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Geoscientific Model Development An interactive open-access journal of the European Geosciences Union
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Discussion papers
https://doi.org/10.5194/gmd-2019-257
© Author(s) 2019. This work is distributed under
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/gmd-2019-257
© Author(s) 2019. This work is distributed under
the Creative Commons Attribution 4.0 License.

Submitted as: development and technical paper 11 Oct 2019

Submitted as: development and technical paper | 11 Oct 2019

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This discussion paper is a preprint. It is a manuscript under review for the journal Geoscientific Model Development (GMD).

Parallel I/O in FMS and MOM5

Rui Yang1, Marshall Ward1,a, and Ben Evans1 Rui Yang et al.
  • 1National ComputationalInfrastructure, the Australian NationalUniversity, Canberra, ACT 0200, Australia
  • anow at: Geophysics Fluid Dynamics Laboratory, National Oceanic & Atmospheric Administration, Princeton, NJ 08540-6649, USA

Abstract. We present an implementation of parallel I/O in the Modular Ocean Model (MOM), a numerical ocean model used for climate forecasting, and determine its optimal performance over a range of tuning parameters. Our implementation uses the parallel API of the netCDF library, and we investigate the potential bottlenecks associated with the model configuration, netCDF implementation, the underpinning MPI-IO library/implementations and Lustre filesystem. We investigate the performance of a global 0.25° resolution model using 240 and 960 CPUs. The best performance is observed when we limit the number of contiguous I/O domains on each compute node and assign one MPI rank to aggregate and write the data from each node, while ensuring that all nodes participate in writing this data to our Lustre filesystem. These best performance configurations are then applied to a higher 0.1° resolution global model using 720 and 1440 CPUs, where we observe even greater performance improvements. In all cases, the tuned parallel I/O implementation achieves much faster write speeds relative to serial single-file I/O, with write speeds up to 60 times faster at higher resolutions. Under the constraints outlined above, we observe that the performance scales as the number of compute nodes and I/O aggregators are increased, ensuring the continued scalability of I/O-intensive MOM5 model runs that will be used in our next generation higher resolution simulations.

Rui Yang et al.
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Status: open (until 06 Dec 2019)
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Short summary
Parallel I/O is implemented in the Modular Ocean Model (MOM) with optimal performance over a range of tuning parameters at model configuration, netCDF, MPI-IO and Lustre filesystem. The scalable parallel I/O performance is observed at 0.1° resolution global model and it could achieve up to 60 times faster in write speed relative to serial single-file I/O running on 960PEs.
Parallel I/O is implemented in the Modular Ocean Model (MOM) with optimal performance over a...
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