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

Example 6 with DataAccessId

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

the class GATJob method processParameters.

private void processParameters(String sandboxPath, ArrayList<String> symlinks, ArrayList<String> lArgs) {
    logger.debug("Processing parameters for GAT job " + this.jobId);
    lArgs.add(Boolean.toString(taskParams.hasTargetObject()));
    // Add return type
    if (taskParams.hasReturnValue()) {
        Parameter returnParam = taskParams.getParameters()[taskParams.getParameters().length - 1];
        lArgs.add(Integer.toString(returnParam.getType().ordinal()));
    } else {
        lArgs.add("null");
    }
    // Add parameters
    int numParams = taskParams.getParameters().length;
    if (taskParams.hasReturnValue()) {
        numParams--;
    }
    lArgs.add(Integer.toString(numParams));
    for (Parameter param : taskParams.getParameters()) {
        DataType type = param.getType();
        lArgs.add(Integer.toString(type.ordinal()));
        lArgs.add(Integer.toString(param.getStream().ordinal()));
        String prefix = param.getPrefix();
        if (prefix == null || prefix.isEmpty()) {
            prefix = Constants.PREFIX_EMTPY;
        }
        lArgs.add(param.getPrefix());
        switch(type) {
            case FILE_T:
                DependencyParameter dFilePar = (DependencyParameter) param;
                java.io.File f = new java.io.File(dFilePar.getDataTarget());
                if (!f.getName().equals(dFilePar.getOriginalName())) {
                    // Add file to manage symlinks and renames
                    String originalName = sandboxPath + File.separator + dFilePar.getOriginalName();
                    symlinks.add(dFilePar.getDataTarget());
                    symlinks.add(dFilePar.getOriginalName());
                    lArgs.add(originalName);
                } else {
                    // Original and target is the same nothing to do
                    lArgs.add(dFilePar.getDataTarget());
                }
                break;
            case PSCO_T:
            case EXTERNAL_OBJECT_T:
                logger.error("GAT Adaptor does not support PSCO Types");
                listener.jobFailed(this, JobEndStatus.SUBMISSION_FAILED);
                break;
            case OBJECT_T:
                DependencyParameter dPar = (DependencyParameter) param;
                DataAccessId dAccId = dPar.getDataAccessId();
                lArgs.add(dPar.getDataTarget());
                if (dAccId instanceof RAccessId) {
                    lArgs.add("R");
                } else {
                    // for the worker to know it must write the object to disk
                    lArgs.add("W");
                }
                break;
            case STRING_T:
                BasicTypeParameter btParS = (BasicTypeParameter) param;
                // Check spaces
                String value = btParS.getValue().toString();
                int numSubStrings = value.split(" ").length;
                lArgs.add(Integer.toString(numSubStrings));
                lArgs.add(value);
                break;
            default:
                // Basic Types
                BasicTypeParameter btParB = (BasicTypeParameter) param;
                lArgs.add(btParB.getValue().toString());
                break;
        }
    }
}

Example 7 with DataAccessId

use of es.bsc.compss.types.data.DataAccessId 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 8 with DataAccessId

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

the class RegisterDataAccessRequest method process.

@Override
public void process(AccessProcessor ap, TaskAnalyser ta, DataInfoProvider dip, TaskDispatcher td) {
    DataAccessId daId = dip.registerDataAccess(this.access);
    this.response = daId;
    sem.release();
}

Example 9 with DataAccessId

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

the class AccessProcessor method mainAccessToFile.

/**
 * Notifies a main access to a given file @sourceLocation in mode @fap
 *
 * @param sourceLocation
 * @param fap
 * @param destDir
 * @return
 */
public DataLocation mainAccessToFile(DataLocation sourceLocation, AccessParams.FileAccessParams fap, String destDir) {
    boolean alreadyAccessed = alreadyAccessed(sourceLocation);
    if (!alreadyAccessed) {
        LOGGER.debug("File not accessed before, returning the same location");
        return sourceLocation;
    }
    // Tell the DM that the application wants to access a file.
    DataAccessId faId = registerDataAccess(fap);
    DataLocation tgtLocation = sourceLocation;
    if (fap.getMode() != AccessMode.W) {
        // Wait until the last writer task for the file has finished
        LOGGER.debug("File " + faId.getDataId() + " mode contains R, waiting until the last writer has finished");
        waitForTask(faId.getDataId(), AccessMode.R);
        if (destDir == null) {
            tgtLocation = transferFileOpen(faId);
        } else {
            DataInstanceId daId;
            if (fap.getMode() == AccessMode.R) {
                RAccessId ra = (RAccessId) faId;
                daId = ra.getReadDataInstance();
            } else {
                RWAccessId ra = (RWAccessId) faId;
                daId = ra.getReadDataInstance();
            }
            String rename = daId.getRenaming();
            String path = DataLocation.Protocol.FILE_URI.getSchema() + destDir + rename;
            try {
                SimpleURI uri = new SimpleURI(path);
                tgtLocation = DataLocation.createLocation(Comm.getAppHost(), uri);
            } catch (Exception e) {
                ErrorManager.error(DataLocation.ERROR_INVALID_LOCATION + " " + path, e);
            }
            transferFileRaw(faId, tgtLocation);
        }
    }
    if (fap.getMode() != AccessMode.R) {
        // Mode contains W
        LOGGER.debug("File " + faId.getDataId() + " mode contains W, register new writer");
        DataInstanceId daId;
        if (fap.getMode() == AccessMode.RW) {
            RWAccessId ra = (RWAccessId) faId;
            daId = ra.getWrittenDataInstance();
        } else {
            WAccessId ra = (WAccessId) faId;
            daId = ra.getWrittenDataInstance();
        }
        String rename = daId.getRenaming();
        String path = DataLocation.Protocol.FILE_URI.getSchema() + Comm.getAppHost().getTempDirPath() + rename;
        try {
            SimpleURI uri = new SimpleURI(path);
            tgtLocation = DataLocation.createLocation(Comm.getAppHost(), uri);
        } catch (Exception e) {
            ErrorManager.error(DataLocation.ERROR_INVALID_LOCATION + " " + path, e);
        }
        Comm.registerLocation(rename, tgtLocation);
    }
    if (DEBUG) {
        LOGGER.debug("File " + faId.getDataId() + " located on " + tgtLocation.toString());
    }
    return tgtLocation;
}

Example 10 with DataAccessId

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

the class AccessProcessor method mainAcessToObject.

/**
 * Notifies a main access to an object @obj
 *
 * @param obj
 * @param hashCode
 * @return
 */
public Object mainAcessToObject(Object obj, int hashCode) {
    if (DEBUG) {
        LOGGER.debug("Requesting main access to object with hash code " + hashCode);
    }
    // Tell the DIP that the application wants to access an object
    AccessParams.ObjectAccessParams oap = new AccessParams.ObjectAccessParams(AccessMode.RW, obj, hashCode);
    DataAccessId oaId = registerDataAccess(oap);
    DataInstanceId wId = ((DataAccessId.RWAccessId) oaId).getWrittenDataInstance();
    String wRename = wId.getRenaming();
    // Wait until the last writer task for the object has finished
    if (DEBUG) {
        LOGGER.debug("Waiting for last writer of " + oaId.getDataId() + " with renaming " + wRename);
    }
    waitForTask(oaId.getDataId(), AccessMode.RW);
    // Ask for the object
    if (DEBUG) {
        LOGGER.debug("Request object transfer " + oaId.getDataId() + " with renaming " + wRename);
    }
    Object oUpdated = obtainObject(oaId);
    if (DEBUG) {
        LOGGER.debug("Object retrieved. Set new version to: " + wRename);
    }
    setObjectVersionValue(wRename, oUpdated);
    return oUpdated;
}