Lung alveolar macrophages (AMs) are in the first line of immune defense against respiratory pathogens and play key roles in the pathogenesis of Mycobacterium tuberculosis (Mtb) in humans. Nevertheless, AMs are available only in limited amounts for in vitro studies, which hamper the detailed molecular understanding of host-Mtb interactions in these macrophages. The recent establishment of the se...

A pure MPI code is not necessarily the best solution to obtain the maximum performance [3]. When the search space is irregular, load balance problems usually appear and they may deteriorate performance as the number of MPI processes increases. For the code to scale to a larger number of cores, one solution is to combine MPI with a threaded model which has load balancing capabilities. The POSIX ...

Message passing using libraries implementing the Message Passing Interface (MPI) standard is the dominant communication mechanism in high performance computing (HPC) applications. Yet, the lack of an implementation independent formal semantics for MPI is a huge void that must be filled, especially given the fact that MPI will be implemented on novel hardware platforms in the near future. To hel...

The Message Passing Interface, MPI, is the standard programming model for high performance computing clusters. However, debugging applications on large scale clusters is difficult. The widely used Message Queue Dumping interface enables inspection of message queue state but there is no general interface for extracting information from MPI objects such as communicators. A developer can debug the...

The collective communication operations of MPI, and in general MPI operations with non-local semantics, require the processes participating in the calls to provide consistent parameters, eg. a unique root process, matching type signatures and amounts for data to be exchanged, or same operator. Exhaustive consistency checks are typically too expensive to perform under normal use of MPI and would...

This paper explores some of the many issues in developing security enhanced versions of MPI. The problems that arise in creating a security enhanced MPI for embedded real-time systems supporting the Department of Defense’s Multi-level Security policy (DoD MLS) are presented along with the preliminary design for such an MPI variant. In addition some of the many issues that need to be addressed i...

This paper introduces FLEX-MPI, a novel runtime approach for the dynamic load balancing of MPI-based SPMD applications running on heterogeneous platforms in the presence of dynamic external loads. To effectively balance the workload, FLEX-MPI monitors the actual performance of applications via hardware counters and the MPI profiling interface—with a negligible overhead and minimal code modifica...

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An MPI implementation of the Basic Linear Communication Subprograms (BLACS) is presented. A wide spectrum of MPI functionality has been used to implement BLACS as succinctly as possible, thus making the implementation concise, but still yielding good performance. We discuss some of the implementation details and present performance results for several parallel architectures with different MPI l...

In this paper we evaluate the current status and performance of several MPI implementations regarding two chapters of the MPI-2 specification. First, we analyze whether the performance using dynamically created communicators is comparable to the approach presented in MPI-1 using a static communicator for different MPI libraries. We then evaluate whether the communication performance of one-side...