8,629 research outputs found
A Tuned and Scalable Fast Multipole Method as a Preeminent Algorithm for Exascale Systems
Among the algorithms that are likely to play a major role in future exascale
computing, the fast multipole method (FMM) appears as a rising star. Our
previous recent work showed scaling of an FMM on GPU clusters, with problem
sizes in the order of billions of unknowns. That work led to an extremely
parallel FMM, scaling to thousands of GPUs or tens of thousands of CPUs. This
paper reports on a a campaign of performance tuning and scalability studies
using multi-core CPUs, on the Kraken supercomputer. All kernels in the FMM were
parallelized using OpenMP, and a test using 10^7 particles randomly distributed
in a cube showed 78% efficiency on 8 threads. Tuning of the
particle-to-particle kernel using SIMD instructions resulted in 4x speed-up of
the overall algorithm on single-core tests with 10^3 - 10^7 particles. Parallel
scalability was studied in both strong and weak scaling. The strong scaling
test used 10^8 particles and resulted in 93% parallel efficiency on 2048
processes for the non-SIMD code and 54% for the SIMD-optimized code (which was
still 2x faster). The weak scaling test used 10^6 particles per process, and
resulted in 72% efficiency on 32,768 processes, with the largest calculation
taking about 40 seconds to evaluate more than 32 billion unknowns. This work
builds up evidence for our view that FMM is poised to play a leading role in
exascale computing, and we end the paper with a discussion of the features that
make it a particularly favorable algorithm for the emerging heterogeneous and
massively parallel architectural landscape
On Designing Multicore-aware Simulators for Biological Systems
The stochastic simulation of biological systems is an increasingly popular
technique in bioinformatics. It often is an enlightening technique, which may
however result in being computational expensive. We discuss the main
opportunities to speed it up on multi-core platforms, which pose new challenges
for parallelisation techniques. These opportunities are developed in two
general families of solutions involving both the single simulation and a bulk
of independent simulations (either replicas of derived from parameter sweep).
Proposed solutions are tested on the parallelisation of the CWC simulator
(Calculus of Wrapped Compartments) that is carried out according to proposed
solutions by way of the FastFlow programming framework making possible fast
development and efficient execution on multi-cores.Comment: 19 pages + cover pag
Hierarchical Parallelisation of Functional Renormalisation Group Calculations -- hp-fRG
The functional renormalisation group (fRG) has evolved into a versatile tool
in condensed matter theory for studying important aspects of correlated
electron systems. Practical applications of the method often involve a high
numerical effort, motivating the question in how far High Performance Computing
(HPC) can leverage the approach. In this work we report on a multi-level
parallelisation of the underlying computational machinery and show that this
can speed up the code by several orders of magnitude. This in turn can extend
the applicability of the method to otherwise inaccessible cases. We exploit
three levels of parallelisation: Distributed computing by means of Message
Passing (MPI), shared-memory computing using OpenMP, and vectorisation by means
of SIMD units (single-instruction-multiple-data). Results are provided for two
distinct High Performance Computing (HPC) platforms, namely the IBM-based
BlueGene/Q system JUQUEEN and an Intel Sandy-Bridge-based development cluster.
We discuss how certain issues and obstacles were overcome in the course of
adapting the code. Most importantly, we conclude that this vast improvement can
actually be accomplished by introducing only moderate changes to the code, such
that this strategy may serve as a guideline for other researcher to likewise
improve the efficiency of their codes
- …