use of org.apache.airavata.cloud.aurora.client.bean.JobConfigBean 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;
}
use of org.apache.airavata.cloud.aurora.client.bean.JobConfigBean in project airavata by apache.
the class AuroraClientSample method getRunningJobsList.
/**
* Gets the job summary.
*
* @param client the client
* @return the job summary
* @throws Exception
*/
public static void getRunningJobsList(String ownerRole) throws Exception {
try {
AuroraThriftClient client = AuroraThriftClient.getAuroraThriftClient();
ResponseBean response = client.getJobList(ownerRole);
System.out.println("Response status: " + response.getResponseCode().name());
if (response instanceof GetJobsResponseBean) {
GetJobsResponseBean result = (GetJobsResponseBean) response;
System.out.println(result);
Set<JobConfigBean> jobConfigs = result.getJobConfigs();
for (JobConfigBean jobConfig : jobConfigs) {
System.out.println(jobConfig);
JobKeyBean jobKey = jobConfig.getJob();
IdentityBean owner = jobConfig.getOwner();
TaskConfigBean taskConfig = jobConfig.getTaskConfig();
Set<ProcessBean> processes = taskConfig.getProcesses();
System.out.println("\n**** JOB CONFIG ****");
System.out.println("\t # cluster: " + jobConfig.getCluster());
System.out.println("\t # instanceCount: " + jobConfig.getInstances());
System.out.println("\t # isService: " + jobConfig.isService());
System.out.println("\t\t # priority: " + jobConfig.getPriority());
System.out.println("\t >> Job Key <<");
System.out.println("\t\t # name: " + jobKey.getName());
System.out.println("\t\t # role: " + jobKey.getRole());
System.out.println("\t\t # environment: " + jobKey.getEnvironment());
System.out.println("\t >> Identity <<");
System.out.println("\t\t # owner: " + owner.getUser());
System.out.println("\t >> Task Config <<");
System.out.println("\t\t >> Resources <<");
System.out.println("\t\t\t # numCPUs: " + taskConfig.getResources().getNumCpus());
System.out.println("\t\t\t # diskMb: " + taskConfig.getResources().getDiskMb());
System.out.println("\t\t\t # ramMb: " + taskConfig.getResources().getRamMb());
System.out.println("\t\t >> Processes <<");
for (ProcessBean process : processes) {
System.out.println("\t\t\t ***** PROCESS *****");
System.out.println("\t\t\t # name: " + process.getName());
System.out.println("\t\t\t # cmdline: " + process.getCmdLine());
}
}
}
} catch (TException e) {
e.printStackTrace();
}
}
use of org.apache.airavata.cloud.aurora.client.bean.JobConfigBean in project airavata by apache.
the class AuroraClientSample method createJob.
public static void createJob() throws Exception {
JobKeyBean jobKey = new JobKeyBean("devel", "centos", "test_job");
IdentityBean owner = new IdentityBean("centos");
ProcessBean proc1 = new ProcessBean("process_1", "echo 'hello_world_1'", false);
ProcessBean proc2 = new ProcessBean("process_2", "echo 'hello_world_2'", false);
Set<ProcessBean> processes = new HashSet<>();
processes.add(proc1);
processes.add(proc2);
ResourceBean resources = new ResourceBean(0.1, 8, 1);
TaskConfigBean taskConfig = new TaskConfigBean("task_hello_world", processes, resources);
JobConfigBean jobConfig = new JobConfigBean(jobKey, owner, taskConfig, "example");
String executorConfigJson = AuroraThriftClientUtil.getExecutorConfigJson(jobConfig);
System.out.println(executorConfigJson);
AuroraThriftClient client = AuroraThriftClient.getAuroraThriftClient();
ResponseBean response = client.createJob(jobConfig);
System.out.println(response);
}
use of org.apache.airavata.cloud.aurora.client.bean.JobConfigBean in project airavata by apache.
the class AuroraClientSample method createAutoDockJob.
public static void createAutoDockJob() throws Exception {
JobKeyBean jobKey = new JobKeyBean("devel", "centos", "test_autodock");
IdentityBean owner = new IdentityBean("centos");
String working_dir = "/home/centos/efs-mount-point/job_" + ThreadLocalRandom.current().nextInt(1, 101) + "/";
String autodock_path = "/home/centos/efs-mount-point/autodock-vina";
ProcessBean proc1 = new ProcessBean("process_1", "mkdir " + working_dir, false);
ProcessBean proc2 = new ProcessBean("process_2", "cp " + autodock_path + "/vina_screenM.sh " + working_dir, false);
ProcessBean proc3 = new ProcessBean("process_3", "cp " + autodock_path + "/ligand* " + working_dir, false);
ProcessBean proc4 = new ProcessBean("process_4", "cd " + working_dir + " && sh vina_screenM.sh", false);
Set<ProcessBean> processes = new LinkedHashSet<>();
processes.add(proc1);
processes.add(proc2);
processes.add(proc3);
processes.add(proc4);
ResourceBean resources = new ResourceBean(1.5, 125, 512);
TaskConfigBean taskConfig = new TaskConfigBean("test_autodock", processes, resources);
JobConfigBean jobConfig = new JobConfigBean(jobKey, owner, taskConfig, "example");
String executorConfigJson = AuroraThriftClientUtil.getExecutorConfigJson(jobConfig);
System.out.println(executorConfigJson);
AuroraThriftClient client = AuroraThriftClient.getAuroraThriftClient();
ResponseBean response = client.createJob(jobConfig);
System.out.println(response);
}
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