Examples with ProcessContext org.apache.airavata.gfac.core.context.ProcessContext used on opensource projects

Example 11 with ProcessContext

use of org.apache.airavata.gfac.core.context.ProcessContext in project airavata by apache.

the class ArchiveTask method execute.

@Override
public TaskStatus execute(TaskContext taskContext) {
    // implement archive logic with jscp
    TaskStatus status = new TaskStatus(TaskState.EXECUTING);
    ProcessContext processContext = taskContext.getParentProcessContext();
    RemoteCluster remoteCluster = processContext.getJobSubmissionRemoteCluster();
    AuthenticationInfo authenticationInfo = null;
    DataStagingTaskModel subTaskModel = null;
    try {
        subTaskModel = (DataStagingTaskModel) ThriftUtils.getSubTaskModel(taskContext.getTaskModel());
    } catch (TException e) {
        String msg = "Error! Deserialization issue with SubTask Model";
        log.error(msg, e);
        status.setState(TaskState.FAILED);
        status.setReason(msg);
        ErrorModel errorModel = new ErrorModel();
        errorModel.setActualErrorMessage(e.getMessage());
        errorModel.setUserFriendlyMessage(msg);
        taskContext.getTaskModel().setTaskErrors(Arrays.asList(errorModel));
        return status;
    }
    try {
        StorageResourceDescription storageResource = taskContext.getParentProcessContext().getStorageResource();
        if (storageResource != null) {
            hostName = storageResource.getHostName();
        } else {
            throw new GFacException("Storage Resource is null");
        }
        userName = processContext.getStorageResourceLoginUserName();
        inputPath = processContext.getStorageFileSystemRootLocation();
        inputPath = (inputPath.endsWith(File.separator) ? inputPath : inputPath + File.separator);
        status = new TaskStatus(TaskState.COMPLETED);
        Session srcSession = Factory.getSSHSession(Factory.getComputerResourceSSHKeyAuthentication(processContext), processContext.getComputeResourceServerInfo());
        Session destSession = Factory.getSSHSession(Factory.getStorageSSHKeyAuthentication(processContext), processContext.getStorageResourceServerInfo());
        URI sourceURI = new URI(subTaskModel.getSource());
        URI destinationURI = null;
        String workingDirName = null, path = null;
        if (sourceURI.getPath().endsWith("/")) {
            path = sourceURI.getPath().substring(0, sourceURI.getPath().length() - 1);
        } else {
            path = sourceURI.getPath();
        }
        workingDirName = path.substring(path.lastIndexOf(File.separator) + 1, path.length());
        // tar working dir
        // cd /Users/syodage/Desktop/temp/.. && tar -cvf path/workingDir.tar temp
        String archiveTar = "archive.tar";
        String resourceAbsTarFilePath = path + "/" + archiveTar;
        CommandInfo commandInfo = new RawCommandInfo("cd " + path + " && tar -cvf " + resourceAbsTarFilePath + " ./* ");
        // move tar to storage resource
        remoteCluster.execute(commandInfo);
        destinationURI = TaskUtils.getDestinationURI(taskContext, hostName, inputPath, archiveTar);
        remoteCluster.scpThirdParty(resourceAbsTarFilePath, srcSession, destinationURI.getPath(), destSession, RemoteCluster.DIRECTION.FROM, true);
        // delete tar in remote computer resource
        commandInfo = new RawCommandInfo("rm " + resourceAbsTarFilePath);
        remoteCluster.execute(commandInfo);
        // untar file and delete tar in storage resource
        String destPath = destinationURI.getPath();
        String destParent = destPath.substring(0, destPath.lastIndexOf("/"));
        String storageArchiveDir = "ARCHIVE";
        commandInfo = new RawCommandInfo("cd " + destParent + " && mkdir " + storageArchiveDir + " && tar -xvf " + archiveTar + " -C " + storageArchiveDir + " && rm " + archiveTar + " && chmod 755 -R " + storageArchiveDir + "/*");
        executeCommand(destSession, commandInfo, new StandardOutReader());
    } catch (CredentialStoreException e) {
        String msg = "Storage authentication issue, make sure you are passing valid credential token";
        log.error(msg, e);
        status.setState(TaskState.FAILED);
        status.setReason(msg);
        status.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
        ErrorModel errorModel = new ErrorModel();
        errorModel.setActualErrorMessage(e.getMessage());
        errorModel.setUserFriendlyMessage(msg);
        taskContext.getTaskModel().setTaskErrors(Arrays.asList(errorModel));
    } catch (URISyntaxException | GFacException e) {
        String msg = "Error! Archive task failed";
        log.error(msg, e);
        status.setState(TaskState.FAILED);
        status.setReason(msg);
        status.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
        ErrorModel errorModel = new ErrorModel();
        errorModel.setActualErrorMessage(e.getMessage());
        errorModel.setUserFriendlyMessage(msg);
        taskContext.getTaskModel().setTaskErrors(Arrays.asList(errorModel));
    }
    return status;
}

Example 12 with ProcessContext

use of org.apache.airavata.gfac.core.context.ProcessContext in project airavata by apache.

the class AuroraJobSubmissionTask method execute.

@Override
public TaskStatus execute(TaskContext taskContext) {
    // set to completed.
    TaskStatus taskStatus = new TaskStatus(TaskState.COMPLETED);
    ProcessContext processContext = taskContext.getParentProcessContext();
    JobModel jobModel = processContext.getJobModel();
    jobModel.setTaskId(taskContext.getTaskId());
    String jobIdAndName = "A" + GFacUtils.generateJobName();
    jobModel.setJobName(jobIdAndName);
    JobStatus jobStatus = new JobStatus();
    jobStatus.setJobState(JobState.SUBMITTED);
    try {
        JobKeyBean jobKey = new JobKeyBean(AuroraUtils.ENVIRONMENT, AuroraUtils.ROLE, jobIdAndName);
        IdentityBean owner = new IdentityBean(AuroraUtils.ROLE);
        GroovyMap groovyMap = GFacUtils.createGroovyMap(processContext, taskContext);
        groovyMap.add(Script.JOB_SUBMITTER_COMMAND, "sh");
        String templateFileName = GFacUtils.getTemplateFileName(ResourceJobManagerType.CLOUD);
        String script = GFacUtils.generateScript(groovyMap, templateFileName);
        Set<ProcessBean> processes = new LinkedHashSet<>();
        ProcessBean process_1 = new ProcessBean("main_process", script, false);
        processes.add(process_1);
        groovyMap.getStringValue(Script.STANDARD_OUT_FILE).ifPresent(stdout -> {
            ProcessBean stdOutProcess = new ProcessBean("stdout_copy_process", "cp .logs/main_process/0/stdout " + stdout, false);
            processes.add(stdOutProcess);
        });
        groovyMap.getStringValue(Script.STANDARD_ERROR_FILE).ifPresent(stderr -> {
            ProcessBean stdErrProcess = new ProcessBean("stderr_copy_process", "cp .logs/main_process/0/stderr " + stderr, false);
            processes.add(stdErrProcess);
        });
        ResourceBean resources = new ResourceBean(1.5, 512, 512);
        TaskConfigBean taskConfig = new TaskConfigBean("Airavata-Aurora-" + jobIdAndName, processes, resources);
        JobConfigBean jobConfig = new JobConfigBean(jobKey, owner, taskConfig, AuroraUtils.CLUSTER);
        String executorConfigJson = AuroraThriftClientUtil.getExecutorConfigJson(jobConfig);
        log.info("Executor Config for Job {} , {}", jobIdAndName, executorConfigJson);
        AuroraThriftClient client = AuroraThriftClient.getAuroraThriftClient();
        ResponseBean response = client.createJob(jobConfig);
        log.info("Response for job {}, {}", jobIdAndName, response);
        jobModel.setJobDescription(resources.toString());
        jobModel.setJobId(jobIdAndName);
        jobStatus.setReason("Successfully Submitted");
        jobModel.setJobStatuses(Arrays.asList(jobStatus));
        jobStatus.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
        taskContext.getParentProcessContext().setJobModel(jobModel);
        GFacUtils.saveJobModel(processContext, jobModel);
        GFacUtils.saveJobStatus(processContext, jobModel);
        taskStatus.setReason("Successfully submitted job to Aurora");
    } catch (Throwable e) {
        String msg = "Error occurred while submitting Aurora job";
        log.error(msg, e);
        taskStatus.setState(TaskState.FAILED);
        taskStatus.setReason(msg);
        taskStatus.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime());
        ErrorModel errorModel = new ErrorModel();
        errorModel.setActualErrorMessage(e.getMessage());
        errorModel.setUserFriendlyMessage(msg);
        taskContext.getTaskModel().setTaskErrors(Arrays.asList(errorModel));
    }
    taskContext.setTaskStatus(taskStatus);
    try {
        GFacUtils.saveAndPublishTaskStatus(taskContext);
    } catch (GFacException e) {
        log.error("Error while saving task status", e);
    }
    return taskStatus;
}

Example 13 with ProcessContext

use of org.apache.airavata.gfac.core.context.ProcessContext 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;
}

Example 14 with ProcessContext

use of org.apache.airavata.gfac.core.context.ProcessContext in project airavata by apache.

the class EmailBasedMonitor method stopMonitor.

@Override
public void stopMonitor(String jobId, boolean runOutflow) {
    TaskContext taskContext = jobMonitorMap.remove(jobId);
    if (taskContext != null && runOutflow) {
        try {
            ProcessContext pc = taskContext.getParentProcessContext();
            if (taskContext.isCancel()) {
                // Moved job status to cancel
                JobModel jobModel = pc.getJobModel();
                JobStatus newJobStatus = new JobStatus(JobState.CANCELED);
                newJobStatus.setReason("Moving job status to cancel, as we didn't see any email from this job " + "for a while after execute job cancel command. This may happen if job was in queued state " + "when we run the cancel command");
                jobModel.setJobStatuses(Arrays.asList(newJobStatus));
                GFacUtils.saveJobStatus(pc, jobModel);
            }
            ProcessStatus pStatus = new ProcessStatus(ProcessState.CANCELLING);
            pStatus.setReason("Job cancelled");
            pc.setProcessStatus(pStatus);
            GFacUtils.saveAndPublishProcessStatus(pc);
            GFacThreadPoolExecutor.getCachedThreadPool().execute(new GFacWorker(pc));
        } catch (GFacException e) {
            log.info("[EJM]: Error while running output tasks", e);
        }
    }
}

Example 15 with ProcessContext

use of org.apache.airavata.gfac.core.context.ProcessContext in project airavata by apache.

the class CancelRequestWatcherImpl method cancelProcess.

private void cancelProcess(int retryAttempt) throws GFacException {
    ProcessContext processContext = Factory.getGfacContext().getProcess(processId);
    if (processContext != null) {
        processContext.setCancel(true);
        log.info("expId {}, processId : {}, Cancelling process", experimentId, processId);
        Factory.getGFacEngine().cancelProcess(processContext);
    } else {
        if (retryAttempt < max_retry) {
            log.info("expId: {}, Cancel request came for processId {} but couldn't find process context. " + "retry in {} s ", experimentId, processId, retryAttempt * 3);
            try {
                Thread.sleep(retryAttempt++ * 3000);
            } catch (InterruptedException e) {
            // ignore we don't care this exception.
            }
            cancelProcess(retryAttempt);
        } else {
            log.info("expId: {}, Cancel request came for processId {} but couldn't find process context.", experimentId, processId);
        }
    }
}