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Fig. 5 | Journal of Cheminformatics

Fig. 5

From: patRoon: open source software platform for environmental mass spectrometry based non-target screening

Fig. 5

Parallelization benchmark results. a Benchmark results for commonly used CLI tools applied in patRoon workflows under varying parallelization conditions. The tested tools were msConvert, FeatureFinderMetabo (FFM), GenForm, SIRIUS and MetFrag. Tests were performed with “simple” (left) and “complex” (right) input conditions (Table 4) to simulate varying workflow complexity. Parallelization was performed with the multiprocessing functionality of patRoon (top) or by using native multithreading (bottom, for tools that supported this). Graphs represent number of processes or threads versus relative execution time (normalized to sequential results). The dotted grey lines represent the theoretical trend if maximum parallelization performance is achieved. The dashed blue line represents the number of physical cores that became the default selection in patRoon based on these results. b Comparison of execution times (normalized to the execution times of the unoptimized results) when tools are executed without optimizations (green), executed with native multithreading (FeatureFinderMetabo, SIRIUS and MetFrag) or batch mode (GenForm) (orange), executed with multiprocessing (purple) or a combination of the latter two (pink), using simple (left) and complex (right) input conditions. c Overview of execution times for a complete patRoon workflow executed under optimized versus unoptimized conditions. All results for msConvert and SIRIUS were obtained without enabling their native batch mode

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