Examples with HpcJobLog edu.pitt.dbmi.tetrad.db.entity.HpcJobLog used on opensource projects

Example 6 with HpcJobLog

use of edu.pitt.dbmi.tetrad.db.entity.HpcJobLog in project tetrad by cmu-phil.

the class HpcJobPreProcessTask method run.

@Override
public void run() {
    TetradDesktop desktop = (TetradDesktop) DesktopController.getInstance();
    while (desktop == null) {
        try {
            Thread.sleep(1000);
        } catch (InterruptedException e) {
            e.printStackTrace();
        }
    }
    final HpcAccountManager hpcAccountManager = desktop.getHpcAccountManager();
    final HpcJobManager hpcJobManager = desktop.getHpcJobManager();
    HpcAccount hpcAccount = hpcJobInfo.getHpcAccount();
    AlgorithmParamRequest algorParamReq = hpcJobInfo.getAlgorithmParamRequest();
    String datasetPath = algorParamReq.getDatasetPath();
    String priorKnowledgePath = algorParamReq.getPriorKnowledgePath();
    try {
        HpcAccountService hpcAccountService = hpcJobManager.getHpcAccountService(hpcAccount);
        HpcJobLog hpcJobLog = hpcJobManager.getHpcJobLog(hpcJobInfo);
        String log = "Initiated connection to " + hpcAccount.getConnectionName();
        LOGGER.debug(log);
        hpcJobManager.logHpcJobLogDetail(hpcJobLog, -1, log);
        log = "datasetPath: " + datasetPath;
        System.out.println(log);
        Path file = Paths.get(datasetPath);
        // Get file's MD5 hash and use it as its identifier
        String md5 = algorParamReq.getDatasetMd5();
        // Initiate data uploading progress
        hpcJobManager.updateUploadFileProgress(datasetPath, 0);
        Path prior = null;
        if (priorKnowledgePath != null) {
            log = "priorKnowledgePath: " + priorKnowledgePath;
            LOGGER.debug(log);
            prior = Paths.get(priorKnowledgePath);
            // Initiate prior knowledge uploading progress
            hpcJobManager.updateUploadFileProgress(priorKnowledgePath, 0);
        }
        // Check if this dataset already exists with this md5 hash
        RemoteDataFileService remoteDataService = hpcAccountService.getRemoteDataService();
        DataFile dataFile = HpcAccountUtils.getRemoteDataFile(hpcAccountManager, remoteDataService, hpcAccount, md5);
        DataUploadService dataUploadService = hpcAccountService.getDataUploadService();
        // If not, upload the file
        if (dataFile == null) {
            log = "Started uploading " + file.getFileName().toString();
            LOGGER.debug(log);
            dataUploadService.startUpload(file, HpcAccountUtils.getJsonWebToken(hpcAccountManager, hpcAccount));
            hpcJobManager.logHpcJobLogDetail(hpcJobLog, -1, log);
            int progress;
            while ((progress = dataUploadService.getUploadJobStatus(file.toAbsolutePath().toString())) < 100) {
                // System.out.println("Uploading "
                // + file.toAbsolutePath().toString() + " Progress: "
                // + progress + "%");
                hpcJobManager.updateUploadFileProgress(datasetPath, progress);
                Thread.sleep(10);
            }
            hpcJobManager.updateUploadFileProgress(datasetPath, progress);
            log = "Finished uploading " + file.getFileName().toString();
            LOGGER.debug(log);
            hpcJobManager.logHpcJobLogDetail(hpcJobLog, -1, log);
            // Get remote datafile
            dataFile = HpcAccountUtils.getRemoteDataFile(hpcAccountManager, remoteDataService, hpcAccount, md5);
            HpcAccountUtils.summarizeDataset(remoteDataService, algorParamReq, dataFile.getId(), HpcAccountUtils.getJsonWebToken(hpcAccountManager, hpcAccount));
            log = "Summarized " + file.getFileName().toString();
            LOGGER.debug(log);
            hpcJobManager.logHpcJobLogDetail(hpcJobLog, -1, log);
        } else {
            log = "Skipped uploading " + file.getFileName().toString();
            LOGGER.debug(log);
            hpcJobManager.updateUploadFileProgress(datasetPath, -1);
            hpcJobManager.logHpcJobLogDetail(hpcJobLog, -1, log);
            if (dataFile.getFileSummary().getVariableType() == null) {
                HpcAccountUtils.summarizeDataset(remoteDataService, algorParamReq, dataFile.getId(), HpcAccountUtils.getJsonWebToken(hpcAccountManager, hpcAccount));
                log = "Summarized " + file.getFileName().toString();
                LOGGER.debug(log);
                hpcJobManager.logHpcJobLogDetail(hpcJobLog, -1, "Summarized " + file.getFileName().toString());
            }
        }
        DataFile priorKnowledgeFile = null;
        // Prior Knowledge File
        if (prior != null) {
            // Get prior knowledge file Id
            md5 = algorParamReq.getPriorKnowledgeMd5();
            priorKnowledgeFile = HpcAccountUtils.getRemotePriorKnowledgeFile(hpcAccountManager, remoteDataService, hpcAccount, md5);
            if (priorKnowledgeFile == null) {
                // Upload prior knowledge file
                dataUploadService.startUpload(prior, HpcAccountUtils.getJsonWebToken(hpcAccountManager, hpcAccount));
                log = "Started uploading Prior Knowledge File";
                LOGGER.debug(log);
                hpcJobManager.logHpcJobLogDetail(hpcJobLog, -1, log);
                int progress;
                while ((progress = dataUploadService.getUploadJobStatus(prior.toAbsolutePath().toString())) < 100) {
                    hpcJobManager.updateUploadFileProgress(priorKnowledgePath, progress);
                    Thread.sleep(10);
                }
                hpcJobManager.updateUploadFileProgress(priorKnowledgePath, progress);
                priorKnowledgeFile = HpcAccountUtils.getRemotePriorKnowledgeFile(hpcAccountManager, remoteDataService, hpcAccount, md5);
                log = "Finished uploading Prior Knowledge File";
                LOGGER.debug(log);
                hpcJobManager.logHpcJobLogDetail(hpcJobLog, -1, log);
            }
        }
        // Algorithm Job Preparation
        edu.pitt.dbmi.ccd.rest.client.dto.algo.AlgorithmParamRequest paramRequest = new edu.pitt.dbmi.ccd.rest.client.dto.algo.AlgorithmParamRequest();
        String algoId = hpcJobInfo.getAlgoId();
        paramRequest.setAlgoId(algoId);
        paramRequest.setDatasetFileId(dataFile.getId());
        // Test
        if (algorParamReq.getTestId() != null) {
            paramRequest.setTestId(algorParamReq.getTestId());
        }
        // Score
        if (algorParamReq.getScoreId() != null) {
            paramRequest.setScoreId(algorParamReq.getScoreId());
        }
        Set<AlgoParameter> algorithmParameters = new HashSet<>();
        for (AlgorithmParameter param : algorParamReq.getAlgorithmParameters()) {
            algorithmParameters.add(new AlgoParameter(param.getParameter(), param.getValue()));
            LOGGER.debug("AlgorithmParameter: " + param.getParameter() + " : " + param.getValue());
        }
        if (priorKnowledgeFile != null) {
            paramRequest.setPriorKnowledgeFileId(priorKnowledgeFile.getId());
            LOGGER.debug("priorKnowledgeFileId: " + priorKnowledgeFile.getId());
        }
        paramRequest.setAlgoParameters(algorithmParameters);
        if (algorParamReq.getJvmOptions() != null) {
            JvmOptions jvmOptions = new JvmOptions();
            jvmOptions.setMaxHeapSize(algorParamReq.getJvmOptions().getMaxHeapSize());
            paramRequest.setJvmOptions(jvmOptions);
        }
        Set<HpcParameter> hpcParameters = algorParamReq.getHpcParameters();
        if (hpcParameters != null) {
            Set<edu.pitt.dbmi.ccd.rest.client.dto.algo.HpcParameter> hpcParams = new HashSet<>();
            for (HpcParameter param : hpcParameters) {
                edu.pitt.dbmi.ccd.rest.client.dto.algo.HpcParameter hpcParam = new edu.pitt.dbmi.ccd.rest.client.dto.algo.HpcParameter();
                hpcParam.setKey(param.getKey());
                hpcParam.setValue(param.getValue());
                hpcParams.add(hpcParam);
                LOGGER.debug("HpcParameter: " + hpcParam.getKey() + " : " + hpcParam.getValue());
            }
            paramRequest.setHpcParameters(hpcParams);
        }
        // Submit a job
        JobQueueService jobQueueService = hpcAccountService.getJobQueueService();
        JobInfo jobInfo = jobQueueService.addToRemoteQueue(paramRequest, HpcAccountUtils.getJsonWebToken(hpcAccountManager, hpcAccount));
        // Log the job submission
        hpcJobInfo.setSubmittedTime(new Date(System.currentTimeMillis()));
        // Submitted
        hpcJobInfo.setStatus(0);
        hpcJobInfo.setPid(jobInfo.getId());
        hpcJobInfo.setResultFileName(jobInfo.getResultFileName());
        hpcJobInfo.setResultJsonFileName(jobInfo.getResultJsonFileName());
        hpcJobInfo.setErrorResultFileName(jobInfo.getErrorResultFileName());
        hpcJobManager.updateHpcJobInfo(hpcJobInfo);
        log = "Submitted job to " + hpcAccount.getConnectionName();
        LOGGER.debug(log);
        hpcJobManager.logHpcJobLogDetail(hpcJobLog, 0, log);
        LOGGER.debug("HpcJobPreProcessTask: HpcJobInfo: id : " + hpcJobInfo.getId() + " : pid : " + hpcJobInfo.getPid() + " : " + hpcJobInfo.getAlgoId() + hpcJobInfo.getAlgorithmParamRequest().getTestId() == null ? "" : " : " + hpcJobInfo.getAlgorithmParamRequest().getTestId() + hpcJobInfo.getAlgorithmParamRequest().getScoreId() == null ? "" : " : " + hpcJobInfo.getAlgorithmParamRequest().getScoreId() + " : " + hpcJobInfo.getResultFileName());
        hpcJobManager.addNewSubmittedHpcJob(hpcJobInfo);
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}

Example 7 with HpcJobLog

use of edu.pitt.dbmi.tetrad.db.entity.HpcJobLog in project tetrad by cmu-phil.

the class KillHpcJobAction method actionPerformed.

@Override
public void actionPerformed(ActionEvent e) {
    JTable table = (JTable) e.getSource();
    int modelRow = Integer.valueOf(e.getActionCommand());
    DefaultTableModel activeJobTableModel = (DefaultTableModel) table.getModel();
    long jobId = Long.valueOf(activeJobTableModel.getValueAt(modelRow, HpcJobActivityEditor.ID_COLUMN).toString()).longValue();
    int answer = JOptionPane.showConfirmDialog(parentComp, "Would you like to cancel this HPC job id: " + jobId + "?", "Cancel HPC job", JOptionPane.YES_NO_OPTION);
    if (answer == JOptionPane.NO_OPTION)
        return;
    TetradDesktop desktop = (TetradDesktop) DesktopController.getInstance();
    final HpcJobManager hpcJobManager = desktop.getHpcJobManager();
    HpcJobInfo hpcJobInfo = hpcJobManager.findHpcJobInfoById(Long.valueOf(activeJobTableModel.getValueAt(modelRow, HpcJobActivityEditor.ID_COLUMN).toString()).longValue());
    if (hpcJobInfo != null) {
        try {
            if (hpcJobInfo.getPid() != null) {
                // Update table
                activeJobTableModel.setValueAt("Kill Request", modelRow, 1);
                table.updateUI();
                hpcJobInfo = hpcJobManager.requestHpcJobKilled(hpcJobInfo);
                // Update hpcJobInfo instance
                hpcJobManager.updateHpcJobInfo(hpcJobInfo);
                // Update hpcJobLog instance
                HpcJobLog hpcJobLog = hpcJobManager.getHpcJobLog(hpcJobInfo);
                if (hpcJobLog != null) {
                    hpcJobLog.setLastUpdatedTime(new Date(System.currentTimeMillis()));
                    hpcJobManager.updateHpcJobLog(hpcJobLog);
                    // Update hpcJobLogDetail instance
                    String log = "Requested job id " + hpcJobLog.getId() + " killed";
                    hpcJobManager.logHpcJobLogDetail(hpcJobLog, 2, log);
                }
            } else {
                // Update table
                activeJobTableModel.removeRow(modelRow);
                table.updateUI();
                hpcJobManager.removePendingHpcJob(hpcJobInfo);
                // Killed
                hpcJobInfo.setStatus(4);
                // Update hpcJobInfo instance
                hpcJobManager.updateHpcJobInfo(hpcJobInfo);
                // Update hpcJobLog instance
                HpcJobLog hpcJobLog = hpcJobManager.getHpcJobLog(hpcJobInfo);
                if (hpcJobLog != null) {
                    hpcJobLog.setCanceledTime(new Date(System.currentTimeMillis()));
                    hpcJobLog.setLastUpdatedTime(new Date(System.currentTimeMillis()));
                    hpcJobManager.updateHpcJobLog(hpcJobLog);
                    // Update hpcJobLogDetail instance
                    String log = "Killed job id " + hpcJobLog.getId();
                    hpcJobManager.logHpcJobLogDetail(hpcJobLog, 4, log);
                }
            }
        } catch (Exception e1) {
            // TODO Auto-generated catch block
            e1.printStackTrace();
        }
    }
}

Example 8 with HpcJobLog

use of edu.pitt.dbmi.tetrad.db.entity.HpcJobLog in project tetrad by cmu-phil.

the class PendingHpcJobUpdaterTask method monitorDataUploadProgress.

private synchronized Set<HpcJobInfo> monitorDataUploadProgress(final Set<HpcJobInfo> pendingDisplayHpcJobInfoSet, final DefaultTableModel model) {
    Map<Long, Integer> rowMap = new HashMap<>();
    for (int row = 0; row < model.getRowCount(); row++) {
        rowMap.put(Long.valueOf(model.getValueAt(row, HpcJobActivityEditor.ID_COLUMN).toString()), row);
    }
    Set<HpcJobInfo> notPendingJobAnymoreSet = new HashSet<>();
    for (HpcJobInfo hpcJobInfo : pendingDisplayHpcJobInfoSet) {
        int status = hpcJobInfo.getStatus();
        if (!rowMap.containsKey(hpcJobInfo.getId())) {
            continue;
        }
        int modelRow = rowMap.get(hpcJobInfo.getId());
        // request was issued
        if (status != -1) {
            notPendingJobAnymoreSet.add(hpcJobInfo);
        } else {
            // Dataset uploading progress
            AlgorithmParamRequest algorParamReq = hpcJobInfo.getAlgorithmParamRequest();
            String datasetPath = algorParamReq.getDatasetPath();
            int dataUploadProgress = hpcJobManager.getUploadFileProgress(datasetPath);
            if (dataUploadProgress > -1 && dataUploadProgress < 100) {
                model.setValueAt("" + dataUploadProgress + "%", modelRow, HpcJobActivityEditor.DATA_UPLOAD_COLUMN);
            } else if (dataUploadProgress == -1) {
                model.setValueAt("Skipped", modelRow, HpcJobActivityEditor.DATA_UPLOAD_COLUMN);
            } else {
                model.setValueAt("Done", modelRow, HpcJobActivityEditor.DATA_UPLOAD_COLUMN);
            }
            // Prior Knowledge uploading progress
            String priorKnowledgePath = algorParamReq.getPriorKnowledgePath();
            int priorKnowledgeUploadProgress = -1;
            if (priorKnowledgePath != null) {
                LOGGER.debug("priorKnowledgePath: " + priorKnowledgePath);
                priorKnowledgeUploadProgress = hpcJobManager.getUploadFileProgress(priorKnowledgePath);
                if (priorKnowledgeUploadProgress > -1 && priorKnowledgeUploadProgress < 100) {
                    model.setValueAt("" + priorKnowledgeUploadProgress + "%", modelRow, HpcJobActivityEditor.KNOWLEDGE_UPLOAD_COLUMN);
                } else {
                    model.setValueAt("Done", modelRow, HpcJobActivityEditor.KNOWLEDGE_UPLOAD_COLUMN);
                }
            } else {
                model.setValueAt("Skipped", modelRow, HpcJobActivityEditor.KNOWLEDGE_UPLOAD_COLUMN);
            }
            if (dataUploadProgress == 100 && (priorKnowledgeUploadProgress == -1 || priorKnowledgeUploadProgress == 100)) {
                LOGGER.debug("HpcJobInfo Id: " + hpcJobInfo.getId() + " done with both uploading");
                Map<HpcAccount, Set<HpcJobInfo>> pendingHpcJobInfoMap = hpcJobManager.getPendingHpcJobInfoMap();
                Map<HpcAccount, Set<HpcJobInfo>> submittedHpcJobInfoMap = hpcJobManager.getSubmittedHpcJobInfoMap();
                if (pendingHpcJobInfoMap != null) {
                    Set<HpcJobInfo> pendingJobSet = pendingHpcJobInfoMap.get(hpcJobInfo.getHpcAccount());
                    // Is the job still stuck in the pre-processed schedule
                    // task?
                    long id = -1;
                    for (HpcJobInfo pendingJob : pendingJobSet) {
                        if (pendingJob.getId() == hpcJobInfo.getId()) {
                            id = pendingJob.getId();
                            continue;
                        }
                    }
                    // The job is not in the pre-processed schedule task
                    if (id == -1 && submittedHpcJobInfoMap != null) {
                        Set<HpcJobInfo> submittedJobSet = submittedHpcJobInfoMap.get(hpcJobInfo.getHpcAccount());
                        // Is the job in the submitted schedule task?
                        for (HpcJobInfo submittedJob : submittedJobSet) {
                            if (submittedJob.getId() == hpcJobInfo.getId()) {
                                // Status
                                switch(submittedJob.getStatus()) {
                                    case -1:
                                        model.setValueAt("Pending", modelRow, HpcJobActivityEditor.STATUS_COLUMN);
                                        break;
                                    case 0:
                                        model.setValueAt("Submitted", modelRow, HpcJobActivityEditor.STATUS_COLUMN);
                                        break;
                                    case 1:
                                        model.setValueAt("Running", modelRow, HpcJobActivityEditor.STATUS_COLUMN);
                                        break;
                                    case 2:
                                        model.setValueAt("Kill Request", modelRow, HpcJobActivityEditor.STATUS_COLUMN);
                                        break;
                                }
                                // Submitted time
                                if (submittedJob.getSubmittedTime() != null) {
                                    model.setValueAt(FilePrint.fileTimestamp(hpcJobInfo.getSubmittedTime().getTime()), modelRow, HpcJobActivityEditor.ACTIVE_SUBMITTED_COLUMN);
                                }
                                // Hpc Pid
                                model.setValueAt(submittedJob.getPid(), modelRow, HpcJobActivityEditor.ACTIVE_HPC_JOB_ID_COLUMN);
                                // last update
                                HpcJobLog hpcJobLog = hpcJobManager.getHpcJobLog(submittedJob);
                                model.setValueAt(FilePrint.fileTimestamp(hpcJobLog.getLastUpdatedTime().getTime()), modelRow, HpcJobActivityEditor.ACTIVE_LAST_UPDATED_COLUMN);
                                // Remove from the pending queue
                                notPendingJobAnymoreSet.add(submittedJob);
                                continue;
                            }
                        }
                    }
                }
            }
        }
    }
    return notPendingJobAnymoreSet;
}

Example 9 with HpcJobLog

use of edu.pitt.dbmi.tetrad.db.entity.HpcJobLog in project tetrad by cmu-phil.

the class SubmittedHpcJobUpdaterTask method monitorSubmittedJobStatus.

private synchronized Set<HpcJobInfo> monitorSubmittedJobStatus(final Set<HpcJobInfo> submittedDisplayHpcJobInfoSet, final DefaultTableModel model) {
    Map<Long, Integer> rowMap = new HashMap<>();
    for (int row = 0; row < model.getRowCount(); row++) {
        rowMap.put(Long.valueOf(model.getValueAt(row, HpcJobActivityEditor.ID_COLUMN).toString()), row);
    }
    Set<HpcJobInfo> finishedJobSet = new HashSet<>();
    for (HpcJobInfo hpcJobInfo : submittedDisplayHpcJobInfoSet) {
        Long id = hpcJobInfo.getId();
        if (!rowMap.containsKey(id)) {
            // System.out.println("hpcJobInfo not found in rowMap");
            continue;
        }
        int modelRow = rowMap.get(id);
        Map<HpcAccount, Set<HpcJobInfo>> submittedHpcJobInfoMap = hpcJobManager.getSubmittedHpcJobInfoMap();
        Set<HpcJobInfo> submittedJobSet = submittedHpcJobInfoMap.get(hpcJobInfo.getHpcAccount());
        if (submittedJobSet != null) {
            for (HpcJobInfo submittedJob : submittedJobSet) {
                if (submittedJob.getId() == hpcJobInfo.getId()) {
                    hpcJobInfo = submittedJob;
                    // submittedHpcJobInfoMap id matched!");
                    continue;
                }
            }
        }
        int status = hpcJobInfo.getStatus();
        // Status
        switch(hpcJobInfo.getStatus()) {
            case -1:
                model.setValueAt("Pending", modelRow, HpcJobActivityEditor.STATUS_COLUMN);
                break;
            case 0:
                model.setValueAt("Submitted", modelRow, HpcJobActivityEditor.STATUS_COLUMN);
                break;
            case 1:
                model.setValueAt("Running", modelRow, HpcJobActivityEditor.STATUS_COLUMN);
                break;
            case 2:
                model.setValueAt("Kill Request", modelRow, HpcJobActivityEditor.STATUS_COLUMN);
                break;
        }
        // last update
        HpcJobLog hpcJobLog = hpcJobManager.getHpcJobLog(hpcJobInfo);
        model.setValueAt(FilePrint.fileTimestamp(hpcJobLog.getLastUpdatedTime().getTime()), modelRow, HpcJobActivityEditor.ACTIVE_LAST_UPDATED_COLUMN);
        // was finished.
        if (status > 2) {
            finishedJobSet.add(hpcJobInfo);
        }
    }
    return finishedJobSet;
}