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References and acknowledgements | ||
=============================== | ||
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Citing tlm_adjoint | ||
------------------ | ||
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tlm_adjoint is described in | ||
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- James R. Maddison, Daniel N. Goldberg, and Benjamin D. Goddard, 'Automated | ||
calculation of higher order partial differential equation constrained | ||
derivative information', SIAM Journal on Scientific Computing, 41(5), pp. | ||
C417--C445, 2019, doi: 10.1137/18M1209465 | ||
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The automated assembly and linear solver caching applied by tlm_adjoint is | ||
based on the approach described in | ||
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- J. R. Maddison and P. E. Farrell, 'Rapid development and adjoining of | ||
transient finite element models', Computer Methods in Applied Mechanics and | ||
Engineering, 276, 95--121, 2014, doi: 10.1016/j.cma.2014.03.010 | ||
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Checkpointing with tlm_adjoint is described in | ||
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- James R. Maddison, 'Step-based checkpointing with high-level algorithmic | ||
differentiation', Journal of Computational Science 82, 102405, 2024, | ||
doi: 10.1016/j.jocs.2024.102405 | ||
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References | ||
---------- | ||
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dolfin-adjoint | ||
`````````````` | ||
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tlm_adjoint implements high-level algorithmic differentiation using an | ||
approach based on that used by dolfin-adjoint, described in | ||
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- P. E. Farrell, D. A. Ham, S. W. Funke, and M. E. Rognes, 'Automated | ||
derivation of the adjoint of high-level transient finite element programs', | ||
SIAM Journal on Scientific Computing 35(4), pp. C369--C393, 2013, | ||
doi: 10.1137/120873558 | ||
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tlm_adjoint was developed from a custom extension to dolfin-adjoint. | ||
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Taylor remainder convergence testing | ||
```````````````````````````````````` | ||
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The functions in `tlm_adjoint/verification.py | ||
<autoapi/tlm_adjoint/verification/index.html>`_ implement Taylor remainder | ||
convergence testing using the approach described in | ||
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- P. E. Farrell, D. A. Ham, S. W. Funke, and M. E. Rognes, 'Automated | ||
derivation of the adjoint of high-level transient finite element programs', | ||
SIAM Journal on Scientific Computing 35(4), pp. C369--C393, 2013, | ||
doi: 10.1137/120873558 | ||
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Differentiating fixed-point problems | ||
```````````````````````````````````` | ||
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The `FixedPointSolver` class in `tlm_adjoint/fixed_point.py | ||
<autoapi/tlm_adjoint/fixed_point/index.html>`_ derives tangent-linear and | ||
adjoint information using the approach described in | ||
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- Jean Charles Gilbert, 'Automatic differentiation and iterative processes', | ||
Optimization Methods and Software, 1(1), pp. 13--21, 1992, | ||
doi: 10.1080/10556789208805503 | ||
- Bruce Christianson, 'Reverse accumulation and attractive fixed points', | ||
Optimization Methods and Software, 3(4), pp. 311--326, 1994, | ||
doi: 10.1080/10556789408805572 | ||
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Binomial checkpointing | ||
`````````````````````` | ||
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The `MultistageCheckpointSchedule` class in | ||
`tlm_adjoint/checkpoint_schedules/binomial.py | ||
<autoapi/tlm_adjoint/checkpoint_schedules/binomial/index.html>`_ implements the | ||
binomial checkpointing strategy described in | ||
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- Andreas Griewank and Andrea Walther, 'Algorithm 799: revolve: an | ||
implementation of checkpointing for the reverse or adjoint mode of | ||
computational differentiation', ACM Transactions on Mathematical Software, | ||
26(1), pp. 19--45, 2000, doi: 10.1145/347837.347846 | ||
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The `MultistageCheckpointSchedule` class determines a memory/disk storage | ||
distribution using an initial run of the checkpoint schedule, leading to a | ||
distribution equivalent to that in | ||
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- Philipp Stumm and Andrea Walther, 'MultiStage approaches for optimal offline | ||
checkpointing', SIAM Journal on Scientific Computing, 31(3), pp. 1946--1967, | ||
2009, doi: 10.1137/080718036 | ||
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The `TwoLevelCheckpointSchedule` class in | ||
`tlm_adjoint/checkpoint_schedules/binomial.py | ||
<autoapi/tlm_adjoint/checkpoint_schedules/binomial/index.html>`_ implements the | ||
two-level mixed periodic/binomial checkpointing approach described in | ||
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- Gavin J. Pringle, Daniel C. Jones, Sudipta Goswami, Sri Hari Krishna | ||
Narayanan, and Daniel Goldberg, 'Providing the ARCHER community with adjoint | ||
modelling tools for high-performance oceanographic and cryospheric | ||
computation', version 1.1, EPCC, 2016 | ||
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and in the supporting information for | ||
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- D. N. Goldberg, T. A. Smith, S. H. K. Narayanan, P. Heimbach, and M. | ||
Morlighem,, 'Bathymetric influences on Antarctic ice-shelf melt rates', | ||
Journal of Geophysical Research: Oceans, 125(11), e2020JC016370, 2020, | ||
doi: 10.1029/2020JC016370 | ||
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PyTorch | ||
``````` | ||
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The PyTorch interface in `tlm_adjoint/torch.py | ||
<autoapi/tlm_adjoint/torch/index.html>`_ follows the same principles as | ||
described in | ||
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- Nacime Bouziani and David A. Ham, 'Physics-driven machine learning models | ||
coupling PyTorch and Firedrake', 2023, arXiv:2303.06871v3 | ||
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Funding | ||
------- | ||
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Early development work leading to tlm_adjoint was conducted as part of a U.K. | ||
Natural Environment Research Council funded project (NE/L005166/1). Further | ||
development has been conducted as part of a U.K. Engineering and Physical | ||
Sciences Research Council funded project (EP/R021600/1) and a Natural | ||
Environment Research Council funded project (NE/T001607/1). |
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