Examples of PBSCluster

Examples of org.apache.airavata.gsi.ssh.impl.PBSCluster

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        // Server info
        ServerInfo serverInfo = new ServerInfo("ogce", "trestles.sdsc.edu");
        Cluster pbsCluster = null;
        try {
            pbsCluster = new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager(app.getInstalledParentPath()));
        } catch (SSHApiException e) {
            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
        }
        GSISecurityContext sshSecurityContext = new GSISecurityContext(pbsCluster);
        return sshSecurityContext;
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Examples of org.apache.airavata.gsi.ssh.impl.PBSCluster

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        // Server info
        ServerInfo serverInfo = new ServerInfo("ogce", hostDescription.getType().getHostAddress());


        Cluster pbsCluster = new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager("/opt/torque/bin/"));


        // 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);
            try {
                org.apache.airavata.gfac.monitor.util.CommonUtils.addMonitortoQueue(pullQueue, monitorID);
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Examples of org.apache.airavata.gsi.ssh.impl.PBSCluster

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                String installedParentPath = "/";
                if (((SSHHostType) registeredHost.getType()).getHpcResource()) {
                    installedParentPath = ((HpcApplicationDeploymentType)
                            jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType()).getInstalledParentPath();
                }
                pbsCluster = new PBSCluster(serverInfo, authenticationInfo,
                        CommonUtils.getPBSJobManager(installedParentPath));
            } catch (SSHApiException e) {
                e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
            }
            sshSecurityContext.setPbsCluster(pbsCluster);
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Examples of org.apache.airavata.gsi.ssh.impl.PBSCluster

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            // Server info
            ServerInfo serverInfo = new ServerInfo(this.userName, this.hostName);
            Cluster pbsCluster = null;
            // here doesn't matter what the job manager is because we are only doing some file handling
            // not really dealing with monitoring or job submission, so we pa
            pbsCluster = new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager("/opt/torque/torque-4.2.3.1/bin/"));
            String parentPath = inputPath + File.separator + jobExecutionContext.getExperimentID() + File.separator + jobExecutionContext.getTaskData().getTaskID();
            (new File(parentPath)).mkdirs();
            MessageContext input = jobExecutionContext.getInMessageContext();
            Set<String> parameters = input.getParameters().keySet();
            for (String paramName : parameters) {
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Examples of org.apache.airavata.gsi.ssh.impl.PBSCluster

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        // Server info
        ServerInfo serverInfo = new ServerInfo("ogce", "login1.stampede.tacc.utexas.edu",2222);


        Cluster pbsCluster = new
                PBSCluster(serverInfo, authenticationInfo, org.apache.airavata.gsi.ssh.util.CommonUtils.getPBSJobManager("/usr/bin/"));


        // 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) {
            e.printStackTrace();
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Examples of org.apache.airavata.gsi.ssh.impl.PBSCluster

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        // Server info
        ServerInfo serverInfo = new ServerInfo("ogce", "trestles.sdsc.edu");
        Cluster pbsCluster = null;
        try {
            pbsCluster = new PBSCluster(serverInfo, authenticationInfo, app.getInstalledParentPath());
        } catch (SSHApiException e) {
            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
        }
        GSISecurityContext sshSecurityContext = new GSISecurityContext(pbsCluster);
        return sshSecurityContext;
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Examples of org.apache.airavata.gsi.ssh.impl.PBSCluster

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        // Server info
        ServerInfo serverInfo = new ServerInfo(this.userName, this.hostName);

        Cluster pbsCluster = null;
        try {
             pbsCluster = new PBSCluster(serverInfo, authenticationInfo,
                     (app.getInstalledParentPath()));
        } catch (SSHApiException e) {
            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
        }
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Examples of org.apache.airavata.gsi.ssh.impl.PBSCluster

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                        requestData.getMyProxyPort(), requestData.getMyProxyLifeTime(), System.getProperty(Constants.TRUSTED_CERTIFICATE_SYSTEM_PROPERTY));
                ServerInfo serverInfo = new ServerInfo(requestData.getMyProxyUserName(), registeredHost.getType().getHostAddress());

                Cluster pbsCluster = null;
                try {
                    pbsCluster = new PBSCluster(serverInfo, authenticationInfo,
                            (((HpcApplicationDeploymentType) jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType()).getInstalledParentPath()));
                } catch (SSHApiException e) {
                    e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
                }

                context.setPbsCluster(pbsCluster);
            }
           
            jobExecutionContext.addSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT, context);
        } else if (registeredHost.getType() instanceof Ec2HostType) {
            if (this.configuration.getAmazonSecurityContext() != null) {
                jobExecutionContext.addSecurityContext(AmazonSecurityContext.AMAZON_SECURITY_CONTEXT,
                        this.configuration.getAmazonSecurityContext());
            }
        } else if (registeredHost.getType() instanceof SSHHostType) {
            String sshUserName = configurationProperties.getProperty(Constants.SSH_USER_NAME);
            String sshPrivateKey = configurationProperties.getProperty(Constants.SSH_PRIVATE_KEY);
            String sshPrivateKeyPass = configurationProperties.getProperty(Constants.SSH_PRIVATE_KEY_PASS);
            String sshPassword = configurationProperties.getProperty(Constants.SSH_PASSWORD);
            String sshPublicKey = configurationProperties.getProperty(Constants.SSH_PUBLIC_KEY);
            SSHSecurityContext sshSecurityContext = new SSHSecurityContext();
            if (((SSHHostType) registeredHost.getType()).getHpcResource()) {
                AuthenticationInfo authenticationInfo = null;
                // we give higher preference to the password over keypair ssh authentication
                if (sshPassword != null) {
                    authenticationInfo = new DefaultPasswordAuthenticationInfo(sshPassword);
                } else {
                    authenticationInfo = new DefaultPublicKeyFileAuthentication(sshPublicKey, sshPrivateKey, sshPrivateKeyPass);
                }
                ServerInfo serverInfo = new ServerInfo(sshUserName, registeredHost.getType().getHostAddress());

                Cluster pbsCluster = null;
                try {
                    pbsCluster = new PBSCluster(serverInfo, authenticationInfo,
                            (((HpcApplicationDeploymentType) jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType()).getInstalledParentPath()));
                } catch (SSHApiException e) {
                    e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
                }
                sshSecurityContext.setPbsCluster(pbsCluster);
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