Parallel algorithms for simulating continuous time Markov chains

We have previously shown that the mathematical technique of uniformization can serve as the basis of synchronization for the parallel simulation of continuous-time Markov chains. This paper reviews the basic method and compares five different methods based on uniformization, evaluating their strengths and weaknesses as a function of problem characteristics. The methods vary in their use of optimism, logical aggregation, communication management, and adaptivity. Performance evaluation is conducted on the Intel Touchstone Delta multiprocessor, using up to 256 processors

Efficient massively parallel simulation of dynamic channel assignment schemes for wireless cellular communications

Fast, efficient parallel algorithms are presented for discrete event simulations of dynamic channel assignment schemes for wireless cellular communication networks. The driving events are call arrivals and departures, in continuous time, to cells geographically distributed across the service area. A dynamic channel assignment scheme decides which call arrivals to accept, and which channels to allocate to the accepted calls, attempting to minimize call blocking while ensuring co-channel interference is tolerably low. Specifically, the scheme ensures that the same channel is used concurrently at different cells only if the pairwise distances between those cells are sufficiently large. Much of the complexity of the system comes from ensuring this separation. The network is modeled as a system of interacting continuous time automata, each corresponding to a cell. To simulate the model, conservative methods are used; i.e., methods in which no errors occur in the course of the simulation and so no rollback or relaxation is needed. Implemented on a 16K processor MasPar MP-1, an elegant and simple technique provides speedups of about 15 times over an optimized serial simulation running on a high speed workstation. A drawback of this technique, typical of conservative methods, is that processor utilization is rather low. To overcome this, new methods were developed that exploit slackness in event dependencies over short intervals of time, thereby raising the utilization to above 50 percent and the speedup over the optimized serial code to about 120 times

Hierarchical fractional-step approximations and parallel kinetic Monte Carlo algorithms

We present a mathematical framework for constructing and analyzing parallel algorithms for lattice Kinetic Monte Carlo (KMC) simulations. The resulting algorithms have the capacity to simulate a wide range of spatio-temporal scales in spatially distributed, non-equilibrium physiochemical processes with complex chemistry and transport micro-mechanisms. The algorithms can be tailored to specific hierarchical parallel architectures such as multi-core processors or clusters of Graphical Processing Units (GPUs). The proposed parallel algorithms are controlled-error approximations of kinetic Monte Carlo algorithms, departing from the predominant paradigm of creating parallel KMC algorithms with exactly the same master equation as the serial one. Our methodology relies on a spatial decomposition of the Markov operator underlying the KMC algorithm into a hierarchy of operators corresponding to the processors' structure in the parallel architecture. Based on this operator decomposition, we formulate Fractional Step Approximation schemes by employing the Trotter Theorem and its random variants; these schemes, (a) determine the communication schedule} between processors, and (b) are run independently on each processor through a serial KMC simulation, called a kernel, on each fractional step time-window. Furthermore, the proposed mathematical framework allows us to rigorously justify the numerical and statistical consistency of the proposed algorithms, showing the convergence of our approximating schemes to the original serial KMC. The approach also provides a systematic evaluation of different processor communicating schedules.Comment: 34 pages, 9 figure

Formalisms for specifying Markovian population models

In this survey, we compare several languages for specifying Markovian population models such as queuing networks and chemical reaction networks. All these languages — matrix descriptions, stochastic Petri nets, stoichiometric equations, stochastic process algebras, and guarded command models — describe continuous-time Markov chains, but they differ according to important properties, such as compositionality, expressiveness and succinctness, executability, and ease of use. Moreover, they provide different support for checking the well-formedness of a model and for analyzing a model

Bloody fast blood collection

This thesis consists of four parts: The first part contains an introduction, the second presents approaches for the evaluation of waiting times at blood collection sites, the third uses these to present approaches that improve waiting times at blood collection sites. The final part shows the application of two of the approaches to data from real blood collection sites, followed by the conclusions that can be drawn from this thesis. Part I: Introduction, contains two chapters. Chapter 1 introduces the context for this thesis: blood banks in general, the Dutch blood bank Sanquin and blood collection sites. The chapter sketches some of the challenges faced with respect to blood collection sites. As blood donors are voluntary and non-remunerated, delays and waiting times within blood collection sites should be kept at acceptable levels. However, waiting times are currently not incorporated in staff planning or in other decisions with respect to blood collection sites. These blood collection sites will be the primary focus of this thesis. This thesis provides methods that do take waiting times into account, aiming to decrease waiting times at blood collection sites and leveling work pressure for staff members, without the need for additional staff. Chapter 2 then presents a technical methods that will be used most of the chapters in this thesis: uniformization. Uniformization can be used to transform Continuous Time Markov Chains (CTMCs) — that are very hard to analyze — into Discrete Time Markov Chains (DTMCs) — that are much easier to analyze. The chapter shows how the method works, provides an extensive overview of the literature related to the method, the (technical) intuition behind the method as well as several extensions and applications. Although not all of the extensions and applications are necessary for this thesis, it does provide an overview of one of the most valuable methods for this thesis. Part II: Evaluation, contains two chapters that propose and adapt several methods to compute waiting times and queues at blood collection sites. A blood collection site is best modeled as a time-dependent queueing network, requiring non-standard approaches. Chapter 3 considers a stationary, i.e. not time-dependent model of blood collection sites as a first step. A blood collection site consists of three main stations: Registration, Interview and Donation. All three of the stations can have their own queue. This means that even the stationary model is non-trivial for some computations. However, for the stationary model, an analytic so-called product form expression is derived. Based on this product form, two more results are shown. The first result is that the standard waiting time distributions from M|M|s queues are applicable, as if the queue is in isolation. It is then concluded that no closed form expression exist for the total waiting or delay time distribution, as the distributions of the three stations in tandem are not independent. Therefore a numerical approach is presented to compute the total delay time distribution of a collection site. All of the results are supported by numerical examples based on a Dutch blood collection site. The approach for the computation of the total delay time distribution can also be combined with the approach from Chapter 4 for an extension to a time-dependent setting. Chapter 4 shows an approach to deal with these time-dependent aspects in queueing systems, as often experienced by blood collection sites and other service systems, typically due to time-dependent arrivals and capacities. Easy and quick to use queueing expressions generally do not apply to time-dependent situations. A large number of computational papers has been written about queue length distributions for time-dependent queues, but these are mostly theoretical and based on single queues. This chapter aims to combine computational methods with more realistic time-dependent queueing networks, with an approach based on uniformization. Although uniformization is generally perceived to be too computationally prohibitive, we show that our method is very effective for practical instances, as shown with an example of a Dutch blood collection site. The objective of the results is twofold: to show that a time-dependent queueing network approach can be beneficial and to evaluate possible improvements for Dutch blood collection sites that can only be properly assessed with a time-dependent queueing method. Part III: Optimization, contains four chapters that aim to improve service levels at Sanquin. The first three chapters focus on three different methods to decrease queues at blood collection sites. Chapters 5 and 6 focus on improving the service by optimizing staff allocation to shifts and stations. Chapter 7 focuses on improving the arrival process with the same goal. Chapter 8 is focused at improving inventory management of red blood cells. Donors do not arrive to blood collection sites uniformly throughout the day, but show clear preferences for certain times of the day. However, the arrival patterns that are shown by historical data, are not used for scheduling staff members at blood collection sites. As a first significant step to shorten waiting times we can align staff capacity and shifts with walk-in arrivals. Chapter 5 aims to optimize shift scheduling for blood collection sites. The chapter proposes a two-step procedure. First, the arrival patterns and methods from queueing theory are used to determine the required number of staff members for every half hour. Second, an integer linear program is used to compute optimal shift lengths and starting times, based on the required number of staff members. The chapter is concluded with numerical experiments that show, depending on the scenario, a reduction of waiting times, a reduction of staff members or a combination of both. At a blood collection site three stations (Registration, Interview and Donation) can roughly be distinguished. Staff members at Dutch blood collection sites are often trained to work at any of these stations, but are usually allocated to one of the stations for large fractions of a shift. If staff members change their allocation this is based on an ad hoc decision. Chapter 6 aims to take advantage of this mostly unused allocation flexibility to reduce queues at blood collection sites. As a collection site is a highly stochastic process, both in arrivals and services, an optimal allocation of staff members to the three stations is unknown, constantly changing and a challenge to determine. Chapter 6 provides and applies a so-called Markov Decision Process (MDP) to compute optimal staff assignments. Extensive numerical and simulation experiments show the potential reductions of queues when the reallocation algorithm would be implemented. Based on Dutch blood collection sites, reductions of 40 to 80% on the number of waiting donors seem attainable, depending on the scenario. Chapter 7 also aims to align the arrival of donors with scheduled staff, similarly to Chapter 5. Chapter 7 tries to achieve this by changing the arrivals of donors. By introducing appointments for an additional part of donors, arrivals can be redirected from the busiest times of the day to quiet times. An extended numerical queueing model with priorities is introduced for blood collection sites, as Sanquin wants to incentive donors to make appointments by prioritizing donors with appointments over donors without appointments. Appointment slots are added if the average queue drops below certain limits. The correct values for these limits, i.e. the values that plan the correct number of appointments, are then determined by binary search. Numerical results show that the method succeeds in decreasing excessive queues. However, the proposed priorities might result in unacceptably high waiting times for donors without appointments, and caution is therefore required before implementation. Although this thesis mainly focuses on blood collection sites, many more logistical challenges are present at a blood bank. One of these challenges arises from the expectation that Sanquin can supply hospitals with extensively typed red blood cell units directly from stock. Chapter 8 deals with this challenge. Currently, all units are issued according to the first-in-first-out principle, irrespective of their specific typing. These kind of issuing policies lead to shortages for rare blood units. Shortages for rare units could be avoided by keeping them in stock for longer, but this could also lead to unnecessary wastage. Therefore, to avoid both wastage and shortages, a trade-off between the age and rarity of a specific unit in stock should be made. For this purpose, we modeled the allocation of the inventory as a circulation flow problem, in which decisions about which units to issue are based on both the age and rarity of the units in stock. We evaluated the model for several settings of the input parameters. It turns out that, especially if only a few donors are typed for some combinations of antigens, shortages can be avoided by saving rare blood products. Moreover, the average issuing age remains unchanged. Part IV: Practice and Outlook concludes this thesis. The first of two chapters in this part shows the combined application of two approaches from this thesis to data from three collection sites in the Netherlands. The final chapter of this thesis presents the conclusions that can be drawn from this thesis and discusses an outlook for further research. Chapter 9 shows the combined application of the methods in Chapters 5 and 6 to three real collection sites in Dutch cities: Nijmegen, Leiden and Almelo. The collection sites in Nijmegen and Leiden are both large fixed collection sites. The collection site in Almelo is a mobile collection site. The application of each one of the methods individually reduce waiting times significantly, and the combined application of the methods reduces waiting times even further. Simultaneously, small reductions in the number of staff hours are attainable. The results from Chapter 9 summarize the main message of this thesis: waiting time for blood donors at blood collection sites can be reduced without the need for more staff members when the working times of staff members are used more effectively and efficiently, and controlling the arrival process of donors. The approaches presented in this thesis can be used for this purpose. This is not only beneficial for blood donors, but will also result in more balanced workload for staff members, as fluctuations in this workload are reduced significantly

Propagation Models for Biochemical Reaction Networks

In this thesis we investigate different ways of approximating the solution of the chemical master equation (CME). The CME is a system of differential equations that models the stochastic transient behaviour of biochemical reaction networks. It does so by describing the time evolution of probability distribution over the states of a Markov chain that represents a biological network, and thus its stochasticity is only implicit. The transient solution of a CME is the vector of probabilities over the states of the corresponding Markov chain at a certain time point t, and it has traditionally been obtained by applying methods that are general to continuous-time Markov chains: uniformization, Krylov subspace methods, and general ordinary differential equation (ODE) solvers such as the fourth order Runge-Kutta method. Even though biochemical reaction networks are the main application of our work, some of our results are presented in the more general framework of propagation models (PM), a computational formalism that we introduce in the first part of this thesis. Each propagation model N has two associated propagation processes, one in discrete-time and a second one in continuous-time. These propagation processes propagate a generic mass through a discrete state space. For example, in order to model a CME, N propagates probability mass. In the discrete-time case the propagation is done step-wise, while in the continuous-time case it is done in a continuous flow defined by a differential equation. Again, in the case of the chemical master equation, this differential equation is the equivalent of the chemical master equation itself where probability mass is propagated through a discrete state space. Discrete-time propagation processes can encode methods such as the uniformization method and the fourth order Runge-Kutta integration method that we have mentioned above, and thus by optimizing propagation algorithms we optimize both of these methods simultaneously. In the second part of our thesis, we define stochastic hybrid models that approximate the stochastic behaviour of biochemical reaction networks by treating some variables of the system deterministically. This deterministic approximation is done for species with large populations, for which stochasticity does not play an important role. We propose three such hybrid models, which we introduce from the coarsest to the most refined one: (i) the first one replaces some variables of the system with their overall expectations, (ii) the second one replaces some variables of the system with their expectations conditioned on the values of the stochastic variables, (iii) and finally, the third one, splits each variable into a stochastic part (for low valuations) and a deterministic part (for high valuations), while tracking the conditional expectation of the deterministic part. For each of these algorithms we give the corresponding propagation models that propagate not only probabilities but also the respective continuous approximations for the deterministic variables