionStatus(startDate, computeHost, lastUpdateDate, endDate, hasData, htcJobID);
                    newJobStatus = new SimulationJobStatus(vcServerID, vcSimDataID.getVcSimID(), jobIndex, submitDate, SchedulerStatus.RUNNING, taskID, workerEventSimulationMessage, newQueueStatus, newExeStatus);
                }
            // }
            }
        }
    } else if (workerEvent.isCompletedEvent()) {
        if (oldSchedulerStatus.isWaiting() || oldSchedulerStatus.isQueued() || oldSchedulerStatus.isDispatched() || oldSchedulerStatus.isRunning()) {
            // new queue status
            SimulationQueueEntryStatus newQueueStatus = new SimulationQueueEntryStatus(queueDate, queuePriority, SimulationJobStatus.SimulationQueueID.QUEUE_ID_NULL);
            // new exe status
            endDate = new Date();
            hasData = true;
            SimulationExecutionStatus newExeStatus = new SimulationExecutionStatus(startDate, computeHost, lastUpdateDate, endDate, hasData, htcJobID);
            newJobStatus = new SimulationJobStatus(vcServerID, vcSimDataID.getVcSimID(), jobIndex, submitDate, SchedulerStatus.COMPLETED, taskID, workerEventSimulationMessage, newQueueStatus, newExeStatus);
        }
    } else if (workerEvent.isFailedEvent()) {
        if (oldSchedulerStatus.isWaiting() || oldSchedulerStatus.isQueued() || oldSchedulerStatus.isDispatched() || oldSchedulerStatus.isRunning()) {
            // new queue status
            SimulationQueueEntryStatus newQueueStatus = new SimulationQueueEntryStatus(queueDate, queuePriority, SimulationJobStatus.SimulationQueueID.QUEUE_ID_NULL);
            // new exe status
            endDate = new Date();
            SimulationExecutionStatus newExeStatus = new SimulationExecutionStatus(startDate, computeHost, lastUpdateDate, endDate, hasData, htcJobID);
            newJobStatus = new SimulationJobStatus(vcServerID, vcSimDataID.getVcSimID(), jobIndex, submitDate, SchedulerStatus.FAILED, taskID, workerEventSimulationMessage, newQueueStatus, newExeStatus);
        }
    } else if (workerEvent.isWorkerExitErrorEvent()) {
        if (oldSchedulerStatus.isWaiting() || oldSchedulerStatus.isQueued() || oldSchedulerStatus.isDispatched() || oldSchedulerStatus.isRunning()) {
            // new queue status
            SimulationQueueEntryStatus newQueueStatus = new SimulationQueueEntryStatus(queueDate, queuePriority, SimulationJobStatus.SimulationQueueID.QUEUE_ID_NULL);
            // new exe status
            endDate = new Date();
            SimulationExecutionStatus newExeStatus = new SimulationExecutionStatus(startDate, computeHost, lastUpdateDate, endDate, hasData, htcJobID);
            SimulationMessage simulationMessage = SimulationMessage.workerFailure("solver stopped unexpectedly, " + workerEventSimulationMessage.getDisplayMessage());
            newJobStatus = new SimulationJobStatus(vcServerID, vcSimDataID.getVcSimID(), jobIndex, submitDate, SchedulerStatus.FAILED, taskID, simulationMessage, newQueueStatus, newExeStatus);
        }
    }
    if (newJobStatus != null) {
        if (!newJobStatus.compareEqual(oldSimulationJobStatus) || workerEvent.isProgressEvent() || workerEvent.isNewDataEvent()) {
            Double progress = workerEvent.getProgress();
            Double timepoint = workerEvent.getTimePoint();
            RunningStateInfo runningStateInfo = null;
            if (progress != null && timepoint != null) {
                runningStateInfo = new RunningStateInfo(progress, timepoint);
            }
            simulationDatabase.updateSimulationJobStatus(newJobStatus, runningStateInfo);
            StatusMessage msgForClient = new StatusMessage(newJobStatus, userName, progress, timepoint);
            msgForClient.sendToClient(session);
            if (lg.isTraceEnabled())
                lg.trace("Send status to client: " + msgForClient);
        } else {
            simulationDatabase.updateSimulationJobStatus(newJobStatus);
            StatusMessage msgForClient = new StatusMessage(newJobStatus, userName, null, null);
            msgForClient.sendToClient(session);
            if (lg.isTraceEnabled())
                lg.trace("Send status to client: " + msgForClient);
        }
    } else if (workerEvent.isProgressEvent() || workerEvent.isNewDataEvent()) {
        Double progress = workerEvent.getProgress();
        Double timepoint = workerEvent.getTimePoint();
        RunningStateInfo runningStateInfo = null;
        if (progress != null && timepoint != null) {
            runningStateInfo = new RunningStateInfo(progress, timepoint);
        }
        simulationDatabase.updateSimulationJobStatus(oldSimulationJobStatus, runningStateInfo);
        StatusMessage msgForClient = new StatusMessage(oldSimulationJobStatus, userName, progress, timepoint);
        msgForClient.sendToClient(session);
        if (lg.isTraceEnabled())
            lg.trace("Send status to client: " + msgForClient);
    } else {
        VCMongoMessage.sendInfo("onWorkerEvent() ignoring WorkerEvent (currState=" + oldSchedulerStatus.getDescription() + "): " + workerEvent.show());
    }
// addStateMachineTransition(new StateMachineTransition(new WorkerStateMachineEvent(taskID, workerEvent), oldSimulationJobStatus, newJobStatus));
}