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

Example 11 with HtcJobID

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

the class SimulationJobTable method getSimulationJobStatus.

/**
 * This method was created in VisualAge.
 * @return VCImage
 * @param rset ResultSet
 * @param log SessionLog
 */
public SimulationJobStatusPersistent getSimulationJobStatus(ResultSet rset) throws SQLException {
    // serverid
    String serID = rset.getString(this.serverID.toString());
    if (rset.wasNull()) {
        serID = null;
    }
    // simRef
    KeyValue parsedSimKey = new KeyValue(rset.getBigDecimal(simRef.toString()));
    // userKey
    KeyValue userKey = new KeyValue(rset.getBigDecimal(SimulationTable.table.ownerRef.toString()));
    // userKey
    String userid = rset.getString(UserTable.table.userid.toString());
    org.vcell.util.document.User owner = new org.vcell.util.document.User(userid, userKey);
    // submitDate
    java.util.Date parsedSubmitDate = rset.getTimestamp(submitDate.toString());
    // taskID
    int parsedTaskID = rset.getInt(taskID.toString());
    // schedulerStatus
    int parsedSchedulerStatusInt = rset.getInt(schedulerStatus.toString());
    SchedulerStatus parsedSchedulerStatus = SchedulerStatus.fromDatabaseNumber(parsedSchedulerStatusInt);
    // statusMsg
    String parsedStatusMsg = TokenMangler.getSQLRestoredString(rset.getString(statusMsg.toString()));
    SimulationMessagePersistent simulationMessage = SimulationMessagePersistent.fromSerialized(parsedSchedulerStatus, parsedStatusMsg);
    // 
    // read queue stuff
    // 
    // queueDate
    java.util.Date parsedQueuedDate = rset.getTimestamp(queueDate.toString());
    // queuePriority
    int parsedQueuePriority = rset.getInt(queuePriority.toString());
    if (rset.wasNull()) {
        parsedQueuePriority = -1;
    }
    // queueID
    int parsedQueueID = rset.getInt(queueID.toString());
    if (rset.wasNull()) {
        parsedQueueID = -1;
    }
    SimulationJobStatusPersistent.SimulationQueueID simulationQueueID = SimulationJobStatusPersistent.SimulationQueueID.fromDatabaseNumber(parsedQueueID);
    SimulationQueueEntryStatusPersistent simQueueEntryStatus = new SimulationQueueEntryStatusPersistent(parsedQueuedDate, parsedQueuePriority, simulationQueueID);
    // 
    // read solver stuff
    // 
    // startDate
    java.util.Date parsedStartDate = rset.getTimestamp(startDate.toString());
    // computeHost
    String parsedComputeHost = rset.getString(computeHost.toString());
    // latestUpdateDate
    java.util.Date parsedLatestUpdateDate = rset.getTimestamp(latestUpdateDate.toString());
    // endDate
    java.util.Date parsedEndDate = rset.getTimestamp(endDate.toString());
    // hasData
    String parsedHasData = rset.getString(hasData.toString());
    HtcJobID parsedHtcJobID = null;
    String htcJobIDString = rset.getString(pbsJobID.toString());
    if (!rset.wasNull() && htcJobIDString != null && htcJobIDString.length() > 0) {
        parsedHtcJobID = SimulationJobTable.fromDatabase(htcJobIDString);
    }
    SimulationExecutionStatusPersistent simExeStatus = new SimulationExecutionStatusPersistent(parsedStartDate, parsedComputeHost, parsedLatestUpdateDate, parsedEndDate, parsedHasData != null, parsedHtcJobID);
    VCSimulationIdentifier parsedVCSimID = new VCSimulationIdentifier(parsedSimKey, owner);
    // jobIndex
    int parsedJobIndex = rset.getInt(jobIndex.toString());
    SimulationJobStatusPersistent simulationJobStatus = new SimulationJobStatusPersistent(VCellServerID.getServerID(serID), parsedVCSimID, parsedJobIndex, parsedSubmitDate, parsedSchedulerStatus, parsedTaskID, simulationMessage, simQueueEntryStatus, simExeStatus);
    // sysDate
    java.util.Date parsedSysDate = rset.getTimestamp(DatabaseConstants.SYSDATE_COLUMN_NAME);
    if (!rset.wasNull()) {
        simulationJobStatus.setTimeDateStamp(parsedSysDate);
    }
    return simulationJobStatus;
}

Example 12 with HtcJobID

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

the class SimulationJobStatusEvent method fromJsonRep.

public static SimulationJobStatusEvent fromJsonRep(Object eventSource, SimulationJobStatusEventRepresentation eventRep) {
    String simid = Simulation.createSimulationID(new KeyValue(eventRep.jobStatus.simulationKey));
    int jobIndex = eventRep.jobStatus.jobIndex;
    int taskID = eventRep.jobStatus.taskID;
    VCellServerID serverID = VCellServerID.getServerID(eventRep.jobStatus.vcellServerID);
    KeyValue simkey = new KeyValue(eventRep.jobStatus.simulationKey);
    User owner = new User(eventRep.jobStatus.owner_userid, new KeyValue(eventRep.jobStatus.onwer_userkey));
    VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(simkey, owner);
    Date submitDate = eventRep.jobStatus.submitDate;
    SchedulerStatus schedulerStatus = null;
    if (eventRep.jobStatus.schedulerStatus != null) {
        schedulerStatus = SchedulerStatus.valueOf(eventRep.jobStatus.schedulerStatus.name());
    }
    HtcJobID htcJobID = null;
    Long htcJobNumber = eventRep.jobStatus.htcJobNumber;
    SimulationJobStatusRepresentation.BatchSystemType htcBatchSystemType = eventRep.jobStatus.htcBatchSystemType;
    if (htcJobNumber != null) {
        htcJobID = new HtcJobID(htcJobNumber.toString(), BatchSystemType.valueOf(htcBatchSystemType.name()));
    }
    SimulationMessage simMessage = null;
    DetailedState detailedState = DetailedState.valueOf(eventRep.jobStatus.detailedState.name());
    String message = eventRep.jobStatus.detailedStateMessage;
    if (detailedState != null) {
        simMessage = SimulationMessage.create(detailedState, message, htcJobID);
    }
    SimulationQueueEntryStatus simQueueStatus = null;
    Date queueDate = eventRep.jobStatus.queueDate;
    Integer queuePriority = eventRep.jobStatus.queuePriority;
    SimulationJobStatusRepresentation.SimulationQueueID queueId2 = eventRep.jobStatus.queueId;
    if (queueDate != null && queuePriority != null) {
        simQueueStatus = new SimulationQueueEntryStatus(queueDate, queuePriority, SimulationQueueID.valueOf(queueId2.name()));
    }
    SimulationExecutionStatus simExeStatus = null;
    Date startDate = eventRep.jobStatus.simexe_startDate;
    String computeHost = eventRep.jobStatus.computeHost;
    Date latestUpdateDate = eventRep.jobStatus.simexe_latestUpdateDate;
    Date endDate = eventRep.jobStatus.simexe_endDate;
    Boolean hasData = eventRep.jobStatus.hasData;
    if (latestUpdateDate != null) {
        simExeStatus = new SimulationExecutionStatus(startDate, computeHost, latestUpdateDate, endDate, hasData, htcJobID);
    }
    SimulationJobStatus jobStatus = new SimulationJobStatus(serverID, vcSimID, jobIndex, submitDate, schedulerStatus, taskID, simMessage, simQueueStatus, simExeStatus);
    Double progress = eventRep.progress;
    Double timepoint = eventRep.timePoint;
    String username = eventRep.username;
    SimulationJobStatusEvent event = new SimulationJobStatusEvent(eventSource, simid, jobStatus, progress, timepoint, username);
    return event;
}

Example 13 with HtcJobID

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

the class SimulationStateMachine method onSystemAbort.

public synchronized void onSystemAbort(SimulationJobStatus oldJobStatus, String failureMessage, SimulationDatabase simulationDatabase, VCMessageSession session) throws VCMessagingException, UpdateSynchronizationException, DataAccessException, SQLException {
    updateSolverProcessTimestamp();
    int taskID = oldJobStatus.getTaskID();
    // 
    // status information (initialized as if new record)
    // 
    Date startDate = null;
    boolean hasData = false;
    HtcJobID htcJobID = null;
    String computeHost = null;
    VCellServerID vcServerID = VCellServerID.getSystemServerID();
    Date submitDate = null;
    Date queueDate = null;
    int queuePriority = PRIORITY_DEFAULT;
    // 
    // update using previously stored status (if available).
    // 
    SimulationExecutionStatus oldSimExeStatus = oldJobStatus.getSimulationExecutionStatus();
    if (oldSimExeStatus != null && oldSimExeStatus.getStartDate() != null) {
        startDate = oldSimExeStatus.getStartDate();
    }
    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 = oldJobStatus.getServerID();
    submitDate = oldJobStatus.getSubmitDate();
    SimulationQueueEntryStatus oldQueueStatus = oldJobStatus.getSimulationQueueEntryStatus();
    if (oldQueueStatus != null && oldQueueStatus.getQueueDate() != null) {
        queueDate = oldQueueStatus.getQueueDate();
    }
    if (oldQueueStatus != null) {
        queuePriority = oldQueueStatus.getQueuePriority();
    }
    SimulationQueueEntryStatus newQueueStatus = new SimulationQueueEntryStatus(queueDate, queuePriority, SimulationJobStatus.SimulationQueueID.QUEUE_ID_NULL);
    Date endDate = new Date();
    Date lastUpdateDate = new Date();
    SimulationExecutionStatus newExeStatus = new SimulationExecutionStatus(startDate, computeHost, lastUpdateDate, endDate, hasData, htcJobID);
    SimulationJobStatus newJobStatus = new SimulationJobStatus(vcServerID, oldJobStatus.getVCSimulationIdentifier(), jobIndex, submitDate, SchedulerStatus.FAILED, taskID, SimulationMessage.jobFailed(failureMessage), newQueueStatus, newExeStatus);
    simulationDatabase.updateSimulationJobStatus(newJobStatus);
    // addStateMachineTransition(new StateMachineTransition(new AbortStateMachineEvent(taskID, failureMessage), oldJobStatus, newJobStatus));
    String userName = VCMessagingConstants.USERNAME_PROPERTY_VALUE_ALL;
    StatusMessage msgForClient = new StatusMessage(newJobStatus, userName, null, null);
    msgForClient.sendToClient(session);
    if (lg.isTraceEnabled())
        lg.trace("Send status to client: " + msgForClient);
}

Example 14 with HtcJobID

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

the class HtcSimulationWorker method submit2PBS.

private HtcJobID submit2PBS(SimulationTask simTask, HtcProxy clonedHtcProxy, PostProcessingChores chores) throws XmlParseException, IOException, SolverException, ExecutableException {
    HtcJobID jobid = null;
    String htcLogDirExternalString = new File(PropertyLoader.getRequiredProperty(PropertyLoader.htcLogDirExternal)).getAbsolutePath();
    if (!htcLogDirExternalString.endsWith("/")) {
        htcLogDirExternalString = htcLogDirExternalString + "/";
    }
    String htcLogDirInternalString = new File(PropertyLoader.getRequiredProperty(PropertyLoader.htcLogDirInternal)).getAbsolutePath();
    if (!htcLogDirInternalString.endsWith("/")) {
        htcLogDirInternalString = htcLogDirInternalString + "/";
    }
    // "S_" + simTask.getSimKey() + "_" + simTask.getSimulationJob().getJobIndex()+ "_" + simTask.getTaskID();
    String jobname = HtcProxy.createHtcSimJobName(new HtcProxy.SimTaskInfo(simTask.getSimKey(), simTask.getSimulationJob().getJobIndex(), simTask.getTaskID()));
    String subFileExternal = htcLogDirExternalString + jobname + clonedHtcProxy.getSubmissionFileExtension();
    String subFileInternal = htcLogDirInternalString + jobname + clonedHtcProxy.getSubmissionFileExtension();
    File parallelDirInternal = new File(chores.runDirectoryInternal);
    File parallelDirExternal = new File(chores.runDirectoryExternal);
    File primaryUserDirInternal = new File(chores.finalDataDirectoryInternal);
    File primaryUserDirExternal = new File(chores.finalDataDirectoryExternal);
    Solver realSolver = (AbstractSolver) SolverFactory.createSolver(primaryUserDirInternal, parallelDirInternal, simTask, true);
    realSolver.setUnixMode();
    String simTaskXmlText = XmlHelper.simTaskToXML(simTask);
    String simTaskFilePathInternal = ResourceUtil.forceUnixPath(new File(primaryUserDirInternal, simTask.getSimulationJobID() + "_" + simTask.getTaskID() + ".simtask.xml").toString());
    String simTaskFilePathExternal = ResourceUtil.forceUnixPath(new File(primaryUserDirExternal, simTask.getSimulationJobID() + "_" + simTask.getTaskID() + ".simtask.xml").toString());
    if (!primaryUserDirInternal.exists()) {
        FileUtils.forceMkdir(primaryUserDirInternal);
        // 
        // directory create from container (possibly) as root, make this user directory accessible from user "vcell"
        // 
        primaryUserDirInternal.setWritable(true, false);
        primaryUserDirInternal.setExecutable(true, false);
        primaryUserDirInternal.setReadable(true, false);
    }
    XmlUtil.writeXMLStringToFile(simTaskXmlText, simTaskFilePathInternal, true);
    final String SOLVER_EXIT_CODE_REPLACE_STRING = "SOLVER_EXIT_CODE_REPLACE_STRING";
    KeyValue simKey = simTask.getSimKey();
    User simOwner = simTask.getSimulation().getVersion().getOwner();
    final int jobId = simTask.getSimulationJob().getJobIndex();
    ExecutableCommand.Container commandContainer = new ExecutableCommand.Container();
    // the post processor command itself is neither messaging nor parallel; it's independent of the previous solver call
    ExecutableCommand postprocessorCmd = new ExecutableCommand(null, false, false, PropertyLoader.getRequiredProperty(PropertyLoader.simulationPostprocessor), simKey.toString(), simOwner.getName(), simOwner.getID().toString(), Integer.toString(jobId), Integer.toString(simTask.getTaskID()), SOLVER_EXIT_CODE_REPLACE_STRING, subFileExternal);
    postprocessorCmd.setExitCodeToken(SOLVER_EXIT_CODE_REPLACE_STRING);
    commandContainer.add(postprocessorCmd);
    // CBN?
    int ncpus = simTask.getSimulation().getSolverTaskDescription().getNumProcessors();
    Collection<PortableCommand> postProcessingCommands = new ArrayList<PortableCommand>();
    if (realSolver instanceof AbstractCompiledSolver) {
        AbstractCompiledSolver compiledSolver = (AbstractCompiledSolver) realSolver;
        List<String> args = new ArrayList<>(4);
        args.add(PropertyLoader.getRequiredProperty(PropertyLoader.simulationPreprocessor));
        args.add(simTaskFilePathExternal);
        args.add(primaryUserDirExternal.getAbsolutePath());
        if (chores.isParallel()) {
            args.add(chores.runDirectoryExternal);
        }
        // compiled solver ...used to be only single executable, now we pass 2 commands to PBSUtils.submitJob that invokes SolverPreprocessor.main() and then the native executable
        // the pre-processor command itself is neither messaging nor parallel; it's independent of the subsequent solver call
        ExecutableCommand preprocessorCmd = new ExecutableCommand(null, false, false, args);
        commandContainer.add(preprocessorCmd);
        for (ExecutableCommand ec : compiledSolver.getCommands()) {
            if (ec.isMessaging()) {
                ec.addArgument("-tid");
                ec.addArgument(simTask.getTaskID());
            }
            commandContainer.add(ec);
        }
        if (chores.isCopyNeeded()) {
            String logName = chores.finalDataDirectoryInternal + '/' + SimulationData.createCanonicalSimLogFileName(simKey, jobId, false);
            CopySimFiles csf = new CopySimFiles(simTask.getSimulationJobID(), chores.runDirectoryInternal, chores.finalDataDirectoryInternal, logName);
            postProcessingCommands.add(csf);
        }
        if (chores.isVtkUser()) {
            VtkMeshGenerator vmg = new VtkMeshGenerator(simOwner, simKey, jobId);
            postProcessingCommands.add(vmg);
        }
    } else {
        ExecutableCommand ec = new ExecutableCommand(null, false, false, PropertyLoader.getRequiredProperty(PropertyLoader.javaSimulationExecutable), simTaskFilePathExternal, ResourceUtil.forceUnixPath(parallelDirExternal.getAbsolutePath()));
        commandContainer.add(ec);
    }
    jobid = clonedHtcProxy.submitJob(jobname, subFileInternal, subFileExternal, commandContainer, ncpus, simTask.getEstimatedMemorySizeMB(), postProcessingCommands);
    if (jobid == null) {
        throw new RuntimeException("Failed. (error message: submitting to job scheduler failed).");
    }
    return jobid;
}

Example 15 with HtcJobID

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

the class SlurmProxy method submitJob.

@Override
public HtcJobID submitJob(String jobName, String sub_file_internal, String sub_file_external, ExecutableCommand.Container commandSet, int ncpus, double memSize, Collection<PortableCommand> postProcessingCommands) throws ExecutableException {
    try {
        if (LG.isDebugEnabled()) {
            LG.debug("generating local SLURM submit script for jobName=" + jobName);
        }
        String text = generateScript(jobName, commandSet, ncpus, memSize, postProcessingCommands);
        File tempFile = File.createTempFile("tempSubFile", ".sub");
        writeUnixStyleTextFile(tempFile, text);
        // move submission file to final location (either locally or remotely).
        if (LG.isDebugEnabled()) {
            LG.debug("moving local SLURM submit file '" + tempFile.getAbsolutePath() + "' to remote file '" + sub_file_external + "'");
        }
        FileUtils.copyFile(tempFile, new File(sub_file_internal));
        tempFile.delete();
    } catch (IOException ex) {
        ex.printStackTrace(System.out);
        return null;
    }
    /**
     * > sbatch /share/apps/vcell2/deployed/test/htclogs/V_TEST_107643258_0_0.slurm.sub
     * Submitted batch job 5174
     */
    String[] completeCommand = new String[] { Slurm_HOME + JOB_CMD_SUBMIT, sub_file_external };
    if (LG.isDebugEnabled()) {
        LG.debug("submitting SLURM job: '" + CommandOutput.concatCommandStrings(completeCommand) + "'");
    }
    CommandOutput commandOutput = commandService.command(completeCommand);
    String jobid = commandOutput.getStandardOutput().trim();
    final String EXPECTED_STDOUT_PREFIX = "Submitted batch job ";
    if (jobid.startsWith(EXPECTED_STDOUT_PREFIX)) {
        jobid = jobid.replace(EXPECTED_STDOUT_PREFIX, "");
    } else {
        LG.error("failed to submit SLURM job '" + sub_file_external + "', stdout='" + commandOutput.getStandardOutput() + "', stderr='" + commandOutput.getStandardError() + "'");
        throw new ExecutableException("unexpected response from '" + JOB_CMD_SUBMIT + "' while submitting simulation: '" + jobid + "'");
    }
    HtcJobID htcJobID = new HtcJobID(jobid, BatchSystemType.SLURM);
    if (LG.isDebugEnabled()) {
        LG.debug("SLURM job '" + CommandOutput.concatCommandStrings(completeCommand) + "' started as htcJobId '" + htcJobID + "'");
    }
    return htcJobID;
}