Mock data loading iterface #336
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grassesi merged 1 commit intoecmwf:grassesi/dev/hackathon_evaluationfrom Jun 13, 2025
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Mock data loading iterface #336grassesi merged 1 commit intoecmwf:grassesi/dev/hackathon_evaluationfrom
grassesi merged 1 commit intoecmwf:grassesi/dev/hackathon_evaluationfrom
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* Implement mock IO (#336) * Adapt score class score class (#339) * Implement mock IO * Adapt score class * Removing unused file (#349) * remove database folder (#355) * Small change - CI - pinning the version of formatting (#361) * changes * changes * Update INSTALL.md * Update INSTALL.md * Fixed Exxx lint issues (#284) * Rebased to the latest changes and linted new changes * addressed review comments * addressed review comments * Linted the latest changes. * corrected the formating * corrected the formating * configured ruff to use LF line endings in pyproject.toml * [357] Sub-package for evaluation (#359) * working * changes * removing deps from non-core project * changes * fixes * comments * Iluise quick fix stac (#374) * remove database folder * fix database * Simplifying workflow for plot_training (#368) * Simplifying workflow for plot_training * Ruffed * Working on implementing exclude_source * Remove unused code * Fixed ruff issue * Fixing bug in lat handling (377) (#378) * Fixing bug in lat handling * Added comment --------- Co-authored-by: Seb Hickman <56727418+shmh40@users.noreply.github.com> * recover num_ranks from previous run to calculate epoch_base (#317) * recover num_ranks from previous run to calculate epoch_base * set email settings for commits * addressing Tim's comment * make ruff happy * improve style * changes (#385) Linter rule so np.ndarray is not used as type * changed the script name from evaluate to inference as it simply gener… (#376) * changed the script name from evaluate to inference as it simply generate infer samples * changed evaluate to inference in the main scripts and corresponding calls in the config * update the main function for the inference script * changed evaluate to inference also in docstring, unit test scripts, and integration test scripts --------- Co-authored-by: Patnala,Ankit <a.patnala@fz-juelich.de> * Introduce tuples instead for strings to avoid TypeError (#392) * Exclude channels from src / target (#363) * Exclude channels from src / target * Simplified code and added comment that pattern matching is used * Adding new stream config * Fixing bug that led to error when accessing self.ds when dataset is empty * Wokign on exlcude_source * work in progress * Fixing incorrect formating for logger (#388) * Ruffed * Refactored and cleaned up channel selection. Also added check that channels are not empty * Cleaned channel parsing and selection * Adjustments * Removing asserts incompatible with empty dataset --------- Co-authored-by: Christian Lessig <christian.lessig@ecwmf.int> * add embed_dropout_rate to config v1 (#358) * [402] adds checks to the pull request (#403) * chanegs * mistake * mistake * mistake * changes * doc * Introduce masking class and incorporate in TokenizerMasking (#383) * creating masking class and adapting tokenizer_masking to use this class * minor changes to masking.py and tokenizer_masking * removed old tokenizer_masking * include masking_strategy in default_config * change ValueError to assert * linting formatting changes files * further linting of docstrings * create mask_source and mask_target in Masker, and update tokenizer_masking to use these, then style improvements * linted masking, tokenizer_masking * modify masker, rng and perm_sel now part of class, remove extra masking_rate, update comments, remove archived class * remove check if all masked, not masked * remove self.masking_rate from MultiStreamDS class, and masking args from batchify_source * update tokenizer utils with description of idx_ord_lens in comment * remove masking args from batchify_, perm_sel removed now internal to Masker class, remove handling special cases of masking (all masked) * adding masking_strategy: to config * remove unused mentions of masking_combination * removed comment about streams * changed assert to check self perm_sel is not None * ruff masking, tokenizer_masking * Ruffed * Added warning to capture corner case, likely due to incorrect user settings. * Fixed incorrect call twice * Fixed missing conditional for logger statement * Required changes for better handling of rngs * Improved handling of rngs * Improved handling of rng --------- Co-authored-by: Christian Lessig <christian.lessig@ecmwf.int> * Implement per-channel logging (#283) * Fix bug with seed being divided by 0 for worker ID=0 * Fix bug causing crash when secrets aren't in private config * Implement logging losses per channel * Fix issue with empty targets * Rework loss logging * ruff * Remove computing max_channels * Change variables names * ruffed * Remove redundant enumerations * Use stages for logging * Add type hints * Apply the review * ruff * fix * Fix type hints * ruff --------- Co-authored-by: Tim Hunter <tim.hunter@ecmwf.int> * [346] Passing options through the slurm script (#400) * changes * fixes * refactor `validation_io.write_validation` to make it more readable * remove legacy code `validation_io.read_validation` * encapsulate artifact path logic in config module * remove redundant attribute `Trainer.path_run` * use config to look up base_path in `write_validation` * remove unused `write_validation` args: `base_path`, `rank` * ensure correct type for pathes * remove streams initialization from `Trainer` * remove path logic from `Trainer.save_model` * simplify conditional * rename mock io module * update uv to include dask * Implement io module to support reading/writing model output * implement new validation_io routine * use new write_validation routine * remove unused code * rename output routine to `write_output` * ruffed and added comments * fixed annotation * use simple __init__ method for `OutputItem` instead of dataclasses magic * address reviewers comments * rename method * add simple docstrings * ruffed * typehint fixes * refactor names * update comments and typehints, dont import pytorch * remove `__post_init__` methods, cache properties * fixes and integration test * final fixes :) * changes * changes * changes * changes * changes * more work * changes * changes * changes * ruffed * ruffed * improve logging and comments * Update to score-class according to internal discussions and feedback in PR. * Add license header. * Ruffed code. * Update to score-class according to internal discussions and feedback in PR. * Add license header. * Ruffed code. * Add doc-string to call-method and provide example usage for efficient graph-construction. * Some fixes to score-class. * Some fixes to handling aggregation dimension. * Add missing import of MockIO. * changes * changes * removing the scores * changes * changes * changes * changes * changes * changes * changes * changes * changes * changes * changes * changes * changes * changes --------- Co-authored-by: Kacper Nowak <kacper.nowak@awi.de> Co-authored-by: Christian Lessig <christian.lessig@ecmwf.int> Co-authored-by: iluise <72020169+iluise@users.noreply.github.com> Co-authored-by: Sindhu-Vasireddy <98752594+Sindhu-Vasireddy@users.noreply.github.com> Co-authored-by: Seb Hickman <56727418+shmh40@users.noreply.github.com> Co-authored-by: Julian Kuehnert <Jubeku@users.noreply.github.com> Co-authored-by: ankitpatnala <ankitpatnala@gmail.com> Co-authored-by: Patnala,Ankit <a.patnala@fz-juelich.de> Co-authored-by: Savvas Melidonis <79579567+SavvasMel@users.noreply.github.com> Co-authored-by: Christian Lessig <christian.lessig@ecwmf.int> Co-authored-by: Till Hauer <till@web-hauer.de> Co-authored-by: Simon Grasse <s.grasse@fz-juelich.de> Co-authored-by: Michael <m.langguth@fz-juelich.de>
jpolz
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Jul 10, 2025
* Implement mock IO (ecmwf#336) * Adapt score class score class (ecmwf#339) * Implement mock IO * Adapt score class * Removing unused file (ecmwf#349) * remove database folder (ecmwf#355) * Small change - CI - pinning the version of formatting (ecmwf#361) * changes * changes * Update INSTALL.md * Update INSTALL.md * Fixed Exxx lint issues (ecmwf#284) * Rebased to the latest changes and linted new changes * addressed review comments * addressed review comments * Linted the latest changes. * corrected the formating * corrected the formating * configured ruff to use LF line endings in pyproject.toml * [357] Sub-package for evaluation (ecmwf#359) * working * changes * removing deps from non-core project * changes * fixes * comments * Iluise quick fix stac (ecmwf#374) * remove database folder * fix database * Simplifying workflow for plot_training (ecmwf#368) * Simplifying workflow for plot_training * Ruffed * Working on implementing exclude_source * Remove unused code * Fixed ruff issue * Fixing bug in lat handling (377) (ecmwf#378) * Fixing bug in lat handling * Added comment --------- Co-authored-by: Seb Hickman <56727418+shmh40@users.noreply.github.com> * recover num_ranks from previous run to calculate epoch_base (ecmwf#317) * recover num_ranks from previous run to calculate epoch_base * set email settings for commits * addressing Tim's comment * make ruff happy * improve style * changes (ecmwf#385) Linter rule so np.ndarray is not used as type * changed the script name from evaluate to inference as it simply gener… (ecmwf#376) * changed the script name from evaluate to inference as it simply generate infer samples * changed evaluate to inference in the main scripts and corresponding calls in the config * update the main function for the inference script * changed evaluate to inference also in docstring, unit test scripts, and integration test scripts --------- Co-authored-by: Patnala,Ankit <a.patnala@fz-juelich.de> * Introduce tuples instead for strings to avoid TypeError (ecmwf#392) * Exclude channels from src / target (ecmwf#363) * Exclude channels from src / target * Simplified code and added comment that pattern matching is used * Adding new stream config * Fixing bug that led to error when accessing self.ds when dataset is empty * Wokign on exlcude_source * work in progress * Fixing incorrect formating for logger (ecmwf#388) * Ruffed * Refactored and cleaned up channel selection. Also added check that channels are not empty * Cleaned channel parsing and selection * Adjustments * Removing asserts incompatible with empty dataset --------- Co-authored-by: Christian Lessig <christian.lessig@ecwmf.int> * add embed_dropout_rate to config v1 (ecmwf#358) * [402] adds checks to the pull request (ecmwf#403) * chanegs * mistake * mistake * mistake * changes * doc * Introduce masking class and incorporate in TokenizerMasking (ecmwf#383) * creating masking class and adapting tokenizer_masking to use this class * minor changes to masking.py and tokenizer_masking * removed old tokenizer_masking * include masking_strategy in default_config * change ValueError to assert * linting formatting changes files * further linting of docstrings * create mask_source and mask_target in Masker, and update tokenizer_masking to use these, then style improvements * linted masking, tokenizer_masking * modify masker, rng and perm_sel now part of class, remove extra masking_rate, update comments, remove archived class * remove check if all masked, not masked * remove self.masking_rate from MultiStreamDS class, and masking args from batchify_source * update tokenizer utils with description of idx_ord_lens in comment * remove masking args from batchify_, perm_sel removed now internal to Masker class, remove handling special cases of masking (all masked) * adding masking_strategy: to config * remove unused mentions of masking_combination * removed comment about streams * changed assert to check self perm_sel is not None * ruff masking, tokenizer_masking * Ruffed * Added warning to capture corner case, likely due to incorrect user settings. * Fixed incorrect call twice * Fixed missing conditional for logger statement * Required changes for better handling of rngs * Improved handling of rngs * Improved handling of rng --------- Co-authored-by: Christian Lessig <christian.lessig@ecmwf.int> * Implement per-channel logging (ecmwf#283) * Fix bug with seed being divided by 0 for worker ID=0 * Fix bug causing crash when secrets aren't in private config * Implement logging losses per channel * Fix issue with empty targets * Rework loss logging * ruff * Remove computing max_channels * Change variables names * ruffed * Remove redundant enumerations * Use stages for logging * Add type hints * Apply the review * ruff * fix * Fix type hints * ruff --------- Co-authored-by: Tim Hunter <tim.hunter@ecmwf.int> * [346] Passing options through the slurm script (ecmwf#400) * changes * fixes * refactor `validation_io.write_validation` to make it more readable * remove legacy code `validation_io.read_validation` * encapsulate artifact path logic in config module * remove redundant attribute `Trainer.path_run` * use config to look up base_path in `write_validation` * remove unused `write_validation` args: `base_path`, `rank` * ensure correct type for pathes * remove streams initialization from `Trainer` * remove path logic from `Trainer.save_model` * simplify conditional * rename mock io module * update uv to include dask * Implement io module to support reading/writing model output * implement new validation_io routine * use new write_validation routine * remove unused code * rename output routine to `write_output` * ruffed and added comments * fixed annotation * use simple __init__ method for `OutputItem` instead of dataclasses magic * address reviewers comments * rename method * add simple docstrings * ruffed * typehint fixes * refactor names * update comments and typehints, dont import pytorch * remove `__post_init__` methods, cache properties * fixes and integration test * final fixes :) * changes * changes * changes * changes * changes * more work * changes * changes * changes * ruffed * ruffed * improve logging and comments * Update to score-class according to internal discussions and feedback in PR. * Add license header. * Ruffed code. * Update to score-class according to internal discussions and feedback in PR. * Add license header. * Ruffed code. * Add doc-string to call-method and provide example usage for efficient graph-construction. * Some fixes to score-class. * Some fixes to handling aggregation dimension. * Add missing import of MockIO. * changes * changes * removing the scores * changes * changes * changes * changes * changes * changes * changes * changes * changes * changes * changes * changes * changes * changes --------- Co-authored-by: Kacper Nowak <kacper.nowak@awi.de> Co-authored-by: Christian Lessig <christian.lessig@ecmwf.int> Co-authored-by: iluise <72020169+iluise@users.noreply.github.com> Co-authored-by: Sindhu-Vasireddy <98752594+Sindhu-Vasireddy@users.noreply.github.com> Co-authored-by: Seb Hickman <56727418+shmh40@users.noreply.github.com> Co-authored-by: Julian Kuehnert <Jubeku@users.noreply.github.com> Co-authored-by: ankitpatnala <ankitpatnala@gmail.com> Co-authored-by: Patnala,Ankit <a.patnala@fz-juelich.de> Co-authored-by: Savvas Melidonis <79579567+SavvasMel@users.noreply.github.com> Co-authored-by: Christian Lessig <christian.lessig@ecwmf.int> Co-authored-by: Till Hauer <till@web-hauer.de> Co-authored-by: Simon Grasse <s.grasse@fz-juelich.de> Co-authored-by: Michael <m.langguth@fz-juelich.de>
tjhunter
added a commit
that referenced
this pull request
Nov 18, 2025
* Revert "Implement per-channel logging (#283)" (#434)
This reverts commit 989ab6e1d6e8c0f69594414c7733adf30acd1c54.
* Fix FESOM datareader and int overflow (#417)
* Fix indexing in DataReaderFesom
* Enforce using only int64 in data loading
* ruff
* ruff2
* Review
* Change int64 back to int32
* changes (#462)
* Fix incorrect handling of empty window (which triggered problem in IO writing code). (#447)
* Update default_config.yml (#446)
analysis_streams_output is missing, which leads to error with val_initial=True and log_validation > 0.
* Re-enabled option to run plot_training as script and fixed -rf argument (#444)
* Re-enabled option to runplot_training as script and removed relative path as default from mutually-exclusive argument -rf.
* Ruffed code.
* Ruff check fix.
* Rename flags for parsing configuration and fixed default handling for standard config YAML-file.
* fix era5 config (#473)
Adding z back in
* [251] Merge new IO class (#469)
* Implement mock IO (#336)
* Adapt score class score class (#339)
* Implement mock IO
* Adapt score class
* Removing unused file (#349)
* remove database folder (#355)
* Small change - CI - pinning the version of formatting (#361)
* changes
* changes
* Update INSTALL.md
* Update INSTALL.md
* Fixed Exxx lint issues (#284)
* Rebased to the latest changes and linted new changes
* addressed review comments
* addressed review comments
* Linted the latest changes.
* corrected the formating
* corrected the formating
* configured ruff to use LF line endings in pyproject.toml
* [357] Sub-package for evaluation (#359)
* working
* changes
* removing deps from non-core project
* changes
* fixes
* comments
* Iluise quick fix stac (#374)
* remove database folder
* fix database
* Simplifying workflow for plot_training (#368)
* Simplifying workflow for plot_training
* Ruffed
* Working on implementing exclude_source
* Remove unused code
* Fixed ruff issue
* Fixing bug in lat handling (377) (#378)
* Fixing bug in lat handling
* Added comment
---------
Co-authored-by: Seb Hickman <56727418+shmh40@users.noreply.github.com>
* recover num_ranks from previous run to calculate epoch_base (#317)
* recover num_ranks from previous run to calculate epoch_base
* set email settings for commits
* addressing Tim's comment
* make ruff happy
* improve style
* changes (#385)
Linter rule so np.ndarray is not used as type
* changed the script name from evaluate to inference as it simply gener… (#376)
* changed the script name from evaluate to inference as it simply generate infer samples
* changed evaluate to inference in the main scripts and corresponding calls in the config
* update the main function for the inference script
* changed evaluate to inference also in docstring, unit test scripts, and integration test scripts
---------
Co-authored-by: Patnala,Ankit <a.patnala@fz-juelich.de>
* Introduce tuples instead for strings to avoid TypeError (#392)
* Exclude channels from src / target (#363)
* Exclude channels from src / target
* Simplified code and added comment that pattern matching is used
* Adding new stream config
* Fixing bug that led to error when accessing self.ds when dataset is empty
* Wokign on exlcude_source
* work in progress
* Fixing incorrect formating for logger (#388)
* Ruffed
* Refactored and cleaned up channel selection. Also added check that channels are not empty
* Cleaned channel parsing and selection
* Adjustments
* Removing asserts incompatible with empty dataset
---------
Co-authored-by: Christian Lessig <christian.lessig@ecwmf.int>
* add embed_dropout_rate to config v1 (#358)
* [402] adds checks to the pull request (#403)
* chanegs
* mistake
* mistake
* mistake
* changes
* doc
* Introduce masking class and incorporate in TokenizerMasking (#383)
* creating masking class and adapting tokenizer_masking to use this class
* minor changes to masking.py and tokenizer_masking
* removed old tokenizer_masking
* include masking_strategy in default_config
* change ValueError to assert
* linting formatting changes files
* further linting of docstrings
* create mask_source and mask_target in Masker, and update tokenizer_masking to use these, then style improvements
* linted masking, tokenizer_masking
* modify masker, rng and perm_sel now part of class, remove extra masking_rate, update comments, remove archived class
* remove check if all masked, not masked
* remove self.masking_rate from MultiStreamDS class, and masking args from batchify_source
* update tokenizer utils with description of idx_ord_lens in comment
* remove masking args from batchify_, perm_sel removed now internal to Masker class, remove handling special cases of masking (all masked)
* adding masking_strategy: to config
* remove unused mentions of masking_combination
* removed comment about streams
* changed assert to check self perm_sel is not None
* ruff masking, tokenizer_masking
* Ruffed
* Added warning to capture corner case, likely due to incorrect user settings.
* Fixed incorrect call twice
* Fixed missing conditional for logger statement
* Required changes for better handling of rngs
* Improved handling of rngs
* Improved handling of rng
---------
Co-authored-by: Christian Lessig <christian.lessig@ecmwf.int>
* Implement per-channel logging (#283)
* Fix bug with seed being divided by 0 for worker ID=0
* Fix bug causing crash when secrets aren't in private config
* Implement logging losses per channel
* Fix issue with empty targets
* Rework loss logging
* ruff
* Remove computing max_channels
* Change variables names
* ruffed
* Remove redundant enumerations
* Use stages for logging
* Add type hints
* Apply the review
* ruff
* fix
* Fix type hints
* ruff
---------
Co-authored-by: Tim Hunter <tim.hunter@ecmwf.int>
* [346] Passing options through the slurm script (#400)
* changes
* fixes
* refactor `validation_io.write_validation` to make it more readable
* remove legacy code `validation_io.read_validation`
* encapsulate artifact path logic in config module
* remove redundant attribute `Trainer.path_run`
* use config to look up base_path in `write_validation`
* remove unused `write_validation` args: `base_path`, `rank`
* ensure correct type for pathes
* remove streams initialization from `Trainer`
* remove path logic from `Trainer.save_model`
* simplify conditional
* rename mock io module
* update uv to include dask
* Implement io module to support reading/writing model output
* implement new validation_io routine
* use new write_validation routine
* remove unused code
* rename output routine to `write_output`
* ruffed and added comments
* fixed annotation
* use simple __init__ method for `OutputItem` instead of dataclasses magic
* address reviewers comments
* rename method
* add simple docstrings
* ruffed
* typehint fixes
* refactor names
* update comments and typehints, dont import pytorch
* remove `__post_init__` methods, cache properties
* fixes and integration test
* final fixes :)
* changes
* changes
* changes
* changes
* changes
* more work
* changes
* changes
* changes
* ruffed
* ruffed
* improve logging and comments
* Update to score-class according to internal discussions and feedback in PR.
* Add license header.
* Ruffed code.
* Update to score-class according to internal discussions and feedback in PR.
* Add license header.
* Ruffed code.
* Add doc-string to call-method and provide example usage for efficient graph-construction.
* Some fixes to score-class.
* Some fixes to handling aggregation dimension.
* Add missing import of MockIO.
* changes
* changes
* removing the scores
* changes
* changes
* changes
* changes
* changes
* changes
* changes
* changes
* changes
* changes
* changes
* changes
* changes
* changes
---------
Co-authored-by: Kacper Nowak <kacper.nowak@awi.de>
Co-authored-by: Christian Lessig <christian.lessig@ecmwf.int>
Co-authored-by: iluise <72020169+iluise@users.noreply.github.com>
Co-authored-by: Sindhu-Vasireddy <98752594+Sindhu-Vasireddy@users.noreply.github.com>
Co-authored-by: Seb Hickman <56727418+shmh40@users.noreply.github.com>
Co-authored-by: Julian Kuehnert <Jubeku@users.noreply.github.com>
Co-authored-by: ankitpatnala <ankitpatnala@gmail.com>
Co-authored-by: Patnala,Ankit <a.patnala@fz-juelich.de>
Co-authored-by: Savvas Melidonis <79579567+SavvasMel@users.noreply.github.com>
Co-authored-by: Christian Lessig <christian.lessig@ecwmf.int>
Co-authored-by: Till Hauer <till@web-hauer.de>
Co-authored-by: Simon Grasse <s.grasse@fz-juelich.de>
Co-authored-by: Michael <m.langguth@fz-juelich.de>
* [459] Attempt to fix ruff differences (#463)
* changes
* debug
* changes
* changes
* Update pyproject.toml (#457)
* Continue training through slurm script (#395)
* train_continue via slurm
* using __main__ as entry point for slurm script
* reverting config files to match base branch
* reverting config files to match base branch
* removing param_sum control logging before and after loading of model weights
* run ruff
* check whether from_run_id is in arguments
* trigger PR check
* remove block to set reuse_run_id=True
---------
Co-authored-by: Julian Kuehnert <julian.kuehnert@ecwmf.int>
* added the .python_version file set to python 3.12 (#482)
Co-authored-by: Kerem Can Tezcan <ktezcan0@login07.leonardo.local>
* script (#489)
* Remove print statements for logging (#421) (#439)
* first change
* removed all prints
* changed model.py back
* adding comments and fixes@
* added ruff fixes
* reverting files for PR
* ruff fixes
* removing run_id.py
* formatting changes
* changing comments in check_gh_issue script
---------
Co-authored-by: owens1 <owens1@jwlogin09.juwels>
Co-authored-by: Timothy Hunter <tim.hunter@ecmwf.int>
* Rename batchsize to batchsize_per_gpu (#475)
* Rename batchsize to batchsize_per_gpu
* Fix ruff stuff
* fix (#490)
* add polar orbiters and abi-goes to the stac database (#426)
* testing adding metopa and metopb as placeholder drafts to stac database
* added the actual json files because I think we have to
* updated metopa metopb jsons and ets
* add fy3 and update metops
* updated names of metops
* updated metopb untarred size inodes and end date
* update names to instrument, satellite
* add untarred data size and inodes for metopa
* updated to oscar naming, with format platform, instrument, and added fengyun satellites
* update size and inodes of fy3c mwhs
* add fengyun jsons, missing before, and update unique ids of metopa and b
* add processing_level field to metopa as a test
* adding processing level field
* fix up processing level
* updated jsons and jsonnets for provenance
* actually include provenance
* updated to include processor and provider, remove provenance
* add abi-goes
* fix abi goes geometry
* fix latitude and longitude
* fix typo
* hopefully this time lat is right..
* update catalogue json for develop
* check catalogue on this branch
* jsonneted for develop
---------
Co-authored-by: iluise <luise.ilaria@gmail.com>
* Added naming convention checks to lint (#501)
* Added naming convention checks to lint
* Implemented python naming conventions and corrected code accordingly
---------
Co-authored-by: Matthias Karlbauer <ecm1575@ac6-102.bullx>
* Correct the in-code-names for rotation matrices (#516)
* Added naming convention checks to lint
* Implemented python naming conventions and corrected code accordingly
* Corrected renaming of rotation matrices from R to rot instead of to r
---------
Co-authored-by: Matthias Karlbauer <ecm1575@ac6-102.bullx>
* extend format string and timedelta to days (#499)
* extend format string and timedelta to days
* replace with pd.to_timedelta
* import pandas
* ruff
* enforce "HH:MM:SS" format
* ruff
* Mlangguth/develop/issue 251 (#495)
* Add score-class to evaluate-package.
* Add score-class to evaluate-package.
* Lintered and ruffed code.
* Add fix to io.py and update dependencies in common.
* Several small fixes to score-class and fast evaluation.
* Add utils for evaluate.
* Moved to_list to utils and improved doc-strings.
* Improve several doc-strings, avoid formatting of logger and other changes from PR review.
* Add xhistogram and xskillscore to dependencies of evaluate.
* Ruffed code.
* Lintered code.
* Fix incorrect retrieval of validation batch size in validation IO.
* Final minor changes to argument-names
* changes (#471)
* Updated to camel case. (#445)
* Updated to camel case.
* Fixed formatting.
* Revert "Updated to camel case. (#445)" (#530)
This reverts commit 4a8bd49067d86c8c9dd2930544d52cb9db8577af.
* [327] Script to create the links to output directories (results, ...) (#528)
* changes
* fixes
* slash
* slash
* checks
* checks
* Update config parameters lr and grad_clip (#545)
* updated lr and grad_clip in config
* modify lr to 1e-4
* Fixed randomization problem with masking (#510)
* Fixed randomization problem with masking (needs to be verified)
* Making sure the seed is ok
* Fixed problem with seed init.
* More improvements. But problem still seems to be there.
* Clean up of rng handling. Re-initalization is passed through to masker, which was the issue.
* - Fixed prime numbers
- Cleaned up unnecessary rng init and added further comments.
---------
Co-authored-by: clessig <christian.lessig@ecwmf.int>
* Sophiex/dev/upper bound targets (#526)
* recovering my stash
* Fix bug
* Clean up pull request
* Clessig/develop/fix forecasting 448 (#449)
* Removed (second) residual connection for forecasting
* Added init to forecasting engine to small values
* Default values for forecasting experiments
* Updated settings
* Setting local engine to empty
* Fix z settings.
* Revised defaults with larger net
* Revised defaults with larger config
* Restoring default config
* Restoring
* Restoring default
---------
Co-authored-by: clessig <christian.lessig@ecwmf.int>
* Restore self.size_time_embedding in tokenizer_forecast.py (#548)
* Restore self.size_time_embedding in tokenizer_forecast.py
Fixes #547
* Remove empty line for ruff
Remove line for ruff?
* Replace cf.rank==0 with utils.distributed.is_root (#535)
Co-authored-by: wang85 <wang85@jwlogin22.juwels>
* Fixed handling of empty streams in plot_train (#552)
* Fixed handling of empty streams
* Fixed
---------
Co-authored-by: clessig <christian.lessig@ecwmf.int>
* Fix train_continue (#556)
* add DocStrings to model (#268)
* added DocStrings for class ModelParams
* added DocStrings for class Model
* Docstring cleanup v1
* Docstring cleanup v2
* Docstring cleanup v3
* Docstring corrections v1
* Docstring corrections v2
* Docstring corrections v3
* ruff check v1
* ruff check v2
* ruff check v3
---------
Co-authored-by: th3002s <till.hauer@alumni.fh-aachen.de>
* Revised structure in metric JSON-file (#549)
* Update score-class to support groupby-operations for per-sample evaluation.
* Update of fast evaluation pipeline to track metrics sample-wise and dump them into the newly structured JSON-files.
* Changes according to PR review and fix for handling situations with a single sample.
* Changes according to PR review and fix to filter channels for score-calculation.
* Fixed handling of empty source/target channels (#558)
Co-authored-by: clessig <christian.lessig@ecwmf.int>
* Fix to peel_tar_channels to allow situations where no data for fstep=0 is present. (#572)
* Update era5.yml: token size 8 (#583)
* [DRAFT] CLI for scoring and plotting (#522)
* first insterface
* working version
* save json
* add omegaconf
* address comment and clean up interface
* add config
* update scoring class
* Fix to allow for channel-selection in get_data and efficiency improvement to plot_data.
* Avoid circulra dependency issues with to_list-function.
* Fix data selection issues.
* Enable proper handling of lists from omegaconf.
* update to mlangguth89 fork
* refactor forecast step
* ruffed
* add printing summary
* add ZarrData class
* adjust size of the plots
* attempt to solve sorting issue
* Rename model to run in config and in code.
* Fixes to Michael's review comments.
* Ruffed code.
* resync with mlangguth89 + add plot titles
* revert mixed
---------
Co-authored-by: Michael <m.langguth@fz-juelich.de>
* 'Handle list input to forecast_steps (Closes #573)' (#581)
* 'fixed bug not handling list input to forecast step #573'
* linted
* replace error with assert
* lint
* roll-back accidental lint
---------
Co-authored-by: Christian Lessig <christian.lessig@ecmwf.int>
* remove plot config (#597)
* first insterface
* working version
* save json
* add omegaconf
* address comment and clean up interface
* add config
* update scoring class
* Fix to allow for channel-selection in get_data and efficiency improvement to plot_data.
* Avoid circulra dependency issues with to_list-function.
* Fix data selection issues.
* Enable proper handling of lists from omegaconf.
* update to mlangguth89 fork
* refactor forecast step
* ruffed
* add printing summary
* add ZarrData class
* adjust size of the plots
* attempt to solve sorting issue
* Rename model to run in config and in code.
* Fixes to Michael's review comments.
* Ruffed code.
* resync with mlangguth89 + add plot titles
* revert mixed
* remove plot config + style addition to evaluation package
* ruffed
---------
Co-authored-by: Michael <m.langguth@fz-juelich.de>
* integrate IFS scores from Quaver into FastEvaluation (#600)
* first insterface
* working version
* save json
* add omegaconf
* address comment and clean up interface
* add config
* update scoring class
* Fix to allow for channel-selection in get_data and efficiency improvement to plot_data.
* Avoid circulra dependency issues with to_list-function.
* Fix data selection issues.
* Enable proper handling of lists from omegaconf.
* update to mlangguth89 fork
* refactor forecast step
* ruffed
* add printing summary
* add ZarrData class
* adjust size of the plots
* attempt to solve sorting issue
* Rename model to run in config and in code.
* Fixes to Michael's review comments.
* Ruffed code.
* resync with mlangguth89 + add plot titles
* revert mixed
* remove plot config + style addition to evaluation package
* ruffed
* add option to comment out plotting
* resync utils to develop
---------
Co-authored-by: Michael <m.langguth@fz-juelich.de>
* [569] Load eagerly the stream content in order (#585)
* changes
* change
* changes
* Remove loading of streams also from inference.
---------
Co-authored-by: Christian Lessig <christian.lessig@ecmwf.int>
* [DRAFT][590] Rename metrics file (#601)
* Implemented backward-compatible function to read and write `{RUN-ID}_train_metrics.json` (new) or `metrics.json` (old)
* Quick fix for #553 NaT from encode_times_target, move offset to before trigs (#589)
* quick fix for 553 NaT from encode_times_target, move offset
* change offset to 10 minutes...
* ruffed
* apply hotfix to deltas_sec
* ruffed
* fix: associate output stream names with correct index (#519)
* fix: associate output stream names with correct index
* ruffed
* fix: iteration over output items
* address comments
* fix: correctly index channels
* fix stream indexing logic, add asserts
* fix: extraction of data/coordinates for sources
* fix assert
* Clessig/develop/channel logging 282 (#615)
* Fix bug with seed being divided by 0 for worker ID=0
* Fix bug causing crash when secrets aren't in private config
* Implement logging losses per channel
* Fix issue with empty targets
* Rework loss logging
* ruff
* Remove computing max_channels
* Change variables names
* ruffed
* Remove redundant enumerations
* Use stages for logging
* Add type hints
* Apply the review
* ruff
* fix
* Fix type hints
* ruff
* Implement sending tensors of different shapes
* ruff
* Fix merge
* Fix docstring
* rerun workflow
* Review
* Change default colums name
* Fix merge
* - Added ddp_average_nan that is robust to NaN/0 entries when computing mean
- Switched from all_gather to this function in trainer to robustly average
- Some code cleanup
* use all_to_all communication
* Fixing problem with single-worker (non-DDP) training
* Ruffed
* Re-enabled validation loss output in terminal
* Simplified handling of dist initalized
---------
Co-authored-by: Kacper Nowak <kacper.nowak@awi.de>
Co-authored-by: Tim Hunter <tim.hunter@ecmwf.int>
Co-authored-by: clessig <christian.lessig@ecwmf.int>
* Fix bug in corner case of data reading (#621)
* Changed logging level for some messages.
* Fix bug in data reading and add assert to better detect these problems.
* Loss class refactoring (#533)
* Fix bug with seed being divided by 0 for worker ID=0
* Fix bug causing crash when secrets aren't in private config
* Implement logging losses per channel
* Fix issue with empty targets
* Rework loss logging
* ruff
* Remove computing max_channels
* Change variables names
* ruffed
* Remove redundant enumerations
* Use stages for logging
* Add type hints
* Apply the review
* ruff
* fix
* Fix type hints
* ruff
* Implement sending tensors of different shapes
* ruff
* Fix merge
* Fix docstring
* rerun workflow
* creating loss class
* Adapted varnames in new compute_loss function to match LossModule
* comments and loss_fcts refactoring
* Suggested a separation of mask creation and loss computation
* first working version of LossModule; added unit test
* Modifications and TODOs after meeting with Christian and Julian
* Added Christian's comments and updated code partially
* Julian & Matze further advances to understand shapes
* New mask_t computations. Not yet correct, thus commented
* Resolved reshaping of tensors for loss computation
* small changes in _prepare_logging
* J&M first refactoring version finished, 2 tests ok
* First round of resolving PR comments
* add ModelLoss dataclass, rearrange mask and loss computation
* Integrating new LossCalculator into trainer.py and adding docstrings
* J&M resolved temp.item() error
* Second round of PR comments integrated
* - Fixed loss accumulation
- Cleaned up variable names
* Renamed weight
* Removed unused vars
* Inspected loss normalization for logging
* Minor clean-up
* Removing unused code.
* More refactoring: breaking code down in smaller pieces
* Fix
* Adding missing copyright
* Adding missing copyright
* Fixing incorrect indent
* Fix
---------
Co-authored-by: Kacper Nowak <kacper.nowak@awi.de>
Co-authored-by: Tim Hunter <tim.hunter@ecmwf.int>
Co-authored-by: Julian Kuehnert <julian.kuehnert@ecwmf.int>
Co-authored-by: Matthias Karlbauer <matthias.karlbauer@ecmwf.int>
Co-authored-by: Christian Lessig <christian.lessig@ecmwf.int>
Co-authored-by: clessig <christian.lessig@ecwmf.int>
* Update momentum (#633)
* Update momentum
* Remove final GELU in MLP
* Adding assert to catch inconsistent config params (#630)
* Update default_config.yml (#641)
Fix incorrect stream
* Backward compatibility of 'loss_avg_mean' metric name (#637)
Co-authored-by: Christian Lessig <christian.lessig@ecmwf.int>
* Iluise/develop/plotting issues (#635)
* fix plotted timestamp
* fix crashing when a run is plot only
* ruffed
* implement comments
* Mlangguth/develop/issue 586 (#625)
* Add options to configure the marker size, the marker type and enable marker-scaling with latitude for map-plots
* Update doc-strings to follow standard format.
* Ruffed code.
* Changes due to review comments.
* Less verbose logging and improved handling of setting to plot histograms.
* Corrected error-message in plot_data.
* [DRAFT]: Prediction head architecture clean-up (#481)
* - Avoid time encoding is 0
- eps in layer norms to 10^-3
- bf16
* Make the attention dtype and norm eps configurable
* Fix gitignore and add config files
* Shuffle config files into sensible folders
* Implement first attempt at new prediction heads
* Fix some bugs
* Fix trainer compile + fsdp
* Fix trainer and better defaults
* Choose AdaLN
* Correlate predictions per cell
Previously this pr treated as independent
* Make things more parameter efficient
* Revert "Make things more parameter efficient"
It made things way worse
This reverts commit 0f31bf11c82ee9f951810ac6782a4b31b83b8757.
* Improve the prediction heads at small sizes
* Improve the stability of training
Two main changes: better beta 1 and beta 2 values in adam w and remove
gelu
* Adding some more regularisation
In particular to prevent training divergences and overfitting
* Forgot the dropout in MLPs
* Tune the learning rate
* Add the original prediction heads
CAREFUL: Untested!!!
* Fix bugs and ruff
* Restore old version last part
* Start fixing the defaults
* Deleting hpc specific configs
* Deleting hpc specific configs
* Defaults and documentation
* Apply ruff
* Clean up code
* Add one more comment
---------
Co-authored-by: Christian Lessig <christian.lessig@ecmwf.int>
* Fix bug in loggin buffer reset (#651)
Co-authored-by: clessig <christian.lessig@ecwmf.int>
* use config dropout_rate in EmbeddingEngine (#646)
* Make numpy argsort version resilient (#645)
* Fix backward compatibility (#655)
* Implement global and per-cell channel masking (#496)
* creating masking class and adapting tokenizer_masking to use this class
* minor changes to masking.py and tokenizer_masking
* removed old tokenizer_masking
* include masking_strategy in default_config
* change ValueError to assert
* linting formatting changes files
* further linting of docstrings
* create mask_source and mask_target in Masker, and update tokenizer_masking to use these, then style improvements
* linted masking, tokenizer_masking
* modify masker, rng and perm_sel now part of class, remove extra masking_rate, update comments, remove archived class
* remove check if all masked, not masked
* remove self.masking_rate from MultiStreamDS class, and masking args from batchify_source
* update tokenizer utils with description of idx_ord_lens in comment
* remove masking args from batchify_, perm_sel removed now internal to Masker class, remove handling special cases of masking (all masked)
* working implementation of healpix level masking in Masker, with too many prints and hardcoded hl_mask and hl_data
* adding masking_strategy: to config
* remove unused mentions of masking_combination
* removed comment about streams
* changed assert to check self perm_sel is not None
* ruff masking, tokenizer_masking
* implementation of healpix masking code with lots of printing
* removed print statements from masking.py
* minor line change
* remove default for strategy_kwargs
* add strategy_kwargs to config, and pass through masker to pass masking strategy specific args
* vectorise child indices calcs, implement masking_rate_sampling, minorly updated docs
* remove print statements
* cf.strategy_kwargs passed to Masker in multi_stream_data_sampler
* masking_strategy random and strategy kwargs passed to config
* ruffed
* pass cf.get(strategy_kwargs or {}) to the Masker and update masking to reflect this
* update config so it does not include strategy_kwargs, no longer needed
* move asserts for healpix to constructor, rename to masking_strategy_config, update config with example of healpix
* test working version, understanding what is happening
* revert breaking develop merge and conflict in config
* default config put channel masking
* reverting the accidental revert...
* small change to config
* implemented global and per-cell per channel masking in masking, change to config
* remove print statements from multistream
* updated config for compatibility to run immediately
* cleaned code, assert to fail for different number of source and target streams
* updated default config to match latest
* fixed _generate_channel_mask to handle empty cells of data
* fixed docstring of masker
* ruffed linted
* rename l in token_lens
* lint ruff, remove prints
* add assert for source and target channels must be the same
* fix config to develop, new assert, remove assert
* revert assert statement for readability
* clip the values in masking_rate_sampling to 0.01 and 0.99
* revert cell name to tl
* remove empty lines from model
* remove empty line from embeddings
* remove empty line tokenizer_masking
* ruff masking, tokenizer_masking
* update config again to develop version
* update config comment for masking strategies
* update channel masking to handle non-data channels for new loss
* ruffed
* Implemented check that for channel masking source and target channel have to be identical
* Minor code improvements
* Fixed incorrect return type for special case
* Ruffed + and reduced magic constants
* Minor fixes to _generate_healpix_mask
* Cleaned up and optimized mask generation for channel masking
* changed to use mode global or per_cell, improved docstring for masking strategies
* added documented valid examples for masking_strategy_config to default_config
* ruffed
* update example masking_strategy_config in default
* Minor adjustments to default settings
* remove mention of hl_data in masking_strat_config
---------
Co-authored-by: clessig <christian.lessig@ecwmf.int>
* Removed that checkpoint is saved at the first batch (#663)
* Clessig/develop/fix data reading anemoi missing date 671 (#672)
* Changed logging level for some messages.
* Fixed unhandled exception with missing dates.
* Fixed debug message
* Make compare_run_config.py usable again (#661)
* Update compare_run_config.py to use existing functions from current repo.
* Ruffed code.
* [595] Changes for running a notebook script (#598)
* Changes
* Chanegs
* work
* change
* changes
* changes
* changes
* changes
* changes
* changes
* changes
* changes
* reverse old changes
* linter
* Implement regional evaluation (#652)
* Add RegionBoundingBox data class to score-utils to handle evaluation for different regions.
* Implement region-specific evaluation in plot_inference.py.
* Adapted utils.
* Introduction of clean RegionLibrary in score_utils.py.
* Ruffed code.
* Updates following reviewer comments.
* Ruffed code.
* Clessig/develop/fix loss 678 (#679)
* Changed logging level for some messages.
* Fixing bug with incorrect counting
* using config results path instead of fixed path (#631)
* using config results path instead of fixed path
* ruff
* Add forgotten LayerNorm (#687)
* Add forgotten LayerNorm
* Apply ruff
---------
Co-authored-by: Sophie Xhonneux <sxhonneux@clariden-ln001.cscs.ch>
* Fix performance degradation in loss computation (#690)
* Changed logging level for some messages.
* Refactored loss computation to improve performance.
* Working around ruff issue
* - Refactored code to improve structure and readability
- Fixed problem with incomplete normalization over loss functions
- Solved problem with mse_weighted as loss function when mse is specified
* Fixed problems with multi-worker training
* Fixed indentation bug and bug in assert
* [DRAFT] Rename plot_inference.py and entrypoint for evaluation (#683)
* Rename plot_inference.py.
* Rename of main-method and move parsing of arguments for entrypoint.
* Introduce entrypoints to fast evaluation.
* Fix to call of main in run_evaluation.py.
* Rename entrypoint and add dependency to weathergen-evaluate.
* Add missing comma in pyproject.toml.
* Option for non-linear output layer in prediction head (#673)
* Add score-class to evaluate-package.
* Add score-class to evaluate-package.
* Lintered and ruffed code.
* Add fix to io.py and update dependencies in common.
* Several small fixes to score-class and fast evaluation.
* Add utils for evaluate.
* Moved to_list to utils and improved doc-strings.
* Improve several doc-strings, avoid formatting of logger and other changes from PR review.
* Add xhistogram and xskillscore to dependencies of evaluate.
* Ruffed code.
* Lintered code.
* Add helper function to get custom last activation.
* Add option to control stream-specific non-linear output layer.
* Controlling print-statement to model.py.
* Corrected handling of config for prediction head.
* Add support for stream-specific, optional non-linear output actiavtion function.
* Provision of ActivationFactory.
* Ruffed.
* Changes following review comments.
* Fix in parsing final_activation-argument.
* Clessig/develop/fix empty 647 (#675)
* Changed logging level for some messages.
* Removed checks that requires non-empty channels
* Adding warning
* Fixed convergence of training (#696)
* Restored old prediction had functionally. Other adjustments/reverts, in particular in attention.
* Ruff'ed
* Addressed reviewer comments and cleaned up minor details
* Fixed bug in obs data reading (#698)
* Restored old prediction had functionally. Other adjustments/reverts, in particular in attention.
* Ruff'ed
* Fixed bug in obs data reading so that data violated window
* Fix
* Update data_reader_obs.py
* Restoring to develop
* Fix
* Ruffed
* Clessig/develop/fix logging verbosity 564 (#619)
* Changed logging level for some messages.
* Added support for more fine grained output control.
* Changed logging setting for inference.
* Minor improvement to doc string
* include run_id in debug log file
* ruff
---------
Co-authored-by: Julian Kuehnert <julian.kuehnert@ecwmf.int>
* Refactor path-setting for 'model' and 'results' to be dynamic (no relative paths) (Closes #591) (#677)
* temp commit wip
* change model_path and run_path setting to dynamic (independent of HPC) (untested)
* removed unnecessary set_paths references
* linted
* remove commented code
* removed commented lines
* Enable plot_train with dynamic paths
* lint
---------
Co-authored-by: Matthias Karlbauer <matthias.karlbauer@ecmwf.int>
* Fix (#715)
* modified evaluation api, callable as python function (#713)
* Fixed bug for degenerate streams (#723)
NaN-robust min/max computation.
* Fixed (#725)
Resolves config loading error when passing a `model_dir`
* Fix on loading model config (#726)
* Small fix on loading model config
* minor change
* Detect if channels for plotting differ from JSON and recompute if necessary (Closes #701) (#718)
* new branch
* detecting changes in channel spec
* style changes
* style changes
* Delete config/plot_config.yml
* incorporated PR feedback
* added run_evaluation (again)
* Clessig/develop/fix logging 719 (#720)
* Cleaned up to use proper logger
* Cleaned up to use proper logger
* Fix logging: needs to be registered per output stream and not per logging level
* Set logging level consistently with debug to file
* Fixes
* Added FSDP-sharding after loading model for train continue (#729)
* Added FSDP-sharding after loading model for train continue
* Improved consistency
* Fixed resetting FSDP after checkpoint saving
* Update handling of `run_path` and `model_path` (Closes #716) (#732)
* proposed solution, untested
* assert instead of error
* lint
* incorporating PR feedback
* lint
* added explicit argument passing
* lint
* Make cartopy map resources a shared asset to prevent downloading from… (#731)
* Make cartopy map resources a shared asset to prevent downloading from the internet which is not always possible
* Replaced print by logger statement
---------
Co-authored-by: xhonneux2 <xhonneux2@jwlogin22.juwels>
Co-authored-by: karlbauer1 <karlbauer1@jwlogin21.juwels>
* Clessig/develop/fixes hackathon (#736)
* Fixed some comments that generated warnings
* Added to create path for log files if it doesn't exist
---------
Co-authored-by: Christian Lessig <christian.lessig@ovgu.de>
* Revised path defaults and output dirctory structure for fast evaluation (#681)
* First changes to path-handling.
* Consistent path for maps and histograms.
* Update of evaluation scipts for proper path defaults and directory structures.
* Make root-path to repo available via common-package.
* Introduce proper defaults to plot_inference.py and set-up desired directory structure for evaluation output.
* Rename of results_dir-parameter to results_base_dir
* Ruffed code.
* Allow for run-specific results-paths and use config to get defaults.
* Several fixes and consistency improvements.
* Remove manual default usage in plotter.py
* Ruffed code.
* Update __init__.py
Remove _REPO_ROOT.
---------
Co-authored-by: Christian Lessig <christian.lessig@ecmwf.int>
* Mk/develop/fix plot train 727 (#738)
* Load model_path from private config if not provided
* Use existing function to get private model path
* Incorporated PR comments
* Fix problems with rel paths in logging files (#742)
* Fixed relative path handling for logging files.
* Adding default argument to _load_private_conf()
* Implement first function for latitude weighting (#705)
* Changed logging level for some messages.
* Refactored loss computation to improve performance.
* Working around ruff issue
* - Refactored code to improve structure and readability
- Fixed problem with incomplete normalization over loss functions
- Solved problem with mse_weighted as loss function when mse is specified
* Fixed problems with multi-worker training
* add location weights, first commit
* assertion on mask and len(location_weights)
* restructuring of location weights and fixes in mse_channel_location_weighted function
* fix coords_raw dependency on offset and fstep
* ruff
* addressing review commits and fixing bug
* rm location_weight from default stream config
---------
Co-authored-by: Christian Lessig <christian.lessig@ecmwf.int>
Co-authored-by: Julian Kuehnert <julian.kuehnert@ecwmf.int>
* Fix failure for notebooks. (#750)
* add proper error message for source_include not equal to target_include (#767)
* Implemented fractional target selection (#751)
* implemented fractional target selection
* ruffed
* fix up configs and <= to accept target_fraction 0.0
* revert to simple implementation of per stream sampling_rate_target
* restore configs
* Corrected formula for L2-error in score-class. (#721)
* Corrected formula for L2-error in score-class.
* Introduced option to get the original or the squared L2-norm.
* Added doc-string for L2-norm.
* Fix sampling rate (#773)
Co-authored-by: clessig <christian.lessig@ecwmf.int>
* Update default_config.yml (#776)
* Adding the animations feature, fixing stable colorbars (not per stream) (#692)
* Adding the animations feature
* keep only the animations and max-min functions.
* Sophiex/dev/name modules (#754)
* Add names to modules as prep for freezing
* Add functionality to freeze modules based on added names
* Ruff
* Clean up
* Wrong import path
* Ruff
* Fix animations bug with paths (#781)
* Fix another bug in animations (#783)
* Work around to allow for model freezing (#785)
* Work around to allow for model freezing.
* Ruff
* fix to avoid whole model element of named_modules and hence freeze whole model
---------
Co-authored-by: clessig <christian.lessig@ecwmf.int>
Co-authored-by: Sebastian Hickman <seb.hickman@ecmwf.int>
Co-authored-by: Seb Hickman <56727418+shmh40@users.noreply.github.com>
* Fast evaluation for integration tests (#770)
* rename module level constant
* split inference into own method
* use proper fast evaluation pipeline for `evaluate_results`
* ruffed
* remove assert => different bug
* adjust tests for new plot template
* Update checking the value of plot_histograms and plot_animations (#788)
* pass StreamData instances to io.py (#779)
* Rename anemoi directories and built backward compatibility (Closes #709) (#771)
* renamed anemoi dirs and built backward compatibility
* ruff
* removed stream directories and updated logging
* renamed all streams
* ruff
* seviri file name change
* cerra_seviri folder update
* cerra path update
---------
Co-authored-by: Christian Lessig <christian.lessig@ecmwf.int>
* Fix IO when targets/preds are empty. (#760)
* Modify DataReaderObs to get base_yyyy... from stream config (#794)
* modify DataReaderObs to get base_yyyy... from stream config, and set it in the ctor, with default of 19700101. Use it in _setup_sample_index. Remove loading obs_id attr. Add igra.yml with example usage.
* add license to igra config
* update to ISO base_datetime, parse to read idx from zarr
* fix integration tests (#796)
* Fixed bug for empty source (#800)
Co-authored-by: clessig <christian.lessig@ecwmf.int>
* Train continue function with arguments (#803)
* add train_continue_from_args to call with arguments
---------
Co-authored-by: Julian Kuehnert <julian.kuehnert@ecwmf.int>
* remove module common/mock_io (#809)
* Update data_reader_obs.py removing asserts (#817)
* Sgrasse/develop/issue 616 (#648)
* encapsulate extraction of source data
* bundle offseting of key attributes
* consolidate calculation of datapoints indices into method
* encapsulate extraction of coordinate axis in function.
* replace attribute `channels` by `target_channels` and `source_channels`
* ruffed
* ruffed
* fixes
* address michas comments
* reactivate assert
* fix typo / renaming
* small fix
* uncomment source_n_empty and target_n_empty unused variables
* fix untit tests (#814)
* Plot substeps (#789)
* Create subplots with grouping by valid_time.
* Create histograms at substeps with grouping by valid_time.
* Make use of inference run config to distinguish between situations where all datapoints of a sample should be plotted or where sub-stepping is required.
* Add helper function to get values of keys from stream configs.
* Corrected loading of model config.
* Ruffed code and turning message-level on cartopy path to debug.
* Revisions following reviewer comments.
* fix histograms
* ruffed
---------
Co-authored-by: Ilaria Luise <iluise00@login05.leonardo.local>
Co-authored-by: ilaria luise <luise.ilaria@gmail.com>
* Add the possibility of common ranges in plots per variable and stream (#801)
* Create subplots with grouping by valid_time.
* Create histograms at substeps with grouping by valid_time.
* Make use of inference run config to distinguish between situations where all datapoints of a sample should be plotted or where sub-stepping is required.
* Add helper function to get values of keys from stream configs.
* Corrected loading of model config.
* Ruffed code and turning message-level on cartopy path to debug.
* Add the possibility of common ranges in plots per variable and stream
* Revisions following reviewer comments.
* fix histograms
* ruffed
* update utils
---------
Co-authored-by: Michael <m.langguth@fz-juelich.de>
Co-authored-by: Ilaria Luise <iluise00@login05.leonardo.local>
Co-authored-by: ilaria luise <luise.ilaria@gmail.com>
* Fix to io problems. (#820)
* Enable histograms for data with some NaNs (#823)
* Fix to filter NaNs before histogram creation.
* Removed unused code lines and correct for bug in marker scaling in plotter.py.
* Clessig/develop/fix empty io 819 2 (#822)
* Fix to io problems.
* Fix issues in input
* Iluise/fix empty io 819 plotting (#826)
* Fix to io problems.
* Fix issues in input
* fix plotting
* ruffed
---------
Co-authored-by: Christian Lessig <christian.lessig@ecmwf.int>
* fix plotting for partially filled first forecast steps (#828)
Co-authored-by: luise1 <luise1@jrc0288.jureca>
* Fix calculation of scores per fstep (#853)
* fix calculation of scores per fstep
* simplified syntax
---------
Co-authored-by: Julian Kuehnert <julian.kuehnert@ecwmf.int>
Co-authored-by: ilaria luise <luise.ilaria@gmail.com>
* Fix Issue 835 (#841)
Enable freezing the target coord embedding when it is just a simple
layer
* Improve r3tos2 (#744)
* vectorized r3tos2
* revise comment
---------
Co-authored-by: Javad Kasravi <j.kasravi@fz-juelich.de>
Co-authored-by: Christian Lessig <christian.lessig@ecmwf.int>
* Sophiex/dev/latent noise (#594)
* - Avoid time encoding is 0
- eps in layer norms to 10^-3
- bf16
* Make the attention dtype and norm eps configurable
* Fix gitignore and add config files
* Shuffle config files into sensible folders
* Implement first attempt at new prediction heads
* Fix some bugs
* Fix trainer compile + fsdp
* Fix trainer and better defaults
* Choose AdaLN
* Correlate predictions per cell
Previously this pr treated as independent
* Make things more parameter efficient
* Revert "Make things more parameter efficient"
It made things way worse
This reverts commit 0f31bf11c82ee9f951810ac6782a4b31b83b8757.
* Improve the prediction heads at small sizes
* Improve the stability of training
Two main changes: better beta 1 and beta 2 values in adam w and remove
gelu
* Adding some more regularisation
In particular to prevent training divergences and overfitting
* Create classes for latent noise
* Add the latent noise after the local engine
* Add the KL loss
* Formatting
* Clean up
* Use the same for loop as before
* Prepare branch for merge
* Remove superfluous configs
* Restore default configs
* Mistake in the merge fixed
* Final beauty changes
* Final clean up
* Ruff
---------
Co-authored-by: Christian Lessig <christian.lessig@ecmwf.int>
* [Hotfix] Fix crash when using list of forecasting steps (#824)
* Fix crash when using list of forecasting steps
* Ruff
* Grammar fix
* Fix grammar
* Add checking forecast steps list
* Review
* Allow 0 as forecast step
* Add list length check
* Assert non-negative forecast step integer, added assertion messages
* Ruff
* ruff
* Move check to config
* what the ruff
---------
Co-authored-by: Matthias Karlbauer <matthias.karlbauer@ecmwf.int>
* add tokenizer base class (#815)
* add tokenizer base class
* ruffed
* ruffed v2
* move calculation of centroids to base_class
* move size_time_embedding initialization
* remove ABC from tokenizer base_class
* renaming
* ruffed
* ruffed v2
* add return value to compute_source_centroids
---------
Co-authored-by: Seb Hickman <56727418+shmh40@users.noreply.github.com>
* vectorize s2tor3 (#745)
* vectorize s2tor3
* ruff code
---------
Co-authored-by: Javad Kasravi <j.kasravi@fz-juelich.de>
* Remove cleaning stream name when logging loss (#763)
* Combine masking strategies during training, with appropriate masking_… (#756)
* combine masking strategies during training, with appropriate masking_strategy_config
* restore config samples per validation
* restore cofigs, and add to masking_strategy_config
* clarify pass to per batch per stream
* updated combination masking to support same masking strategy for all streams in the batch. Strategy resampled for every batch.
* rename so we have masking_strategy and masking_strategy_per_batch
* ruffed
* clean, default to different strategy per batch for combination
* ruff
* remove unused variable
* updated docstrings (#875)
Co-authored-by: Patnala,Ankit <a.patnala@fz-juelich.de>
* Enable correct reading of channels, forecast_step, sample variables in plot config file (Closes #717) (#755)
* adjusted run_evaluation and utils code to take into account forecast_step variable from config
(cherry picked from commit 26c26a923cabc5777bc75ef911f0fc3c61397e1a)
* print statement change
* catching error when fstep not present in zarr file
* upgrades based on PR feedback
* intermediate commit
* intermediate commit
* new functions _get_channels_fsteps_samples and check_metric
* edited plotting
* inter commit
* fixed bug in get_data
* self review
* refactor
* dummy commit
* inter commit
* feedback appleid
* incorporate review feedback
* removed sorting of fsteps_final
* remove comments
---------
Co-authored-by: ilaria luise <luise.ilaria@gmail.com>
* Implement causal masking as MTM strategy (#798)
* first rough implementation of causal masking
* incorporated combine masking strategies
* include per stream sampling rate target in tokenizer_masking based on other PR
* clean up implementation of causal masking
* remove TODO
* remove old causal masking function
* add latest error message for channel
* change if to elif for causal masking
* if to elif in mask_target
* cleaned up causal masking code
* tokenizer_masking small change
* updated config
* fix up config
* restore era5 config
* ruffed
* update config and masking.py with causal masking specific masking rate, and some comments
* ruffed
* roll back causal_masking_rate changes, return to just use masking_rate
* faster version of causal masking, vectorise where possible. Need list comprehension for variable length tokens
* ruffed
* add log scale and refactor plot_summary (#865)
* add log scale and refactor plot_summary
* add plot_utils
* add grid
* ruffed
* fix marker size
* fix global plotting options
* add types
* ruffed
* Fixed stream name factoring (#534)
* Updated to camel case.
* Fixed formatting.
* to reflect upstream develop
* got rid of regex and changed formatting of str names
* pulled recent changes from upstream develop
* Removed refactoring of lf_name.
* clean_name with the new changes
* Fetched latest changes to the branch
* Fixed linting
* Fixed stream name without touching the losses dict
* fixed type annotation
* add srun to integration-test in actions script (#886)
* add srun to integration-test in actions script
* add --offline flag to integration-test in actions.sh
* Merge compare_run_configs.py with markdown table version (#699)
* initial comments to outline implementation
* Refactor config comparison script to support YAML input and enhance output formatting
* remove unused code
* Add example configuration for model run IDs and display patterns
* shorten
* Add 'tabulate' dependency to enhance table formatting capabilities
* add instructions to config
* restore option for command line run ids and model dirs
* ruff
* fix arg parsing
* add option to show specific or all parameters in config comparison
* ruff
* Remove 'tabulate' from dependencies
Removed 'tabulate' dependency from project requirements.
* logging, imports and dependency in compare_run_configs.py
* fix logging and dependencies
* ruff
* set default
* fix arg order and checks
* improve model directory handling and add exception when there is not latest model
* refactor error handling in main function to omit exception details in logs
* ruff
* ruff
* add weathergen dependency
* make file executable
* add private home argument
* revert to default model path argument assuming symlink to shared folder is set
* ruff
* Implement splitting zarr and regex filenames (#524)
* Implement splitting zarr and regex filenames
* Optimize dask reading operations
* Ruff
* Review
* Ruff
* Remove stream name cleaning when logging loss
* Add tolerance to setting std to 1.0
* Implement input column reordering and channel exclusion
* Update stream config
* Ruff
* Add config file
* Implement variable state persistance
* ruffffff
* ruffa
* ruf ruf
* Add select channels method
* updating .gitignore file to include all development directories without / (#900)
* [804] vectorize tokenize_window_space (with test) (#893)
* vectorize tokenize_window_space
* import pad_sequence from torch
* change vari names, remove device, add comments, ruff code
* changes
* changes
* changes
* simplify
* small change
* unit tests
* unit tests
* unit tests
---------
Co-authored-by: Javad Kasravi <j.kasravi@fz-juelich.de>
* [812] efficient tcs computation (with tests) (#894)
* efficient tcs computation
* revise vectorize tcs_optimized, ruff code
* add typing
* changes
* changes
* merge
---------
Co-authored-by: Javad Kasravi <j.kasravi@fz-juelich.de>
* [811] Improve perf locs to cell coords ctrs (#895)
* optimize locs_to_cell_coords_ctrs
* revise get_target_coords_local_ffast for new optimized locs_to_cell_coords_ctrs
* changes
* changes
* tests
---------
Co-authored-by: Javad Kasravi <j.kasravi@fz-juelich.de>
Co-authored-by: Sophie X <24638638+sophie-xhonneux@users.noreply.github.com>
* [810] optimize locs_to_ctr_coords (with tests) (#896)
* optimize locs_to_ctr_coords
* changes
* changes
* changes
* changes
* merge
* changes
---------
Co-authored-by: Javad Kasravi <j.kasravi@fz-juelich.de>
* Migrated Config to common (#607)
* Updated to camel case.
* Fixed formatting.
* to reflect upstream develop
* got rid of regex and changed formatting of str names
* pulled recent changes from upstream develop
* migrated config to common
* fixed lint issues
* Corrected all the changes
* syntax err fixed
* Fixed import
* Latest upstream changes pulled
* Fixed Linting errors
* Lint fix
* Pulled latest
* fixed other occurences
* Fix compare_config after config went to common (#903)
* fix after config went to common
* Change argument type for --show option from int to str in main function
* Update default config path in main function to compare_config_list.yml
* Iluise/develop/add io reader (#891)
* first implementation of reader class for evaluation package
* add io reader
* move check_availability to reader
* update to develop
* fix retrive results
* address comments
* Fix minor bug in modules (#909)
---------
Co-authored-by: Savvas Melidonis <79579567+SavvasMel@users.noreply.github.com>
* [908] Harmonize the linter check between the CI and our CLI (#910)
* changes
* changes
* [554] Updates the PR template (#912)
* changes
* changes
* changes
* comments
* [906] Bug fix in tokenizer (#907)
* changes
* changes
* changes
* changes
* changes
* changes
* changes
* changes
* cleanups
* changes
* comments
---------
Co-authored-by: Seb Hickman <56727418+shmh40@users.noreply.github.com>
* Add levels (#916)
* changes to include discrete levels in colormap if needed
* Change slightly the position of the feature
* Lint
* changes (#920)
* [926][evaluation] weatherGen reader for evaluation package (#927)
* weatherGen reader for evaluation package
* ruffed
* [939] Fix CI (#940)
* changes
* changes
* Implement forecast activity metrics (#892)
* Add forecast activity calculations and update fstep handling in utils
* Add forecast rate of change metrics (froct, troct) to score calculations
* update description
* add next data to verified data
* move cases for kwargs to score
* refactor froct adn troct to use calc_change_rate
* remove metric specific kwargs in calc_scores_per_stream
* calc_change_rate now gives NaN array when next step is None
* fix nans
---------
Co-authored-by: Julian Kuehnert <julian.b.kuehnert@gmail.com>
Co-authored-by: Ilaria Luise <luise.ilaria@gmail.com>
* added IFS-FESOM streams and updated all stac files using jsonnet (#934)
* added IFS-FESOM streams and updated all stac files using jsonnet
* changes according to comments by Ilaria
* resolved by using providers from common.jsonnet file
* changed refererrence to ecmwf and develop branch
---------
Co-authored-by: Patnala,Ankit <a.patnala@fz-juelich.de>
* [939] Catches failures of labeling CI job (#950)
* changes
* more permissions
* more permissions
* [880] Informative type checks in the CI (#915)
* attempt
* fixing pyrefly
* changes
* changes
* changes
* Sets dropout rate to 0 in eval mode for flash_attn (#923)
* added check for train/eval for setting dropout_p value
* ruff
* rm ceil, conj, floor, and matmul from annotations.json (#951)
Co-authored-by: Javad Kasravi <j.kasravi@fz-juelich.de>
* Add the calculation of 10ff for ERA5 and CERRA (#914)
* Add the calculation of 10ff
* Caring for cases were 10ff cannot be calculated
* Create a new script for derived_channels, minor changes to reader_io
* Remove stream specific settings add regex
* Add more datetime formats (#962)
* fix error when global_plotting_opt does not exist (#964)
* fix error when global_plotting_opt does not exist
* fix linter
* changes (#1009)
* Revert "changes (#1009)" (#1012)
This reverts commit 2af1c09a11e6dd027d247b670737bbac0cd1a766.
* sorcha/dev/500 (#1001)
* lint reformatting + fixing get_channels
* debug messages
* [datasets] move to new cerra and new era5 (#995)
* move to new cerra and new era5
* fix cerra
* Removed the method freeze_weights_forecast and all forecast_freeze_model flag occurences (#924)
* Add Coordinate System Conversion to DataReaderFesom (#1024)
* Add coordinates conversion
* Ruff
* Add check for longitude
* Sophiex/dev/fsdp2 fix (#959)
* Save current state
* Save current state
* Barebone FSDP2 prototype TODO save checkpoints
* First version of saving model
* Fix save_model
* Log everything and log to files
* Remove redundant path creation
* Allow for both slurm and torchrun + fewer log files
* Cleaning up init_ddp
* Ruff
* Attempt to avoid duplicate logging
* FSDP2 with mixed precision policy
* Ruff
* Clean up and logging
* Try to get loggers to behave as we want
* Makes ruff unhappy but works
* Fixed ruff issue
* Fixed problems with multi-node training.
* Fix for interactive/non-DDP runs
* No idea why, but this seems to work so far
Committing simply so it is saved, obviously needs cleanup
* Still works! So which is it memory or the grad scaler?
* Also still works, I now strongly suspect the amp.gradscaler
* This still works, I have no clue anymore why but whatever it works
now....
* Enable loading model from absolute paths
* Enable loading for 1 GPU only
* Fix 1 GPU train continue
* Appease ruff
* Fix saving the model more regularly and perf logging
* Fixed problem when training with 2 nodes.
* Fix data loader seed
* Appease ruff
* Shouldn't overwrite with_fsdp like this
* Potential fix for FSDP2 issue
with different ranks using different model parts
* Fix loss scaling and logging of dummy data loss
* Clean up
* Appease ruff
* Fixed problem when source channels are empty (i.e. with diagnostic trainings).
* Update io.py
* FSDP2 suggestions from Tim (#1015)
* comments
* sophie's comments
* removed logger suggestions
* Clean up deadcode etc
* Removing unused imports that the linter didn't like
---------
Co-authored-by: Christian Lessig <christian.lessig@ecmwf.int>
Co-authored-by: Tim Hunter <tim.hunter@ecmwf.int>
* Ensure sample coordinate is repeated along ipoint for single sample cases in WeatherGenReader (#1026)
Co-authored-by: Savvas Melidonis <79579567+SavvasMel@users.noreply.github.com>
* Fix change rate calculation by aligning s1 with s0 (#1007)
* Fix change rate calculation by aligning s1 with s0
* Refactor score calculation to remove unnecessary alignment and add sorting function for coordinates
* use .values option
* Optimize pos enc harmonic (#1033)
* add device & dtype
* ruffed
---------
Co-authored-by: Javad Kasravi <j.kasravi@fz-juelich.de>
* [evaluation] fix score computation with empty cerra samples (#1039)
* fix samples
* riffed
* answer comments
* ruffed
* Add score cards plotting feature (#1041)
* add the feature of score_cards
* Refactor, fix error when sample are different for each run, linting
* fix bug, fix sizes when skill difference is huge
* linting
* changes on comments
* linting
* Clessig/develop/fix inference 1049 (#1053)
* add device & dtype
* ruffed
* Fix inference
---------
Co-authored-by: Javad Kasravi <j.kasravi@fz-juelich.de>
* Channel weighting in loss computation (#753)
* introducing channel weights
* tested channel weighting
* adding target_channel_weights to data_reader_base
* uncomment target channel parsing in anemoi dataset
* remove channel weights from default stream config
* Adds default config for run_evaluation (#1028)
* adding default config + changing yml path locations
* linter checks
* linter checks
* revert .yml file
* updates
---------
Co-authored-by: iluise <72020169+iluise@users.noreply.github.com>
* Fix CERRA eval breaking with coord sorting in `froct` (#1057)
* Move coord sorting inside score function to be metric-specific
* Linting: Removed unused import
* Return nan data array to prevent crash
* fix nans shape in calc_change_rate
---------
Co-authored-by: ilaria luise <luise.ilaria@gmail.com>
* [1059][eval] Fix eval crash of inference models from other HPCs (#1060)
* Read model path from private repo instead of inference config
* Linting: Organized imports
* Interface improvements
* [1022] Getting WG to work on santis (#1023)
* working pytorch
* changes
* Fix for code to work on Alps-Santis
* changes
* cleanups
* changes
* reverting change
* having issues with the latest branch on santis
* changes
* changes
* changes
* override with cpu
* working for cpu
* flash-attn moved to gpu
* remove contstraint
* simplifying
* trying
* working on atos
* changes
* macos
* chanegs
* cleanups
* actions
* actions
* actions
* actions
* changes
---------
Co-authored-by: Christian Lessig <christian.lessig@ecmwf.int>
* fix crash in case of missing streams (#1058)
* fix issue with empty region
* fix non existing stream
* fix channel order in evaluation (#1066)
* New templates for issues (#1017)
* changes
* changes
* Revert "New templates for issues (#1017)" (#1071)
This reverts commit 3a6e7b826b7b29a6df4af27b6771567474302fb3.
* [1002] Template for issues try 2 (#1072)
* changes
* changes
* issue with template
* updates
* changes
* issue
* issue
* [1073][model] Adds latent noise imputation (#1074)
* Add latent noise imputation to model.py with backwards compatibility
* Linted
* Resetting default_config, except for new flag
* Resetting default_config 2nd try
* add modules to annotations.json (#1035)
Co-authored-by: Javad Kasravi <j.kasravi@fz-juelich.de>
* Jk/develop/gamma decay (#998)
* Update to develop, prepare for new experiment series
* gamma decay over fsteps first commit
* add gamma decay factor to config
* working gamma decay weighting
* rm breakpoint
* rm eval and plot configs
* reverting default config
---------
Co-authored-by: Matthias Karlbauer <matthias.karlbauer@ecmwf.int>
Co-authored-by: Julian Kuehnert <julian.kuehnert@ecwmf.int>
* Add materialisation of new modules before loading checkpoint (#1030)
* Add materialisation of new modules before loading checkpoint
* Initialize new modules in load_model
* Fix adding new embedding networks
* Clessig/develop/fix kcrps 1077 (#1078)
* Improved robustness for loss fcts where ch loss does not make sense
* Re-enabled kernel CRPS and added weighting options
* Fixes
* Improved tensor reordering
* Sgrasse/develop/issue 898 checkpoint freq conf (#905)
* add new/changed parameters in default_config
* implement backward compatibility
* remove `train_log.log_interval` from default config
* use new configuration arguments in Trainer
* fix: wrong variable name
* ruffed
* Rework method structure
* fix bug
* rename `log_intevals` to `train_log_freq`
* fix integration tests
* fix forgot renaming
* fix rebasing artifact
* Sorcha/dev/571 (#957)
* debug for netcdf pipeline
* zarr_netcdf first draft
* fixing pipeline
* linter checks
* removing debug prints from io.py
* refactoring, found issue with forecast_ref_time
* deleting unnecessary lines
* proper docstrings
* moving filepaths
* linting
* multithread processing added
* debug info
* debugging
* refactoring
* linting
* fstep as argument
* change assert
---------
Co-authored-by: owens1 <owens1@jrlogin09.jureca>
Co-authored-by: iluise <72020169+iluise@users.noreply.github.com>
Co-authored-by: ilaria luise <luise.ilaria@gmail.com>
* pyproject.toml checks (#1042)
* adding chceks for toml files into actions
* lint fixes
* lint checks
* link fixes
* changes
* disabling ruff check
* change to path info instead
* adding E501 and E721 to be ignored for now
---------
Co-authored-by: Tim Hunter <tim.hunter@ecmwf.int>
* Implement EMA of the model (#1005)
* Save current state
* Save current state
* Barebone FSDP2 prototype TODO save checkpoints
* First version of saving model
* Fix save_model
* Log everything and log to files
* Remove redundant path creation
* Allow for both slurm and torchrun + fewer log files
* Cleaning up init_ddp
* Ruff
* Attempt to avoid duplicate logging
* FSDP2 with mixed precision policy
* Ruff
* Clean up and logging
* Try to get loggers to behave as we want
* Makes ruff unhappy but works
* Fixed ruff issue
* Fixed problems with multi-node training.
* Fix for interactive/non-DDP runs
* No idea why, but this seems to work so far
Committing simply so it is saved, obviously needs cleanup
* Still works! So which is it memory or the grad scaler?
* Also still works, I now strongly suspect the amp.gradscaler
* This still works, I have no clue anymore why but whatever it works
now....
* Enable loading model from absolute paths
* Enable loading for 1 GPU only
* Fix 1 GPU train continue
* Appease ruff
* Fix saving the model more regularly and perf logging
* Fixed problem when training with 2 nodes.
* Fix data loader seed
* Appease ruff
* Shouldn't overwrite with_fsdp like this
* Potential fix for FSDP2 issue
with different ranks using different model parts
* Fix loss scaling and logging of dummy data loss
* Clean up
* Appease ruff
* Start implementing EMA, works for 1 GPU
* Make EMA model multi-gpu compatible
…
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