Examples with ResourceJobManager org.apache.airavata.model.appcatalog.computeresource.ResourceJobManager used on opensource projects

Example 11 with ResourceJobManager

use of org.apache.airavata.model.appcatalog.computeresource.ResourceJobManager in project airavata by apache.

the class DocumentCreatorNew method createBigRedAmberDocs.

public String createBigRedAmberDocs() throws InvalidRequestException, AiravataClientException, AiravataSystemException, TException, AppCatalogException {
    ComputeResourceDescription host = DocumentCreatorUtils.createComputeResourceDescription("bigred2", null, null);
    host.addToHostAliases(bigRed2HostAddress);
    host.addToIpAddresses(bigRed2HostAddress);
    host.setComputeResourceId(client.registerComputeResource(authzToken, host));
    Map<JobManagerCommand, String> commands = new HashMap<JobManagerCommand, String>();
    commands.put(JobManagerCommand.SUBMISSION, "aprun -n 4");
    ResourceJobManager resourceJobManager = DocumentCreatorUtils.createResourceJobManager(ResourceJobManagerType.UGE, "/opt/torque/torque-4.2.3.1/bin/", commands, null);
    SSHJobSubmission sshJobSubmission = new SSHJobSubmission();
    sshJobSubmission.setResourceJobManager(resourceJobManager);
    sshJobSubmission.setSecurityProtocol(SecurityProtocol.SSH_KEYS);
    sshJobSubmission.setSshPort(22);
    client.addSSHJobSubmissionDetails(authzToken, host.getComputeResourceId(), 1, sshJobSubmission);
    SCPDataMovement scpDataMovement = new SCPDataMovement();
    scpDataMovement.setSecurityProtocol(SecurityProtocol.SSH_KEYS);
    scpDataMovement.setSshPort(22);
    client.addSCPDataMovementDetails(authzToken, host.getComputeResourceId(), 1, scpDataMovement);
    ApplicationModule amodule = DocumentCreatorUtils.createApplicationModule("Amber", "12.0", null);
    amodule.setAppModuleId(client.registerApplicationModule(authzToken, DEFAULT_GATEWAY, amodule));
    ApplicationInterfaceDescription application = new ApplicationInterfaceDescription();
    application.setApplicationName("AmberBR2");
    application.addToApplicationModules(amodule.getAppModuleId());
    application.addToApplicationInputs(DocumentCreatorUtils.createAppInput("AMBER_HEAT_RST", "AMBER_HEAT_RST", null, null, DataType.URI));
    application.addToApplicationInputs(DocumentCreatorUtils.createAppInput("AMBER_PROD_IN", "AMBER_PROD_IN", null, null, DataType.URI));
    application.addToApplicationInputs(DocumentCreatorUtils.createAppInput("AMBER_PRMTOP", "AMBER_PRMTOP", null, null, DataType.URI));
    application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("AMBER_Prod.info", null, DataType.URI));
    application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("AMBER_Prod.mdcrd", null, DataType.URI));
    application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("AMBER_Prod.out", null, DataType.URI));
    application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("AMBER_Prod.rst", null, DataType.URI));
    application.setApplicationInterfaceId(client.registerApplicationInterface(authzToken, DEFAULT_GATEWAY, application));
    ApplicationDeploymentDescription deployment = DocumentCreatorUtils.createApplicationDeployment(host.getComputeResourceId(), amodule.getAppModuleId(), "/N/u/cgateway/BigRed2/sandbox/amber_wrapper.sh", ApplicationParallelismType.SERIAL, "AmberBR2");
    deployment.setAppDeploymentId(client.registerApplicationDeployment(authzToken, DEFAULT_GATEWAY, deployment));
    String date = (new Date()).toString();
    date = date.replaceAll(" ", "_");
    date = date.replaceAll(":", "_");
    String tempDir = "/N/u/cgateway/BigRed2/sandbox/jobs";
    tempDir = tempDir + File.separator + "Amber";
    client.addGatewayComputeResourcePreference(authzToken, getGatewayResourceProfile().getGatewayID(), host.getComputeResourceId(), DocumentCreatorUtils.createComputeResourcePreference(host.getComputeResourceId(), tempDir, null, false, null, null, null));
    return host.getComputeResourceId() + "," + application.getApplicationInterfaceId();
}

Example 12 with ResourceJobManager

use of org.apache.airavata.model.appcatalog.computeresource.ResourceJobManager in project airavata by apache.

the class DocumentCreatorNew method createPBSDocsForOGCE_WRF.

public String createPBSDocsForOGCE_WRF() throws AppCatalogException, InvalidRequestException, AiravataClientException, AiravataSystemException, TException {
    ComputeResourceDescription host = DocumentCreatorUtils.createComputeResourceDescription(trestleshpcHostAddress, null, null);
    host.addToIpAddresses(trestleshpcHostAddress);
    host.addToHostAliases(trestleshpcHostAddress);
    host.setComputeResourceId(client.registerComputeResource(authzToken, host));
    SSHJobSubmission sshJobSubmission = new SSHJobSubmission();
    ResourceJobManager resourceJobManager = DocumentCreatorUtils.createResourceJobManager(ResourceJobManagerType.PBS, "/opt/torque/bin/", null, null);
    sshJobSubmission.setResourceJobManager(resourceJobManager);
    sshJobSubmission.setSecurityProtocol(SecurityProtocol.GSI);
    sshJobSubmission.setSshPort(22);
    client.addSSHJobSubmissionDetails(authzToken, host.getComputeResourceId(), 1, sshJobSubmission);
    SCPDataMovement scpDataMovement = new SCPDataMovement();
    scpDataMovement.setSecurityProtocol(SecurityProtocol.GSI);
    scpDataMovement.setSshPort(22);
    client.addSCPDataMovementDetails(authzToken, host.getComputeResourceId(), 1, scpDataMovement);
    client.addGatewayComputeResourcePreference(authzToken, getGatewayResourceProfile().getGatewayID(), host.getComputeResourceId(), DocumentCreatorUtils.createComputeResourcePreference(host.getComputeResourceId(), "/oasis/scratch/trestles/ogce/temp_project/", "sds128", false, null, null, null));
    ApplicationModule module2 = DocumentCreatorUtils.createApplicationModule("wrf", "1.0.0", null);
    module2.setAppModuleId(client.registerApplicationModule(authzToken, DEFAULT_GATEWAY, module2));
    ApplicationInterfaceDescription application2 = new ApplicationInterfaceDescription();
    // application2.setIsEmpty(false);
    application2.setApplicationName("WRF");
    application2.addToApplicationModules(module2.getAppModuleId());
    application2.addToApplicationInputs(DocumentCreatorUtils.createAppInput("WRF_Namelist", "WRF_Namelist", null, null, DataType.URI));
    application2.addToApplicationInputs(DocumentCreatorUtils.createAppInput("WRF_Boundary_File", "WRF_Boundary_File", null, null, DataType.URI));
    application2.addToApplicationInputs(DocumentCreatorUtils.createAppInput("WRF_Input_File", "WRF_Input_File", null, null, DataType.URI));
    application2.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("WRF_Output", null, DataType.URI));
    application2.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("WRF_Execution_Log", null, DataType.URI));
    application2.setApplicationInterfaceId(client.registerApplicationInterface(authzToken, DEFAULT_GATEWAY, application2));
    ApplicationDeploymentDescription deployment2 = DocumentCreatorUtils.createApplicationDeployment(host.getComputeResourceId(), module2.getAppModuleId(), "/home/ogce/production/app_wrappers/wrf_wrapper.sh", ApplicationParallelismType.MPI, "WRF");
    deployment2.setAppDeploymentId(client.registerApplicationDeployment(authzToken, DEFAULT_GATEWAY, deployment2));
    return host.getComputeResourceId() + "," + application2.getApplicationInterfaceId();
}

Example 13 with ResourceJobManager

use of org.apache.airavata.model.appcatalog.computeresource.ResourceJobManager in project airavata by apache.

the class DocumentCreatorNew method createSSHHostDocs.

public String createSSHHostDocs() throws AppCatalogException, InvalidRequestException, AiravataClientException, AiravataSystemException, TException {
    ComputeResourceDescription host = DocumentCreatorUtils.createComputeResourceDescription("gw111.iu.xsede.org", null, null);
    host.addToIpAddresses("gw111.iu.xsede.org");
    host.addToHostAliases("gw111.iu.xsede.org");
    host.setResourceDescription("gw111 ssh access");
    host.setComputeResourceId(client.registerComputeResource(authzToken, host));
    SSHJobSubmission jobSubmission = new SSHJobSubmission();
    jobSubmission.setSshPort(22);
    jobSubmission.setSecurityProtocol(SecurityProtocol.SSH_KEYS);
    ResourceJobManager resourceJobManager = DocumentCreatorUtils.createResourceJobManager(ResourceJobManagerType.FORK, null, null, null);
    jobSubmission.setResourceJobManager(resourceJobManager);
    client.addSSHJobSubmissionDetails(authzToken, host.getComputeResourceId(), 1, jobSubmission);
    SCPDataMovement scpDataMovement = new SCPDataMovement();
    scpDataMovement.setSecurityProtocol(SecurityProtocol.SSH_KEYS);
    scpDataMovement.setSshPort(22);
    client.addSCPDataMovementDetails(authzToken, host.getComputeResourceId(), 1, scpDataMovement);
    ApplicationModule module = DocumentCreatorUtils.createApplicationModule("echo", "1.1", null);
    module.setAppModuleId(client.registerApplicationModule(authzToken, DEFAULT_GATEWAY, module));
    ApplicationDeploymentDescription deployment = DocumentCreatorUtils.createApplicationDeployment(host.getComputeResourceId(), module.getAppModuleId(), "/bin/echo", ApplicationParallelismType.SERIAL, "SSHEchoApplication");
    client.registerApplicationDeployment(authzToken, DEFAULT_GATEWAY, deployment);
    ApplicationInterfaceDescription application = new ApplicationInterfaceDescription();
    // application.setIsEmpty(false);
    application.setApplicationName("SSHEcho1");
    application.addToApplicationModules(module.getAppModuleId());
    application.addToApplicationInputs(DocumentCreatorUtils.createAppInput("echo_input", "echo_input", null, null, DataType.STRING));
    application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("echo_output", null, DataType.STRING));
    client.registerApplicationInterface(authzToken, DEFAULT_GATEWAY, application);
    client.addGatewayComputeResourcePreference(authzToken, getGatewayResourceProfile().getGatewayID(), host.getComputeResourceId(), DocumentCreatorUtils.createComputeResourcePreference(host.getComputeResourceId(), "/tmp", null, false, null, null, null));
    return host.getComputeResourceId() + "," + application.getApplicationInterfaceId();
}

Example 14 with ResourceJobManager

use of org.apache.airavata.model.appcatalog.computeresource.ResourceJobManager in project airavata by apache.

the class DocumentCreatorNew method createTrestlesAmberDocs.

public String createTrestlesAmberDocs() throws InvalidRequestException, AiravataClientException, AiravataSystemException, TException, AppCatalogException {
    ComputeResourceDescription host = DocumentCreatorUtils.createComputeResourceDescription(trestleshpcHostAddress, null, null);
    host.addToIpAddresses(trestleshpcHostAddress);
    host.addToHostAliases(trestleshpcHostAddress);
    host.setComputeResourceId(client.registerComputeResource(authzToken, host));
    SSHJobSubmission sshJobSubmission = new SSHJobSubmission();
    ResourceJobManager resourceJobManager = DocumentCreatorUtils.createResourceJobManager(ResourceJobManagerType.PBS, "/opt/torque/bin/", null, null);
    sshJobSubmission.setResourceJobManager(resourceJobManager);
    sshJobSubmission.setSecurityProtocol(SecurityProtocol.GSI);
    sshJobSubmission.setSshPort(22);
    client.addSSHJobSubmissionDetails(authzToken, host.getComputeResourceId(), 1, sshJobSubmission);
    SCPDataMovement scpDataMovement = new SCPDataMovement();
    scpDataMovement.setSecurityProtocol(SecurityProtocol.GSI);
    scpDataMovement.setSshPort(22);
    client.addSCPDataMovementDetails(authzToken, host.getComputeResourceId(), 1, scpDataMovement);
    ApplicationModule amodule = DocumentCreatorUtils.createApplicationModule("Amber", "12.0", null);
    amodule.setAppModuleId(client.registerApplicationModule(authzToken, DEFAULT_GATEWAY, amodule));
    ApplicationInterfaceDescription application = new ApplicationInterfaceDescription();
    application.setApplicationName("AmberTrestles");
    application.addToApplicationModules(amodule.getAppModuleId());
    application.addToApplicationInputs(DocumentCreatorUtils.createAppInput("AMBER_HEAT_RST", "AMBER_HEAT_RST", null, null, DataType.URI));
    application.addToApplicationInputs(DocumentCreatorUtils.createAppInput("AMBER_PROD_IN", "AMBER_PROD_IN", null, null, DataType.URI));
    application.addToApplicationInputs(DocumentCreatorUtils.createAppInput("AMBER_PRMTOP", "AMBER_PRMTOP", null, null, DataType.URI));
    application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("AMBER_Prod.info", null, DataType.URI));
    application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("AMBER_Prod.mdcrd", null, DataType.URI));
    application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("AMBER_Prod.out", null, DataType.URI));
    application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("AMBER_Prod.rst", null, DataType.URI));
    application.setApplicationInterfaceId(client.registerApplicationInterface(authzToken, DEFAULT_GATEWAY, application));
    ApplicationDeploymentDescription deployment = DocumentCreatorUtils.createApplicationDeployment(host.getComputeResourceId(), amodule.getAppModuleId(), "/home/ogce/production/app_wrappers/amber_wrapper.sh", ApplicationParallelismType.SERIAL, "AmberStampede");
    deployment.setAppDeploymentId(client.registerApplicationDeployment(authzToken, DEFAULT_GATEWAY, deployment));
    client.addGatewayComputeResourcePreference(authzToken, getGatewayResourceProfile().getGatewayID(), host.getComputeResourceId(), DocumentCreatorUtils.createComputeResourcePreference(host.getComputeResourceId(), "/oasis/scratch/trestles/ogce/temp_project/", "sds128", false, null, null, null));
    return host.getComputeResourceId() + "," + application.getApplicationInterfaceId();
}

Example 15 with ResourceJobManager

use of org.apache.airavata.model.appcatalog.computeresource.ResourceJobManager in project airavata by apache.

the class GFacEngineImpl method getResourceJobManager.

public static ResourceJobManager getResourceJobManager(ProcessContext processCtx) throws AppCatalogException, GFacException {
    List<JobSubmissionInterface> jobSubmissionInterfaces = Factory.getDefaultAppCatalog().getComputeResource().getComputeResource(processCtx.getComputeResourceId()).getJobSubmissionInterfaces();
    ResourceJobManager resourceJobManager = null;
    JobSubmissionInterface jsInterface = null;
    for (JobSubmissionInterface jobSubmissionInterface : jobSubmissionInterfaces) {
        if (jobSubmissionInterface.getJobSubmissionProtocol() == processCtx.getJobSubmissionProtocol()) {
            jsInterface = jobSubmissionInterface;
            break;
        }
    }
    if (jsInterface == null) {
        throw new GFacException("Job Submission interface cannot be empty at this point");
    } else if (jsInterface.getJobSubmissionProtocol() == JobSubmissionProtocol.SSH) {
        SSHJobSubmission sshJobSubmission = Factory.getDefaultAppCatalog().getComputeResource().getSSHJobSubmission(jsInterface.getJobSubmissionInterfaceId());
        // fixme - Move this to populate process
        processCtx.setMonitorMode(sshJobSubmission.getMonitorMode());
        // context method.
        resourceJobManager = sshJobSubmission.getResourceJobManager();
    } else if (jsInterface.getJobSubmissionProtocol() == JobSubmissionProtocol.LOCAL) {
        LOCALSubmission localSubmission = Factory.getDefaultAppCatalog().getComputeResource().getLocalJobSubmission(jsInterface.getJobSubmissionInterfaceId());
        resourceJobManager = localSubmission.getResourceJobManager();
    } else if (jsInterface.getJobSubmissionProtocol() == JobSubmissionProtocol.SSH_FORK) {
        SSHJobSubmission sshJobSubmission = Factory.getDefaultAppCatalog().getComputeResource().getSSHJobSubmission(jsInterface.getJobSubmissionInterfaceId());
        // fixme - Move this to populate process
        processCtx.setMonitorMode(sshJobSubmission.getMonitorMode());
        resourceJobManager = sshJobSubmission.getResourceJobManager();
    } else if (jsInterface.getJobSubmissionProtocol() == JobSubmissionProtocol.CLOUD) {
        return null;
    } else {
        throw new GFacException("Unsupported JobSubmissionProtocol - " + jsInterface.getJobSubmissionProtocol().name());
    }
    if (resourceJobManager == null) {
        throw new GFacException("Resource Job Manager is empty.");
    }
    return resourceJobManager;
}