feat(jax/array-api): se_e2_a #4217
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Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
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📝 Walkthrough📝 WalkthroughWalkthroughThe changes in this pull request involve modifications to the Changes
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🧰 Additional context used🔇 Additional comments (11)
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Actionable comments posted: 4
🧹 Outside diff range and nitpick comments (4)
source/tests/array_api_strict/descriptor/se_e2_a.py (2)
23-25: Consider usingcopy.deepcopyinstead of serializing and deserializingIn the assignment of the
embeddingsattribute, you serializevalueand then immediately deserialize it usingNetworkCollection.deserialize(value.serialize()). If the intention is to create a deep copy ofvalue, usingcopy.deepcopy(value)would be more direct and efficient.Apply this change:
+ from copy import deepcopy elif name in {"embeddings"}: if value is not None: - value = NetworkCollection.deserialize(value.serialize()) + value = deepcopy(value)
26-28: Clarify the purpose of theenv_matattribute assignmentWhen
name == "env_mat", the code executes apassstatement, indicating that no action is taken upon assignment. While there is a comment# env_mat doesn't store any value, consider expanding this comment to provide more context on why no value is stored forenv_mat, enhancing code readability and maintainability.deepmd/jax/descriptor/se_e2_a.py (2)
24-26: Optimize 'embeddings' assignment to avoid unnecessary serializationWhen assigning to
embeddings, the code serializes and then deserializesvalue. This could introduce unnecessary overhead ifvalueis already in the correct format. Consider checking if serialization is necessary or ifvaluecan be assigned directly to improve efficiency.
27-29: Clarify handling of 'env_mat' attribute assignmentIn the
__setattr__method, when the attributenameis"env_mat", the code does nothing (pass). If the intent is to preventenv_matfrom being set or stored, consider explicitly documenting this behavior or using a more explicit mechanism to prevent unintended assignments.
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📒 Files selected for processing (5)
- deepmd/dpmodel/descriptor/se_e2_a.py (5 hunks)
- deepmd/dpmodel/utils/nlist.py (1 hunks)
- deepmd/jax/descriptor/se_e2_a.py (1 hunks)
- source/tests/array_api_strict/descriptor/se_e2_a.py (1 hunks)
- source/tests/consistent/descriptor/test_se_e2_a.py (4 hunks)
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🪛 Ruff
deepmd/dpmodel/utils/nlist.py
171-171: Local variable
snselis assigned to but never usedRemove assignment to unused variable
snsel(F841)
🔇 Additional comments (17)
source/tests/array_api_strict/descriptor/se_e2_a.py (1)
19-32: LGTM!The implementation of the
DescrptSeAclass and the overridden__setattr__method appropriately handle custom attribute assignments. The usage ofto_array_api_strict_array,NetworkCollection, andPairExcludeMaskappears correct and in line with best practices.deepmd/jax/descriptor/se_e2_a.py (1)
21-33: Override of__setattr__is well-structured and maintains class integrityThe custom
__setattr__method effectively handles specific attributes with necessary transformations while preserving the base class behavior throughsuper().__setattr__(name, value). This ensures controlled attribute assignment and maintains the integrity of the class.source/tests/consistent/descriptor/test_se_e2_a.py (4)
15-16: Imports ofINSTALLED_ARRAY_API_STRICTandINSTALLED_JAXare correctly addedThe inclusion of
INSTALLED_ARRAY_API_STRICTandINSTALLED_JAXin the imports enhances the conditional handling of different backends.
139-140: Class attributes for JAX and Array API Strict are appropriately assignedThe
jax_classandarray_api_strict_classattributes are correctly set to their respective descriptor classes.
226-234: Ensureeval_array_api_strict_descriptormethod existsThe method
eval_array_api_strictinvokesself.eval_array_api_strict_descriptor, but its definition isn't present in the provided code. Verify that this method is implemented to avoid runtime errors.Run the following script to confirm the existence of
eval_array_api_strict_descriptor:#!/bin/bash # Description: Verify if 'eval_array_api_strict_descriptor' method is defined in the codebase. # Test: Search for the definition of 'eval_array_api_strict_descriptor'. Expect: At least one match indicating the method definition. rg --type python -A 2 -B 2 'def eval_array_api_strict_descriptor\('
217-225: Ensureeval_jax_descriptormethod existsThe method
eval_jaxcallsself.eval_jax_descriptor, but it's not shown in the provided code whethereval_jax_descriptoris defined. Verify that this method exists to preventAttributeError.Run the following script to confirm the existence of
eval_jax_descriptor:✅ Verification successful
eval_jax_descriptormethod is defined insource/tests/consistent/descriptor/common.py.🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify if 'eval_jax_descriptor' method is defined in the codebase. # Test: Search for the definition of 'eval_jax_descriptor'. Expect: At least one match indicating the method definition. rg --type python -A 2 -B 2 'def eval_jax_descriptor\('Length of output: 100
Script:
#!/bin/bash # Description: Verify if 'eval_jax_descriptor' method is defined in the codebase. # Test: Search for the definition of 'eval_jax_descriptor'. Expect: At least one match indicating the method definition. rg -g "*.py" -A 2 -B 2 'def eval_jax_descriptor\('Length of output: 413
deepmd/dpmodel/utils/nlist.py (1)
166-180: Changes enhance clarity and efficiency in neighbor list handling.The modifications to the
nlist_distinguish_typesfunction improve the handling of atomic types and neighbor lists. The use ofxp.whereandxp_take_along_axissimplifies the logic and enhances code readability.🧰 Tools
🪛 Ruff
171-171: Local variable
snselis assigned to but never usedRemove assignment to unused variable
snsel(F841)
deepmd/dpmodel/descriptor/se_e2_a.py (10)
10-10: Ensurearray_api_compatis included in dependenciesThe import statement for
array_api_compatis added. Please verify thatarray_api_compatis installed in the environment and included in your project's dependencies, such as inrequirements.txtorsetup.py, to prevent import issues.
18-20: Import ofto_numpy_arrayis appropriateThe import of
to_numpy_arrayfromdeepmd.dpmodel.commonis necessary for serialization purposes later in the code.
193-201: Initialization of embeddings is correctly updatedThe modification initializes the
embeddingsusingNetworkCollectionwith appropriate dimensions based onself.type_one_side. The loop correctly iterates over the embedding indices, and each embedding is instantiated with the given parameters.
209-219: Proper assignment and initialization of class variablesThe assignments to
self.embeddings,self.env_mat, and other class variables likeself.nnei,self.davg,self.dstd, andself.sel_cumsumare correctly implemented. The use of.item()afternp.sum(self.sel)ensures thatself.nneiis a scalar, which is appropriate.
330-332: Utilization ofarray_api_compatfor array operationsThe
cal_gmethod now usesarray_api_compatto obtain the array namespacexp, enhancing compatibility with different array backends. The reshaping ofssusingxp.reshapeensures that the code is compatible with the selected array API.
454-455: Serialization uses consistent data typesConverting
self.davgandself.dstdto numpy arrays usingto_numpy_arrayensures consistent data types during serialization, which is important for data integrity when saving and loading models.
509-591: Addition ofDescrptSeAArrayAPIclass enhances array compatibilityThe new class
DescrptSeAArrayAPIextendsDescrptSeAand overrides thecallmethod to utilize the array API provided byarray_api_compat. This includes:
- Checking
self.type_one_sideand raisingNotImplementedErrorif it'sFalse, which correctly reflects the current limitations.- Deleting the
mappingparameter as it's unused.- Using
xpfor array operations, ensuring compatibility with different array libraries.- Replacing
np.einsumwith equivalent operations usingxp.sumand broadcasting, which can offer performance benefits and compatibility.
546-549: Informative error message for unsupported configurationThe check for
self.type_one_sideand the subsequentNotImplementedErrorprovide a clear indication thattype_one_side == Falseis not supported inDescrptSeAArrayAPI. This helps users understand the limitations of the new class.
551-551: Unused parametermappingis appropriately handledThe deletion of the unused parameter
mappingwithdel mappingprevents potential confusion and indicates that it is intentionally not used in this method.
579-587: Optimized array operationsThe replacement of
xp.einsumwith explicit sum and multiplication operations:
- Line 579:
gr_tmp = xp.sum(gg[:, :, :, None] * tr[:, :, None, :], axis=1)- Line 587:
grrg = xp.sum(gr[:, :, :, None, :] * gr1[:, :, None, :, :], axis=4)These changes improve compatibility with array APIs that may not support
einsumand can lead to performance improvements.
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## devel #4217 +/- ##
==========================================
+ Coverage 83.50% 83.52% +0.01%
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Files 541 542 +1
Lines 52488 52538 +50
Branches 3047 3043 -4
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+ Hits 43831 43882 +51
Misses 7709 7709
+ Partials 948 947 -1 ☔ View full report in Codecov by Sentry. |
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Summary by CodeRabbit
New Features
DescrptSeAArrayAPIfor enhanced array compatibility.DescrptSeAintegrated with the Flax library for neural network modules.Tests