Vital-IT project submissions – Guidelines
General considerations
The Vital-IT project is sponsored by the Universities of Lausanne, Geneva and Basel, by the Swiss Federal Polytechnic in Lausanne (EPFL), by the Ludwig Institute for Cancer Research (LICR), by the Swiss Institute of Bioinformatics (SIB), and by the industrial partners Hewlett-Packard and Intel. The management of the project has been entrusted to the SIB. The goals of the project are to make available to its partner institutions a highperformance computing environment for the life sciences, particularly genomics and proteomics, and to develop in these fields high-quality software that is tuned to the VitalIT hardware architecture (a cluster of Itanium-based servers running Linux). These dual aims should be kept in mind when submitting projects.
Who can apply?
Any researcher working at one of the Vital-IT partner institutions can apply. It should be stressed, however, that the applicant or his/her delegate will have primary responsibility for supervising the project, and that s/he should thus have sufficient expertise to interact productively with a team of computer professionals. It is strongly recommended that supervision of projects be entrusted to people with a solid background in bioinformatics. The role of the Vital-IT team is to provide high-level expertise in software development and management of a HPC infrastructure, not to propose solutions to basic biological data analysis and management problems.
Types of project
There are three major types of projects that can make use of the Vital-IT infrastructure: 1. Development: Projects aimed at producing software that will perform optimally in the Vital-IT environment. 2. Access to HPC: Projects that require access to a high-performance computer. 3. Support: Projects to provide computational infrastructure to core facilities. Examples of eligible projects: • • • • Adapting an existing program to run in a cluster environment (NB: the source code must be available) - Development Optimizing a program or parts thereof for the Itanium 2 processor – Development Producing high-quality code to implement an algorithm designed and tested by the user - Development Running computationally expensive jobs for a user’s research project – Access to HPC
• • • •
Installing a large database that requires disk and CPU resources beyond those provided by a standard workgroup server – Support Providing a computational back-end for Web-based services offered to the partner institutions or to the biomedical community – Access to HPC Setting up a batch queue to run computationally intensive jobs for a core facility – Support Providing data storage and backup for large bioscience projects - Support
Examples of ineligible projects: • • • • • Developing software from scratch for an ad hoc analysis of user data Helping a user to find the best method to interpret his/her data Modifying commercial software for which the source code is not available Running applications under operating systems other than Linux (e.g. Vital-IT cannot host an Access database) Providing help with the use of standard office productivity or scientific applications
Access to the Vital-IT machines
Three types of machines are available within the Vital-IT facility: 1. A “development cluster” consisting of a front-end and several compute nodes. This is primarily intended for development and testing activities. 2. A “production cluster” consisting of a front-end and 640 compute CPU cores with Itanium 2 or EM64T (64-bit Xeon) processors. These are primarily intended for running jobs after software has been validated on the development cluster, and as a computational back-end for jobs submitted remotely (e.g. through the Web or a Grid). 3. One or more machines running relational database engines (MySQL and Oracle). The hardware architecture on these machines has been optimized for database applications. Depending on the project, the person in charge may require access to one or more of these machines. Please note that installation of software on the production cluster can be performed only by Vital-IT staff.
Project evaluation
Projects will be evaluated by the Vital-IT Technical Committee. Its decisions will be based on the scientific and technical merits of the project, as well as on available human and computational resources. Every effort will be made to accommodate the needs of all of the partner institutions. Decisions of the Technical Committee are final, and appeals have to be addressed to the Vital-IT Steering Committee.