16,059 research outputs found
Fat vs. thin threading approach on GPUs: application to stochastic simulation of chemical reactions
We explore two different threading approaches on a graphics processing unit (GPU) exploiting two different characteristics of the current GPU architecture. The fat thread approach tries to minimise data access time by relying on shared memory and registers potentially sacrificing parallelism. The thin thread approach maximises parallelism and tries to hide access latencies. We apply these two approaches to the parallel stochastic simulation of chemical reaction systems using the stochastic simulation algorithm (SSA) by Gillespie (J. Phys. Chem, Vol. 81, p. 2340-2361, 1977). In these cases, the proposed thin thread approach shows comparable performance while eliminating the limitation of the reaction systemâs size
Molecular dynamics recipes for genome research
Molecular dynamics (MD) simulation allows one to predict the time evolution of a system of interacting particles. It is widely used in physics, chemistry and biology to address specific questions about the structural properties and dynamical mechanisms of model systems. MD earned a great success in genome research, as it proved to be beneficial in sorting pathogenic from neutral genomic mutations. Considering their computational requirements, simulations are commonly performed on HPC computing devices, which are generally expensive and hard to administer. However, variables like the software tool used for modeling and simulation or the size of the molecule under investigation might make one hardware type or configuration more advantageous than another or even make the commodity hardware definitely suitable for MD studies. This work aims to shed lights on this aspect
Parallel simulation of Population Dynamics P systems: updates and roadmap
Population Dynamics P systems are a type of
multienvironment P systems that serve as a formal modeling
framework for real ecosystems. The accurate simulation of
these probabilisticmodels, e.g. with Direct distribution based
on Consistent Blocks Algorithm, entails large run times.
Hence, parallel platforms such as GPUs have been employed
to speedup the simulation. In 2012, the first GPU simulator of
PDP systems was presented. However, it was able to run only
randomly generated PDP systems. In this paper, we present
current updates made on this simulator, involving an input
modu le for binary files and an output module for CSV files.
Finally, the simulator has been experimentally validated with
a real ecosystem model, and its performance has been tested
with two high-end GPUs: Tesla C1060 and K40.Ministerio de EconomĂa y Competitividad TIN2012-37434Junta de AndalucĂa P08-TIC-0420
GPU accelerated biochemical network simulation.
Motivation: Mathematical modelling is central to systems and synthetic biology. Using simulations to calculate statistics or to explore parameter space is a common means for analysing these models and can be computationally intensive. However, in many cases, the simulations are easily parallelizable. Graphics processing units (GPUs) are capable of efficiently running highly parallel programs and outperform CPUs in terms of raw computing power. Despite their computational advantages, their adoption by the systems biology community is relatively slow, since differences in hardware architecture between GPUs and CPUs complicate the porting of existing code. Results: We present a Python package, cuda-sim, that provides highly parallelized algorithms for the repeated simulation of biochemical network models on NVIDIA CUDA GPUs. Algorithms are implemented for the three popular types of model formalisms: the LSODA algorithm for ODE integration, the Euler-Maruyama algorithm for SDE simulation and the Gillespie algorithm for MJP simulation. No knowledge of GPU computing is required from the user. Models can be specified in SBML format or provided as CUDA code. For running a large number of simulations in parallel, up to 360-fold decrease in simulation runtime is attained when compared to single CPU implementations
A GPU-based multi-criteria optimization algorithm for HDR brachytherapy
Currently in HDR brachytherapy planning, a manual fine-tuning of an objective
function is necessary to obtain case-specific valid plans. This study intends
to facilitate this process by proposing a patient-specific inverse planning
algorithm for HDR prostate brachytherapy: GPU-based multi-criteria optimization
(gMCO).
Two GPU-based optimization engines including simulated annealing (gSA) and a
quasi-Newton optimizer (gL-BFGS) were implemented to compute multiple plans in
parallel. After evaluating the equivalence and the computation performance of
these two optimization engines, one preferred optimization engine was selected
for the gMCO algorithm. Five hundred sixty-two previously treated prostate HDR
cases were divided into validation set (100) and test set (462). In the
validation set, the number of Pareto optimal plans to achieve the best plan
quality was determined for the gMCO algorithm. In the test set, gMCO plans were
compared with the physician-approved clinical plans.
Over 462 cases, the number of clinically valid plans was 428 (92.6%) for
clinical plans and 461 (99.8%) for gMCO plans. The number of valid plans with
target V100 coverage greater than 95% was 288 (62.3%) for clinical plans and
414 (89.6%) for gMCO plans. The mean planning time was 9.4 s for the gMCO
algorithm to generate 1000 Pareto optimal plans.
In conclusion, gL-BFGS is able to compute thousands of SA equivalent
treatment plans within a short time frame. Powered by gL-BFGS, an ultra-fast
and robust multi-criteria optimization algorithm was implemented for HDR
prostate brachytherapy. A large-scale comparison against physician approved
clinical plans showed that treatment plan quality could be improved and
planning time could be significantly reduced with the proposed gMCO algorithm.Comment: 18 pages, 7 figure
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