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

Example 1 with SSHJobSubmission

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

the class SSHAccountManager method setupSSHAccount.

/**
 * Add SSH key to compute resource on behalf of user.
 * @param gatewayId
 * @param computeResourceId
 * @param userId Airavata user id
 * @param sshCredential
 * @return a populated but not persisted UserComputeResourcePreference instance
 * @throws InvalidSetupException
 * @throws InvalidUsernameException
 */
public static UserComputeResourcePreference setupSSHAccount(String gatewayId, String computeResourceId, String userId, SSHCredential sshCredential) throws InvalidSetupException, InvalidUsernameException {
    // get compute resource preferences for the gateway and hostname
    RegistryService.Client registryServiceClient = getRegistryServiceClient();
    ComputeResourcePreference computeResourcePreference = null;
    ComputeResourceDescription computeResourceDescription = null;
    SSHJobSubmission sshJobSubmission = null;
    try {
        computeResourcePreference = registryServiceClient.getGatewayComputeResourcePreference(gatewayId, computeResourceId);
        computeResourceDescription = registryServiceClient.getComputeResource(computeResourceId);
        // Find the SSHJobSubmission
        for (JobSubmissionInterface jobSubmissionInterface : computeResourceDescription.getJobSubmissionInterfaces()) {
            if (jobSubmissionInterface.getJobSubmissionProtocol() == JobSubmissionProtocol.SSH) {
                sshJobSubmission = registryServiceClient.getSSHJobSubmission(jobSubmissionInterface.getJobSubmissionInterfaceId());
                break;
            }
        }
    } catch (TException e) {
        throw new RuntimeException("Failed to retrieve compute resource information for [" + gatewayId + "] and " + "[" + computeResourceId + "]: " + e.getMessage(), e);
    } finally {
        if (registryServiceClient.getInputProtocol().getTransport().isOpen()) {
            registryServiceClient.getInputProtocol().getTransport().close();
        }
        if (registryServiceClient.getOutputProtocol().getTransport().isOpen()) {
            registryServiceClient.getOutputProtocol().getTransport().close();
        }
    }
    if (sshJobSubmission == null) {
        throw new InvalidSetupException("Compute resource [" + computeResourceId + "] does not have an SSH Job Submission " + "interface.");
    }
    // get the account provisioner and config values for the preferences
    if (!computeResourcePreference.isSetSshAccountProvisioner()) {
        throw new InvalidSetupException("Compute resource [" + computeResourceId + "] does not have an SSH Account Provisioner " + "configured for it.");
    }
    // instantiate and init the account provisioner
    SSHAccountProvisioner sshAccountProvisioner = createSshAccountProvisioner(gatewayId, computeResourcePreference);
    boolean canCreateAccount = SSHAccountProvisionerFactory.canCreateAccount(computeResourcePreference.getSshAccountProvisioner());
    // First check if userId has an account
    boolean hasAccount = false;
    try {
        hasAccount = sshAccountProvisioner.hasAccount(userId);
    } catch (InvalidUsernameException e) {
        throw e;
    } catch (Exception e) {
        throw new RuntimeException("hasAccount call failed for userId [" + userId + "]: " + e.getMessage(), e);
    }
    if (!hasAccount && !canCreateAccount) {
        throw new InvalidSetupException("User [" + userId + "] doesn't have account and [" + computeResourceId + "] doesn't " + "have a SSH Account Provisioner that supports creating accounts.");
    }
    // TODO: create account for user if user doesn't have account
    String username = null;
    // Install SSH key
    try {
        username = sshAccountProvisioner.installSSHKey(userId, sshCredential.getPublicKey());
    } catch (InvalidUsernameException e) {
        throw e;
    } catch (Exception e) {
        throw new RuntimeException("installSSHKey call failed for userId [" + userId + "]: " + e.getMessage(), e);
    }
    // Verify can authenticate to host
    String sshHostname = getSSHHostname(computeResourceDescription, sshJobSubmission);
    int sshPort = sshJobSubmission.getSshPort();
    boolean validated = false;
    try {
        validated = SSHUtil.validate(sshHostname, sshPort, username, sshCredential);
    } catch (Exception e) {
        throw new RuntimeException("Failed to validate SSH public key installation for account for user [" + username + "] on host [" + sshHostname + "]: " + e.getMessage(), e);
    }
    if (!validated) {
        throw new RuntimeException("Failed to validate installation of key for [" + username + "] on [" + computeResourceDescription.getHostName() + "] using SSH Account Provisioner [" + computeResourcePreference.getSshAccountProvisioner() + "]");
    }
    // create the scratch location on the host
    String scratchLocation = sshAccountProvisioner.getScratchLocation(userId);
    try {
        SSHUtil.execute(sshHostname, sshPort, username, sshCredential, "mkdir -p " + scratchLocation);
    } catch (Exception e) {
        throw new RuntimeException("Failed to create scratch location [" + scratchLocation + "] for user [" + username + "] on host [" + sshHostname + "]: " + e.getMessage(), e);
    }
    UserComputeResourcePreference userComputeResourcePreference = new UserComputeResourcePreference();
    userComputeResourcePreference.setComputeResourceId(computeResourceId);
    userComputeResourcePreference.setLoginUserName(username);
    userComputeResourcePreference.setScratchLocation(scratchLocation);
    userComputeResourcePreference.setValidated(true);
    return userComputeResourcePreference;
}

Example 2 with SSHJobSubmission

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

the class DocumentCreatorNew method createStampedeAmberDocs.

public String createStampedeAmberDocs() throws InvalidRequestException, AiravataClientException, AiravataSystemException, TException, AppCatalogException {
    ComputeResourceDescription host = DocumentCreatorUtils.createComputeResourceDescription(stampedeHostAddress, null, null);
    host.addToHostAliases(stampedeHostAddress);
    host.addToIpAddresses(stampedeHostAddress);
    host.setComputeResourceId(client.registerComputeResource(authzToken, host));
    ResourceJobManager resourceJobManager = DocumentCreatorUtils.createResourceJobManager(ResourceJobManagerType.SLURM, "/usr/bin/", null, "push");
    SSHJobSubmission sshJobSubmission = new SSHJobSubmission();
    sshJobSubmission.setResourceJobManager(resourceJobManager);
    sshJobSubmission.setSecurityProtocol(SecurityProtocol.GSI);
    sshJobSubmission.setSshPort(2222);
    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("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(), "/home1/01437/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(), "/home1/01437/ogce", "TG-STA110014S", false, null, null, null));
    return host.getComputeResourceId() + "," + application.getApplicationInterfaceId();
}

Example 3 with SSHJobSubmission

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

the class DocumentCreatorNew method createPBSDocsForOGCE_Echo.

// 
// public void createGramDocs() {
// //        /*
// //           creating host descriptor for gram
// //        */
// //        HostDescription host = new HostDescription(GlobusHostType.type);
// //        host.getType().setHostAddress(trestleshpcHostAddress);
// //        host.getType().setHostName(trestleshpcHostAddress);
// //        ((GlobusHostType) host.getType()).setGlobusGateKeeperEndPointArray(new String[]{gramAddress});
// //        ((GlobusHostType) host.getType()).setGridFTPEndPointArray(new String[]{gridftpAddress});
// //        try {
// //            airavataAPI.getApplicationManager().saveHostDescription(host);
// //        } catch (AiravataAPIInvocationException e) {
// //            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
// //        }
// //
// //
// //        /*
// //        * Service Description creation and saving
// //        */
// //        String serviceName = "SimpleEcho1";
// //        ServiceDescription serv = new ServiceDescription();
// //        serv.getType().setName(serviceName);
// //
// //        List<InputParameterType> inputList = new ArrayList<InputParameterType>();
// //        List<OutputParameterType> outputList = new ArrayList<OutputParameterType>();
// //
// //        InputParameterType input = InputParameterType.Factory.newInstance();
// //        input.setParameterName("echo_input");
// //        ParameterType parameterType = input.addNewParameterType();
// //        parameterType.setType(DataType.STRING);
// //        parameterType.setName("String");
// //
// //        OutputParameterType output = OutputParameterType.Factory.newInstance();
// //        output.setParameterName("echo_output");
// //        ParameterType parameterType1 = output.addNewParameterType();
// //        parameterType1.setType(DataType.STRING);
// //        parameterType1.setName("String");
// //
// //        inputList.add(input);
// //        outputList.add(output);
// //
// //        InputParameterType[] inputParamList = inputList.toArray(new InputParameterType[inputList.size()]);
// //        OutputParameterType[] outputParamList = outputList.toArray(new OutputParameterType[outputList.size()]);
// //
// //        serv.getType().setInputParametersArray(inputParamList);
// //        serv.getType().setOutputParametersArray(outputParamList);
// //        try {
// //            airavataAPI.getApplicationManager().saveServiceDescription(serv);
// //        } catch (AiravataAPIInvocationException e) {
// //            e.printStackTrace();
// //        }
// //
// //        /*
// //            Application descriptor creation and saving
// //         */
// //        ApplicationDescription appDesc = new ApplicationDescription(HpcApplicationDeploymentType.type);
// //        HpcApplicationDeploymentType app = (HpcApplicationDeploymentType) appDesc.getType();
// //        ApplicationDeploymentDescriptionType.ApplicationName name = ApplicationDeploymentDescriptionType.ApplicationName.Factory.newInstance();
// //        name.setStringValue("EchoLocal");
// //        app.setApplicationName(name);
// //        ProjectAccountType projectAccountType = app.addNewProjectAccount();
// //        projectAccountType.setProjectAccountNumber("sds128");
// //
// //        QueueType queueType = app.addNewQueue();
// //        queueType.setQueueName("normal");
// //
// //        app.setCpuCount(1);
// //        app.setJobType(JobTypeType.SERIAL);
// //        app.setNodeCount(1);
// //        app.setProcessorsPerNode(1);
// //
// //        /*
// //           * Use bat file if it is compiled on Windows
// //           */
// //        app.setExecutableLocation("/bin/echo");
// //
// //        /*
// //           * Default tmp location
// //           */
// //        String tempDir = "/home/ogce/scratch";
// //        app.setScratchWorkingDirectory(tempDir);
// //        app.setMaxMemory(10);
// //
// //
// //        try {
// //            airavataAPI.getApplicationManager().saveApplicationDescription(serviceName, trestleshpcHostAddress, appDesc);
// //        } catch (AiravataAPIInvocationException e) {
// //            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
// //        }
// }
// 
public String createPBSDocsForOGCE_Echo() 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);
    ApplicationModule module1 = DocumentCreatorUtils.createApplicationModule("echo", "1.2", null);
    module1.setAppModuleId(client.registerApplicationModule(authzToken, DEFAULT_GATEWAY, module1));
    ApplicationInterfaceDescription application = new ApplicationInterfaceDescription();
    // application.setIsEmpty(false);
    application.setApplicationName("SimpleEcho2");
    application.addToApplicationModules(module1.getAppModuleId());
    application.addToApplicationInputs(DocumentCreatorUtils.createAppInput("echo_input", "echo_input", "echo_input", null, DataType.STRING));
    application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("echo_output", null, DataType.STRING));
    application.setApplicationInterfaceId(client.registerApplicationInterface(authzToken, DEFAULT_GATEWAY, application));
    ApplicationDeploymentDescription deployment = DocumentCreatorUtils.createApplicationDeployment(host.getComputeResourceId(), module1.getAppModuleId(), "/home/ogce/echo.sh", ApplicationParallelismType.SERIAL, "Echo application");
    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 4 with SSHJobSubmission

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

the class DocumentCreatorNew method createSlurmDocs.

public String createSlurmDocs() throws AppCatalogException, InvalidRequestException, AiravataClientException, AiravataSystemException, TException {
    ComputeResourceDescription host = DocumentCreatorUtils.createComputeResourceDescription(stampedeHostAddress, null, null);
    host.addToHostAliases(stampedeHostAddress);
    host.addToIpAddresses(stampedeHostAddress);
    host.setComputeResourceId(client.registerComputeResource(authzToken, host));
    ResourceJobManager resourceJobManager = DocumentCreatorUtils.createResourceJobManager(ResourceJobManagerType.SLURM, "/usr/bin/", null, "push");
    SSHJobSubmission sshJobSubmission = new SSHJobSubmission();
    sshJobSubmission.setResourceJobManager(resourceJobManager);
    sshJobSubmission.setSecurityProtocol(SecurityProtocol.GSI);
    sshJobSubmission.setSshPort(2222);
    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 module = DocumentCreatorUtils.createApplicationModule("echo", "1.3", null);
    module.setAppModuleId(client.registerApplicationModule(authzToken, DEFAULT_GATEWAY, module));
    ApplicationInterfaceDescription application = new ApplicationInterfaceDescription();
    // application.setIsEmpty(false);
    application.setApplicationName("SimpleEcho3");
    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));
    application.setApplicationInterfaceId(client.registerApplicationInterface(authzToken, DEFAULT_GATEWAY, application));
    ApplicationDeploymentDescription deployment = DocumentCreatorUtils.createApplicationDeployment(host.getComputeResourceId(), module.getAppModuleId(), "/bin/echo", ApplicationParallelismType.SERIAL, "EchoLocal");
    deployment.setAppDeploymentId(client.registerApplicationDeployment(authzToken, DEFAULT_GATEWAY, deployment));
    client.addGatewayComputeResourcePreference(authzToken, getGatewayResourceProfile().getGatewayID(), host.getComputeResourceId(), DocumentCreatorUtils.createComputeResourcePreference(host.getComputeResourceId(), "/home1/01437/ogce", "TG-STA110014S", false, null, null, null));
    return host.getComputeResourceId() + "," + application.getApplicationInterfaceId();
}

Example 5 with SSHJobSubmission

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

the class DocumentCreatorNew method createSlumWRFDocs.

public String createSlumWRFDocs() throws AppCatalogException, TException {
    ComputeResourceDescription host = DocumentCreatorUtils.createComputeResourceDescription(stampedeHostAddress, null, null);
    host.addToHostAliases(stampedeHostAddress);
    host.addToIpAddresses(stampedeHostAddress);
    host.setComputeResourceId(client.registerComputeResource(authzToken, host));
    ResourceJobManager resourceJobManager = DocumentCreatorUtils.createResourceJobManager(ResourceJobManagerType.SLURM, "/usr/bin/", null, "push");
    SSHJobSubmission sshJobSubmission = new SSHJobSubmission();
    sshJobSubmission.setResourceJobManager(resourceJobManager);
    sshJobSubmission.setSecurityProtocol(SecurityProtocol.GSI);
    sshJobSubmission.setSshPort(2222);
    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.addSCPDataMovementDetails(authzToken, host.getComputeResourceId(), 1, scpDataMovement);
    client.addGatewayComputeResourcePreference(authzToken, getGatewayResourceProfile().getGatewayID(), host.getComputeResourceId(), DocumentCreatorUtils.createComputeResourcePreference(host.getComputeResourceId(), "/home1/01437/ogce", "TG-STA110014S", 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(), "/home1/01437/ogce/production/app_wrappers/wrf_wrapper.sh", ApplicationParallelismType.MPI, "WRF");
    deployment2.setAppDeploymentId(client.registerApplicationDeployment(authzToken, DEFAULT_GATEWAY, deployment2));
    return host.getComputeResourceId() + "," + application2.getApplicationInterfaceId();
}