Package org.apache.airavata.gsi.ssh.api.job

Examples of org.apache.airavata.gsi.ssh.api.job.JobDescriptor

92
93
94
95
96
97
98
99
100
101
102
103
            ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType();
            String remoteFile = app.getStaticWorkingDirectory() + File.separatorChar + Constants.EXECUTABLE_NAME;
            details.setJobID(taskID);
            details.setJobDescription(remoteFile);
            jobExecutionContext.setJobDetails(details);
            JobDescriptor jobDescriptor = GFACSSHUtils.createJobDescriptor(jobExecutionContext, app, null);
            details.setJobDescription(jobDescriptor.toXML());

            GFacUtils.saveJobStatus(jobExecutionContext, details, JobState.SETUP);
            log.info(remoteFile);
            try {
                File runscript = createShellScript(jobExecutionContext);
View Full Code Here
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
                        throw new GFacProviderException("Security context is not set properly");
                    } else {
                        log.info("Successfully retrieved the Security Context");
                    }
                    // This installed path is a mandetory field, because this could change based on the computing resource
                    JobDescriptor jobDescriptor = GFACSSHUtils.createJobDescriptor(jobExecutionContext, app, cluster);

                    log.info(jobDescriptor.toXML());

                    jobDetails.setJobDescription(jobDescriptor.toXML());

                    String jobID = cluster.submitBatchJob(jobDescriptor);
                    jobExecutionContext.setJobDetails(jobDetails);
                    if (jobID == null) {
                        jobDetails.setJobID("none");
View Full Code Here
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
                    throw new GFacHandlerException("Error retrieving job details from Registry", e);
                }
                JobDetails jobDetails = taskData.getJobDetailsList().get(0);
                String jobDescription = jobDetails.getJobDescription();
                if (jobDescription != null) {
                    JobDescriptor jobDescriptor = null;
                    try {
                        jobDescriptor = JobDescriptor.fromXML(jobDescription);
                    } catch (XmlException e1) {
                        e1.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
                    }
                    applicationDeploymentDescription.getType().setScratchWorkingDirectory(
                            jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getWorkingDirectory());
                    applicationDeploymentDescription.getType().setInputDataDirectory(jobDescriptor.getInputDirectory());
                    applicationDeploymentDescription.getType().setOutputDataDirectory(jobDescriptor.getOutputDirectory());
                    applicationDeploymentDescription.getType().setStandardError(jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getStandardErrorFile());
                    applicationDeploymentDescription.getType().setStandardOutput(jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getStandardOutFile());
                }
            }
        }
        try {
            if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) == null) {
View Full Code Here
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151

        // Execute command
        System.out.println("Target PBS file path: " + workingDirectory);
        // constructing the job object
        JobDescriptor jobDescriptor = new JobDescriptor();
        jobDescriptor.setWorkingDirectory(workingDirectory);
        jobDescriptor.setShellName("/bin/bash");
        jobDescriptor.setJobName("GSI_SSH_SLEEP_JOB");
        jobDescriptor.setExecutablePath("/bin/echo");
        jobDescriptor.setAllEnvExport(true);
        jobDescriptor.setMailOptions("n");
        jobDescriptor.setStandardOutFile(workingDirectory + File.separator + "application.out");
        jobDescriptor.setStandardErrorFile(workingDirectory + File.separator + "application.err");
        jobDescriptor.setNodes(1);
        jobDescriptor.setProcessesPerNode(1);
        jobDescriptor.setQueueName("normal");
        jobDescriptor.setMaxWallTime("60");
        jobDescriptor.setAcountString("sds128");
        List<String> inputs = new ArrayList<String>();
        jobDescriptor.setOwner("ogce");
        inputs.add("Hello World");
        jobDescriptor.setInputValues(inputs);
        //finished construction of job object
        System.out.println(jobDescriptor.toXML());
        for (int i = 0; i < 1; i++) {
            String jobID = pbsCluster.submitBatchJob(jobDescriptor);
            System.out.println("Job submitted successfully, Job ID: " +  jobID);
            MonitorID monitorID = new HPCMonitorID(hostDescription, jobID,null,null,null, "ogce");
            ((HPCMonitorID)monitorID).setAuthenticationInfo(authenticationInfo);
View Full Code Here
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
            jobExecutionContext.addSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT, sshSecurityContext);
        }
    }
    public static JobDescriptor createJobDescriptor(JobExecutionContext jobExecutionContext,
                                                    ApplicationDeploymentDescriptionType app, Cluster cluster) {
        JobDescriptor jobDescriptor = new JobDescriptor();
        // this is common for any application descriptor
        jobDescriptor.setInputDirectory(app.getInputDataDirectory());
        jobDescriptor.setOutputDirectory(app.getOutputDataDirectory());
        jobDescriptor.setExecutablePath(app.getExecutableLocation());
        jobDescriptor.setStandardOutFile(app.getStandardOutput());
        jobDescriptor.setStandardErrorFile(app.getStandardError());
        Random random = new Random();
        int i = random.nextInt();
        jobDescriptor.setJobName(app.getApplicationName().getStringValue() + String.valueOf(i));
        jobDescriptor.setWorkingDirectory(app.getStaticWorkingDirectory());


        List<String> inputValues = new ArrayList<String>();
        MessageContext input = jobExecutionContext.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, " ");
                inputValues.add(value);
            } else {
                String paramValue = MappingFactory.toString(actualParameter);
                inputValues.add(paramValue);
            }
        }
        jobDescriptor.setInputValues(inputValues);

        // this part will fill out the hpcApplicationDescriptor
        if (app instanceof HpcApplicationDeploymentType) {
            HpcApplicationDeploymentType applicationDeploymentType
                    = (HpcApplicationDeploymentType) app;
            jobDescriptor.setShellName("/bin/bash");
            jobDescriptor.setAllEnvExport(true);
            jobDescriptor.setMailOptions("n");
            jobDescriptor.setNodes(applicationDeploymentType.getNodeCount());
            jobDescriptor.setProcessesPerNode(applicationDeploymentType.getProcessorsPerNode());
            jobDescriptor.setMaxWallTime(String.valueOf(applicationDeploymentType.getMaxWallTime()));
            jobDescriptor.setJobSubmitter(applicationDeploymentType.getJobSubmitterCommand());
            if (applicationDeploymentType.getProjectAccount() != null) {
                if (applicationDeploymentType.getProjectAccount().getProjectAccountNumber() != null) {
                    jobDescriptor.setAcountString(applicationDeploymentType.getProjectAccount().getProjectAccountNumber());
                }
            }
            if (applicationDeploymentType.getQueue() != null) {
                if (applicationDeploymentType.getQueue().getQueueName() != null) {
                    jobDescriptor.setQueueName(applicationDeploymentType.getQueue().getQueueName());
                }
            }
            jobDescriptor.setOwner(((PBSCluster) cluster).getServerInfo().getUserName());
            TaskDetails taskData = jobExecutionContext.getTaskData();
            if (taskData != null && taskData.isSetTaskScheduling()) {
                ComputationalResourceScheduling computionnalResource = taskData.getTaskScheduling();
                if (computionnalResource.getNodeCount() > 0) {
                    jobDescriptor.setNodes(computionnalResource.getNodeCount());
                }
                if (computionnalResource.getComputationalProjectAccount() != null) {
                    jobDescriptor.setAcountString(computionnalResource.getComputationalProjectAccount());
                }
                if (computionnalResource.getQueueName() != null) {
                    jobDescriptor.setQueueName(computionnalResource.getQueueName());
                }
                if (computionnalResource.getTotalCPUCount() > 0) {
                    jobDescriptor.setProcessesPerNode(computionnalResource.getTotalCPUCount());
                }
                if (computionnalResource.getWallTimeLimit() > 0) {
                    jobDescriptor.setMaxWallTime(String.valueOf(computionnalResource.getWallTimeLimit()));
                }
            }

        }
        return jobDescriptor;
View Full Code Here
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
                throw new GFacProviderException("Security context is not set properly");
            } else {
                log.info("Successfully retrieved the Security Context");
            }
            // This installed path is a mandetory field, because this could change based on the computing resource
            JobDescriptor jobDescriptor = GFACGSISSHUtils.createJobDescriptor(jobExecutionContext, app, cluster);

            log.info(jobDescriptor.toXML());
           
            jobDetails.setJobDescription(jobDescriptor.toXML());
           
            String jobID = cluster.submitBatchJob(jobDescriptor);
            jobExecutionContext.setJobDetails(jobDetails);
            if(jobID == null){
                jobDetails.setJobID("none");
View Full Code Here
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153

        // Execute command
        System.out.println("Target PBS file path: " + workingDirectory);
        // constructing the job object
        JobDescriptor jobDescriptor = new JobDescriptor();
        jobDescriptor.setWorkingDirectory(workingDirectory);
        jobDescriptor.setShellName("/bin/bash");
        jobDescriptor.setJobName("GSI_SSH_SLEEP_JOB");
        jobDescriptor.setExecutablePath("/bin/echo");
        jobDescriptor.setAllEnvExport(true);
        jobDescriptor.setMailOptions("n");
        jobDescriptor.setStandardOutFile(workingDirectory + File.separator + "application.out");
        jobDescriptor.setStandardErrorFile(workingDirectory + File.separator + "application.err");
        jobDescriptor.setNodes(1);
        jobDescriptor.setProcessesPerNode(1);
        jobDescriptor.setQueueName("normal");
        jobDescriptor.setMaxWallTime("60");
        jobDescriptor.setAcountString("TG-STA110014S");
        List<String> inputs = new ArrayList<String>();
        jobDescriptor.setOwner("ogce");
        inputs.add("Hello World");
        jobDescriptor.setInputValues(inputs);
        //finished construction of job object
        System.out.println(jobDescriptor.toXML());
        String jobID = pbsCluster.submitBatchJob(jobDescriptor);
        System.out.println(jobID);
        try {
            pushQueue.add(new MonitorID(hostDescription, jobID,null,null,null, "ogce"));
        } catch (Exception e) {
View Full Code Here
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
                    throw new GFacHandlerException("Error retrieving job details from Registry", e);
                }
                JobDetails jobDetails = taskData.getJobDetailsList().get(0);
                String jobDescription = jobDetails.getJobDescription();
                if (jobDescription != null) {
                    JobDescriptor jobDescriptor = null;
                    try {
                        jobDescriptor = JobDescriptor.fromXML(jobDescription);
                    } catch (XmlException e1) {
                        e1.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
                    }
                    applicationDeploymentDescription.getType().setScratchWorkingDirectory(
                            jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getWorkingDirectory());
                    applicationDeploymentDescription.getType().setInputDataDirectory(jobDescriptor.getInputDirectory());
                    applicationDeploymentDescription.getType().setOutputDataDirectory(jobDescriptor.getOutputDirectory());
                    applicationDeploymentDescription.getType().setStandardError(jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getStandardErrorFile());
                    applicationDeploymentDescription.getType().setStandardOutput(jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getStandardOutFile());
                }
            }
        }

        try {
View Full Code Here
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
        }
        jobExecutionContext.addSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT,context);
    }
    public static JobDescriptor createJobDescriptor(JobExecutionContext jobExecutionContext,
                                                    ApplicationDeploymentDescriptionType app, Cluster cluster) {
        JobDescriptor jobDescriptor = new JobDescriptor();
        // this is common for any application descriptor
        jobDescriptor.setInputDirectory(app.getInputDataDirectory());
        jobDescriptor.setOutputDirectory(app.getOutputDataDirectory());
        jobDescriptor.setExecutablePath(app.getExecutableLocation());
        jobDescriptor.setStandardOutFile(app.getStandardOutput());
        jobDescriptor.setStandardErrorFile(app.getStandardError());
        Random random = new Random();
        int i = random.nextInt();
        jobDescriptor.setJobName(app.getApplicationName().getStringValue() + String.valueOf(i));
        jobDescriptor.setWorkingDirectory(app.getStaticWorkingDirectory());


        List<String> inputValues = new ArrayList<String>();
        MessageContext input = jobExecutionContext.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, " ");
                inputValues.add(value);
            } else {
                String paramValue = MappingFactory.toString(actualParameter);
                inputValues.add(paramValue);
            }
        }
        jobDescriptor.setInputValues(inputValues);

        // this part will fill out the hpcApplicationDescriptor
        if (app instanceof HpcApplicationDeploymentType) {
            HpcApplicationDeploymentType applicationDeploymentType
                    = (HpcApplicationDeploymentType) app;
            jobDescriptor.setShellName("/bin/bash");
            jobDescriptor.setAllEnvExport(true);
            jobDescriptor.setMailOptions("n");
            jobDescriptor.setNodes(applicationDeploymentType.getNodeCount());
            jobDescriptor.setProcessesPerNode(applicationDeploymentType.getProcessorsPerNode());
            jobDescriptor.setMaxWallTime(String.valueOf(applicationDeploymentType.getMaxWallTime()));
            jobDescriptor.setJobSubmitter(applicationDeploymentType.getJobSubmitterCommand());
            if (applicationDeploymentType.getProjectAccount() != null) {
                if (applicationDeploymentType.getProjectAccount().getProjectAccountNumber() != null) {
                    jobDescriptor.setAcountString(applicationDeploymentType.getProjectAccount().getProjectAccountNumber());
                }
            }
            if (applicationDeploymentType.getQueue() != null) {
                if (applicationDeploymentType.getQueue().getQueueName() != null) {
                    jobDescriptor.setQueueName(applicationDeploymentType.getQueue().getQueueName());
                }
            }
            jobDescriptor.setOwner(((PBSCluster) cluster).getServerInfo().getUserName());
            TaskDetails taskData = jobExecutionContext.getTaskData();
            if (taskData != null && taskData.isSetTaskScheduling()) {
                ComputationalResourceScheduling computionnalResource = taskData.getTaskScheduling();
                if (computionnalResource.getNodeCount() > 0) {
                    jobDescriptor.setNodes(computionnalResource.getNodeCount());
                }
                if (computionnalResource.getComputationalProjectAccount() != null) {
                    jobDescriptor.setAcountString(computionnalResource.getComputationalProjectAccount());
                }
                if (computionnalResource.getQueueName() != null) {
                    jobDescriptor.setQueueName(computionnalResource.getQueueName());
                }
                if (computionnalResource.getTotalCPUCount() > 0) {
                    jobDescriptor.setProcessesPerNode(computionnalResource.getTotalCPUCount());
                }
                if (computionnalResource.getWallTimeLimit() > 0) {
                    jobDescriptor.setMaxWallTime(String.valueOf(computionnalResource.getWallTimeLimit()));
                }
            }

        }
        return jobDescriptor;
View Full Code Here
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161

        // Execute command
        System.out.println("Target PBS file path: " + workingDirectory);
        // constructing the job object
        JobDescriptor jobDescriptor = new JobDescriptor();
        jobDescriptor.setWorkingDirectory(workingDirectory);
        jobDescriptor.setShellName("/bin/bash");
        jobDescriptor.setJobName("GSI_SSH_SLEEP_JOB");
        jobDescriptor.setExecutablePath("/bin/echo");
        jobDescriptor.setAllEnvExport(true);
        jobDescriptor.setMailOptions("n");
        jobDescriptor.setStandardOutFile(workingDirectory + File.separator + "application.out");
        jobDescriptor.setStandardErrorFile(workingDirectory + File.separator + "application.err");
        jobDescriptor.setNodes(1);
        jobDescriptor.setProcessesPerNode(1);
        jobDescriptor.setQueueName("normal");
        jobDescriptor.setMaxWallTime("60");
        jobDescriptor.setAcountString("sds128");
        List<String> inputs = new ArrayList<String>();
        inputs.add("Hello World");
        jobDescriptor.setInputValues(inputs);
        //finished construction of job object
        System.out.println(jobDescriptor.toXML());
        jobID = pbsCluster.submitBatchJob(jobDescriptor);
        System.out.println("JobID returned : " + jobID);

        //Cluster cluster = sshApi.getCluster(serverInfo, authenticationInfo);
        Thread.sleep(1000);
        JobDescriptor jobById = pbsCluster.getJobDescriptorById(jobID);

        //printing job data got from previous call
        AssertJUnit.assertEquals(jobById.getJobId(), jobID);
        System.out.println(jobById.getAcountString());
        System.out.println(jobById.getAllEnvExport());
        System.out.println(jobById.getCompTime());
        System.out.println(jobById.getExecutablePath());
        System.out.println(jobById.getEllapsedTime());
        System.out.println(jobById.getQueueName());
        System.out.println(jobById.getExecuteNode());
        System.out.println(jobById.getJobName());
        System.out.println(jobById.getCTime());
        System.out.println(jobById.getSTime());
        System.out.println(jobById.getMTime());
        System.out.println(jobById.getCompTime());
        System.out.println(jobById.getOwner());
        System.out.println(jobById.getQTime());
        System.out.println(jobById.getUsedCPUTime());
        System.out.println(jobById.getUsedMemory());
        System.out.println(jobById.getVariableList());
    }
View Full Code Here
TOP

Related Classes of org.apache.airavata.gsi.ssh.api.job.JobDescriptor

  • org.apache.airavata.gfac.gsissh.handler.GSISSHOutputHandler
  • org.apache.airavata.gfac.gsissh.provider.impl.GSISSHProvider
  • org.apache.airavata.gfac.gsissh.util.GFACGSISSHUtils
  • org.apache.airavata.gfac.provider.impl.GSISSHProvider
  • org.apache.airavata.gfac.ssh.handler.SSHOutputHandler
  • org.apache.airavata.gfac.ssh.provider.impl.SSHProvider
  • org.apache.airavata.gfac.ssh.util.GFACSSHUtils
  • org.apache.airavata.gsi.ssh.impl.DefaultSSHApiTest
  • org.apache.airavata.gsi.ssh.impl.DefaultSSHApiTestWithMyProxyAuth
  • org.apache.airavata.gsi.ssh.impl.GSISSHAbstractCluster
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.