Apache Airavata

 Introduction to PHP Reference Gateway

PHP Reference gateway is the interface developed by the Airavata team for demonstration purposes and also for interested science communities to work with. This guide provides step-by-step information on obtaining a complete science gateway experience for science and scholarly communities using Airavata as a middleware platform. Here we also discuss main features and services provided for gateway communities via Airavata.

End of the tutorial you will know;

  • How to create and activate user account in the gateway.

  • How to create and modify projects

  • How to create, execute and monitor, etc... experiments.

  • How to communicate your issues, feedback, and request.

For more details on Airavata please visit Airavata site

Test/Demo Environment Details

  1. PHP Reference Gateway link;
    https://testdrive.airavata.org/
  2. Download application sample input files from;
    https://cwiki.apache.org/confluence/display/AIRAVATA/XSEDE14+Gateway+Tutorial+Application+Input+Files+and+Parameters 

Tutorial I - Gateway Login

Create Account or Use CILogon

  1. Create a user account or use CILogon using 'Create Account' on the home page.
  2. For account creation,
    1. Account creation page link:https://testdrive.airavata.org/create
    2. Please enter the required information and submit.
    3. Important;
      1. Username cannot have spaces.
      2. Username cannot be an email address.
      3. Username & password must be longer than 5 characters.
      4. The password is case sensitive.
      5. All the mandatory fields indicated by a star; *.
  3. Users could use CILogon and get access to the gateway through using campus credential or Gmail account.
  4. Account activation;
    1. The user will receive an email upon creating the account to provided email to confirm the creation. Follow the instructions and login to the gateway using the username and password.
    2. Once the account is confirmed gateway admin has to provide gateway access after validating the user account.
    3. The user will be notified gateway access via email.
       

Login to Account

  1. Once the account is created or CILogon is used successfully, then access will be granted to login to the gateway through 'Log In' link in the home page.
    1.  Link: https://testdrive.airavata.org/login

Password Recovery

  1. Gateway user can recover the forgotten password using '(Forgot Password? Click here)' link in the login page.
  2. When the username is submitted user will receive an email to the email box linked to the username.
  3. The email will have instructions on changing the password.

Tutorial II - Create & Search Projects

Create Project

  1. 'Projects' in the gateway is simply a grouping of experiments with sharing capability. 
  2. Every user will have a pre-created 'Default Project'.
  3. To create Projects navigate to ‘Project → Create’ from the main menu. Mandatory fields indicated by star; *.
  4. When creating the project user has the option of sharing it with other gateway users. Simply navigate to sharing window using 'Share with Other Users'. Here search users by their email, name or username and share.
    1. When sharing can give read or write access.
    2. Read access: They can only view, clone and download files of the experiment within the project.
    3. Write access: Users can clone, edit, launch or cancel the experiment. When cloning can use the primary owner's project as well.
    4. When the project is shared with a user cannot remove that sharing at experiment level from the user.
    5. By editing the project users can modify sharing statuses as well.
  5. The user is directed to Project Summary page upon successful creation of the project. A project shared users will also be listed with their access level in the project summary.

Search Projects

  1. To browse existing projects, 'Project → Browse' from the main menu.
  2. In the project list, projects shared by other users will also be listed. Depending on the access given you would be able to either just view or edit the project.
    <add project list image with shared projects>
  3. Search keys are;
    1. Project Name
    2. Project Description
  4. After selecting the search key, the user has to give a value to search using the selected key.
  5. All the Projects will be listed with pagination. By clicking ‘View’ at the end of the row user can navigate to ‘Project Summary’ page. 
  6. The user can also search using (*) as a wild character. 
  7. Project summary will list all the experiments within the project.
  8. To edit the project use the 'pen' icon on project summary. 

Tutorial III - Create & Launch Experiment

Create Experiment

  1. To create an experiment navigate to Experiment → Create from the main menu.
  2. The user needs to enter/select given fields in order to continue.
    1. Experiment Name (Mandatory)
    2. Experiment Description (Optional)
    3. Project (Select from the available LOV)
    4. Application (Select from the available LOV)
    and click ‘Continue’ button. At this point, the user can restart by clicking ‘Reset Values’.
  3. By using 'Share with other Users' can share this experiment with other users. If the project used in the experiment is already shared with users, the shared users will be displayed here.
    1. When sharing can either provide read or write access to the experiment.
    2. Search for users using the username, name or email.
  4. Then continue entering application configuration information.
    1. Experiment application input - Application input can be in the form of entering data or uploading a single or multiple files.
      NOTE: Uploading file content validity is not checked by the gateway. The user is responsible for uploading correct files.
    2. If defined in the application interface the experiment might have the possibility of uploading 'Optional Inputs'. Here the user has the option of using or not using and also can upload single or multiple optional input files.
    3. The compute resource (select from the available LOV. If the application is existing in a single resource, it will be the default value)
      1. When the compute resource is selected, if the user has an own allocation in the particular resource and if it's configured in the gateway a checkbox with 'use my own allocatiobn' will be selected by default.
    4. Queue (a default value will be taken if not changed by the user)
    5. Node Count (If not entered default value will be taken as the input)
    6. Total Core Count (If not entered default value will be taken as the input)
    7. Wall Time Limit (If not entered default value will be taken as the input)
    8. Total Physical Memory (If not entered the default value 0 will be taken as the input)
  5. For some compute resources default values in e, f and g will not be accurate, in such cases the user needs to change the node count in such cases.
  6. While entering application configurations user can start over from the beginning using ‘Start Over’ button.
  7. Once saved or saved and launched user will be directed to ‘Experiment Summary’ page. The summary page is auto-refreshing to update and display current status when the experiment is in progress. 

Launch Experiment

  1. The user can launch an experiment just after creating it or launch previously saved from 'Experiment Summary' Page. 
  2. Experiments can be accessed through 'Experiment → Browse' or 'Project →Browse →View Project' pages.
  3. If the experiment is not supposed to launch e.g.: a COMPLETED, LAUNCHED experiment, then the launch button will be disabled.

Tutorial IV - Browse Experiments

  1. User can search for experiment created by him/her and once shared with them through

    1. Experiments → Browse

    2. Projects → Browse → View Project → View Experiment (by clicking on the name of the experiment) - Please refer 'Search Projects' in Tutorial II above.

  2. Search keys are;

    1. Experiment Name

    2. Experiment Description

    3. Application

    4. Creation Time

  3. All the experiments of the user and the shared ones will be listed; latest on top. The user can also search specifically for experiments using a search key. Can use partial values, complete values, (*) wildcard to search.

  4. The user can combine one of the above search keys with experiment status to search experiments.

  5. By clicking on the 'Status' user will be navigated to ‘Experiment Summary’ screen of each experiment.

  6. In experiment summary users can;

    1. Launch experiment - Explained in above Tutorial III

    2. Cancel experiment

    3. Clone experiment

    4. Edit experiment

    5. Share experiment

Tutorial V - Edit, Cancel, Clone & Share Experiments

Edit Experiment

  1. Edit experiment by clicking on the edit icon (pen) next to experiment name OR by clicking on ‘Edit’ button in Experiment Summary Page.

  2. The user can modify all available fields except project, experiment status, application & experiment ID.  

  3. The user can only edit experiments in CREATED status.

  4. After editing user can either save for later launch or save and launch at the same time.

Cancel Experiment 

  1. Experiments can be canceled by navigating to 'Experiment Summary’ screen.
  2. Experiments can be canceled with statuses;
    1. LAUNCHED
    2. EXECUTING
    3. SCHEDULED
  3. Click on ‘Cancel’ button and the experiment status will change to CANCELING.
  4. If the job is already COMPLETED in the resource the job will proceed to COMPLETE and upon completing the experiment status will change to CANCELED. 
  5. If the output is already transferred to gateway they will be available even when the experiment is canceled. But if the outputs were not transferred they will not be available for the user since the cancellation was initiated by the user.
  6. If the job was successfully CANCELED upon changing the job state to CANCELED experiment status will also change to CANCELED.
  7. CANCELED experiments are only available to clone.

Clone Experiment

  1. Experiments can be cloned irrespective of the experiment status by clicking ‘Clone’ in ‘Experiment Summary’ page.
  2. When cloned the user will be navigated to ‘Edit Experiment’ page of the new experiment. The new experiment will have exact same information as the earlier existing experiment.   
  3. The new experiment will have a new experiment ID and the status will always be CREATED.
    New experiment name = Clone of + Old experiment name
  4. The user can change existing information (except the project and application) in ‘Edit Experiment’ page and save or save & launch. 

Share Experiment

  1. The user can share the experiment at creation or at any stage of the experiment from experiment summary page.
  2. Owner can share the experiment with 'READ' or 'WRITE' access
  3. When shared with 'READ' access, shared user can
    1. View the experiment.
    2. Clone and create a new one using one of the own projects.
    3. Download both input and output files.
  4. When shared with write access, shared user can
    1. View the experiment.
    2. Edit, launch and cancel the experiment.
    3. Clone and create a new one using one of the own projects OR with one of the original owner's projects ( To use someone else's project to create an experiment need to have write access to the project).
    4. Download both input and output files.
  5. With 'READ' or 'WRITE' access shared users cannot change the owners 'Shared User's list. Only the owner can change the 'Shared Users' list.
  6. Shared experiments are available in Experiment → Browse.

Tutorial VI - User Settings

User settings are to add user's own allocation account details and storage details into the gateway. Gateway user can provide their resource allocation details and also add an SSH key for secure communication.

Compute Resource

  1. Users can select the compute resource which they have an allocation and enter details.
  2. Can use the default credential store key generated by the system or can generate new keys and assign.

Storage Resource

Credential Store

 

 

Tutorial VII - User Assistance

Contact Gateway Administrator

  1. Gateway users can contact gateway admins to; 

    1. Report an issue
    2. Request a feature
    3. Suggest improvements
    4. Request for an Application
    5. Seek assistance
  2. To make these requests to gateway admin use the email address provided in 'Contact Us' in home page. 

 

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For an overview of Apache Airavata visit the Website - https://airavata.apache.org/