Tracing long running applications: A case study using Gromacs
Michael Wagner, Jens Doleschal, Andreas Knüpfer · 2015
Performance analysis is inevitable to develop applications that utilize the enormous capabilities of current HPC systems. While many recent tool studies focused on large scales, performance analysis of long-running applications has not been paid much attention. This paper investigates challenges that arise from monitoring long-running real-life applications, in particular, the disruptive bias of intermediate memory buffer flushes in the measurement environment. We propose a concept for an in-memory event tracing that completely avoids intermediate memory buffer flushes. We evaluate to which extent such an in-memory event tracing workflow helps overcoming the critical properties, such as resulting trace size, application slow down, and measurement bias. We utilize a prototype implementation, based on Score-P and OTF2, with the molecular dynamics packages Gromacs, an application currently infeasible to monitor in a full production run.