Parallel Performance and I/O Profiling of HPC RNA-Seq Applications

Lucas Cruz, Micaella Coelho, Marcelo Galheigo, Andre Carneiro, Diego Carvalho, Luiz Gadelha, Francieli Boito, Philippe Navaux, Carla Osthoff, Kary Ocaña


Transcriptomics experiments are often expressed as scientific workflows and benefit from high-performance computing environments. In these environments, workflow management systems can allow handling independent or communicating tasks across nodes, which may be heterogeneous. Specifically, transcriptomics workflows may treat large volumes of data. ParslRNA-Seq is a workflow for analyzing RNA-Seq experiments, which efficiently manages the estimation of differential gene expression levels from raw sequencing reads and can be executed in varied computational environments, ranging from personal computers to high-performance computing environments with parallel scripting library Parsl. In this work, we aim to investigate CPU and I/O metrics critical for improving the efficiency and resilience of current and upcoming RNA-Seq workflows. Based on the resulting profiling of CPU and I/O data collection, we demonstrate that we can correctly identify anomalies of transcriptomics workflow performance that is an essential resource to optimize its use of high-performance computing systems.


Supercomputing, sorkflow, RNA-seq

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