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The central management piece for each KNSG application is KNSGFrame, an extension of BardFrame that registers tupelo utility methods for CETBeans used by the KNSG framework. In For the remainder of this document , we will will use the name term BardFrame since our extension (KNSGFrame) only overrides the method for registering beans, the rest is the same. BardFrame provides an interface for working with the Tupelo semantic content repository and is responsible for managing contexts, bean sessions, data, firing events, etc. The use of Tupelo beans will be a core concept for persisting information in the KNSG framework so all beans will need to descend from CETBean to remain compatible with the framework and other CET projects. Because every application will have its own bean requirements, each KNSG application should have its own instance of BardFrame to handle this as well as along with an ontology to define domain specific concepts. All application bean types should register with BardFrame and the IBardFrameService should provide the correct instance of BardFrame at runtime.

Tupelo Beans

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These are This section outlines the bean classes that will be required for the KNSG framework. Where possible, the core CETBeans will be used to minimize the work required and maximize compatibility across projects. Some beans will be marked optional if they are part of PTPFlow and if it is uncertain that they will be managed by Tupelo or continue to be managed by PTPFlow's current repository.

Scenario Bean

A scenario bean will be used to organize things such as user data and workflows specific to a scenario (or project). This will include datasets (input and output), workflows, and possibly the RMI service for launching jobs. A snippet of what the scenario bean might look like is below:

private String title;  // scenario title
private String description;  // scenario description
private Date date = new Date();  // date scenario created
private PersonBean creator;  // scenario creator
private Set<DatasetBean> dataSets;  // datasets associated with scenario
private List<WorkflowBean> workflows;  // workflows associated with this scenario, if possible, this needs to be able to wrap ptpflow workflow xml files, or we need our own bean type

This scenario bean will evolve as the application framework is built and more final documentation will be put here as the design matures. The main parts of this bean are: DatasetBean's will be used to manage all of the input/output datasets and the WorkflowBean List will contain the workflows associated with this scenario. A user might extend the ScenarioBean if their application has other things that logically belong to their scenarios, but this is unlikely. Most changes will happen at the metadata level (e.g. this dataset is a mesh, a result, etc).

Dataset Bean

This section is intended to talk about the types of concepts that the Ontology needs to capture. We will break this into two parts: general framework concepts (e.g. result) and eAIRS specific (e.g. mesh). We don't anticipate any changes to the DatasetBean class that is provided as part edu.uiuc.ncsa.cet.bean plug-in.

WorkflowBean & WorkflowStepBean

Below you will find an example of a PTPFlow workflow.xml file. This file cannot be altered since it is understood by PTPFlow and outlines the steps in the workflow including which resource to run on, executables that will be launched, input files to use, etc. Ideally, this file would be wrapped into the current WorkflowBean and/or WorkflowStepBean in the edu.uiuc.ncsa.cet.bean plug-in. If this is not possible, the KNSG framework will need its own workflow bean.

If a bean is from the set of beans provided by edu.uiuc.ncsa.cet.bean it will be noted so we differentiate between new beans for KNSG and the use of existing beans (e.g. the ScenarioBean below is new, but has the same name as the scenario bean in edu.uiuc.ncsa.cet.bean).

Scenario Bean

A scenario bean will be used to organize things such as user data and workflows specific to a scenario (or project). This will include datasets (input and output), workflows, and possibly the RMI service for launching jobs. The RMI service was previously part of the scenario, but since this is a system wide object, it will probably not be tracked as part of the scenario in version 2.0. A snippet of what the scenario bean might look like is below:

private String title;  // scenario title
private String description;  // scenario description
private Date date = new Date();  // date scenario created
private PersonBean creator;  // scenario creator
private Set<DatasetBean> dataSets;  // datasets associated with scenario
private List<WorkflowBean> workflows;  // workflows associated with this scenario, if possible, this needs to be able to wrap ptpflow workflow xml files, or we need our own bean type
private List<VisualizationBean> visualizations; // it is possible in the future that visualizations might be part of a scenario so we know which datasets/tools are required to generate visualizations

While this bean looks very similar to the ScenarioBean in the cet bean plug-in, it is unclear if some of the internal bean types will match what is required for eAIRS/KNSG (e.g. the workflow bean, the visualization bean). As the scenario bean evolves, it will become more clear whether we can replace our bean with the one in the cet bean plug-in. More final documentation will be put here as this design matures.

The main parts of this bean are: DatasetBean's will be used to manage all of the input/output datasets and the WorkflowBean List will contain the workflows associated with this scenario. A user might extend the ScenarioBean if their application has other things that logically belong to their scenarios, but it is envisioned that most changes will happen at the metadata level (e.g. this dataset is a mesh, a result, etc) since the scenario bean should be a generic container that satisfies most users needs.

Dataset Bean

This section is intended to talk about the types of concepts that the Ontology needs to capture. We will break this into two parts: general framework concepts (e.g. a result) and eAIRS specific (e.g. a mesh). We don't anticipate any changes to the DatasetBean class that is provided as part edu.uiuc.ncsa.cet.bean plug-in.

WorkflowBean & WorkflowStepBean

Below you will find an example of a PTPFlow workflow.xml file. Right now, this file cannot be altered since it is understood by PTPFlow and outlines the steps in the workflow including which resource to run on, executables that will be launched, input files to use, etc. Ideally, this file would be wrapped into the current WorkflowBean and/or WorkflowStepBean in the edu.uiuc.ncsa.cet.bean plug-in. If this is not possible, the KNSG framework will need its own workflow bean.

<workflow-builder name="eAIRS-Single" experimentId="singleCFDWorkflow" eventLevel="DEBUG">
  <!-- <global-resource>grid-abe.ncsa.teragrid.org</global-resource> -->
  <global-resource></global-resource>
  <scheduling>
    <profile name="batch">
      <property name="submissionType">
        <value>batch</value>
      </property>
    </profile>
  </scheduling>
  <execution>
     <profile name="mesh0">

<workflow-builder name="eAIRS-Single" experimentId="singleCFDWorkflow" eventLevel="DEBUG">
  <!-- <global-resource>grid-abe.ncsa.teragrid.org</global-resource> -->
  <global-resource></global-resource>
  <scheduling>
    <profile name="batch">
      <property name="submissionType">
        <value>batch</value>
      </property>
    </profile>
  </scheduling>
  <execution>
     <profile name="mesh0">
     	 <property name="RESULT_LOC">
     	 	<value>some-file-uri</value>
     	 </property>
     	 <property name="executableRESULT_LOC">
     	 	<value>some-file-uri</value>
     	 </property>
        	 <property name="meshTypeexecutable">
     	      	<value>some-file-uri</value>
     	 </property>
         <property name="meshType">
           <value>some-file-uri</value>
         </property>
         <property name="inputParam">
           <value>some-file-uri</value>
         </property>
     </profile>
  </execution>
  <graph>
    <execute name="compute0">
      <scheduler-constraints>batch</scheduler-constraints>
      <execute-profiles>mesh0</execute-profiles>
      <payload>2DComp</payload>
    </execute>
  </graph>
  <scripts>
    <payload name="2DComp" type="elf">
      <elf>
        <serial-scripts>
          <ogrescript>
            <echo message="Result location = file:${RESULT_LOC}/${service.job.name} result directory is file:${runtime.dir}/result, copy target is file:${RESULT_LOC}/${service.job.name}"/>
            <simple-process execution-dir="${runtime.dir}" out-file="cfd.out" >
              <command-line>${executable} -mesh ${meshType} -param ${inputParam}</command-line>
             <!-- <command-line>${runtime.dir}/2D_Comp-2.0 -mesh ${meshType} -param ${inputParam}</command-line> -->
            </simple-process>
            <mkdir>
            	<uri>file:${RESULT_LOC}/${service.job.name}</uri>
            </mkdir>
            <copy sourceDir="file:${runtime.dir}/result" target="file:${RESULT_LOC}/${service.job.name}"/>
          </ogrescript>
        </serial-scripts>
      </elf>
    </payload>
  </scripts>
</workflow-builder>

RMIService Info Bean (optional)

The information about each service installation will be stored in an RMIServiceBean and will be used to launch and start the service. All of this information is currently used in PTPFlow and is stored in xml files. Bringing in tupelo to the service stack will allow us to store this information in tupelo.

// Service Info
private String name;
private String platform;
private String deployUsingURI;  // e.g. file:/
private String launchUsingURI;
private String installLocation;  // e.g. /home/user_home/ptpflow
private String rmiContactURI;
private int rmiPortLowerBound;
private int rmiPortUpperBound;
private int gridftpPortLowerBound;
private int gridftpPortUpperBound;
private Date installedDate;
private boolean running;
private Set<HostResourceBean> knownHosts;  // all of the known hosts associated with this service

Known Host Bean (optional)

Below is the bean structure that is anticipated:

A HostResourceBean defines the hpc host and its properties.

_LOC}/${service.job.name}</uri>
            </mkdir>
            <copy sourceDir="file:${runtime.dir}/result" target="file:${RESULT_LOC}/${service.job.name}"/>
          </ogrescript>
        </serial-scripts>
      </elf>
    </payload>
  </scripts>
</workflow-builder>

RMIService Bean (optional)

PTPFlow's RMI Service is the service that manages the execution of PTPFlow workflows and records event information. It is the service through which clients communicate to find the status of their workflows. This information could be managed by Tupelo (at some future date) using an RMIServiceBean. This information is currently stored in xml files and managed by PTPFlow's repository system.

// Service Info
private String name;
private String platform;
private String deployUsingURI;  // e.g. file:/
private String launchUsingURI;
private String installLocation;  // e.g. /home/user_home/ptpflow
private String rmiContactURI;
private int rmiPortLowerBound;
private int rmiPortUpperBound;
private int gridftpPortLowerBound;
private int gridftpPortUpperBound;
private Date installedDate;
private boolean running;
private Set<HostResourceBean> knownHosts;  // all of the known hosts associated with this service

Host Resource Bean (optional)

Below is the bean structure that is anticipated:

A HostResourceBean defines the hpc host and its properties.

private String osName;  // host os name
private String osVersion; // host os version
private String architecture; // host architecture
private String id; // host id
private Set<PropertyBean> envProperties;  // environment properties on host
private Set<NodeBean> nodes;  // properties of each node
private Set<UserPropertyBean> users;  // user properties on the host - userHome, userNameOnHost, userName

A NodeBean defines an HPC nodes properties such as the protocols used and nodeId.

private String osNamenodeId;  // hostid osof name
private String osVersion; // host os version
private String architecture; // host architecture
private String id; // host id
private Set<PropertyBean> envProperties;  // environment properties on host
private Set<NodeBean> nodes;  // properties of each node
private Set<UserPropertyBean> users;  // user properties on the host - userHome, userNameOnHost, userName

A NodeBean defines an HPC nodes properties such as the protocols used and nodeId.

private String nodeId;  // id of the node, e.g. grid-abe.ncsa.teragrid.org
private List<FileProtocolBean> fileProtocols;
private List<BatchProtocolBean> batchProtocols;
private List<InteractiveProtocolBean> interactiveProtocols;

A UserPropertyBean defines the users properties on the host

private String userHome;
private String userName;
private String userNameOnHost;

Metadata Requirements

General Framework Metadata

What we need to capture:

• Is this dataset a result or output dataset?
• Is this dataset an input dataset?

the node, e.g. grid-abe.ncsa.teragrid.org
private List<FileProtocolBean> fileProtocols;
private List<BatchProtocolBean> batchProtocols;
private List<InteractiveProtocolBean> interactiveProtocols;

A UserPropertyBean defines the users properties on the host

private String userHome;
private String userName;
private String userNameOnHost;

Metadata Requirements

This is a list of information we would like to capture with Tupelo using an ontology that is built by NCSA and KISTI (note that KISTI has not provided input on the domain concepts they would like captured).

General Framework Metadata

What we need to capture:

• Is this dataset a result or output dataset?
• Which workflow created this dataset?
• Is this dataset an input dataset?
• Who imported the dataset and when was it imported
• What tags and annotations are associated with the dataset

//Namespace for KNSG
public static final String NS = "http://cet.ncsa.illinois.edu/2011/";

// KNSG Scenario
public static final Resource SCENARIO = newResourceSuffix("/knsg/scenario/KNSGScenario");
public static final Resource HAS_DATA = newResourceSuffix("/knsg/scenario/hasData");

eAIRS Metadata

What we need to capture:

• Is this dataset an eAirs mesh (*.msh)?
• Is this dataset an eAirs input file (*.inp)
• Result files: coefhist.rlt, error.rlt, result.rlt, time.rlt, cp.rlt, force_com.rlt, result.vtk. We should capture enough information to know what each of these files represent as far as outputs (need input from KISTI).

Mime types of the files that are outputs from the eAIRS workflowassociated with the eAIRS workflow

• Input
  • .inp
  • .msh
• Output
  • .rlt
  • .vtk

Views

Scenarios View

A primary view provided by the KNSG framework will be the ScenariosView that displays user scenario(s) and all sub-parts (most likely in some kinda of Tree viewer). A scenario is similar to the concept of a project and is simply a way of organizing things that belong together. The scenario is responsible for managing all of the pieces that it contains including input datasets, output datasets and workflows. Users will be able to launch jobs on available HPC machines through an RMI Service (provided by PTPFlow) that use the inputs in their scenario and when a project completes, the outputs should be added back to that scenario, possibly through a thread that is polling the Tupelo server for new data). A user can have multiple scenarios open at once, close scenarios, or even delete scenarios from their scenario view (deleted from the view, but still in the repository) so we'll need to manage which scenarios are in a session and possibly what is their current state (open/closed). It is anticipated that new applications might extend this view to organize their view differently for their specific domain (e.g. use different icons, possibly organize data into different categories, etc).

RMI Service Registry View

This view shows all of the machines defined as available to the user for installing the RMI service and PTPFlow plugins required to run HPC jobs and return status information to the client. Below you will see a partial specification for what an RMI Service stored as a tupelo bean might look like. This is not a requirement for version 2.0.

Datasets View

Most of the views in the framework will display data stored either by Tupelo or the current PTPFlow Repository. Instead of a single repository view showing everything, there will be multiple views (similar to Medici/Cyberintegrator) that are configured to show a particular type of bean(s) coming from a content provider. The content provider would get the data required from the configured tupelo context. For example, we will need a "Dataset View" that shows all datasets (e.g. input/output datasets) and a way to manipulate them (e.g. add tags, annotations, etc), "Workflow view" that shows all of the workflows that have been ran, "Scenarios View" that shows all scenarios (probably sorted by current user/all users), "Service Registry View" that shows defined RMI service endpoints for launching jobs, and a "Known Hosts View" for showing known hosts that can accept jobs. The last two will be provided by PTPFlow's repository if those PTPFlow objects are not stored in a tupelo context. Each of the views described below that use tupelo beans will extend BardFrameView since the BardFrame will be required to get the information required for each view.

Scenarios View

A primary view provided by the KNSG framework will be the ScenariosView that displays user scenario(s) and all sub-parts (most likely in some kinda of Tree viewer). A scenario is similar to the concept of a project and is simply a way of organizing things that belong together. The scenario is responsible for managing all of the pieces that it contains including input datasets, output datasets and workflows. Users will be able to launch jobs on available HPC machines through an RMI Service (provided by PTPFlow) that use the inputs in their scenario and when a project completes, the outputs should be added back to that scenario, possibly through a thread that is polling the Tupelo server for new data). A user can have multiple scenarios open at once, close scenarios, or even delete scenarios from their scenario view (deleted from the view, but still in the repository) so we'll need to manage which scenarios are in a session and possibly what is their current state (open/closed). The idea of open/closed scenarios is open for debate about whether that is useful to track or if it doesn't matter since no data would be pulled unless a user selected or expanded a scenario. It is anticipated that new applications might extend this view to organize their view differently for their specific domain (e.g. use different icons, possibly organize data into different categories defined by their ontology, etc).

RMI Service Registry View

This view shows all of the machines defined as available to the user for installing the RMI service and PTPFlow plugins required to run HPC jobs and return status information to the client. Below you will see a partial specification for what an RMI Service stored as a tupelo bean might look like. This is not a requirement for version 2.0.

Datasets View

This view will display the datasets that are stored in the tupelo context that the system is connected to. Users should be able to import/export datasets from this view, tag datasets, annotate datasets, etcThis view will display the datasets that are stored in the tupelo context that the system is connected to. Users should be able to import/export datasets from this view, tag datasets, etc.
Rather than a single repository view, this will be multiple views that are configured to show a particular type of bean(s) coming from a content provider. The content provider would get the data required from the configured tupelo context(s). For example, we will need a "Dataset Repository View" that shows all datasets (e.g. input/output datasets) and a way to manipulate them (e.g. add tags, annotations, etc), "Workflow Repository View" that shows all imported workflows, "Scenario Repository View" that shows all saved scenarios, "Service Repository View" that shows defined RMI service endpoints for launching jobs, and a "Known Hosts View" for showing known hosts that can accept jobs. This seems like too much disparate information to display in a single view. All Repository views will descend from BardFrameView since the BardFrame will be required to get the data required for each view.

Functional Requirements

1. Import datasets that will be used as input to HPC workflows such as Mesh files, input files (e.g. mach number, poisson ratio, etc)
2. Store output datasets from workflow runs, some workflows will be parameterized and have multiple outputs
3. Export datasets
4. Dataset tagging, Annotation, etc
5. Other functionality?

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The analysis framework will allow users to register HPC workflows, modify the workflow inputs through a graphical user interface, and execute HPC jobs when all inputs are satisfied. The UI will need information from the metadata to determine if an input is valid for the field (e.g. this field needs a mesh).