Cipres Science Gateway

This page provides information about requesting a research allocation.

The closing dates for submission of research requests are the 15th Jan (awards beginning April 1), Apr (awards beginning July 1), July (awards beginning October 1), and October (awards beginning Jan 1).

The application process consists of filling out a series of on-line forms and uploading documents. Here we review the documents you will need to upload. In Step 3, we will guide you through the selections you need to make as you fill in the forms. The full step by step protocol is available at the XSEDE User Portal under the tab /ALLOCATIONS/Request Steps. The application document is intended to provide reviewers with information that assures them that the problem is important (the PI has peer reviewed funding to do the research), that the resource use is appropriate (supercomputers are used efficiently), and will accelerate the research described.

Most CIPRES users are expected to request allocations in one of these supported categories:

• Single Principal Investigator (PI): A single PI and possibly a small research group working closely and co-authoring papers.
• Multi-PI, Large Research Collaborations: Characterized by a single PI representing a large group of collaborating co-PIs who are working on sub-projects within the overall collaboration.

In both cases above, a single proposal is submitted; account management and resource use is at the discretion of the PI.

Required Documents: A short abstract, a main proposal document (10 pages or less), CVs of the PI and any co-PIs, and a list of references (no page limit). Special requirements can be (optionally) described in a 1 page document.

ABSTRACT: Your abstract is pasted into a form rather than uploaded, but it is usually easiest to prepare it ahead of time in a word processor, and just cut and paste when filling out the form. The Abstract should describe your domain science and your planned use of TeraGrid resources. It should include text specifying the use of the CIPRES Science Gateway. Some sample text is provided here.

Main Document (10 page maximum):

The main document describes the research to be performed and illustrates its scientific merit. The emphasis here should be on describing

1. The importance of the domain project and how access to XSEDE resources will accelerate the discovery process.
2. The codes that the investigations will require ( a section entitled Codes and Methods is appropriate)
3. Justification for the magnitude of the request: how many separate analyses of what size are required. (a section entitled Justification of the Request is appropriate).

For guidance in describing the domain problem, its signficance, and the importance of computational resources, the user is referred to the successful request proposals here (the proposal examples are at the bottom of the page).

In Codes and Methods, you want to address these issues:

• Are the codes relevant to the problem?
• Are the codes deployed in a way that makes efficient use of XSEDE resources?

Addressing the relevance of the codes to the domain problem will be specific to your individual proposal. The reviewers will want to know breifly what codes are to be used, and why specific codes have been chosen to address the domain problem.

To address the issue of code efficiency, you want to address how the codes will be run on the XSEDE resources. This is based in turn on how well the codes scale for your particular code/data set. If you plan to deploy jobs exclusively through the CIPRES Science Gateway, this information is provided here. These documents describe how codes deployed on the CSG are run. Since the run strategies used by CIPRES Gateway have already passed peer review by the XRAC Committee, it should be sufficient for users to refer to this documentation.

In Justification of the Resource Request you want explain how the requested number of SUs (CPU hours) was arrived at. A responsive request would include, for example:

• how many MrBayes/RAxML/MAFFT/BEAST/GARLI runs do you require?
• how many taxa and characters do your data sets have?
• how long are the runs?
• how many cores does each run consume?

If you are running on the CIPRES Science Gateway, the number of cores to be used for specific runs is given here.

This section is important because reviewers are awarding a limited number of CPU hrs, and these are usually overrequested. They need to insure that your request is based on some specific knowledge of how the problems scale. For this reason, it is a good idea to use the CIPRES Gateway community account to build an undertsanding of your needs, and then relate your understanding in the proposal. Make it clear you are using the CIPRES Gateway codes, and that you have specific experience in making these runs to justify your request.

Once you have prepared the main document, and assembled the CVs for the PI and co-PI, you are ready to prepare the allocation request submittal.

If you would like feedback on your proposal, you can send it to us for quick review/suggestions. Please do this in plenty of time before the submission deadline, though.

CV: The CV has no page limit. It is a single document that includes CV's for the PI and all co-PIs. The two-page NSF or NIH formats are highly recommended.

Go to Step 3. Submit the allocation request.