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Overview

This is the parent page for information on the iPlant Collaborative Research Environment.  iPlant provides computational resources for biological researchers.  iPlant is not strictly limited to plant genomics research.

Major components of interest to users include the following:

  • Discovery Environment - Condor-driven canned applications
  • Atmosphere - similar to Amazon EC2 - discrete virtual machine (VM) instances
  • Data Store - personal data storage - keep private, or share publicly or with limited set of collaborators

Basic User Account

A basic user account entitles the user to access most of the computational services of iPlant, with the exception of the "Atmosphere".  To gain access to Atmosphere, submit a request with a brief statement of research intentions.  Approval is generally granted the same day.

User accounts are afforded the following initial resources:

  • 100GB of storage on the Data Store
  • Access to run jobs in the Discovery Environment
  • The ability to create "apps" which are based-upon existing bioinformatics tools
  • 168 Atmosphere Units (AUs) - 1 cpu hour is equivalent to 1 AU
  • Maximum 16 processing cores (SandyBridge) in the Atmosphere
  • Maximum 128GB of RAM in the Atmosphere
  • 1.2 TB of storage per Atmosphere VM instance
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Due to the prodigious use of Java by iPlant, it is strongly recommended that users access the site using the Firefox browser. Chrome, Safari, and other browsers often lack the Java support to make certain portions of the site accessible.

Basic information on accessing iPlant, moving data, and utilizing its various resources are summarized in a brief one-page cheatsheet.

Data Store

Users are provided with 100GB initially of storage space as part of the iPlant Data Store.  Data Stores are accessible from any iPlant resource, such as the Discovery Environment (DE) or Atmosphere.  In the former case, the Data Store may be accessed at the time applications are selected via an intuitive browser-based user interface.  For Atmosphere, the Data Store must be "connected" and mounted to the Atmosphere instance in order to be accessible.

Data Stores may be shared with collaborators with an iPlant account, either through the DE or via a URL.  Both the DE and Atmosphere are discussed in the following sections in greater detail.

For more information on connecting the Data Store to an Atmosphere instance, please read the wiki page on Data Store Connection to Atmosphere.

If you are configuring your own Atmosphere Instance, please first refer to Atmosphere Configuration for Data Store before attempting to establish a Data Store connection.

 

Data can be moved directly between the HPCC and the iPlant Data Store by following these instructions on using iCommands

Atmosphere 

The iPlant "Atmosphere" enables users to create customized virtual machine (VM) instances from existing templates, and to customize those instances to fit their needs.  Customized instances may be "imaged" (saved) by submitting a ticketing request to iPlant staff.  Imaging requests are generally approved in a couple of hours, and the saved image can be located for subsequent uses by entering the saved image name into the search box that is available after signing into Atmosphere, and clicking the "launch" icon.

Tested and confirmed capabilities of the iPlant Atmosphere VM include (but are not necessarily limited to):

  • Command line software
  • Web-based visualization tools
  • Database-driven applications such as MySQL and Postgres
  • Conventional SSH capability (users can connect through terminal after the instance starts)
  • Outgoing email support

Preliminary testing indicates that Atmosphere VMs provide very much the same capabilities as hardware-based servers, with the exception that instance run time is limited by the number of AUs the user has available on their account.

Atmosphere AUs

Atmosphere AUs are the units by which iPlant controls VM runtime.  Users are initially provided with an allocation of 168 AUs that decline at the rate of 1 CPU hour per AU.  For example, an instance which uses 10 CPU cores for 15 hours will use 150 AUs.

AUs are renewed on a monthly basis.  It is possible to obtain additional AUs by submitting a request with justification to iPlant (for example, analyses which will require more than 1 week of CPU hours).

AUs are counted against the user's balance whenever, and for as long as the instance is active.  This includes instances which have been spawned but in a "shutdown" state.  AUs still accrue for shutdown but active Atmosphere VMs, because the resources assigned to the instance are still held in reserve for the user and are not placed back into the pool for others until the instance is actually suspended or terminated.

Therefore, it is important to shutdown and either suspend, or fully terminate your instance in-between analytical activities, because failing to do so will continue to count against the user's allocation.

 

 

 

 

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