Search in sources :

Example 1 with JobSubmissionTaskModel

use of org.apache.airavata.model.task.JobSubmissionTaskModel in project airavata by apache.

the class GFacUtils method createGroovyMap.

public static GroovyMap createGroovyMap(ProcessContext processContext, TaskContext taskContext) throws GFacException, AppCatalogException, ApplicationSettingsException {
    GroovyMap groovyMap = new GroovyMap();
    ProcessModel processModel = processContext.getProcessModel();
    ResourceJobManager resourceJobManager = getResourceJobManager(processContext);
    // set email options and addresses
    setMailAddresses(processContext, groovyMap);
    groovyMap.add(Script.INPUT_DIR, processContext.getInputDir());
    groovyMap.add(Script.OUTPUT_DIR, processContext.getOutputDir());
    groovyMap.add(Script.EXECUTABLE_PATH, processContext.getApplicationDeploymentDescription().getExecutablePath());
    groovyMap.add(Script.STANDARD_OUT_FILE, processContext.getStdoutLocation());
    groovyMap.add(Script.STANDARD_ERROR_FILE, processContext.getStderrLocation());
    groovyMap.add(Script.SCRATCH_LOCATION, processContext.getScratchLocation());
    groovyMap.add(Script.GATEWAY_ID, processContext.getGatewayId());
    groovyMap.add(Script.GATEWAY_USER_NAME, processContext.getProcessModel().getUserName());
    groovyMap.add(Script.APPLICATION_NAME, processContext.getApplicationInterfaceDescription().getApplicationName());
    groovyMap.add(Script.QUEUE_SPECIFIC_MACROS, processContext.getQueueSpecificMacros());
    groovyMap.add(Script.ACCOUNT_STRING, processContext.getAllocationProjectNumber());
    groovyMap.add(Script.RESERVATION, processContext.getReservation());
    // To make job name alpha numeric
    groovyMap.add(Script.JOB_NAME, "A" + String.valueOf(generateJobName()));
    groovyMap.add(Script.WORKING_DIR, processContext.getWorkingDir());
    List<String> inputValues = getProcessInputValues(processModel.getProcessInputs());
    inputValues.addAll(getProcessOutputValues(processModel.getProcessOutputs()));
    groovyMap.add(Script.INPUTS, inputValues);
    groovyMap.add(Script.USER_NAME, processContext.getJobSubmissionRemoteCluster().getServerInfo().getUserName());
    groovyMap.add(Script.SHELL_NAME, "/bin/bash");
    // get walltime
    if (taskContext != null) {
        try {
            JobSubmissionTaskModel jobSubmissionTaskModel = ((JobSubmissionTaskModel) taskContext.getSubTaskModel());
            if (jobSubmissionTaskModel.getWallTime() > 0) {
                groovyMap.add(Script.MAX_WALL_TIME, GFacUtils.maxWallTimeCalculator(jobSubmissionTaskModel.getWallTime()));
                if (resourceJobManager != null) {
                    if (resourceJobManager.getResourceJobManagerType().equals(ResourceJobManagerType.LSF)) {
                        groovyMap.add(Script.MAX_WALL_TIME, GFacUtils.maxWallTimeCalculatorForLSF(jobSubmissionTaskModel.getWallTime()));
                    }
                }
            }
        } catch (TException e) {
            log.error("Error while getting job submission sub task model", e);
        }
    }
    // NOTE: Give precedence to data comes with experiment
    // qos per queue
    String qoS = getQoS(processContext.getQualityOfService(), processContext.getQueueName());
    if (qoS != null) {
        groovyMap.add(Script.QUALITY_OF_SERVICE, qoS);
    }
    ComputationalResourceSchedulingModel scheduling = processModel.getProcessResourceSchedule();
    if (scheduling != null) {
        int totalNodeCount = scheduling.getNodeCount();
        int totalCPUCount = scheduling.getTotalCPUCount();
        if (isValid(scheduling.getQueueName())) {
            groovyMap.add(Script.QUEUE_NAME, scheduling.getQueueName());
        }
        if (totalNodeCount > 0) {
            groovyMap.add(Script.NODES, totalNodeCount);
        }
        if (totalCPUCount > 0) {
            int ppn = totalCPUCount / totalNodeCount;
            groovyMap.add(Script.PROCESS_PER_NODE, ppn);
            groovyMap.add(Script.CPU_COUNT, totalCPUCount);
        }
        // if so we ignore scheduling configuration.
        if (scheduling.getWallTimeLimit() > 0 && groovyMap.get(Script.MAX_WALL_TIME) == null) {
            groovyMap.add(Script.MAX_WALL_TIME, GFacUtils.maxWallTimeCalculator(scheduling.getWallTimeLimit()));
            if (resourceJobManager != null) {
                if (resourceJobManager.getResourceJobManagerType().equals(ResourceJobManagerType.LSF)) {
                    groovyMap.add(Script.MAX_WALL_TIME, GFacUtils.maxWallTimeCalculatorForLSF(scheduling.getWallTimeLimit()));
                }
            }
        }
        if (scheduling.getTotalPhysicalMemory() > 0) {
            groovyMap.add(Script.USED_MEM, scheduling.getTotalPhysicalMemory());
        }
        if (isValid(scheduling.getOverrideLoginUserName())) {
            groovyMap.add(Script.USER_NAME, scheduling.getOverrideLoginUserName());
        }
        if (isValid(scheduling.getOverrideAllocationProjectNumber())) {
            groovyMap.add(Script.ACCOUNT_STRING, scheduling.getOverrideAllocationProjectNumber());
        }
        if (isValid(scheduling.getStaticWorkingDir())) {
            groovyMap.add(Script.WORKING_DIR, scheduling.getStaticWorkingDir());
        }
    } else {
        log.error("Task scheduling cannot be null at this point..");
    }
    ApplicationDeploymentDescription appDepDescription = processContext.getApplicationDeploymentDescription();
    List<CommandObject> moduleCmds = appDepDescription.getModuleLoadCmds();
    if (moduleCmds != null) {
        List<String> modulesCmdCollect = moduleCmds.stream().sorted((e1, e2) -> e1.getCommandOrder() - e2.getCommandOrder()).map(map -> map.getCommand()).collect(Collectors.toList());
        groovyMap.add(Script.MODULE_COMMANDS, modulesCmdCollect);
    }
    List<CommandObject> preJobCommands = appDepDescription.getPreJobCommands();
    if (preJobCommands != null) {
        List<String> preJobCmdCollect = preJobCommands.stream().sorted((e1, e2) -> e1.getCommandOrder() - e2.getCommandOrder()).map(map -> parseCommands(map.getCommand(), groovyMap)).collect(Collectors.toList());
        groovyMap.add(Script.PRE_JOB_COMMANDS, preJobCmdCollect);
    }
    List<CommandObject> postJobCommands = appDepDescription.getPostJobCommands();
    if (postJobCommands != null) {
        List<String> postJobCmdCollect = postJobCommands.stream().sorted((e1, e2) -> e1.getCommandOrder() - e2.getCommandOrder()).map(map -> parseCommands(map.getCommand(), groovyMap)).collect(Collectors.toList());
        groovyMap.add(Script.POST_JOB_COMMANDS, postJobCmdCollect);
    }
    ApplicationParallelismType parallelism = appDepDescription.getParallelism();
    if (parallelism != null) {
        if (parallelism != ApplicationParallelismType.SERIAL) {
            Map<ApplicationParallelismType, String> parallelismPrefix = processContext.getResourceJobManager().getParallelismPrefix();
            if (parallelismPrefix != null) {
                String parallelismCommand = parallelismPrefix.get(parallelism);
                if (parallelismCommand != null) {
                    groovyMap.add(Script.JOB_SUBMITTER_COMMAND, parallelismCommand);
                } else {
                    throw new GFacException("Parallelism prefix is not defined for given parallelism type " + parallelism + ".. Please define the parallelism prefix at App Catalog");
                }
            }
        }
    }
    return groovyMap;
}
Also used : TException(org.apache.thrift.TException) CreateMode(org.apache.zookeeper.CreateMode) TemplateEngine(groovy.text.TemplateEngine) URL(java.net.URL) URISyntaxException(java.net.URISyntaxException) LoggerFactory(org.slf4j.LoggerFactory) TaskContext(org.apache.airavata.gfac.core.context.TaskContext) Stat(org.apache.zookeeper.data.Stat) ByteBuffer(java.nio.ByteBuffer) InetAddress(java.net.InetAddress) SecureRandom(java.security.SecureRandom) ZKPaths(org.apache.curator.utils.ZKPaths) Matcher(java.util.regex.Matcher) Document(org.w3c.dom.Document) CredentialReaderImpl(org.apache.airavata.credential.store.store.impl.CredentialReaderImpl) org.apache.airavata.model.data.replica(org.apache.airavata.model.data.replica) ProcessContext(org.apache.airavata.gfac.core.context.ProcessContext) DataType(org.apache.airavata.model.application.io.DataType) org.apache.airavata.common.utils(org.apache.airavata.common.utils) JobSubmissionTaskModel(org.apache.airavata.model.task.JobSubmissionTaskModel) Collectors(java.util.stream.Collectors) CuratorFramework(org.apache.curator.framework.CuratorFramework) ErrorModel(org.apache.airavata.model.commons.ErrorModel) GStringTemplateEngine(groovy.text.GStringTemplateEngine) Pattern(java.util.regex.Pattern) org.apache.airavata.model.appcatalog.computeresource(org.apache.airavata.model.appcatalog.computeresource) java.util(java.util) JobModel(org.apache.airavata.model.job.JobModel) ACL(org.apache.zookeeper.data.ACL) Writable(groovy.lang.Writable) javax.xml.xpath(javax.xml.xpath) CredentialReader(org.apache.airavata.credential.store.store.CredentialReader) Node(org.w3c.dom.Node) MessageContext(org.apache.airavata.messaging.core.MessageContext) RegistryFactory(org.apache.airavata.registry.core.experiment.catalog.impl.RegistryFactory) InputDataObjectType(org.apache.airavata.model.application.io.InputDataObjectType) Logger(org.slf4j.Logger) NodeList(org.w3c.dom.NodeList) Constants(org.apache.airavata.registry.cpi.utils.Constants) TException(org.apache.thrift.TException) FileUtils(org.apache.commons.io.FileUtils) org.apache.airavata.model.status(org.apache.airavata.model.status) ApplicationParallelismType(org.apache.airavata.model.parallelism.ApplicationParallelismType) org.apache.airavata.registry.cpi(org.apache.airavata.registry.cpi) UnknownHostException(java.net.UnknownHostException) ComputeResourcePreference(org.apache.airavata.model.appcatalog.gatewayprofile.ComputeResourcePreference) Element(org.w3c.dom.Element) ExperimentModel(org.apache.airavata.model.experiment.ExperimentModel) ZooDefs(org.apache.zookeeper.ZooDefs) java.io(java.io) ApplicationDeploymentDescription(org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription) ComputationalResourceSchedulingModel(org.apache.airavata.model.scheduling.ComputationalResourceSchedulingModel) org.apache.airavata.model.messaging.event(org.apache.airavata.model.messaging.event) ProcessModel(org.apache.airavata.model.process.ProcessModel) ApplicationSettingsException(org.apache.airavata.common.exception.ApplicationSettingsException) CommandObject(org.apache.airavata.model.appcatalog.appdeployment.CommandObject) OutputDataObjectType(org.apache.airavata.model.application.io.OutputDataObjectType) ProcessModel(org.apache.airavata.model.process.ProcessModel) ApplicationDeploymentDescription(org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription) ApplicationParallelismType(org.apache.airavata.model.parallelism.ApplicationParallelismType) CommandObject(org.apache.airavata.model.appcatalog.appdeployment.CommandObject) JobSubmissionTaskModel(org.apache.airavata.model.task.JobSubmissionTaskModel) ComputationalResourceSchedulingModel(org.apache.airavata.model.scheduling.ComputationalResourceSchedulingModel)

Example 2 with JobSubmissionTaskModel

use of org.apache.airavata.model.task.JobSubmissionTaskModel in project airavata by apache.

the class GFacEngineImpl method executeJobSubmission.

private boolean executeJobSubmission(TaskContext taskContext, boolean recovery) throws GFacException {
    TaskStatus taskStatus = new TaskStatus(TaskState.EXECUTING);
    taskStatus.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
    taskContext.setTaskStatus(taskStatus);
    GFacUtils.saveAndPublishTaskStatus(taskContext);
    try {
        JobSubmissionTaskModel jobSubmissionTaskModel = ((JobSubmissionTaskModel) taskContext.getSubTaskModel());
        JobSubmissionTask jobSubmissionTask = Factory.getJobSubmissionTask(jobSubmissionTaskModel.getJobSubmissionProtocol());
        ProcessContext processContext = taskContext.getParentProcessContext();
        taskStatus = executeTask(taskContext, jobSubmissionTask, recovery);
        taskStatus.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
        taskContext.setTaskStatus(taskStatus);
        GFacUtils.saveAndPublishTaskStatus(taskContext);
        checkFailures(taskContext, taskStatus, jobSubmissionTask);
        return false;
    } catch (TException e) {
        throw new GFacException(e);
    }
}
Also used : TException(org.apache.thrift.TException) GFacException(org.apache.airavata.gfac.core.GFacException) JobSubmissionTask(org.apache.airavata.gfac.core.task.JobSubmissionTask) TaskStatus(org.apache.airavata.model.status.TaskStatus) JobSubmissionTaskModel(org.apache.airavata.model.task.JobSubmissionTaskModel) ProcessContext(org.apache.airavata.gfac.core.context.ProcessContext)

Aggregations

ProcessContext (org.apache.airavata.gfac.core.context.ProcessContext)2 JobSubmissionTaskModel (org.apache.airavata.model.task.JobSubmissionTaskModel)2 Writable (groovy.lang.Writable)1 GStringTemplateEngine (groovy.text.GStringTemplateEngine)1 TemplateEngine (groovy.text.TemplateEngine)1 java.io (java.io)1 InetAddress (java.net.InetAddress)1 URISyntaxException (java.net.URISyntaxException)1 URL (java.net.URL)1 UnknownHostException (java.net.UnknownHostException)1 ByteBuffer (java.nio.ByteBuffer)1 SecureRandom (java.security.SecureRandom)1 java.util (java.util)1 Matcher (java.util.regex.Matcher)1 Pattern (java.util.regex.Pattern)1 Collectors (java.util.stream.Collectors)1 javax.xml.xpath (javax.xml.xpath)1 ApplicationSettingsException (org.apache.airavata.common.exception.ApplicationSettingsException)1 org.apache.airavata.common.utils (org.apache.airavata.common.utils)1 CredentialReader (org.apache.airavata.credential.store.store.CredentialReader)1