Package org.globus.gram

Examples of org.globus.gram.GramAttributes

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    private static final Logger log = LoggerFactory.getLogger(GramJobSubmissionListener.class);

    public static GramJob setupEnvironment(JobExecutionContext jobExecutionContext, boolean enableTwoPhase) throws GFacProviderException {
        log.debug("Searching for Gate Keeper");
        try {
            GramAttributes jobAttr = GramRSLGenerator.configureRemoteJob(jobExecutionContext);
            String rsl = jobAttr.toRSL();

            if (enableTwoPhase) {
                rsl = rsl + "(twoPhase=yes)";
            }
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    ;

    public static GramAttributes configureRemoteJob(JobExecutionContext context) throws ToolsException {
        HpcApplicationDeploymentType app = (HpcApplicationDeploymentType) context.getApplicationContext().getApplicationDeploymentDescription().getType();
        GramAttributes jobAttr = new GramAttributes();
        jobAttr.setExecutable(app.getExecutableLocation());
        jobAttr.setDirectory(app.getStaticWorkingDirectory());
        jobAttr.setStdout(app.getStandardOutput());
        jobAttr.setStderr(app.getStandardError());
        /*
         * The env here contains the env of the host and the application. i.e the env specified in the host description
         * and application description documents
         */
        NameValuePairType[] env = app.getApplicationEnvironmentArray();
        if (env.length != 0) {
            Map<String, String> nv = new HashMap<String, String>();
            for (int i = 0; i < env.length; i++) {
                String key = env[i].getName();
                String value = env[i].getValue();
                nv.put(key, value);
            }

            for (Map.Entry<String, String> entry : nv.entrySet()) {
                jobAttr.addEnvVariable(entry.getKey(), entry.getValue());
            }
        }
        jobAttr.addEnvVariable(Constants.INPUT_DATA_DIR_VAR_NAME, app.getInputDataDirectory());
        jobAttr.addEnvVariable(Constants.OUTPUT_DATA_DIR_VAR_NAME, app.getOutputDataDirectory());

   

        if (app.getStandardInput() != null && !"".equals(app.getStandardInput())) {
            jobAttr.setStdin(app.getStandardInput());
        } else {
            MessageContext input = context.getInMessageContext();;
            Map<String,Object> inputs = input.getParameters();
            Set<String> keys = inputs.keySet();
            for (String paramName : keys ) {
               ActualParameter actualParameter = (ActualParameter) inputs.get(paramName);
                if ("URIArray".equals(actualParameter.getType().getType().toString())) {
                    String[] values = ((URIArrayType) actualParameter.getType()).getValueArray();
                    for (String value : values) {
                        jobAttr.addArgument(value);
                    }
                } else {
                    String paramValue = MappingFactory.toString(actualParameter);
                    jobAttr.addArgument(paramValue);
                }
            }
        }
        // Using the workflowContext Header values if user provided them in the request and overwrite the default values in DD
        //todo finish the scheduling based on workflow execution context
        ContextHeaderDocument.ContextHeader currentContextHeader = context.getContextHeader();
        if(currentContextHeader != null){
        if (currentContextHeader.getWorkflowSchedulingContext() != null) {
            if (currentContextHeader != null &&
                    currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray() != null &&
                    currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray().length > 0) {
                try {
                    int cpuCount = currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray()[0].getCpuCount();
                    if(cpuCount>0){
                        app.setCpuCount(cpuCount);
                    }
                } catch (NullPointerException e) {
                    log.debug("No Value sent in WorkflowContextHeader for CPU Count, value in the Deployment Descriptor will be used");
                    new GFacProviderException("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used",e);
                }
                try {
                    int nodeCount = currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray()[0].getNodeCount();
                    if(nodeCount>0){
                        app.setNodeCount(nodeCount);
                    }
                } catch (NullPointerException e) {
                    log.debug("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used");
                     new GFacProviderException("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used",e);
                }
                try {
                    String queueName = currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray()[0].getQueueName();
                    if (queueName != null) {
                        if(app.getQueue() == null){
                            QueueType queueType = app.addNewQueue();
                            queueType.setQueueName(queueName);
                        }else{
                            app.getQueue().setQueueName(queueName);
                        }
                    }
                } catch (NullPointerException e) {
                    log.debug("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used");
                     new GFacProviderException("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used",e);
                }
                try {
                    int maxwallTime = currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray()[0].getMaxWallTime();
                    if(maxwallTime>0){
                        app.setMaxWallTime(maxwallTime);
                    }
                } catch (NullPointerException e) {
                    log.debug("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used");
                     new GFacProviderException("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used",e);
                }
            }
        }
//        if(currentContextHeader.getWorkflowOutputDataHandling() != null){
//            if(currentContextHeader.getWorkflowOutputDataHandling().getApplicationOutputDataHandlingArray().length != 0)
//            app.setOutputDataDirectory(currentContextHeader.getWorkflowOutputDataHandling().getApplicationOutputDataHandlingArray()[0].getOutputDataDirectory());
//        }
        }
        if (app.getNodeCount() > 0) {
            jobAttr.set("hostCount", String.valueOf(app.getNodeCount()));
            log.debug("Setting number of Nodes to " + app.getCpuCount());
        }
        if (app.getCpuCount() > 0) {
            log.debug("Setting number of procs to " + app.getCpuCount());
            jobAttr.setNumProcs(app.getCpuCount());
        }
        if (app.getMinMemory() > 0) {
            log.debug("Setting minimum memory to " + app.getMinMemory());
            jobAttr.setMinMemory(app.getMinMemory());
        }
        if (app.getMaxMemory() > 0) {
            log.debug("Setting maximum memory to " + app.getMaxMemory());
            jobAttr.setMaxMemory(app.getMaxMemory());
        }
        if (app.getProjectAccount() != null) {
            if (app.getProjectAccount().getProjectAccountNumber() != null) {
                log.debug("Setting project to " + app.getProjectAccount().getProjectAccountNumber());
                jobAttr.setProject(app.getProjectAccount().getProjectAccountNumber());
            }
        }
        if (app.getQueue() != null) {
            if (app.getQueue().getQueueName() != null) {
                log.debug("Setting job queue to " + app.getQueue().getQueueName());
                jobAttr.setQueue(app.getQueue().getQueueName());
            }
        }
        if (app.getMaxWallTime() > 0) {
            log.debug("Setting max wall clock time to " + app.getMaxWallTime());

            if (app.getMaxWallTime() > 30 && app.getQueue() != null && app.getQueue().getQueueName().equals("debug")) {
                throw new ToolsException("NCSA debug Queue only support jobs < 30 minutes");
            }

            jobAttr.setMaxWallTime(app.getMaxWallTime());
            jobAttr.set("proxy_timeout", "1");
        } else {
            jobAttr.setMaxWallTime(30);
        }
        String jobType = JobType.SINGLE.toString();
        if (app.getJobType() != null) {
            jobType = app.getJobType().toString();
        }
        if (jobType.equalsIgnoreCase(JobType.SINGLE.toString())) {
            log.debug("Setting job type to single");
            jobAttr.setJobType(GramAttributes.JOBTYPE_SINGLE);
        } if (jobType.equalsIgnoreCase(JobType.SERIAL.toString())) {
            log.debug("Setting job type to single");
            jobAttr.setJobType(GramAttributes.JOBTYPE_SINGLE);
        } else if (jobType.equalsIgnoreCase(JobType.MPI.toString())) {
            log.debug("Setting job type to mpi");
            jobAttr.setJobType(GramAttributes.JOBTYPE_MPI);
        } else if (jobType.equalsIgnoreCase(JobType.MULTIPLE.toString())) {
            log.debug("Setting job type to multiple");
            jobAttr.setJobType(GramAttributes.JOBTYPE_MULTIPLE);
        } else if (jobType.equalsIgnoreCase(JobType.CONDOR.toString())) {
            jobAttr.setJobType(GramAttributes.JOBTYPE_CONDOR);
        }

        return jobAttr;
    }
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            gateKeeper = tmp[0];
        }
        log.info("Using Globus GateKeeper " + gateKeeper);

        try {
            GramAttributes jobAttr = GramRSLGenerator.configureRemoteJob(invocationContext);
            String rsl = jobAttr.toRSL();

            log.info("RSL = " + rsl);

            job = new GramJob(rsl);
            listener = new JobSubmissionListener(job, invocationContext);
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    ;

    public static GramAttributes configureRemoteJob(InvocationContext context) throws ToolsException {
        GramApplicationDeploymentType app = (GramApplicationDeploymentType) context.getExecutionDescription().getApp().getType();
        GramAttributes jobAttr = new GramAttributes();
        jobAttr.setExecutable(app.getExecutableLocation());
        jobAttr.setDirectory(app.getStaticWorkingDirectory());
        jobAttr.setStdout(app.getStandardOutput());
        jobAttr.setStderr(app.getStandardError());

        /*
         * The env here contains the env of the host and the application. i.e the env specified in the host description
         * and application description documents
         */
        NameValuePairType[] env = app.getApplicationEnvironmentArray();
        if (env.length != 0) {
            Map<String, String> nv = new HashMap<String, String>();
            for (int i = 0; i < env.length; i++) {
                String key = env[i].getName();
                String value = env[i].getValue();
                nv.put(key, value);
            }

            for (Entry<String, String> entry : nv.entrySet()) {
                jobAttr.addEnvVariable(entry.getKey(), entry.getValue());
            }
        }
        jobAttr.addEnvVariable(GFacConstants.INPUT_DATA_DIR_VAR_NAME, app.getInputDataDirectory());
        jobAttr.addEnvVariable(GFacConstants.OUTPUT_DATA_DIR_VAR_NAME, app.getOutputDataDirectory());

        if (app.getMaxWallTime() > 0) {
            log.info("Setting max wall clock time to " + app.getMaxWallTime());

            if (app.getMaxWallTime() > 30 && app.getQueue() != null && app.getQueue().getQueueName().equals("debug")) {
                throw new ToolsException("NCSA debug Queue only support jobs < 30 minutes");
            }

            jobAttr.setMaxWallTime(app.getMaxWallTime());
            jobAttr.set("proxy_timeout", "1");
        } else {
            jobAttr.setMaxWallTime(30);
        }

        if (app.getStandardInput() != null && !"".equals(app.getStandardInput())) {
            jobAttr.setStdin(app.getStandardInput());
        } else {
            MessageContext<Object> input = context.getInput();
            for (Iterator<String> iterator = input.getNames(); iterator.hasNext(); ) {
                String paramName = iterator.next();
                ActualParameter actualParameter = (ActualParameter) input.getValue(paramName);
                if ("URIArray".equals(actualParameter.getType().getType().toString())) {
                    String[] values = ((URIArrayType) actualParameter.getType()).getValueArray();
                    for (String value : values) {
                        jobAttr.addArgument(value);
                    }
                } else {
                    String paramValue = input.getStringValue(paramName);
                    jobAttr.addArgument(paramValue);
                }
            }
        }
        // Using the workflowContext Header values if user provided them in the request and overwrite the default values in DD
        ContextHeaderDocument.ContextHeader currentContextHeader = WorkflowContextHeaderBuilder.getCurrentContextHeader();
        if (currentContextHeader.getWorkflowSchedulingContext() != null) {
            if (currentContextHeader != null &&
                    currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray() != null &&
                    currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray().length > 0) {
                try {
                    int cpuCount = currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray()[0].getCpuCount();
                    app.setCpuCount(cpuCount);
                } catch (NullPointerException e) {
                    log.info("No Value sent in WorkflowContextHeader for CPU Count, value in the Deployment Descriptor will be used");
                    context.getExecutionContext().getNotifier().executionFail(context, e, "No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used");
                }
                try {
                    int nodeCount = currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray()[0].getNodeCount();
                    app.setNodeCount(nodeCount);
                } catch (NullPointerException e) {
                    log.info("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used");
                    context.getExecutionContext().getNotifier().executionFail(context, e, "No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used");
                }
                try {
                    String queueName = currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray()[0].getQueueName();
                    if (queueName != null) {
                        if(app.getQueue() == null){
                            QueueType queueType = app.addNewQueue();
                            queueType.setQueueName(queueName);
                        }else{
                            app.getQueue().setQueueName(queueName);
                        }
                    }
                } catch (NullPointerException e) {
                    log.info("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used");
                    context.getExecutionContext().getNotifier().executionFail(context, e, "No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used");
                }
            }
        }
        if (app.getNodeCount() > 0) {
            jobAttr.set("hostCount", String.valueOf(app.getNodeCount()));
            log.info("Setting number of Nodes to " + app.getCpuCount());
        }
        if (app.getCpuCount() > 0) {
            log.info("Setting number of procs to " + app.getCpuCount());
            jobAttr.setNumProcs(app.getCpuCount());
        }
        if (app.getMinMemory() > 0) {
            log.info("Setting minimum memory to " + app.getMinMemory());
            jobAttr.setMinMemory(app.getMinMemory());
        }
        if (app.getMaxMemory() > 0) {
            log.info("Setting maximum memory to " + app.getMaxMemory());
            jobAttr.setMaxMemory(app.getMaxMemory());
        }
        if (app.getProjectAccount() != null) {
            if (app.getProjectAccount().getProjectAccountNumber() != null) {
                log.info("Setting project to " + app.getProjectAccount().getProjectAccountNumber());
                jobAttr.setProject(app.getProjectAccount().getProjectAccountNumber());
            }
        }
        if (app.getQueue() != null) {
            if (app.getQueue().getQueueName() != null) {
                System.out.println("Testing");
                log.info("Setting job queue to " + app.getQueue().getQueueName());
                jobAttr.setQueue(app.getQueue().getQueueName());
            }
        }
        String jobType = JobType.SINGLE.toString();
        if (app.getJobType() != null) {
            jobType = app.getJobType().toString();
        }
        if (jobType.equalsIgnoreCase(JobType.SINGLE.toString())) {
            log.info("Setting job type to single");
            jobAttr.setJobType(GramAttributes.JOBTYPE_SINGLE);
        } else if (jobType.equalsIgnoreCase(JobType.MPI.toString())) {
            log.info("Setting job type to mpi");
            jobAttr.setJobType(GramAttributes.JOBTYPE_MPI);
        } else if (jobType.equalsIgnoreCase(JobType.MULTIPLE.toString())) {
            log.info("Setting job type to multiple");
            jobAttr.setJobType(GramAttributes.JOBTYPE_MULTIPLE);
        } else if (jobType.equalsIgnoreCase(JobType.CONDOR.toString())) {
            jobAttr.setJobType(GramAttributes.JOBTYPE_CONDOR);
        }

        return jobAttr;
    }
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    private static final Logger log = LoggerFactory.getLogger(GramProviderUtils.class);

    public static GramJob setupEnvironment(JobExecutionContext jobExecutionContext, boolean enableTwoPhase) throws GFacProviderException {
        log.debug("Searching for Gate Keeper");
        try {
            GramAttributes jobAttr = GramRSLGenerator.configureRemoteJob(jobExecutionContext);
            String rsl = jobAttr.toRSL();

            if (enableTwoPhase) {
                rsl = rsl + "(twoPhase=yes)";
            }
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    ;

    public static GramAttributes  configureRemoteJob(JobExecutionContext context) throws ToolsException {
        HpcApplicationDeploymentType app = (HpcApplicationDeploymentType) context.getApplicationContext().getApplicationDeploymentDescription().getType();
        GramAttributes jobAttr = new GramAttributes();
        jobAttr.setExecutable(app.getExecutableLocation());
        jobAttr.setDirectory(app.getStaticWorkingDirectory());
        jobAttr.setStdout(app.getStandardOutput());
        jobAttr.setStderr(app.getStandardError());
        /*
         * The env here contains the env of the host and the application. i.e the env specified in the host description
         * and application description documents
         */
        NameValuePairType[] env = app.getApplicationEnvironmentArray();
        if (env.length != 0) {
            Map<String, String> nv = new HashMap<String, String>();
            for (int i = 0; i < env.length; i++) {
                String key = env[i].getName();
                String value = env[i].getValue();
                nv.put(key, value);
            }

            for (Map.Entry<String, String> entry : nv.entrySet()) {
                jobAttr.addEnvVariable(entry.getKey(), entry.getValue());
            }
        }
        jobAttr.addEnvVariable(Constants.INPUT_DATA_DIR_VAR_NAME, app.getInputDataDirectory());
        jobAttr.addEnvVariable(Constants.OUTPUT_DATA_DIR_VAR_NAME, app.getOutputDataDirectory());

   

        if (app.getStandardInput() != null && !"".equals(app.getStandardInput())) {
            jobAttr.setStdin(app.getStandardInput());
        } else {
            MessageContext input = context.getInMessageContext();;
            Map<String,Object> inputs = input.getParameters();
            Set<String> keys = inputs.keySet();
            for (String paramName : keys ) {
               ActualParameter actualParameter = (ActualParameter) inputs.get(paramName);
                if ("URIArray".equals(actualParameter.getType().getType().toString()) || "StringArray".equals(actualParameter.getType().getType().toString())
                        || "FileArray".equals(actualParameter.getType().getType().toString())) {
                    String[] values = null;
                    if (actualParameter.getType() instanceof URIArrayType) {
                        values = ((URIArrayType) actualParameter.getType()).getValueArray();
                    } else if (actualParameter.getType() instanceof StringArrayType) {
                        values = ((StringArrayType) actualParameter.getType()).getValueArray();
                    } else if (actualParameter.getType() instanceof FileArrayType) {
                        values = ((FileArrayType) actualParameter.getType()).getValueArray();
                    }
                    String value = StringUtil.createDelimiteredString(values, " ");
                    jobAttr.addArgument(value);
                } else {
                    String paramValue = MappingFactory.toString(actualParameter);
                    jobAttr.addArgument(paramValue);
                }
            }
        }
        // Using the workflowContext Header values if user provided them in the request and overwrite the default values in DD
        //todo finish the scheduling based on workflow execution context
        TaskDetails taskData = context.getTaskData();
        if(taskData != null && taskData.isSetTaskScheduling()){
           ComputationalResourceScheduling computionnalResource = taskData.getTaskScheduling();
                try {
                    int cpuCount = computionnalResource.getTotalCPUCount();
                    if(cpuCount>0){
                        app.setCpuCount(cpuCount);
                    }
                } catch (NullPointerException e) {
                    log.debug("No Value sent in WorkflowContextHeader for CPU Count, value in the Deployment Descriptor will be used");
                    new GFacProviderException("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used",e);
                }
                try {
                    int nodeCount = computionnalResource.getNodeCount();
                    if(nodeCount>0){
                        app.setNodeCount(nodeCount);
                    }
                } catch (NullPointerException e) {
                    log.debug("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used");
                     new GFacProviderException("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used",e);
                }
                try {
                    String queueName = computionnalResource.getQueueName();
                    if (queueName != null) {
                        if(app.getQueue() == null){
                            QueueType queueType = app.addNewQueue();
                            queueType.setQueueName(queueName);
                        }else{
                            app.getQueue().setQueueName(queueName);
                        }
                    }
                } catch (NullPointerException e) {
                    log.debug("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used");
                     new GFacProviderException("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used",e);
                }
                try {
                    int maxwallTime = computionnalResource.getWallTimeLimit();
                    if(maxwallTime>0){
                        app.setMaxWallTime(maxwallTime);
                    }
                } catch (NullPointerException e) {
                    log.debug("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used");
                     new GFacProviderException("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used",e);
                }
        }
        if (app.getNodeCount() > 0) {
            jobAttr.set("hostCount", String.valueOf(app.getNodeCount()));
            log.debug("Setting number of Nodes to " + app.getCpuCount());
        }
        if (app.getCpuCount() > 0) {
            log.debug("Setting number of procs to " + app.getCpuCount());
            jobAttr.setNumProcs(app.getCpuCount());
        }
        if (app.getMinMemory() > 0) {
            log.debug("Setting minimum memory to " + app.getMinMemory());
            jobAttr.setMinMemory(app.getMinMemory());
        }
        if (app.getMaxMemory() > 0) {
            log.debug("Setting maximum memory to " + app.getMaxMemory());
            jobAttr.setMaxMemory(app.getMaxMemory());
        }
        if (app.getProjectAccount() != null) {
            if (app.getProjectAccount().getProjectAccountNumber() != null) {
                log.debug("Setting project to " + app.getProjectAccount().getProjectAccountNumber());
                jobAttr.setProject(app.getProjectAccount().getProjectAccountNumber());
            }
        }
        if (app.getQueue() != null) {
            if (app.getQueue().getQueueName() != null) {
                log.debug("Setting job queue to " + app.getQueue().getQueueName());
                jobAttr.setQueue(app.getQueue().getQueueName());
            }
        }
        if (app.getMaxWallTime() > 0) {
            log.debug("Setting max wall clock time to " + app.getMaxWallTime());

            jobAttr.setMaxWallTime(app.getMaxWallTime());
            jobAttr.set("proxy_timeout", "1");
        } else {
            jobAttr.setMaxWallTime(30);
        }
        String jobType = JobType.SINGLE.toString();
        if (app.getJobType() != null) {
            jobType = app.getJobType().toString();
        }
        if (jobType.equalsIgnoreCase(JobType.SINGLE.toString())) {
            log.debug("Setting job type to single");
            jobAttr.setJobType(GramAttributes.JOBTYPE_SINGLE);
        } if (jobType.equalsIgnoreCase(JobType.SERIAL.toString())) {
            log.debug("Setting job type to single");
            jobAttr.setJobType(GramAttributes.JOBTYPE_SINGLE);
        } else if (jobType.equalsIgnoreCase(JobType.MPI.toString())) {
            log.debug("Setting job type to mpi");
            jobAttr.setJobType(GramAttributes.JOBTYPE_MPI);
        } else if (jobType.equalsIgnoreCase(JobType.MULTIPLE.toString())) {
            log.debug("Setting job type to multiple");
            jobAttr.setJobType(GramAttributes.JOBTYPE_MULTIPLE);
        } else if (jobType.equalsIgnoreCase(JobType.CONDOR.toString())) {
            jobAttr.setJobType(GramAttributes.JOBTYPE_CONDOR);
        }

        return jobAttr;
    }
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    };

    public static GramAttributes configureRemoteJob(InvocationContext context) throws ToolsException {
        GramApplicationDeploymentType app = (GramApplicationDeploymentType) context.getExecutionDescription().getApp().getType();

        GramAttributes jobAttr = new GramAttributes();
        jobAttr.setExecutable(app.getExecutableLocation());
        jobAttr.setDirectory(app.getStaticWorkingDirectory());
        jobAttr.setStdout(app.getStandardOutput());
        jobAttr.setStderr(app.getStandardError());

        /*
         * The env here contains the env of the host and the application. i.e the env specified in the host description
         * and application description documents
         */
        NameValuePairType[] env = app.getApplicationEnvironmentArray();
        if(env.length != 0){
            Map<String, String> nv =new HashMap<String, String>();
            for (int i = 0; i < env.length; i++) {
                String key = env[i].getName();
                String value = env[i].getValue();
                nv.put(key, value);
            }

            for (Entry<String, String> entry : nv.entrySet()) {
                jobAttr.addEnvVariable(entry.getKey(), entry.getValue());
            }
        }
        jobAttr.addEnvVariable(GFacConstants.INPUT_DATA_DIR_VAR_NAME, app.getInputDataDirectory());
        jobAttr.addEnvVariable(GFacConstants.INPUT_DATA_DIR_VAR_NAME, app.getOutputDataDirectory());

        if (app.getMaxWallTime() > 0) {
            log.info("Setting max wall clock time to " + app.getMaxWallTime());

            if (app.getMaxWallTime() > 30 && app.getQueue() != null && app.getQueue().getQueueName().equals("debug")) {
                throw new ToolsException("NCSA debug Queue only support jobs < 30 minutes");
            }

            jobAttr.setMaxWallTime(app.getMaxWallTime());
            jobAttr.set("proxy_timeout", "1");
        } else {
            jobAttr.setMaxWallTime(29);
        }

        if (app.getStandardInput() != null) {
            jobAttr.setStdin(app.getStandardInput());
        } else {
            // input parameter
            for (Iterator<String> iterator = context.getInput().getNames(); iterator.hasNext();) {
                String key = iterator.next();
                jobAttr.addArgument(context.getInput().getStringValue(key));
            }
        }

        if (app.getNodeCount() > 1) {
            jobAttr.set("hostCount", String.valueOf(app.getNodeCount()));
        }
        if (app.getCpuCount() > 1) {
            log.info("Setting number of procs to " + app.getCpuCount());
            jobAttr.setNumProcs(app.getCpuCount());
        }
        if (app.getProjectAccount().getProjectAccountNumber() != null) {
            log.info("Setting project to " + app.getProjectAccount().getProjectAccountNumber());
            jobAttr.setProject(app.getProjectAccount().getProjectAccountNumber());
        }
        if(app.getQueue() != null){
        if (app.getQueue().getQueueName() != null) {
            System.out.println("Testing");
            log.info("Setting job queue to " + app.getQueue().getQueueName());
            jobAttr.setQueue(app.getQueue().getQueueName());
        }
        }

        String jobType = JobType.SINGLE.toString();
        if (app.getJobType() != null) {
            jobType = app.getJobType().toString();
        }

        if (jobType.equalsIgnoreCase(JobType.SINGLE.toString())) {
            log.info("Setting job type to single");
            jobAttr.setJobType(GramAttributes.JOBTYPE_SINGLE);
        } else if (jobType.equalsIgnoreCase(JobType.MPI.toString())) {
            log.info("Setting job type to mpi");
            jobAttr.setJobType(GramAttributes.JOBTYPE_MPI);
        } else if (jobType.equalsIgnoreCase(JobType.MULTIPLE.toString())) {
            log.info("Setting job type to multiple");
            jobAttr.setJobType(GramAttributes.JOBTYPE_MULTIPLE);
        } else if (jobType.equalsIgnoreCase(JobType.CONDOR.toString())) {
            jobAttr.setJobType(GramAttributes.JOBTYPE_CONDOR);
        }

        // TODO rsl parameter & urgency/SPRUCE

        return jobAttr;
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            gateKeeper = tmp[0];
        }
        log.info("Using Globus GateKeeper " + gateKeeper);

        try {
            GramAttributes jobAttr = GramRSLGenerator.configureRemoteJob(invocationContext);
            String rsl = jobAttr.toRSL();

            log.info("RSL = " + rsl);

            job = new GramJob(rsl);
            listener = new JobSubmissionListener(job, invocationContext);
View Full Code Here
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    };

    public static GramAttributes configureRemoteJob(InvocationContext context) throws ToolsException {
        GramApplicationDeploymentType app = (GramApplicationDeploymentType) context.getExecutionDescription().getApp().getType();

        GramAttributes jobAttr = new GramAttributes();
        jobAttr.setExecutable(app.getExecutableLocation());
        jobAttr.setDirectory(app.getStaticWorkingDirectory());
        jobAttr.setStdout(app.getStandardOutput());
        jobAttr.setStderr(app.getStandardError());

        /*
         * The env here contains the env of the host and the application. i.e the env specified in the host description
         * and application description documents
         */
        NameValuePairType[] env = app.getApplicationEnvironmentArray();
        if(env.length != 0){
            Map<String, String> nv =new HashMap<String, String>();
            for (int i = 0; i < env.length; i++) {
                String key = env[i].getName();
                String value = env[i].getValue();
                nv.put(key, value);
            }

            for (Entry<String, String> entry : nv.entrySet()) {
                jobAttr.addEnvVariable(entry.getKey(), entry.getValue());
            }
        }
        jobAttr.addEnvVariable(GFacConstants.INPUT_DATA_DIR_VAR_NAME, app.getInputDataDirectory());
        jobAttr.addEnvVariable(GFacConstants.OUTPUT_DATA_DIR_VAR_NAME, app.getOutputDataDirectory());

        if (app.getMaxWallTime() > 0) {
            log.info("Setting max wall clock time to " + app.getMaxWallTime());

            if (app.getMaxWallTime() > 30 && app.getQueue() != null && app.getQueue().getQueueName().equals("debug")) {
                throw new ToolsException("NCSA debug Queue only support jobs < 30 minutes");
            }

            jobAttr.setMaxWallTime(app.getMaxWallTime());
            jobAttr.set("proxy_timeout", "1");
        } else {
            jobAttr.setMaxWallTime(30);
        }

        if (app.getStandardInput() != null && !"".equals(app.getStandardInput())) {
            jobAttr.setStdin(app.getStandardInput());
        } else {
            // input parameter
            for (Iterator<String> iterator = context.getInput().getNames(); iterator.hasNext();) {
                String key = iterator.next();
                jobAttr.addArgument(context.getInput().getStringValue(key));
            }
        }
        // Using the workflowContext Header values if user provided them in the request and overwrite the default values in DD
        ContextHeaderDocument.ContextHeader currentContextHeader = WorkflowContextHeaderBuilder.getCurrentContextHeader();
        if (currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray() != null &&
                currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray().length > 0) {
            try {
                int cpuCount = currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray()[0].getCpuCount();
                app.setCpuCount(cpuCount);
            } catch (NullPointerException e) {
                log.info("No Value sent in WorkflowContextHeader for CPU Count, value in the Deployment Descriptor will be used");
            }
            try {
                int nodeCount = currentContextHeader.getWorkflowSchedulingContext().getApplicationSchedulingContextArray()[0].getNodeCount();
                app.setNodeCount(nodeCount);
            } catch (NullPointerException e) {
                log.info("No Value sent in WorkflowContextHeader for Node Count, value in the Deployment Descriptor will be used");
            }
        }
        if (app.getNodeCount() > 0) {
            jobAttr.set("hostCount", String.valueOf(app.getNodeCount()));
        }
        if (app.getCpuCount() > 0) {
            log.info("Setting number of procs to " + app.getCpuCount());
            jobAttr.setNumProcs(app.getCpuCount());
        }
        if (app.getMinMemory() > 0) {
            log.info("Setting minimum memory to " + app.getMinMemory());
            jobAttr.setMinMemory(app.getMinMemory());
        }
        if (app.getMaxMemory() > 0) {
            log.info("Setting maximum memory to " + app.getMaxMemory());
            jobAttr.setMaxMemory(app.getMaxMemory());
        }
        if (app.getProjectAccount() != null) {
            if (app.getProjectAccount().getProjectAccountNumber() != null) {
                log.info("Setting project to " + app.getProjectAccount().getProjectAccountNumber());
                jobAttr.setProject(app.getProjectAccount().getProjectAccountNumber());
            }
        }
        if(app.getQueue() != null){
        if (app.getQueue().getQueueName() != null) {
            System.out.println("Testing");
            log.info("Setting job queue to " + app.getQueue().getQueueName());
            jobAttr.setQueue(app.getQueue().getQueueName());
        }
        }

        String jobType = JobType.SINGLE.toString();
        if (app.getJobType() != null) {
            jobType = app.getJobType().toString();
        }

        if (jobType.equalsIgnoreCase(JobType.SINGLE.toString())) {
            log.info("Setting job type to single");
            jobAttr.setJobType(GramAttributes.JOBTYPE_SINGLE);
        } else if (jobType.equalsIgnoreCase(JobType.MPI.toString())) {
            log.info("Setting job type to mpi");
            jobAttr.setJobType(GramAttributes.JOBTYPE_MPI);
        } else if (jobType.equalsIgnoreCase(JobType.MULTIPLE.toString())) {
            log.info("Setting job type to multiple");
            jobAttr.setJobType(GramAttributes.JOBTYPE_MULTIPLE);
        } else if (jobType.equalsIgnoreCase(JobType.CONDOR.toString())) {
            jobAttr.setJobType(GramAttributes.JOBTYPE_CONDOR);
        }

        return jobAttr;
    }
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            gateKeeper = tmp[0];
        }
        log.info("Using Globus GateKeeper " + gateKeeper);

        try {
            GramAttributes jobAttr = GramRSLGenerator.configureRemoteJob(invocationContext);
            String rsl = jobAttr.toRSL();

            log.info("RSL = " + rsl);

            job = new GramJob(rsl);
            listener = new JobSubmissionListener(job, invocationContext);
View Full Code Here
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  • org.apache.airavata.core.gfac.provider.impl.GramProvider
  • org.apache.airavata.core.gfac.provider.utils.GramRSLGenerator
  • org.apache.airavata.gfac.gram.util.GramProviderUtils
  • org.apache.airavata.gfac.gram.util.GramRSLGenerator
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