Examples with ExecutableException org.vcell.util.exe.ExecutableException used on opensource projects

Example 1 with ExecutableException

use of org.vcell.util.exe.ExecutableException in project vcell by virtualcell.

the class BNGExecutorServiceNative method executeBNG.

/**
 * Insert the method's description here.
 * Creation date: (6/23/2005 3:57:30 PM)
 */
@Override
public BNGOutput executeBNG() throws BNGException {
    if (executable != null) {
        throw new BNGException("You can only run BNG one at a time!");
    }
    BNGOutput bngOutput = null;
    startTime = System.currentTimeMillis();
    File workingDir = null;
    try {
        workingDir = Files.createTempDirectory("Bng_working_").toFile();
        File bngInputFile = null;
        FileOutputStream fos = null;
        String tempFilePrefix = workingDir.getName();
        try {
            bngInputFile = new File(workingDir, tempFilePrefix + suffix_input);
            fos = new java.io.FileOutputStream(bngInputFile);
        } catch (java.io.IOException e) {
            if (LG.isWarnEnabled()) {
                LG.warn("error opening input file '" + bngInputFile, e);
            }
            e.printStackTrace(System.out);
            throw new RuntimeException("error opening input file '" + bngInputFile.getName() + ": " + e.getMessage());
        }
        PrintWriter inputFile = new PrintWriter(fos);
        System.out.println("Input file is: " + bngInputFile.getPath());
        inputFile.print(bngInput.getInputString());
        inputFile.close();
        // System.out.println("BNGExecutorService.executeBNG(): input = \n"+bngInput.getInputString());
        String[] cmd = null;
        OperatingSystemInfo osi = OperatingSystemInfo.getInstance();
        if (osi.isWindows()) {
            System.out.println("BNGExecutorService.executeBNG() " + (osi.is64bit() ? "64bit" : "32bit") + " as standalone executable\n");
            cmd = new String[] { ResourceUtil.getBNG2StandaloneWin(osi.is64bit()), bngInputFile.getAbsolutePath() };
        } else {
            // Execute as perl script
            System.out.println("BNGExecutorService.executeBNG() as perl script\n");
            String bngPerlFilePath = ResourceUtil.getBNG2_perl_file();
            cmd = new String[] { ResourceUtil.getPerlExe().getAbsolutePath(), bngPerlFilePath, bngInputFile.getAbsolutePath() };
        }
        // run BNG
        long timeoutMS = 0;
        if (timeoutDurationMS != null) {
            timeoutMS = timeoutDurationMS.longValue();
        }
        executable = new BioNetGenExecutable(cmd, timeoutMS, workingDir);
        executable.addEnvironmentVariable("LD_LIBRARY_PATH", "");
        executable.inheritCallbacks(getCallbacks());
        int[] expectedReturnCodes = new int[] { 0 };
        executable.start(expectedReturnCodes);
        String stdoutString;
        if (executable.getStatus() != org.vcell.util.exe.ExecutableStatus.STOPPED) {
            stdoutString = executable.getStdoutString();
        } else {
            stdoutString = "Stopped by user. Output from BioNetGen may be truncated";
        }
        if (executable.getExitValue() == 1) {
            String stderrString = executable.getStderrString();
            if (stderrString.contains("run_network")) {
                stdoutString = "run_network not supported on this operating system; partial data may be available\n" + executable.getStdoutString();
            }
        }
        File[] files = workingDir.listFiles();
        ArrayList<String> filenames = new ArrayList<String>();
        ArrayList<String> filecontents = new ArrayList<String>();
        for (File file : files) {
            String filename = file.getName();
            if (LG.isDebugEnabled()) {
                LG.debug("BNG executor trying to read " + filename);
            }
            filenames.add(filename);
            filecontents.add(FileUtils.readFileToString(file));
        }
        bngOutput = new BNGOutput(stdoutString, filenames.toArray(new String[0]), filecontents.toArray(new String[0]));
    } catch (ExecutableException | IOException ex) {
        if (LG.isWarnEnabled()) {
            LG.warn("error executable BNG", ex);
        }
        if (executable == null || executable.getStderrString().trim().length() == 0) {
            throw new BNGException("Error executing BNG", ex);
        }
        throw new BNGException(executable.getStderrString(), ex);
    } finally {
        if (workingDir != null) {
            File[] files = workingDir.listFiles();
            for (File file : files) {
                file.delete();
            }
            workingDir.delete();
        }
    }
    return bngOutput;
}

Example 2 with ExecutableException

use of org.vcell.util.exe.ExecutableException in project vcell by virtualcell.

the class CopasiServicePython method runCopasiPython.

public static void runCopasiPython(File copasiOptProblemFile, File copasiResultsFile) throws IOException {
    // It's 2015 -- forward slash works for all operating systems
    File PYTHON = PythonSupport.getPythonExe();
    InstallStatus copasiInstallStatus = PythonSupport.getPythonPackageStatus(PythonPackage.COPASI);
    if (copasiInstallStatus == InstallStatus.FAILED) {
        throw new RuntimeException("failed to install COPASI python package, consider re-installing VCell-managed python\n ...see Preferences->Python->Re-install");
    }
    if (copasiInstallStatus == InstallStatus.INITIALIZING) {
        throw new RuntimeException("VCell is currently installing or verifying the COPASI python package ... please try again in a minute");
    }
    File vcellOptDir = ResourceUtil.getVCellOptPythonDir();
    File optServicePythonFile = new File(vcellOptDir, "optService.py");
    if (PYTHON == null || !PYTHON.exists()) {
        throw new RuntimeException("python executable not specified, set python location in VCell menu File->Preferences...->Python Properties");
    }
    String[] cmd = new String[] { PYTHON.getAbsolutePath(), optServicePythonFile.getAbsolutePath(), copasiOptProblemFile.getAbsolutePath(), copasiResultsFile.getAbsolutePath() };
    IExecutable exe = prepareExecutable(cmd);
    try {
        exe.start(new int[] { 0 });
        if (exe.getExitValue() != 0) {
            throw new RuntimeException("copasi python solver (optService.py) failed with return code " + exe.getExitValue() + ": " + exe.getStderrString());
        }
    } catch (ExecutableException e) {
        e.printStackTrace();
        throw new RuntimeException("optService.py invocation failed: " + e.getMessage(), e);
    }
}

Example 3 with ExecutableException

use of org.vcell.util.exe.ExecutableException in project vcell by virtualcell.

the class SlurmProxy method submitJobFile.

HtcJobID submitJobFile(File sub_file_external) throws ExecutableException {
    final String JOB_CMD_SBATCH = PropertyLoader.getProperty(PropertyLoader.slurm_cmd_sbatch, "sbatch");
    String[] completeCommand = new String[] { JOB_CMD_SBATCH, sub_file_external.getAbsolutePath() };
    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_SBATCH + "' 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;
}

Example 4 with ExecutableException

use of org.vcell.util.exe.ExecutableException in project vcell by virtualcell.

the class SlurmProxy method killJobSafe.

@Override
public void killJobSafe(HtcJobInfo htcJobInfo) throws ExecutableException, HtcException {
    final String JOB_CMD_DELETE = PropertyLoader.getProperty(PropertyLoader.slurm_cmd_scancel, "scancel");
    String[] cmd = new String[] { JOB_CMD_DELETE, "--jobname", htcJobInfo.getJobName(), Long.toString(htcJobInfo.getHtcJobID().getJobNumber()) };
    try {
        // CommandOutput commandOutput = commandService.command(cmd, new int[] { 0, QDEL_JOB_NOT_FOUND_RETURN_CODE });
        if (LG.isDebugEnabled()) {
            LG.debug("killing SLURM job htcJobId=" + htcJobInfo + ": '" + CommandOutput.concatCommandStrings(cmd) + "'");
        }
        CommandOutput commandOutput = commandService.command(cmd, new int[] { 0, SCANCEL_JOB_NOT_FOUND_RETURN_CODE });
        Integer exitStatus = commandOutput.getExitStatus();
        String standardOut = commandOutput.getStandardOutput();
        if (exitStatus != null && exitStatus.intValue() == SCANCEL_JOB_NOT_FOUND_RETURN_CODE && standardOut != null && standardOut.toLowerCase().contains(SCANCEL_UNKNOWN_JOB_RESPONSE.toLowerCase())) {
            LG.error("failed to cancel SLURM htcJobId=" + htcJobInfo + ", job not found");
            throw new HtcJobNotFoundException(standardOut, htcJobInfo);
        }
    } catch (ExecutableException e) {
        LG.error("failed to cancel SLURM htcJobId=" + htcJobInfo, e);
        if (!e.getMessage().toLowerCase().contains(SCANCEL_UNKNOWN_JOB_RESPONSE.toLowerCase())) {
            throw e;
        } else {
            throw new HtcJobNotFoundException(e.getMessage(), htcJobInfo);
        }
    }
}

Example 5 with ExecutableException

use of org.vcell.util.exe.ExecutableException in project vcell by virtualcell.

the class SlurmProxyTest method testSLURM.

@Test
public void testSLURM() throws IOException, ExecutableException {
    System.setProperty("log4j2.trace", "true");
    System.setProperty(PropertyLoader.vcellServerIDProperty, "Test2");
    System.setProperty(PropertyLoader.htcLogDirExternal, "/Volumes/vcell/htclogs");
    VCMongoMessage.enabled = false;
    String[] partitions = new String[] { "vcell", "vcell2" };
    System.setProperty(PropertyLoader.slurm_partition, partitions[0]);
    CommandServiceSshNative cmd = null;
    try {
        cmd = new CommandServiceSshNative(new String[] { "vcell-service.cam.uchc.edu" }, "vcell", new File("/Users/schaff/.ssh/schaff_rsa"));
        SlurmProxy slurmProxy = new SlurmProxy(cmd, "vcell");
        Map<HtcJobInfo, HtcJobStatus> runningJobs = slurmProxy.getRunningJobs();
        for (HtcJobInfo jobInfo : runningJobs.keySet()) {
            HtcJobStatus jobStatus = runningJobs.get(jobInfo);
            System.out.println("job " + jobInfo.getHtcJobID() + " " + jobInfo.getJobName() + ", status=" + jobStatus.toString());
        }
        for (String partition : partitions) {
            System.setProperty(PropertyLoader.slurm_partition, partition);
            PartitionStatistics partitionStatistics = slurmProxy.getPartitionStatistics();
            System.out.println("partition statistics for partition " + partition + ": " + partitionStatistics);
            System.out.println("number of cpus allocated = " + partitionStatistics.numCpusAllocated);
            System.out.println("load = " + partitionStatistics.load);
            System.out.println("number of cpus total = " + partitionStatistics.numCpusTotal);
        }
    } catch (Exception e) {
        e.printStackTrace();
        fail(e.getMessage());
    } finally {
        if (cmd != null) {
            cmd.close();
        }
    }
}