ICHEC Summer Scholarships 2010

Overview

The ICHEC Summer Scholarships provides funding for a select number of talented senior undergraduate students to undertake 10-week summer projects located in Galway or Dublin. It provides exciting opportunities for students worldwide to undertake projects related to HPC/computational science, all in the environment of a national HPC centre under the supervision of ICHEC's computational scientists and systems staff.

Important Dates

Funding

Successful candidates will be given a stipend of EUR 2750 for the duration of the project to cover living expenses (paid fortnightly over 10 weeks). Appropriate accommodation is provided at no extra cost (may or may not include utility bills). ICHEC also subsidises travel expenses up to a capped amount based on the location of the candidate (EU countries: EUR 300; Rest of the world: EUR 800).

Projects

Each applicant must specify at least one preferred project (chosen from the list below). Up to 4 projects can be specified in order of preference. Please note that applicants will be asked to comment briefly on their motivation in selecting a particular project.

1. Implementation of the multiple polynomial sieve factoring algorithm on the GPU architecture

   Integer factorisation is a classic problem in number theory, and it forms the basis for encryption methodologies that facilitate secure e-commerce. While factorisation may be trivial for small integers, the problem becomes much harder for extremely large numbers (e.g. over 100 digits). The multiple polynomial quadratic sieve factoring algorithm, implemented on a powerful computer, makes it feasible to factorise such large numbers. The algorithm is very parallelisable which makes it an ideal candidate for implementation on HPC architectures. Thus the challenge for this project is to implement this algorithm on the GPU and to evaluate its performance. Working C code for CPUs will be provided as a starting point.

2. Development of a General Matrix Multiply (GEMM) library for hybrid CPU-GPU architectures

   General Matrix Multiply (GEMM) is a matrix multiplication subroutine in the Basic Linear Algebra Subprograms (BLAS) that is often optimised for HPC architectures. It has significant impact on performance as it is the foundation of many other subroutines, scientific codes and the LINPACK benchmark. As hybrid CPU-GPU architectures becomes more prevalent in HPC, Massimiliano Fatica¹ developed a host library that intercepts double-precision DGEMM calls and distributes the workload to be executed on both CPUs and GPUs simultaneously. The results showed that improved Linpack performance is readily achievable on hybrid CPU-GPU architectures.

   Following on from that work, the goal of this project is to develop a more general-purpose version of the host library that will handle single-precision (SGEMM), complex double-precision (ZGEMM), as well as DGEMM operations. It will also ensure that best performance is obtained regardless of matrix dimension and form. As the [SDZ]GEMM subroutines are widely used, this project has the potential to benefit a large community.

   ¹Fatica, M. (2009) Accelerating Linpack with CUDA on heterogeneous clusters. ACM ICPS 383: 46-51. [Link]

3. Porting EXCITON for the GPU architecture

   EXCITON is an electronic structure code under development in the School of Physics, Trinity College Dublin and ICHEC. Its purpose is computation of excitations in solids using state of the art methods such as the GW approximation and the Bethe-Salpeter Equation. It is written in C and is parallelised with MPI. We are investigating how the numerically intensive parts of EXCITON can be accelerated on Graphical Processor Unit (GPU) architectures. This project will involve porting EXCITON to GPU and use of the CUDA language.

4. Bioinformatics on the GPU

   Many bioinformatics software tools follow the single instruction, multiple data (SIMD) paradigm. Hence GPGPU has the potential to provide relatively inexpensive, scalable solutions to increasingly data-intensive problems in biology. There are already a number of algorithms which has been implemented on the GPU (e.g. Smith-Waterman, BLASTP), most of which report significant speed-ups over CPU implementations.

   The goal of this project is to implement some of the existing bioinformatics GPGPU codes on ICHEC hardware and to assess their behaviour, applicability and useability. In collaboration with the Molecular Evolution and Bioinformatics Unit at NUI Maynooth, there are opportunities to carry out real scientific analyses and to enable previously-infeasible computations. The codes will cover a range of areas including biological sequence comparisons, molecular phylogenetics and high-throughput DNA sequencing.

5. Parallelism improvements of the GIPAW Nuclear Magnetic Resonance module for HPC users

   GIPAW is a module within the Quantum ESPRESSO distribution that models NMR experiments (e.g. chemical shifts) from first principles. Until now, NMR modelling has been applied to relatively simple systems of tens of atoms in the unit cell at most. The current scalability of GIPAW is limited to a few hundreds of cores at most. In order to make GIPAW useful in biomedical and industrial applications, we need to extend its range to systems having hundreds to thousands of atoms, and to extend scalability up to thousands of cores. The aim of this project is to improve the parallelism inside GIPAW, by further distributing large arrays across processors and by adding a further parallelisation level on electronic states.

6. Parallelisation of mesh-free computational fluid dynamics (CFD) code

   Methods for Computational Fluid Dynamics (CFD) has become increasingly important in many aspects of engineering. Traditionally, methods for CFD have been mesh-based, i.e. the computational nodes are interconnected and fixed in space. Mesh-free methods for CFD are a relatively recent development. These methods offer greater flexibility than traditional mesh-based approaches because the computational nodes can move with the fluid and have no pre-defined connectivity.

   Code for mesh-free CFD has been developed at Mechanical and Biomedical Engineering at NUI Galway. This project will involve the parallelisation of certain elements of this mesh-free CFD code and will be conducted in collaboration with the research group of Dr. Nathan Quinlan at NUI, Galway.

7. Visualisation of nested climate and weather datasets

   Nested models are increasingly used in climate and weather, with a regional model running within a larger global model. Incorrectly nested models can have issues due to artificial noise at the model boundaries, or incorrectly filtered dynamics that remove the desired signals in the model.

   The aim of the project is to investigate and implement techniques for showing the results of two nested models within VTK or paraview, enabling the users to distinguish the different datasets and investigate potential issues due to resolution, artificial noise or filtering within the nested system.

8. Development of wizard interfaces for efficient job submission on HPC systems

   The input file syntax required for running HPC jobs while reasonably straight-forward and deterministic can be confusing for new users. Similarly debugging and scaling work can require modifications of normal production jobs which can be error prone, if it is not a day-to-day activity. The aim of this project is to develop a series of 'Wizard' based interfaces, probably web-based, which can be used to generate job submission and related files for users in a user-friendly manner. The generated files could then be used by users directly or as a basis for further customisation.

9. Instrumentation of taskfarming on ICHEC systems

   One method commonly used for large-scale parameter studies and other ideally-parallel workloads is so-called taskfarming. ICHEC's current taskfarm utility is light-weight and adaptable but it currently assumes that users have a good understanding of the system load and run-times of their jobs. However a more sophisticated taskfarming approach could automatically harvest and log performance data producing a summary, both textual and graphical, of the properties of a given run. This could benefit users by helping them to readily spot problematic tasks or inefficiencies.

Eligibility

Undergraduate students from third-level institutions worldwide are eligible to apply. Candidates are expected to be proficient in English for every-day communication and completion of a written report at the end of the project (with perhaps a short presentation). Since the projects require a computational background and proficiency at programming, preferences will be given to senior undergraduates (those in the final 2 years of their degrees).

How do I apply?

Before you begin the application process, please ensure the following:

• You have your CV in electronic format (preferably in PDF format)
• From the list of projects above, you have identified at least one preferred project; up to 4 preferred projects in order of preference. You are also expected to state briefly your motivation for each selection.
• You are available to work on the project for the entire 10-week duration (see above for start and end dates) in Ireland. Small deviations may be possible to suit your schedule but please state this clearly in your application (in the Additional Info section).

--> Proceed to ICHEC Summer Scholarship application form.

Further Information

For further information regarding the Summer Scholarships, please contact our Education & Training Coordinator.