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NEMO on HECToR A
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NEMO on HECToR A
Contents
Introduction
The NEMO dCSE Project
What is NEMO?
HECToR
Introduction
Architecture
Modes of operation
Communication and I/O networks
Operating systems
Compiling NEMO on HECToR
PGI
PathScale
Running NEMO on HECToR: creating new experiment data, verifying the output and visualising data
Creating a new set of NEMO experiment data
Combining the output data
Using CDFTOOLS for verification of NEMO output
Visualising the NEMO output
NEMO performance
Scaling for equal grid dimensions
Single core versus dual core performance
Performance for different grid dimensions
Scaling plot
Removing the land only grid cells
Compiler optimisations
Summary of benchmarking study
Optimal processor count
Time spent in file I/O and initialisation
Aside on I/O strategies for parallel codes
NEMO file I/O
NetCDF performance and installation
NetCDF 3.6.2 performance on HECToR
Installing zlib 1.2.3
Installing HDF5 1.8.1
Installing netCDF 4.0
NOCSCOMBINE performance on HECToR for different versions of netCDF
NEMO V3.0
Compilation
Performance for different compiler flags
Performance of NEMO V3.0
Converting NEMO to use netCDF 4.0
NEMO AGRIF nested model running/debugging
Introduction to the nested model problem
BASIC nested model
MERGED nested model
Conclusions and future work
Summary of work and conclusions
Other work
Future work
NEMO output comparison scripts
Some notes on HDF5 datasets
HDF5 Filters
Bibliography