Evaluating kernels on Xeon Phi to accelerate Gysela application

This work describes the challenges presented by porting parts ofthe Gysela code to the Intel Xeon Phi coprocessor, as well as techniques used for optimization, vectorization and tuning that can be applied to other applications. We evaluate the performance of somegeneric micro-benchmark on Phi versus Intel Sandy Bridge. Several interpolation kernels useful for the Gysela application are analyzed and the performance are shown. Some memory-bound and compute-bound kernels are accelerated by a factor 2 on the Phi device compared to Sandy architecture. Nevertheless, it is hard, if not impossible, to reach a large fraction of the peek performance on the Phi device,especially for real-life applications as Gysela. A collateral benefit of this optimization and tuning work is that the execution time of Gysela (using 4D advections) has decreased on a standard architecture such as Intel Sandy Bridge.Comment: submitted to ESAIM proceedings for CEMRACS 2014 summer school version reviewe

Translating international HIV treatment guidelines into local priorities in Indonesia

Objective: International guidelines recommend countries to expand antiretroviral therapy (ART) to all HIV-infected individuals and establish local-level priorities in relation to other treatment, prevention and mitigation interventions through fair processes. However, no practical guidance is provided for such priority-setting processes. Evidence-informed deliberative processes (EDPs) fill this gap and combine stakeholder deliberation to incorporate relevant social values with rational decision-making informed by evidence on these values. This study reports on the first-time implementation and evaluation of an EDP in HIV control, organised to support the AIDS Commission in West Java province, Indonesia, in the development of its strategic plan for 2014–2018. Methods: Under the responsibility of the provincial AIDS Commission, an EDP was implemented to select priority interventions using six steps: (i) situational analysis; (ii) formation of a multistakeholder Consultation Panel; (iii) selection of criteria; (iv) identification and assessment of interventions’ performance; (v) deliberation; and (vi) selection of funding and implementing institutions. An independent researcher conducted in-depth interviews (n = 21) with panel members to evaluate the process. Results: The Consultation Pa

Translating international HIV treatment guidelines into local priorities in Indonesia

Contains fulltext : 189873.pdf (publisher's version ) (Open Access

Benefits of SMT and of Parallel Transpose Algorithm for the Large-Scale GYSELA Application

International audienceThis article describes how we manage to increase performance and to extend features of a large parallel application through the use of simultaneous multithreading (SMT) and by designing a robust parallel transpose algorithm. The semi-Lagrangian code Gysela typically performs large physics simulations using a few thousands of cores, between 1k cores up to 16k on x86-based clusters. However, simulations with finer resolutions and with kinetic electrons increase those needs by a huge factor, providing a good example of applications requiring Exascale machines. To improve Gysela compute times, we take advantage of efficient SMT implementations available on recent INTEL architectures. We also analyze the cost of a transposition communication scheme that involves a large number of cores in our case. Adaptation of the code for balance load whenever using both SMT and good deployment strategy led to a significant reduction that can be up to 38% of the execution times