Benjamin Jones - courses.csail.mit.edu€¦ · Benjamin Jones . Biophysical Model Overview...
Transcript of Benjamin Jones - courses.csail.mit.edu€¦ · Benjamin Jones . Biophysical Model Overview...
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Benjamin Jones
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Biophysical Model Overview
Numerically solve some form of the conservation laws. Fortran / MPI models:
ROMS HYCOM FVCOM
Optionally add subgrid scale processes as a stochastic component.
Integrate larval trajectories, including growth, behavior, etc.
Postprocess the data to extract information. Write analyses in Python, R, MATLAB, Fortran, C, etc
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MPI fork()
OpenMP CUDA
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OpenMP Parallelization
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MPI
MPI Parallelization
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Shared memory
Multi-process parallelization
POSIX Signals
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CUDA
Pointer
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Flow field and parameterization
� 2D steadily translated Rankine vortex � 500km X 1000km grid � 1.5km and 4km lattice
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Possible Extensions: Features
� Support for real ocean models � FVCOM * � HYCOM � ROMS
� Advection-diffusion module * � Biological module
� Density-dependence * � Growth � Movement
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Possible Extensions: MPI
� Try MPICH2 � Minimize communication � Optimize arrangement of nodes � OpenMP within each node � Dynamically balance number of grid
controllers and particle controllers
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Possible Extensions: CUDA
� Tune threads per block vs. number of blocks
� Reduce data movement � Make used of shared or thread memory � Move temporal interpolation to GPU � Integrate analyses into the model
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Conclusions
� Optimization level matters � GPUs can offer cheap parallelism � Beware of context switching � Communication is expensive � Lots of opportunity for improvement