[TYPO] #3635
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[TYPO] #3635
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Set the default `save_ckpt` to `model.ckpt` as the prefix. When saving checkpoints, `model.ckpt-100.pt` will be saved, and `model.ckpt.pt` will be symlinked to `model.ckpt-100.pt`. A `checkpoint` file will be dedicated to record `model.ckpt-100.pt`. This keeps the same behavior as the TF backend. One can do the below using the PT backend just like the TF backend: ```sh dp --pt train input.json # one can cancel the training before it finishes dp --pt freeze ``` --------- Signed-off-by: Jinzhe Zeng <[email protected]>
…eling#3195) Fix https://github.com/deepmodeling/deepmd-kit/security/code-scanning/2096 --------- Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
per discussion. Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: Han Wang <[email protected]>
```
- source
- tests
- common
- tf
- pt
```
---------
Signed-off-by: Jinzhe Zeng <[email protected]>
Co-authored-by: Han Wang <[email protected]>
Fix deepmodeling#3121. There are TODOs: (1) PyTorch-backend specific features and arguments; (2) Python interface installation. Currently, the TensorFlow backend is always installed, and I am considering rewriting the logic; (3) Unsupported features - write docs when implemented. --------- Signed-off-by: Jinzhe Zeng <[email protected]>
The default one from PyPI is for CU12. --------- Signed-off-by: Jinzhe Zeng <[email protected]>
…pmodeling#3201) If so, throw the following error: ``` -- PyTorch CXX11 ABI: 0 CMake Error at CMakeLists.txt:162 (message): PyTorch CXX11 ABI mismatch TensorFlow: 0 != 1 ``` Signed-off-by: Jinzhe Zeng <[email protected]>
…deling#3200) Fix deepmodeling#3120. One can disable building the TensorFlow backend during `pip install` by setting `DP_ENABLE_TENSORFLOW=0`. --------- Signed-off-by: Jinzhe Zeng <[email protected]>
…g net. (deepmodeling#3199) - add dp model format (backend independent definition) for the fitting - refactor torch support, compatible with dp model format - fix mlp issue: the idt should only be used when a skip connection is available. - add tools `to_numpy_array` and `to_torch_tensor`. --------- Co-authored-by: Han Wang <[email protected]>
Co-authored-by: Han Wang <[email protected]>
This PR fixes GPU UTs; Delete the PREPROCESS_DEVICE in torch data preprocess and use training DEVICE instead, which will be removed after the dataset is refomated. --------- Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Jinzhe Zeng <[email protected]> Co-authored-by: Han Wang <[email protected]> Co-authored-by: Han Wang <[email protected]>
Today [GitHub introduced the new M1 runners](https://github.blog/changelog/2024-01-30-github-actions-introducing-the-new-m1-macos-runner-available-to-open-source/), making it possible to build macos-arm64 wheels without cross-building. Remove old hacked codes for cross-building.
Signed-off-by: Jinzhe Zeng <[email protected]>
Migrated from this [PR](dptech-corp/deepmd-pytorch#174). This is to reimplement the PairTab Model in Pytorch. Notes: 1. Different from the tensorflow version, the pytorch version abstracts away all the post energy conversion operations (force, virial). 2. Added extrapolation when `rcut` > `rmax`. The pytorch version overwrite energy beyond extrapolation endpoint to `0`. These features are not available in the tensorflow version. The extrapolation uses a cubic spline form, the 1st order derivation for the starting point is estimated using the last two rows in the user defined table. See example below:     --------- Co-authored-by: Anyang Peng <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Signed-off-by: Jinzhe Zeng <[email protected]>
Use the same arguments as TF. [PyTorch on Tensorboard](https://pytorch.org/docs/stable/tensorboard.html):  [PyTorch Profiler on Tensorboard](https://pytorch.org/tutorials/intermediate/tensorboard_profiler_tutorial.html):  --------- Signed-off-by: Jinzhe Zeng <[email protected]>
…ng#3208) Features: - abstract base classes for atomic model, fitting and descriptor. - dp model format for atomic models - dp model format for models. - torch support for atomic model format. - torch support `fparam` and `aparam`. This pr also introduces the following updates: - support region and nlist in numpy code. - class decorator like `fitting_check_output` gives human readable class names. - support int types in precision dict. - fix descriptor interfaces. - refactor torch atomic model impl. introduces dirty hacks to be fixed. - provide `format_nlist` that format the nlist in forward_lower method. Known limitations: - torch atomic model has dirty hacks - interfaces for descriptor, fitting and model statistics was not considered, should be fixed in future PRs. Will be fixed - [x] dp model module path is a mess to be refactorized. - [x] nlist consistency should be checked. if not format nlist. - [x] doc strings. - [x] `fparam` and `aparam` support. --------- Co-authored-by: Han Wang <[email protected]>
Fix deepmodeling#3214. In the gmx patch file, `${TENSORFLOW_ROOT}` is used other than `${TensorFlow_LIBRARY_PATH}$` or `${TENSORFLOW_INCLUDE_DIRS}`, so the fastest workaround is to set `${TENSORFLOW_ROOT}`. https://github.com/deepmodeling/deepmd-kit/blob/eb9b2efedf4efc946894800a0d7abf5056f4bb7a/source/gmx/patches/2020.2/CMakeLists.txt.patch.in#L14-L18 Signed-off-by: Jinzhe Zeng <[email protected]>
…ng#3219) Co-authored-by: Han Wang <[email protected]>
Fix deepmodeling#3214. Signed-off-by: Jinzhe Zeng <[email protected]>
Fix deepmodeling#3045. All memory leaks have been fixed! --------- Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
This PR is to provide backend independent implementation of PairTabModel in `numpy`. Also the cross framework `serialization` and `deserialization` are added. --------- Co-authored-by: Anyang Peng <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
add shape hit to doc string. Co-authored-by: Han Wang <[email protected]>
…ling#3226) To be consistent with TF, as discussed in deepmodeling#3213 (comment). Old PT models are expected to be incompatible. Signed-off-by: Jinzhe Zeng <[email protected]>
We can change the format of the global logger in the future if the additional information is helpful (e.g., time, path, etc). --------- Signed-off-by: Jinzhe Zeng <[email protected]>
Signed-off-by: Jinzhe Zeng <[email protected]>
Avoid installing tensorflow as build requires when `DP_ENABLE_TENSORFLOW` is `0`. Signed-off-by: Jinzhe Zeng <[email protected]>
- mv all dpmodel related UTs to a separate directory - split the large test_model_format_utils.py as tests for different modules. --------- Co-authored-by: Han Wang <[email protected]>
…modeling#3235) Co-authored-by: Han Wang <[email protected]>
Co-authored-by: Han Wang <[email protected]>
…eepmodeling#3618) Signed-off-by: Jinzhe Zeng <[email protected]>
deepmodeling#3578 deepmodeling#3579 --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
deepmodeling#3475 --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Signed-off-by: Jinzhe Zeng <[email protected]>
Only conduct file renaming in this PR. --------- Signed-off-by: Jinzhe Zeng <[email protected]>
The wrong type hint appeared in f5c67af, very old... Signed-off-by: Jinzhe Zeng <[email protected]>
Signed-off-by: Jinzhe Zeng <[email protected]>
…ng#3626) - also add missing UT for execute_all --------- Co-authored-by: Han Wang <[email protected]>
…modeling#3631) Signed-off-by: Jinzhe Zeng <[email protected]>
- add UT for it. - at the moment, only energy is supported in the `base_atomic_model`. handling of multiple output stat will be implemented in a future PR. --------- Co-authored-by: Han Wang <[email protected]>
Signed-off-by: Jinzhe Zeng <[email protected]>
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