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

Example 6 with HpcJobInfo

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

the class HpcJobManager method addNewSubmittedHpcJob.

public synchronized void addNewSubmittedHpcJob(final HpcJobInfo hpcJobInfo) {
    HpcAccount hpcAccount = hpcJobInfo.getHpcAccount();
    LOGGER.debug("addNewSubmittedHpcJob: connection: " + hpcAccount.getConnectionName());
    LOGGER.debug("addNewSubmittedHpcJob: algorithm: " + hpcJobInfo.getAlgoId());
    LOGGER.debug("addNewSubmittedHpcJob: status: " + hpcJobInfo.getStatus());
    LOGGER.debug("addNewSubmittedHpcJob: " + "pid: " + hpcJobInfo.getPid());
    Set<HpcJobInfo> hpcJobInfos = submittedHpcJobInfoMap.get(hpcAccount);
    if (hpcJobInfos == null) {
        hpcJobInfos = new LinkedHashSet<>();
    }
    hpcJobInfos.add(hpcJobInfo);
    submittedHpcJobInfoMap.put(hpcAccount, hpcJobInfos);
    removePendingHpcJob(hpcJobInfo);
}

Example 7 with HpcJobInfo

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

the class GeneralAlgorithmEditor method doRemoteCompute.

private void doRemoteCompute(final GeneralAlgorithmRunner runner, final HpcAccount hpcAccount) throws Exception {
    // **********************
    // Show progress panel *
    // **********************
    Frame ancestor = (Frame) JOptionUtils.centeringComp().getTopLevelAncestor();
    final JDialog progressDialog = new JDialog(ancestor, "HPC Job Submission's Progress...", false);
    Dimension progressDim = new Dimension(500, 150);
    JTextArea progressTextArea = new JTextArea();
    progressTextArea.setPreferredSize(progressDim);
    progressTextArea.setEditable(false);
    JScrollPane progressScroller = new JScrollPane(progressTextArea);
    progressScroller.setAlignmentX(LEFT_ALIGNMENT);
    progressDialog.setLayout(new BorderLayout());
    progressDialog.getContentPane().add(progressScroller, BorderLayout.CENTER);
    progressDialog.pack();
    Dimension screenDim = Toolkit.getDefaultToolkit().getScreenSize();
    progressDialog.setLocation((screenDim.width - progressDim.width) / 2, (screenDim.height - progressDim.height) / 2);
    progressDialog.setVisible(true);
    int totalProcesses = 4;
    String newline = "\n";
    String tab = "\t";
    int progressTextLength = 0;
    DataModel dataModel = runner.getDataModel();
    // 1. Generate temp file
    Path file = null;
    Path prior = null;
    try {
        // ****************************
        // Data Preparation Progress *
        // ****************************
        String dataMessage = String.format("1/%1$d Data Preparation", totalProcesses);
        progressTextArea.append(dataMessage);
        progressTextArea.append(tab);
        progressTextLength = progressTextArea.getText().length();
        progressTextArea.append("Preparing...");
        progressTextArea.updateUI();
        file = Files.createTempFile("Tetrad-data-", ".txt");
        // LOGGER.info(file.toAbsolutePath().toString());
        List<String> tempLine = new ArrayList<>();
        // Header
        List<Node> variables = dataModel.getVariables();
        if ((variables == null || variables.isEmpty()) && runner.getSourceGraph() != null) {
            variables = runner.getSourceGraph().getNodes();
        }
        String vars = StringUtils.join(variables.toArray(), tab);
        tempLine.add(vars);
        // Data
        DataSet dataSet = (DataSet) dataModel;
        for (int i = 0; i < dataSet.getNumRows(); i++) {
            String line = null;
            for (int j = 0; j < dataSet.getNumColumns(); j++) {
                String cell = null;
                if (dataSet.isContinuous()) {
                    cell = String.valueOf(dataSet.getDouble(i, j));
                } else {
                    cell = String.valueOf(dataSet.getInt(i, j));
                }
                if (line == null) {
                    line = cell;
                } else {
                    line = line + "\t" + cell;
                }
            }
            tempLine.add(line);
        }
        // for (String line : tempLine) {
        // LOGGER.info(line);
        // }
        Files.write(file, tempLine);
        // Get file's MD5 hash and use it as its identifier
        String datasetMd5 = MessageDigestHash.computeMD5Hash(file);
        progressTextArea.replaceRange("Done", progressTextLength, progressTextArea.getText().length());
        progressTextArea.append(newline);
        progressTextArea.updateUI();
        // ***************************************
        // Prior Knowledge Preparation Progress *
        // ***************************************
        String priorMessage = String.format("2/%1$d Prior Knowledge Preparation", totalProcesses);
        progressTextArea.append(priorMessage);
        progressTextArea.append(tab);
        progressTextLength = progressTextArea.getText().length();
        progressTextArea.append("Preparing...");
        progressTextArea.updateUI();
        // 2. Generate temp prior knowledge file
        Knowledge2 knowledge = (Knowledge2) dataModel.getKnowledge();
        if (knowledge != null && !knowledge.isEmpty()) {
            prior = Files.createTempFile(file.getFileName().toString(), ".prior");
            knowledge.saveKnowledge(Files.newBufferedWriter(prior));
            progressTextArea.replaceRange("Done", progressTextLength, progressTextArea.getText().length());
            progressTextArea.append(newline);
            progressTextArea.updateUI();
        } else {
            progressTextArea.replaceRange("Skipped", progressTextLength, progressTextArea.getText().length());
            progressTextArea.append(newline);
            progressTextArea.updateUI();
        }
        // Get knowledge file's MD5 hash and use it as its identifier
        String priorKnowledgeMd5 = null;
        if (prior != null) {
            priorKnowledgeMd5 = MessageDigestHash.computeMD5Hash(prior);
        }
        // *******************************************
        // Algorithm Parameter Preparation Progress *
        // *******************************************
        String algorMessage = String.format("3/%1$d Algorithm Preparation", totalProcesses);
        progressTextArea.append(algorMessage);
        progressTextArea.append(tab);
        progressTextLength = progressTextArea.getText().length();
        progressTextArea.append("Preparing...");
        progressTextArea.updateUI();
        // 3.1 Algorithm Id, Independent Test Id, Score Id
        AlgorithmModel algoModel = algorithmList.getSelectedValue();
        String algoId = algoModel.getAlgorithm().getAnnotation().command();
        // Test
        String testId = null;
        if (indTestComboBox.isEnabled()) {
            IndependenceTestModel indTestModel = indTestComboBox.getItemAt(indTestComboBox.getSelectedIndex());
            testId = indTestModel.getIndependenceTest().getAnnotation().command();
        }
        // Score
        String scoreId = null;
        if (scoreComboBox.isEnabled()) {
            ScoreModel scoreModel = scoreComboBox.getItemAt(scoreComboBox.getSelectedIndex());
            scoreId = scoreModel.getScore().getAnnotation().command();
        }
        // 3.2 Parameters
        AlgorithmParamRequest algorithmParamRequest = new AlgorithmParamRequest();
        // Test and score
        algorithmParamRequest.setTestId(testId);
        algorithmParamRequest.setScoreId(scoreId);
        // Dataset and Prior paths
        String datasetPath = file.toAbsolutePath().toString();
        LOGGER.info(datasetPath);
        algorithmParamRequest.setDatasetPath(datasetPath);
        algorithmParamRequest.setDatasetMd5(datasetMd5);
        if (prior != null) {
            String priorKnowledgePath = prior.toAbsolutePath().toString();
            LOGGER.info(priorKnowledgePath);
            algorithmParamRequest.setPriorKnowledgePath(priorKnowledgePath);
            algorithmParamRequest.setPriorKnowledgeMd5(priorKnowledgeMd5);
        }
        // VariableType
        if (dataModel.isContinuous()) {
            algorithmParamRequest.setVariableType("continuous");
        } else if (dataModel.isDiscrete()) {
            algorithmParamRequest.setVariableType("discrete");
        } else {
            algorithmParamRequest.setVariableType("mixed");
        }
        // FileDelimiter
        // Pre-determined
        String fileDelimiter = "tab";
        algorithmParamRequest.setFileDelimiter(fileDelimiter);
        Set<AlgorithmParameter> AlgorithmParameters = new HashSet<>();
        Parameters parameters = runner.getParameters();
        List<String> parameterNames = runner.getAlgorithm().getParameters();
        for (String parameter : parameterNames) {
            String value = parameters.get(parameter).toString();
            LOGGER.info("parameter: " + parameter + "\tvalue: " + value);
            if (value != null) {
                AlgorithmParameter algorParam = new AlgorithmParameter();
                algorParam.setParameter(parameter);
                algorParam.setValue(value);
                AlgorithmParameters.add(algorParam);
            }
        }
        algorithmParamRequest.setAlgorithmParameters(AlgorithmParameters);
        String maxHeapSize = null;
        do {
            maxHeapSize = JOptionPane.showInputDialog(progressDialog, "Enter Your Request Java Max Heap Size (GB):", "5");
        } while (maxHeapSize != null && !StringUtils.isNumeric(maxHeapSize));
        if (maxHeapSize != null) {
            JvmOptions jvmOptions = new JvmOptions();
            jvmOptions.setMaxHeapSize(Integer.parseInt(maxHeapSize));
            algorithmParamRequest.setJvmOptions(jvmOptions);
        }
        // Hpc parameters
        final HpcAccountManager hpcAccountManager = desktop.getHpcAccountManager();
        JsonWebToken jsonWebToken = HpcAccountUtils.getJsonWebToken(hpcAccountManager, hpcAccount);
        if (jsonWebToken.getWallTime() != null) {
            // User allowed to customize the job's wall time
            String[] wallTime = jsonWebToken.getWallTime();
            Object userwallTime = JOptionPane.showInputDialog(progressDialog, "Wall Time:", "Choose Your Wall Time (in Hour)", JOptionPane.QUESTION_MESSAGE, null, wallTime, wallTime[0]);
            if (wallTime != null && userwallTime != null) {
                HpcParameter hpcParameter = new HpcParameter();
                hpcParameter.setKey("walltime");
                hpcParameter.setValue(userwallTime.toString());
                LOGGER.info("walltime: " + userwallTime.toString());
                Set<HpcParameter> hpcParameters = new HashSet<>();
                hpcParameters.add(hpcParameter);
                algorithmParamRequest.setHpcParameters(hpcParameters);
            }
        }
        progressTextArea.replaceRange("Done", progressTextLength, progressTextArea.getText().length());
        progressTextArea.append(newline);
        progressTextArea.updateUI();
        // ********************************
        // Adding HPC Job Queue Progress *
        // ********************************
        String dbMessage = String.format("4/%1$d HPC Job Queue Submission", totalProcesses);
        progressTextArea.append(dbMessage);
        progressTextArea.append(tab);
        progressTextLength = progressTextArea.getText().length();
        progressTextArea.append("Preparing...");
        progressTextArea.updateUI();
        HpcJobManager hpcJobManager = desktop.getHpcJobManager();
        // 4.1 Save HpcJobInfo
        hpcJobInfo = new HpcJobInfo();
        hpcJobInfo.setAlgoId(algoId);
        hpcJobInfo.setAlgorithmParamRequest(algorithmParamRequest);
        hpcJobInfo.setStatus(-1);
        hpcJobInfo.setHpcAccount(hpcAccount);
        hpcJobManager.submitNewHpcJobToQueue(hpcJobInfo, this);
        progressTextArea.replaceRange("Done", progressTextLength, progressTextArea.getText().length());
        progressTextArea.append(newline);
        progressTextArea.updateUI();
        this.jsonResult = null;
        JOptionPane.showMessageDialog(ancestor, "The " + hpcJobInfo.getAlgoId() + " job on the " + hpcJobInfo.getHpcAccount().getConnectionName() + " node is in the queue successfully!");
    } catch (IOException exception) {
        LOGGER.error("", exception);
    } finally {
        progressDialog.setVisible(false);
        progressDialog.dispose();
    }
    (new HpcJobActivityAction("")).actionPerformed(null);
}

Example 8 with HpcJobInfo

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

the class HpcJobActivityEditor method removeSubmittedDisplayJobFromActiveTableModel.

public synchronized void removeSubmittedDisplayJobFromActiveTableModel(final Set<HpcJobInfo> finishedJobSet) {
    DefaultTableModel model = (DefaultTableModel) jobsTable.getModel();
    Map<Long, Integer> rowMap = new HashMap<>();
    for (int row = 0; row < model.getRowCount(); row++) {
        rowMap.put(Long.valueOf(model.getValueAt(row, ID_COLUMN).toString()), row);
    }
    for (final HpcJobInfo hpcJobInfo : finishedJobSet) {
        if (rowMap.containsKey(hpcJobInfo.getId())) {
            model.removeRow(rowMap.get(hpcJobInfo.getId()));
        }
    }
}

Example 9 with HpcJobInfo

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

the class HpcJobActivityEditor method getFinishedRowData.

private Vector<Vector<String>> getFinishedRowData(final TetradDesktop desktop, final List<HpcAccount> exclusiveHpcAccounts) throws Exception {
    final Vector<Vector<String>> finishedRowData = new Vector<>();
    HpcJobManager hpcJobManager = desktop.getHpcJobManager();
    Map<Long, HpcJobInfo> finishedHpcJobIdMap = null;
    // Finished jobs
    Map<HpcAccount, Set<HpcJobInfo>> finishedHpcJobInfoMap = hpcJobManager.getFinishedHpcJobInfoMap();
    for (HpcAccount hpcAccount : finishedHpcJobInfoMap.keySet()) {
        if (exclusiveHpcAccounts != null && !exclusiveHpcAccounts.contains(hpcAccount)) {
            continue;
        }
        Set<HpcJobInfo> finishedHpcJobSet = finishedHpcJobInfoMap.get(hpcAccount);
        for (HpcJobInfo hpcJobInfo : finishedHpcJobSet) {
            if (finishedHpcJobIdMap == null) {
                finishedHpcJobIdMap = new HashMap<>();
            }
            finishedHpcJobIdMap.put(hpcJobInfo.getId(), hpcJobInfo);
        }
    }
    if (finishedHpcJobIdMap != null) {
        List<Long> finishedJobIds = new ArrayList<>(finishedHpcJobIdMap.keySet());
        Collections.sort(finishedJobIds);
        Collections.reverse(finishedJobIds);
        for (Long jobId : finishedJobIds) {
            final HpcJobInfo hpcJobInfo = finishedHpcJobIdMap.get(jobId);
            Vector<String> rowData = new Vector<>();
            HpcJobLog hpcJobLog = hpcJobManager.getHpcJobLog(hpcJobInfo);
            // Local job id
            rowData.add(hpcJobInfo.getId().toString());
            int status = hpcJobInfo.getStatus();
            switch(status) {
                case 3:
                    rowData.add("Finished");
                    break;
                case 4:
                    rowData.add("Canceled");
                    break;
                case 5:
                    rowData.add("Finished");
                    break;
                case 6:
                    rowData.add("Error");
                    break;
            }
            // Locally added time
            rowData.add(FilePrint.fileTimestamp(hpcJobLog.getAddedTime().getTime()));
            // HPC node name
            HpcAccount hpcAccount = hpcJobInfo.getHpcAccount();
            rowData.add(hpcAccount.getConnectionName());
            // Algorithm
            rowData.add(hpcJobInfo.getAlgoId());
            // Submitted time
            rowData.add(hpcJobInfo.getSubmittedTime() != null ? FilePrint.fileTimestamp(hpcJobInfo.getSubmittedTime().getTime()) : "");
            // HPC job id
            rowData.add("" + hpcJobInfo.getPid());
            // Result Name
            switch(status) {
                case 3:
                    rowData.add(hpcJobInfo.getResultFileName());
                    break;
                case 4:
                    rowData.add("");
                    break;
                case 5:
                    rowData.add(hpcJobInfo.getResultFileName());
                    break;
                case 6:
                    rowData.add(hpcJobInfo.getErrorResultFileName());
                    break;
            }
            // Finished time
            if (status != 4) {
                rowData.add(FilePrint.fileTimestamp(hpcJobLog.getEndedTime().getTime()));
            } else {
                rowData.add("");
            }
            // Canceled time
            if (status == 4) {
                rowData.add(hpcJobLog.getCanceledTime() != null ? FilePrint.fileTimestamp(hpcJobLog.getCanceledTime().getTime()) : "");
            } else {
                rowData.add("");
            }
            // Last update time
            rowData.add(FilePrint.fileTimestamp(hpcJobLog.getLastUpdatedTime().getTime()));
            // Delete job from db
            rowData.add("Delete");
            finishedRowData.add(rowData);
        }
    }
    return finishedRowData;
}

Example 10 with HpcJobInfo

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

the class HpcJobManager method updateSubmittedHpcJobInfo.

public synchronized void updateSubmittedHpcJobInfo(final HpcJobInfo hpcJobInfo) {
    final HpcAccount hpcAccount = hpcJobInfo.getHpcAccount();
    Set<HpcJobInfo> hpcJobInfos = submittedHpcJobInfoMap.get(hpcAccount);
    if (hpcJobInfos != null) {
        for (HpcJobInfo jobInfo : hpcJobInfos) {
            if (jobInfo.getId() == hpcJobInfo.getId()) {
                // LOGGER.debug("updateSubmittedHpcJobInfo: Found
                // hpcJobInfo in the submittedHpcJobInfoMap & removed it!");
                hpcJobInfos.remove(jobInfo);
            }
        }
        hpcJobInfos.add(hpcJobInfo);
        submittedHpcJobInfoMap.put(hpcAccount, hpcJobInfos);
    }
}