Examples with LogicalData es.bsc.compss.types.data.LogicalData used on opensource projects

Example 11 with LogicalData

use of es.bsc.compss.types.data.LogicalData in project compss by bsc-wdc.

the class Resource method getData.

/**
 * Retrieves a given data
 *
 * @param dataId
 * @param tgtDataId
 * @param reason
 * @param listener
 */
public void getData(String dataId, String tgtDataId, Transferable reason, EventListener listener) {
    LogicalData srcData = Comm.getData(dataId);
    LogicalData tgtData = null;
    if (tgtDataId != null) {
        tgtData = Comm.getData(tgtDataId);
    }
    getData(srcData, dataId, tgtData, reason, listener);
}

Example 12 with LogicalData

use of es.bsc.compss.types.data.LogicalData in project compss by bsc-wdc.

the class Resource method getTracingPackageToMaster.

private void getTracingPackageToMaster() {
    COMPSsNode masterNode = Comm.getAppHost().getNode();
    Semaphore sem = new Semaphore(0);
    String fileName = getName() + "_compss_trace.tar.gz";
    SimpleURI fileOriginURI = node.getCompletePath(DataType.FILE_T, fileName);
    if (DEBUG) {
        LOGGER.debug("Copying tracing package from : " + fileOriginURI.getPath() + ",to : " + Comm.getAppHost().getAppLogDirPath() + "trace" + File.separator + fileName);
    }
    TracingCopyListener tracingListener = new TracingCopyListener(sem);
    tracingListener.addOperation();
    // Source data location
    DataLocation source;
    try {
        source = DataLocation.createLocation(this, fileOriginURI);
    } catch (Exception e) {
        ErrorManager.error(DataLocation.ERROR_INVALID_LOCATION + " " + fileOriginURI.getPath(), e);
        return;
    }
    // Target data location
    DataLocation tgt;
    String targetPath = Protocol.FILE_URI.getSchema() + Comm.getAppHost().getAppLogDirPath() + "trace" + File.separator + fileName;
    try {
        SimpleURI uri = new SimpleURI(targetPath);
        tgt = DataLocation.createLocation(Comm.getAppHost(), uri);
    } catch (Exception e) {
        ErrorManager.error(DataLocation.ERROR_INVALID_LOCATION + " " + targetPath);
        return;
    }
    // Ask for data
    masterNode.obtainData(new LogicalData("tracing" + this.getName()), source, tgt, new LogicalData("tracing" + this.getName()), new TracingCopyTransferable(), tracingListener);
    tracingListener.enable();
    try {
        sem.acquire();
    } catch (InterruptedException ex) {
        LOGGER.error("Error waiting for tracing files in resource " + getName() + " to get saved");
    }
    if (DEBUG) {
        LOGGER.debug("Removing " + this.getName() + " tracing temporary files");
    }
    File f = null;
    try {
        f = new File(source.getPath());
        if (!f.delete()) {
            LOGGER.error("Unable to remove tracing temporary files of node " + this.getName());
        }
    } catch (Exception e) {
        LOGGER.error("Unable to remove tracing temporary files of node " + this.getName(), e);
    }
}

Example 13 with LogicalData

use of es.bsc.compss.types.data.LogicalData in project compss by bsc-wdc.

the class Resource method retrieveData.

/**
 * Retrieves all the data from the Resource
 *
 * @param saveUniqueData
 */
public void retrieveData(boolean saveUniqueData) {
    if (DEBUG) {
        LOGGER.debug("Retrieving data resource " + this.getName());
    }
    Semaphore sem = new Semaphore(0);
    SafeCopyListener listener = new SafeCopyListener(sem);
    Set<LogicalData> lds = getAllDataFromHost();
    Map<String, String> disks = SharedDiskManager.terminate(this);
    COMPSsNode masterNode = Comm.getAppHost().getNode();
    for (LogicalData ld : lds) {
        ld.notifyToInProgressCopiesEnd(listener);
        DataLocation lastLoc = ld.removeHostAndCheckLocationToSave(this, disks);
        if (lastLoc != null && saveUniqueData) {
            listener.addOperation();
            DataLocation safeLoc = null;
            String safePath = Protocol.FILE_URI.getSchema() + Comm.getAppHost().getTempDirPath() + ld.getName();
            try {
                SimpleURI uri = new SimpleURI(safePath);
                safeLoc = DataLocation.createLocation(Comm.getAppHost(), uri);
            } catch (Exception e) {
                ErrorManager.error(DataLocation.ERROR_INVALID_LOCATION + " " + safePath, e);
            }
            masterNode.obtainData(ld, lastLoc, safeLoc, ld, new SafeCopyTransferable(), listener);
        }
    }
    if (DEBUG) {
        LOGGER.debug("Waiting for finishing saving copies for " + this.getName());
    }
    listener.enable();
    try {
        sem.acquire();
    } catch (InterruptedException ex) {
        LOGGER.error("Error waiting for files in resource " + getName() + " to get saved");
    }
    if (DEBUG) {
        LOGGER.debug("Unique files saved for " + this.getName());
    }
    if (this.getType() != Type.SERVICE) {
        shutdownExecutionManager();
        if (Tracer.isActivated()) {
            if (node.generatePackage()) {
                getTracingPackageToMaster();
                if (DEBUG) {
                    LOGGER.debug("Tracing package obtained for " + this.getName());
                }
            }
        }
        if (DEBUG) {
            if (node.generateWorkersDebugInfo()) {
                getWorkersDebugInfo();
                LOGGER.debug("Workers Debug files obtained for " + this.getName());
            }
        }
    }
}

Example 14 with LogicalData

use of es.bsc.compss.types.data.LogicalData in project compss by bsc-wdc.

the class GATJob method prepareJob.

private JobDescription prepareJob() throws Exception {
    // Get the information related to the job
    logger.debug("Preparing GAT Job " + this.jobId);
    TaskDescription taskParams = this.taskParams;
    String targetPath = getResourceNode().getInstallDir();
    String targetHost = getResourceNode().getHost();
    String targetUser = getResourceNode().getUser();
    if (userNeeded && !targetUser.isEmpty()) {
        targetUser += "@";
    } else {
        targetUser = "";
    }
    SoftwareDescription sd = new SoftwareDescription();
    sd.setExecutable(targetPath + WORKER_SCRIPT_PATH + WORKER_SCRIPT_NAME);
    ArrayList<String> lArgs = new ArrayList<String>();
    // Common arguments: language working_dir lib_path num_obsolete [obs1... obsN] tracing [event_type task_id
    // slot_id]
    lArgs.add(LANG);
    lArgs.add(getResourceNode().getWorkingDir());
    lArgs.add(getResourceNode().getLibPath());
    LogicalData[] obsoleteFiles = getResource().pollObsoletes();
    if (obsoleteFiles != null) {
        lArgs.add("" + obsoleteFiles.length);
        for (LogicalData ld : obsoleteFiles) {
            String renaming = ld.getName();
            lArgs.add(renaming);
        }
    } else {
        lArgs.add("0");
    }
    // Check sandbox working dir
    boolean isSpecific = false;
    String sandboxDir = null;
    AbstractMethodImplementation absImpl = (AbstractMethodImplementation) this.impl;
    switch(absImpl.getMethodType()) {
        case BINARY:
            BinaryImplementation binaryImpl = (BinaryImplementation) absImpl;
            sandboxDir = binaryImpl.getWorkingDir();
            isSpecific = true;
            break;
        case MPI:
            MPIImplementation mpiImpl = (MPIImplementation) absImpl;
            sandboxDir = mpiImpl.getWorkingDir();
            isSpecific = true;
            break;
        case DECAF:
            DecafImplementation decafImpl = (DecafImplementation) absImpl;
            sandboxDir = decafImpl.getWorkingDir();
            isSpecific = true;
            break;
        case OMPSS:
            OmpSsImplementation ompssImpl = (OmpSsImplementation) absImpl;
            sandboxDir = ompssImpl.getWorkingDir();
            isSpecific = true;
            break;
        case OPENCL:
            OpenCLImplementation openclImpl = (OpenCLImplementation) absImpl;
            sandboxDir = openclImpl.getWorkingDir();
            isSpecific = true;
            break;
        case METHOD:
            sandboxDir = null;
            break;
    }
    if (sandboxDir == null || sandboxDir.isEmpty() || sandboxDir.equals(Constants.UNASSIGNED)) {
        sandboxDir = getResourceNode().getWorkingDir() + File.separator + "sandBox" + File.separator + "job_" + this.jobId;
        isSpecific = false;
    }
    // Processing parameters to get symlinks pairs to create (symlinks) and how to pass parameters in the GAT
    // Job(paramArgs)
    ArrayList<String> symlinks = new ArrayList<>();
    ArrayList<String> paramArgs = new ArrayList<>();
    processParameters(sandboxDir, symlinks, paramArgs);
    // Adding info to create symlinks between renamed files and original names
    lArgs.add(Boolean.toString(isSpecific));
    lArgs.add(sandboxDir);
    if (symlinks.size() > 0) {
        lArgs.add(String.valueOf(symlinks.size()));
        lArgs.addAll(symlinks);
    } else {
        lArgs.add("0");
    }
    lArgs.add(Boolean.toString(Tracer.isActivated()));
    lArgs.add(getHostName());
    if (debug) {
        logger.debug("hostName " + getHostName());
    }
    if (Tracer.isActivated()) {
        // event type
        lArgs.add(String.valueOf(Tracer.getTaskEventsType()));
        // task id
        lArgs.add(String.valueOf(this.taskParams.getId() + 1));
        int slot = Tracer.getNextSlot(targetHost);
        // slot id
        lArgs.add(String.valueOf(slot));
        sd.addAttribute("slot", slot);
    }
    // Language-dependent arguments: taskSandbox_dir app_dir classpath pythonpath debug storage_conf
    // method_impl_type method_impl_params
    // numSlaves [slave1,..,slaveN] numCus
    // has_target num_params par_type_1 par_1 ... par_type_n par_n
    lArgs.add(sandboxDir);
    lArgs.add(getResourceNode().getAppDir());
    lArgs.add(getClasspath());
    lArgs.add(getPythonpath());
    lArgs.add(String.valueOf(debug));
    lArgs.add(STORAGE_CONF);
    lArgs.add(String.valueOf(absImpl.getMethodType()));
    switch(absImpl.getMethodType()) {
        case METHOD:
            MethodImplementation methodImpl = (MethodImplementation) absImpl;
            lArgs.add(methodImpl.getDeclaringClass());
            String methodName = methodImpl.getAlternativeMethodName();
            if (methodName == null || methodName.isEmpty()) {
                methodName = taskParams.getName();
            }
            lArgs.add(methodName);
            break;
        case MPI:
            MPIImplementation mpiImpl = (MPIImplementation) absImpl;
            lArgs.add(mpiImpl.getMpiRunner());
            lArgs.add(mpiImpl.getBinary());
            break;
        case DECAF:
            DecafImplementation decafImpl = (DecafImplementation) absImpl;
            lArgs.add(targetPath + DecafImplementation.SCRIPT_PATH);
            String dfScript = decafImpl.getDfScript();
            if (!dfScript.startsWith(File.separator)) {
                String appPath = getResourceNode().getAppDir();
                dfScript = appPath + File.separator + dfScript;
            }
            lArgs.add(dfScript);
            String dfExecutor = decafImpl.getDfExecutor();
            if (dfExecutor == null || dfExecutor.isEmpty() || dfExecutor.equals(Constants.UNASSIGNED)) {
                dfExecutor = "executor.sh";
            }
            if (!dfExecutor.startsWith(File.separator) && !dfExecutor.startsWith("./")) {
                dfExecutor = "./" + dfExecutor;
            }
            lArgs.add(dfExecutor);
            String dfLib = decafImpl.getDfLib();
            if (dfLib == null || dfLib.isEmpty()) {
                dfLib = Constants.UNASSIGNED;
            }
            lArgs.add(dfLib);
            lArgs.add(decafImpl.getMpiRunner());
            break;
        case OMPSS:
            OmpSsImplementation ompssImpl = (OmpSsImplementation) absImpl;
            lArgs.add(ompssImpl.getBinary());
            break;
        case OPENCL:
            OpenCLImplementation openclImpl = (OpenCLImplementation) absImpl;
            lArgs.add(openclImpl.getKernel());
            break;
        case BINARY:
            BinaryImplementation binaryImpl = (BinaryImplementation) absImpl;
            lArgs.add(binaryImpl.getBinary());
            break;
    }
    // Slave nodes and cus description
    lArgs.add(String.valueOf(slaveWorkersNodeNames.size()));
    lArgs.addAll(slaveWorkersNodeNames);
    lArgs.add(String.valueOf(((MethodResourceDescription) this.impl.getRequirements()).getTotalCPUComputingUnits()));
    // Add parameter arguments already processed
    lArgs.addAll(paramArgs);
    // Conversion vector -> array
    String[] arguments = new String[lArgs.size()];
    arguments = lArgs.toArray(arguments);
    try {
        sd.setArguments(arguments);
    } catch (NullPointerException e) {
        StringBuilder sb = new StringBuilder("Null argument parameter of job " + this.jobId + " " + absImpl.getMethodDefinition() + "\n");
        int i = 0;
        for (Parameter param : taskParams.getParameters()) {
            sb.append("Parameter ").append(i).append("\n");
            DataType type = param.getType();
            sb.append("\t Type: ").append(param.getType()).append("\n");
            if (type == DataType.FILE_T || type == DataType.OBJECT_T) {
                DependencyParameter dPar = (DependencyParameter) param;
                DataAccessId dAccId = dPar.getDataAccessId();
                sb.append("\t Target: ").append(dPar.getDataTarget()).append("\n");
                if (type == DataType.OBJECT_T) {
                    if (dAccId instanceof RAccessId) {
                        sb.append("\t Direction: " + "R").append("\n");
                    } else {
                        // for the worker to know it must write the object to disk
                        sb.append("\t Direction: " + "W").append("\n");
                    }
                }
            } else if (type == DataType.STRING_T) {
                BasicTypeParameter btParS = (BasicTypeParameter) param;
                // Check spaces
                String value = btParS.getValue().toString();
                int numSubStrings = value.split(" ").length;
                sb.append("\t Num Substrings: " + Integer.toString(numSubStrings)).append("\n");
                sb.append("\t Value:" + value).append("\n");
            } else {
                // Basic types
                BasicTypeParameter btParB = (BasicTypeParameter) param;
                sb.append("\t Value: " + btParB.getValue().toString()).append("\n");
            }
            i++;
        }
        logger.error(sb.toString());
        listener.jobFailed(this, JobEndStatus.SUBMISSION_FAILED);
    }
    sd.addAttribute("jobId", jobId);
    // JEA Changed to allow execution in MN
    sd.addAttribute(SoftwareDescription.WALLTIME_MAX, absImpl.getRequirements().getWallClockLimit());
    if (absImpl.getRequirements().getHostQueues().size() > 0) {
        sd.addAttribute(SoftwareDescription.JOB_QUEUE, absImpl.getRequirements().getHostQueues().get(0));
    }
    sd.addAttribute("coreCount", absImpl.getRequirements().getTotalCPUComputingUnits());
    sd.addAttribute("gpuCount", absImpl.getRequirements().getTotalGPUComputingUnits());
    sd.addAttribute("fpgaCount", absImpl.getRequirements().getTotalFPGAComputingUnits());
    sd.addAttribute(SoftwareDescription.MEMORY_MAX, absImpl.getRequirements().getMemorySize());
    // sd.addAttribute(SoftwareDescription.SANDBOX_ROOT, "/tmp/");
    sd.addAttribute(SoftwareDescription.SANDBOX_ROOT, getResourceNode().getWorkingDir());
    sd.addAttribute(SoftwareDescription.SANDBOX_USEROOT, "true");
    sd.addAttribute(SoftwareDescription.SANDBOX_DELETE, "false");
    /*
         * sd.addAttribute(SoftwareDescription.SANDBOX_PRESTAGE_STDIN, "false");
         * sd.addAttribute(SoftwareDescription.SANDBOX_POSTSTAGE_STDOUT, "false");
         * sd.addAttribute(SoftwareDescription.SANDBOX_POSTSTAGE_STDERR, "false");
         */
    if (debug) {
        // Set standard output file for job
        File outFile = GAT.createFile(context, Protocol.ANY_URI.getSchema() + File.separator + JOBS_DIR + "job" + jobId + "_" + this.getHistory() + ".out");
        sd.setStdout(outFile);
    }
    if (debug || usingGlobus) {
        // Set standard error file for job
        File errFile = GAT.createFile(context, Protocol.ANY_URI.getSchema() + File.separator + JOBS_DIR + "job" + jobId + "_" + this.getHistory() + ".err");
        sd.setStderr(errFile);
    }
    Map<String, Object> attributes = new HashMap<String, Object>();
    attributes.put(RES_ATTR, Protocol.ANY_URI.getSchema() + targetUser + targetHost);
    attributes.put("Jobname", "compss_remote_job_" + jobId);
    ResourceDescription rd = new HardwareResourceDescription(attributes);
    if (debug) {
        logger.debug("Ready to submit job " + jobId + ":");
        logger.debug("  * Host: " + targetHost);
        logger.debug("  * Executable: " + sd.getExecutable());
        StringBuilder sb = new StringBuilder("  - Arguments:");
        for (String arg : sd.getArguments()) {
            sb.append(" ").append(arg);
        }
        logger.debug(sb.toString());
    }
    JobDescription jd = new JobDescription(sd, rd);
    // jd.setProcessCount(method.getRequirements().getProcessorCoreCount());
    return jd;
}

Example 15 with LogicalData

use of es.bsc.compss.types.data.LogicalData in project compss by bsc-wdc.

the class NIOWorkerNode method newVersion.

private void newVersion(StorageCopy sc) {
    String targetHostname = this.getName();
    LogicalData srcLD = sc.getSourceData();
    LogicalData targetLD = sc.getTargetData();
    boolean preserveSource = sc.mustPreserveSourceData();
    if (DEBUG) {
        LOGGER.debug("Ask for new Version of " + srcLD.getName() + " with id " + srcLD.getId() + " to " + targetHostname + " with must preserve " + preserveSource);
    }
    // Get the PSCOId to replicate
    String pscoId = srcLD.getId();
    // Perform version
    LOGGER.debug("Performing new version for PSCO " + pscoId);
    if (NIOTracer.isActivated()) {
        NIOTracer.emitEvent(NIOTracer.Event.STORAGE_NEWVERSION.getId(), NIOTracer.Event.STORAGE_NEWVERSION.getType());
    }
    try {
        String newId = StorageItf.newVersion(pscoId, preserveSource, Comm.getAppHost().getName());
        LOGGER.debug("Register new new version of " + pscoId + " as " + newId);
        sc.setFinalTarget(newId);
        if (targetLD != null) {
            targetLD.setId(newId);
        }
    } catch (Exception e) {
        sc.end(OpEndState.OP_FAILED, e);
        return;
    } finally {
        if (NIOTracer.isActivated()) {
            NIOTracer.emitEvent(NIOTracer.EVENT_END, NIOTracer.Event.STORAGE_NEWVERSION.getType());
        }
    }
    // Notify successful end
    sc.end(OpEndState.OP_OK);
}