Preface

This volume contains the final versions of the papers presented at the 3rd International Workshop on Computational Models for Cell Processes (CompMod 2011). The workshop took place on September 10, 2011 at the University of Aachen, Germany, in conjunction with CONCUR 2011. The first edition of the workshop (2008) took place in Turku, Finland, in conjunction with F

Device Cooperation in Ad-hoc Multimedia Ensembles

Users can be overwhelmed by the abundance of functionality that smart ad-hoc environments offer. This thesis investigates how to assist the user in controlling such environments. We present an approach that enables the devices in an ad-hoc environment to cooperatively generate and execute an action sequence to fulfill the user's goals. Device cooperation happens spontaneously and in a completely distributed fashion. In a quantitative user study, we show that users accept the assistance such a system provides even if it is suboptimal.Nutzer von intelligenten Ad-hoc-Umgebungen sind oft überfordert von der Fülle an Funktionalität, die solche Umgebungen bieten. Im Mittelpunkt dieser Arbeit steht die Frage, wie man Nutzern solcher Umgebungen assistieren kann. Der vorgestellte Ansatz versetzt die Geräte in Ad-hoc-Umgebungen in die Lage, kooperativ eine Aktionssequenz zu generieren und auszuführen, die die Nutzerziele erfüllt. Die Gerätekooperation erfolgt spontan und komplett verteilt. In einer quantitativen Nutzerstudie zeigen wir, dass Nutzer die Assistenz eines solchen Systems akzeptieren, auch wenn sie suboptimal ist

Parallel Programming with Global Asynchronous Memory: Models, C++ APIs and Implementations

In the realm of High Performance Computing (HPC), message passing has been the programming paradigm of choice for over twenty years. The durable MPI (Message Passing Interface) standard, with send/receive communication, broadcast, gather/scatter, and reduction collectives is still used to construct parallel programs where each communication is orchestrated by the developer-based precise knowledge of data distribution and overheads; collective communications simplify the orchestration but might induce excessive synchronization. Early attempts to bring shared-memory programming model—with its programming advantages—to distributed computing, referred as the Distributed Shared Memory (DSM) model, faded away; one of the main issue was to combine performance and programmability with the memory consistency model. The recently proposed Partitioned Global Address Space (PGAS) model is a modern revamp of DSM that exposes data placement to enable optimizations based on locality, but it still addresses (simple) data- parallelism only and it relies on expensive sharing protocols. We advocate an alternative programming model for distributed computing based on a Global Asynchronous Memory (GAM), aiming to avoid coherency and consistency problems rather than solving them. We materialize GAM by designing and implementing a distributed smart pointers library, inspired by C++ smart pointers. In this model, public and pri- vate pointers (resembling C++ shared and unique pointers, respectively) are moved around instead of messages (i.e., data), thus alleviating the user from the burden of minimizing transfers. On top of smart pointers, we propose a high-level C++ template library for writing applications in terms of dataflow-like networks, namely GAM nets, consisting of stateful processors exchanging pointers in fully asynchronous fashion. We demonstrate the validity of the proposed approach, from the expressiveness perspective, by showing how GAM nets can be exploited to implement both standalone applications and higher-level parallel program- ming models, such as data and task parallelism. As for the performance perspective, preliminary experiments show both close-to-ideal scalability and negligible overhead with respect to state-of-the-art benchmark implementations. For instance, the GAM implementation of a high-quality video restoration filter sustains a 100 fps throughput over 70%-noisy high-quality video streams on a 4-node cluster of Graphics Processing Units (GPUs), with minimal programming effort

Proceedings of the Third International Workshop on Computational Models for Cell Processes (CompMod 2011, Aachen, Germany, September 10, 2011)

This volume contains the final versions of the papers presented at the 3rd International Workshop on Computational Models for Cell Processes (CompMod 2011). The workshop took place on September 10, 2011 at the University of Aachen, Germany, in conjunction with CONCUR 2011. The first edition of the workshop (2008) took place in Turku, Finland, in conjunction with Formal Methods 2008 and the second edition (2009) took place in Eindhoven, the Netherlands, as well in conjunction with Formal Methods 2009. The goal of the CompMod workshop series is to bring together researchers in Computer Science (especially in Formal Methods) and Mathematics (both discrete and continuous), interested in the opportunities and the challenges of Systems Biology

Proceedings of the Third International Workshop on Computational Models for Cell Processes (CompMod 2011, Aachen, Germany, September 10, 2011)

This volume contains the final versions of the papers presented at the 3rd International Workshop on Computational Models for Cell Processes (CompMod 2011). The workshop took place on September 10, 2011 at the University of Aachen, Germany, in conjunction with CONCUR 2011. The first edition of the workshop (2008) took place in Turku, Finland, in conjunction with Formal Methods 2008 and the second edition (2009) took place in Eindhoven, the Netherlands, as well in conjunction with Formal Methods 2009. The goal of the CompMod workshop series is to bring together researchers in Computer Science (especially in Formal Methods) and Mathematics (both discrete and continuous), interested in the opportunities and the challenges of Systems Biology