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

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

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

Reversible GANs for Memory-efficient Image-to-Image Translation

The Pix2pix and CycleGAN losses have vastly improved the qualitative and quantitative visual quality of results in image-to-image translation tasks. We extend this framework by exploring approximately invertible architectures which are well suited to these losses. These architectures are approximately invertible by design and thus partially satisfy cycle-consistency before training even begins. Furthermore, since invertible architectures have constant memory complexity in depth, these models can be built arbitrarily deep. We are able to demonstrate superior quantitative output on the Cityscapes and Maps datasets at near constant memory budget

QTM: computational package using MPI protocol for quantum trajectories method

The Quantum Trajectories Method (QTM) is one of {the} frequently used methods for studying open quantum systems. { The main idea of this method is {the} evolution of wave functions which {describe the system (as functions of time). Then,} so-called quantum jumps are applied at {a} randomly selected point in time. {The} obtained system state is called as a trajectory. After averaging many single trajectories{,} we obtain the approximation of the behavior of {a} quantum system.} {This fact also allows} us to use parallel computation methods. In the article{,} we discuss the QTM package which is supported by the MPI technology. Using MPI allowed {utilizing} the parallel computing for calculating the trajectories and averaging them -- as the effect of these actions{,} the time {taken by} calculations is shorter. In spite of using the C++ programming language, the presented solution is easy to utilize and does not need any advanced programming techniques. At the same time{,} it offers a higher performance than other packages realizing the QTM. It is especially important in the case of harder computational tasks{,} and the use of MPI allows {improving the} performance of particular problems which can be solved in the field of open quantum systems.Comment: 28 pages, 9 figure

PARALLEL NUMERICAL COMPUTATION: A COMPARATIVE STUDY ON CPU-GPU PERFORMANCE IN PI DIGITS COMPUTATION

As the usage of GPU (Graphical Processing Unit) for non-graphical computation is rising, one important area is to study how the device helps improve numerical calculations. In this work, we present a time performance comparison between purely CPU (serial) and GPU-assisted (parallel) programs in numerical computation. Specifically, we design and implement the calculation of the hexadecimal -digit of the irrational number Pi in two ways: serial and parallel. Both programs are based upon the BBP formula for Pi in the form of infinite series identity. We then provide a detailed time performance analysis of both programs based on the magnitude. Our result shows that the GPU-assisted parallel algorithm ran a hundred times faster than the serial algorithm. To be more precise, we offer that as the value  grows, the ratio between the execution time of the serial and parallel algorithms also increases. Moreover, when  it is large enough, that is This GPU efficiency ratio converges to a constant, showing the GPU's maximally utilized capacity. On the other hand, for sufficiently small enough, the serial algorithm performed solely on the CPU works faster since the GPU's small usage of parallelism does not help much compared to the arithmetic complexity