Examples with KeyValue org.vcell.util.document.KeyValue used on opensource projects

Example 71 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class FieldDataDBOperationDriver method getFunctionFileNamesAndSimKeys.

public static synchronized HashMap<String, KeyValue> getFunctionFileNamesAndSimKeys(User user) throws DataAccessException {
    String sql = "SELECT " + SimulationJobTable.table.simRef.getQualifiedColName() + "," + SimulationJobTable.table.jobIndex.getQualifiedColName() + " FROM " + SimulationJobTable.table.getTableName() + "," + SimulationTable.table.getTableName() + " WHERE " + SimulationTable.table.ownerRef.getQualifiedColName() + " = " + user.getID() + " AND " + SimulationTable.table.id.getQualifiedColName() + " = " + SimulationJobTable.table.simRef.getQualifiedColName() + " UNION " + " SELECT " + SimulationTable.table.id.getQualifiedColName() + "," + // SimulationJobTable.table.jobIndex.getUnqualifiedColName()+
    "TO_NUMBER(NULL) " + " FROM " + SimulationTable.table.getTableName() + " WHERE " + SimulationTable.table.ownerRef.getQualifiedColName() + "=" + user.getID() + " AND " + SimulationTable.table.id.getQualifiedColName() + " NOT IN (SELECT " + SimulationJobTable.table.simRef.getQualifiedColName() + " FROM " + SimulationJobTable.table.getTableName() + " )" + " UNION " + " SELECT " + ExternalDataTable.table.id.getQualifiedColName() + "," + "TO_NUMBER(0) " + " FROM " + ExternalDataTable.table.getTableName() + " WHERE " + ExternalDataTable.table.ownerRef.getQualifiedColName() + "=" + user.getID();
    Statement stmt = null;
    HashMap<String, KeyValue> functionNamesH = new HashMap<String, KeyValue>();
    try {
        stmt = getConnection().createStatement();
        ResultSet rset = stmt.executeQuery(sql);
        while (rset.next()) {
            KeyValue simKey = new KeyValue(rset.getBigDecimal(1));
            BigDecimal jobIndex = rset.getBigDecimal(2);
            boolean isOldStyle = rset.wasNull();
            functionNamesH.put(SimulationData.createCanonicalFunctionsFileName(simKey, (isOldStyle ? 0 : jobIndex.intValue()), isOldStyle), simKey);
        }
    } catch (Exception e) {
        e.printStackTrace();
        throw new DataAccessException("Error: getFunctionFileNamesAndSimKeys", e);
    } finally {
        if (stmt != null) {
            try {
                stmt.close();
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    }
    return functionNamesH;
}

Example 72 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class SimulationControllerImpl method onSimJobQueue_SimulationTask.

private void onSimJobQueue_SimulationTask(VCMessage vcMessage) {
    SimulationTask simTask = null;
    try {
        SimulationTaskMessage simTaskMessage = new SimulationTaskMessage(vcMessage);
        simTask = simTaskMessage.getSimulationTask();
        LocalSolverController solverController = getOrCreateSolverController(simTask);
        // can only start after updating the database is done
        solverController.startSimulationJob();
    } catch (Exception e) {
        lg.error(e.getMessage(), e);
        KeyValue simKey = simTask.getSimKey();
        VCSimulationIdentifier vcSimID = simTask.getSimulationJob().getVCDataIdentifier().getVcSimID();
        int jobIndex = simTask.getSimulationJob().getJobIndex();
        int taskID = simTask.getTaskID();
        SimulationJobStatus newJobStatus = new SimulationJobStatus(VCellServerID.getSystemServerID(), vcSimID, jobIndex, null, SchedulerStatus.FAILED, taskID, SimulationMessage.jobFailed(e.getMessage()), null, null);
        SimulationJobStatusEvent event = new SimulationJobStatusEvent(this, Simulation.createSimulationID(simKey), newJobStatus, null, null, vcSimID.getOwner().getName());
        fireSimulationJobStatusEvent(event);
    }
}

Example 73 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class BatchScheduler method schedule.

/**
 * Insert the method's description here.
 * Creation date: (5/11/2006 9:32:58 AM)
 */
public static WaitingJob[] schedule(SimulationJobStatus[] activeJobsThisSite, Map<KeyValue, SimulationRequirements> simulationRequirementsMap, int siteJobQuota, int userQuotaOde, int userQuotaPde, VCellServerID systemID) {
    Hashtable<User, Integer> userPdeRunningJobsThisSite = new Hashtable<User, Integer>();
    Hashtable<User, Integer> userOdeRunningJobsThisSite = new Hashtable<User, Integer>();
    cbit.vcell.server.SimulationJobStatus jobStatus = null;
    int numRunningJobsThisSite = 0;
    for (int i = 0; i < activeJobsThisSite.length; i++) {
        jobStatus = activeJobsThisSite[i];
        if (!jobStatus.getSchedulerStatus().isActive()) {
            continue;
        }
        if (jobStatus.getSchedulerStatus().isWaiting()) {
            // we only do statistics on running jobs;
            continue;
        }
        numRunningJobsThisSite++;
        if (jobStatus.getServerID().equals(systemID)) {
            // the number of running jobs on this site
            User user = activeJobsThisSite[i].getVCSimulationIdentifier().getOwner();
            SimulationRequirements simRequirements = simulationRequirementsMap.get(jobStatus.getVCSimulationIdentifier().getSimulationKey());
            if (simRequirements != null && simRequirements.isPDE()) {
                Integer numUserPdeJobs = userPdeRunningJobsThisSite.get(user);
                if (numUserPdeJobs == null) {
                    userPdeRunningJobsThisSite.put(user, 1);
                } else {
                    userPdeRunningJobsThisSite.put(user, numUserPdeJobs.intValue() + 1);
                }
            } else {
                Integer numUserOdeJobs = userOdeRunningJobsThisSite.get(user);
                if (numUserOdeJobs == null) {
                    userOdeRunningJobsThisSite.put(user, 1);
                } else {
                    userOdeRunningJobsThisSite.put(user, numUserOdeJobs.intValue() + 1);
                }
            }
        }
    }
    ArrayList<WaitingJob> waitingJobs = new ArrayList<WaitingJob>();
    for (int i = 0; i < activeJobsThisSite.length; i++) {
        jobStatus = activeJobsThisSite[i];
        if (!jobStatus.getSchedulerStatus().isWaiting()) {
            // ignore non-waiting job
            continue;
        }
        if (!jobStatus.getServerID().equals(systemID)) {
            // doesn't belong
            continue;
        }
        User user = activeJobsThisSite[i].getVCSimulationIdentifier().getOwner();
        Integer numRunningPDEsThisSite = userPdeRunningJobsThisSite.get(user);
        if (numRunningPDEsThisSite == null) {
            numRunningPDEsThisSite = new Integer(0);
        }
        Integer numRunningODEsThisSite = userOdeRunningJobsThisSite.get(user);
        if (numRunningODEsThisSite == null) {
            numRunningODEsThisSite = new Integer(0);
        }
        long waitingTimeStamp = jobStatus.getSimulationQueueEntryStatus().getQueueDate().getTime();
        KeyValue simKey = jobStatus.getVCSimulationIdentifier().getSimulationKey();
        waitingJobs.add(new WaitingJob(user, numRunningPDEsThisSite, numRunningODEsThisSite, waitingTimeStamp, jobStatus, simulationRequirementsMap.get(simKey)));
    }
    Collections.sort(waitingJobs, new Comparator<WaitingJob>() {

        @Override
        public int compare(WaitingJob o1, WaitingJob o2) {
            // 
            if (!o1.getNumRunningJobs().equals(o2.getNumRunningJobs())) {
                return o1.getNumRunningJobs().compareTo(o2.getNumRunningJobs());
            }
            // 
            if (o1.simRequirements.isPDE() != o2.simRequirements.isPDE()) {
                if (o1.simRequirements.isPDE()) {
                    return 1;
                } else {
                    return -1;
                }
            }
            // 
            return o1.waitingTimeStamp.compareTo(o2.waitingTimeStamp);
        }
    });
    // 
    // enforce quota for each user
    // 
    HashSet<User> users = new HashSet<User>();
    users.addAll(userPdeRunningJobsThisSite.keySet());
    users.addAll(userOdeRunningJobsThisSite.keySet());
    for (User user : users) {
        Integer numRunningPDEsThisSite = userPdeRunningJobsThisSite.get(user);
        int numRunningPDEs = 0;
        if (numRunningPDEsThisSite != null) {
            numRunningPDEs = numRunningPDEsThisSite;
        }
        Integer numRunningODEsThisSite = userOdeRunningJobsThisSite.get(user);
        int numRunningODEs = 0;
        if (numRunningODEsThisSite != null) {
            numRunningODEs = numRunningODEsThisSite;
        }
        // 
        // go full list and remove any jobs that would exceed this users quota
        // 
        Iterator<WaitingJob> waitingJobIter = waitingJobs.iterator();
        while (waitingJobIter.hasNext()) {
            WaitingJob waitingJob = waitingJobIter.next();
            if (waitingJob.user.equals(user)) {
                if (waitingJob.simRequirements.isPDE()) {
                    if (numRunningPDEs < userQuotaPde) {
                        numRunningPDEs++;
                    } else {
                        waitingJobIter.remove();
                    }
                } else {
                    if (numRunningODEs < userQuotaOde) {
                        numRunningODEs++;
                    } else {
                        waitingJobIter.remove();
                    }
                }
            }
        }
    }
    // 
    // enforce site quota (keep only first N jobs) where currentRunning + N <= quota
    // 
    int numJobsSlotsAvailable = Math.max(0, siteJobQuota - numRunningJobsThisSite);
    int numJobsEligible = waitingJobs.size();
    int numJobsToDispatch = Math.min(numJobsSlotsAvailable, numJobsEligible);
    if (numJobsToDispatch == 0) {
        return new WaitingJob[0];
    } else {
        return waitingJobs.subList(0, numJobsToDispatch).toArray(new WaitingJob[0]);
    }
}

Example 74 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class SimulationDatabaseDirect method getFieldDataIdentifierSpecs.

@Override
public FieldDataIdentifierSpec[] getFieldDataIdentifierSpecs(Simulation sim) throws DataAccessException {
    try {
        KeyValue simKey = sim.getKey();
        if (lg.isTraceEnabled())
            lg.trace("Get FieldDataIdentifierSpec for [" + simKey + "]");
        FieldDataIdentifierSpec[] fieldDataIDSs = (FieldDataIdentifierSpec[]) simFieldDataIDMap.get(simKey);
        if (fieldDataIDSs != null) {
            return fieldDataIDSs;
        }
        FieldFunctionArguments[] fieldFuncArgs = FieldUtilities.getFieldFunctionArguments(sim.getMathDescription());
        if (fieldFuncArgs == null || fieldFuncArgs.length == 0) {
            fieldDataIDSs = new FieldDataIdentifierSpec[0];
            simFieldDataIDMap.put(simKey, fieldDataIDSs);
            return fieldDataIDSs;
        }
        fieldDataIDSs = new FieldDataIdentifierSpec[0];
        User owner = sim.getVersion().getOwner();
        FieldDataDBOperationSpec fieldDataDbOperationSpec = FieldDataDBOperationSpec.createGetExtDataIDsSpec(owner);
        FieldDataDBOperationResults fieldDataDBOperationResults = databaseServerImpl.fieldDataDBOperation(owner, fieldDataDbOperationSpec);
        ExternalDataIdentifier[] externalDataIDs = fieldDataDBOperationResults.extDataIDArr;
        if (externalDataIDs != null && externalDataIDs.length != 0 && fieldFuncArgs != null && fieldFuncArgs.length > 0) {
            Vector<FieldDataIdentifierSpec> fieldDataIdV = new Vector<FieldDataIdentifierSpec>();
            for (int j = 0; fieldFuncArgs != null && j < fieldFuncArgs.length; j += 1) {
                for (int i = 0; i < externalDataIDs.length; i += 1) {
                    if (externalDataIDs[i].getName().equals(fieldFuncArgs[j].getFieldName())) {
                        fieldDataIdV.add(new FieldDataIdentifierSpec(fieldFuncArgs[j], externalDataIDs[i]));
                        break;
                    }
                }
            }
            if (fieldDataIdV.size() > 0) {
                fieldDataIDSs = new FieldDataIdentifierSpec[fieldDataIdV.size()];
                fieldDataIdV.copyInto(fieldDataIDSs);
            }
        }
        simFieldDataIDMap.put(simKey, fieldDataIDSs);
        return fieldDataIDSs;
    } catch (Exception ex) {
        lg.error(ex.getMessage(), ex);
        throw new DataAccessException(ex.getMessage());
    }
}

Example 75 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class SimulationDispatcherEngine method onSystemAbort.

public void onSystemAbort(SimulationJobStatus jobStatus, String failureMessage, SimulationDatabase simulationDatabase, VCMessageSession session) {
    try {
        KeyValue simKey = jobStatus.getVCSimulationIdentifier().getSimulationKey();
        int jobIndex = jobStatus.getJobIndex();
        SimulationStateMachine simStateMachine = getSimulationStateMachine(simKey, jobIndex);
        simStateMachine.onSystemAbort(jobStatus, failureMessage, simulationDatabase, session);
    } catch (Exception ex) {
        lg.error(ex.getMessage(), ex);
    }
}