Examples with VtkMeshGenerator cbit.vcell.simdata.VtkMeshGenerator used on opensource projects

Example 1 with VtkMeshGenerator

use of cbit.vcell.simdata.VtkMeshGenerator 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;
}