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feat(jax/array-api): hybrid descriptor #4275

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merged 2 commits into from
Oct 31, 2024

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@njzjz njzjz commented Oct 29, 2024

Summary by CodeRabbit

  • New Features

    • Introduced support for the JAX backend in the hybrid descriptor framework.
    • Added a new DescrptHybrid class with specialized attribute handling.
    • Enhanced testing framework to support additional backends, including JAX and strict array API.
  • Bug Fixes

    • Improved attribute handling in multiple descriptor classes to ensure proper deserialization and registration.
  • Documentation

    • Updated documentation to reflect the addition of JAX as a supported backend for hybrid descriptors.

njzjz added 2 commits October 29, 2024 19:58
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
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coderabbitai bot commented Oct 30, 2024

📝 Walkthrough

Walkthrough

The pull request introduces several modifications primarily to the DescrptHybrid class and related components across multiple files. Key changes include the adjustment of variable scope in the initialization of DescrptHybrid, the adoption of array API compatibility in array operations, and the introduction of new classes and methods for handling descriptors in JAX. Additionally, documentation is updated to reflect the support for JAX as a backend for hybrid descriptors. Overall, these changes enhance the flexibility and compatibility of the descriptor framework.

Changes

File Change Summary
deepmd/dpmodel/descriptor/hybrid.py Modified DescrptHybrid class: changed self.nlist_cut_idx to local variable, updated call method for array API compatibility. Updated method signatures for __init__, call, and update_sel.
deepmd/jax/descriptor/__init__.py Added import for DescrptHybrid and updated __all__ list to include it.
deepmd/jax/descriptor/hybrid.py Introduced DescrptHybrid class extending DescrptHybridDP, added custom __setattr__ method for attribute handling.
doc/model/train-hybrid.md Updated to include JAX as a supported backend for hybrid descriptors.
source/tests/array_api_strict/descriptor/__init__.py Added imports for DescrptDPA1, DescrptHybrid, DescrptSeA, DescrptSeR and updated __all__ list.
source/tests/array_api_strict/descriptor/base_descriptor.py Created new file for BaseDescriptor, includes license and imports.
source/tests/array_api_strict/descriptor/dpa1.py Modified DescrptDPA1 class with new imports and attribute handling in __setattr__. Registered with BaseDescriptor.
source/tests/array_api_strict/descriptor/hybrid.py Introduced DescrptHybrid class extending DescrptHybridDP, added custom __setattr__ method.
source/tests/array_api_strict/descriptor/se_e2_a.py Introduced DescrptSeA class with custom __setattr__ and registration with BaseDescriptor.
source/tests/array_api_strict/descriptor/se_e2_r.py Introduced DescrptSeR class with custom __setattr__ and registration with BaseDescriptor.
source/tests/consistent/descriptor/test_hybrid.py Enhanced testing framework for hybrid descriptors with support for JAX and array API strict classes. Added new methods and properties in TestHybrid.

Possibly related PRs

Suggested labels

Python, Docs

Suggested reviewers

  • wanghan-iapcm
  • iProzd

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Actionable comments posted: 1

🧹 Outside diff range and nitpick comments (6)
source/tests/array_api_strict/descriptor/se_e2_r.py (1)

Line range hint 33-34: Enhance the env_mat comment documentation

The current comment "env_mat doesn't store any value" could be more descriptive about why this is the case.

-            # env_mat doesn't store any value
+            # env_mat is a computed property and doesn't persist any value
source/tests/array_api_strict/descriptor/se_e2_a.py (1)

Line range hint 24-36: Add return type hint to setattr.

The method signature should include the return type hint for better type safety and code clarity.

-    def __setattr__(self, name: str, value: Any) -> None:
+    def __setattr__(self, name: str, value: Any) -> None:  # type: ignore

Enhance the env_mat comment.

The current comment could be more descriptive about why env_mat doesn't store any value.

-            # env_mat doesn't store any value
+            # env_mat is a computed property and doesn't store any value directly
doc/model/train-hybrid.md (1)

Line range hint 1-100: Consider adding JAX-specific usage examples.

While the documentation comprehensively covers the theory and general usage, it might be helpful to add JAX-specific examples or notes, particularly if there are any unique considerations when using the hybrid descriptor with JAX.

Would you like me to help draft JAX-specific usage examples or notes to add to the documentation?

source/tests/array_api_strict/descriptor/dpa1.py (1)

Line range hint 78-85: Consider adding docstring explaining multiple identifiers

The class is registered with two different identifiers ("dpa1" and "se_atten"). Consider adding a docstring to explain why both identifiers exist and their intended usage.

 @BaseDescriptor.register("dpa1")
 @BaseDescriptor.register("se_atten")
 class DescrptDPA1(DescrptDPA1DP):
+    """Descriptor implementation that can be accessed via 'dpa1' or 'se_atten' identifiers.
+    
+    The dual registration supports both the standard name (dpa1) and the
+    implementation-specific name (se_atten) for backward compatibility.
+    """
     def __setattr__(self, name: str, value: Any) -> None:
source/tests/consistent/descriptor/test_hybrid.py (1)

152-168: Consider using more specific return type annotations.

The implementation of the evaluation methods is correct and consistent with existing patterns. However, consider replacing Any with a more specific return type annotation to improve type safety.

For example:

-    def eval_array_api_strict(self, array_api_strict_obj: Any) -> Any:
+    def eval_array_api_strict(self, array_api_strict_obj: Any) -> tuple[np.ndarray, ...]:

-    def eval_jax(self, jax_obj: Any) -> Any:
+    def eval_jax(self, jax_obj: Any) -> tuple[np.ndarray, ...]:

This matches the return type used in extract_ret method and provides better type information.

deepmd/dpmodel/descriptor/hybrid.py (1)

Line range hint 247-275: Consider adding error handling for array operations.

While the array operations are now backend-agnostic, it would be beneficial to add error handling for potential array operation failures, especially when dealing with different backends that might have varying support for these operations.

Consider wrapping the array operations in try-except blocks:

 def call(self, coord_ext, atype_ext, nlist, mapping: Optional[np.ndarray] = None):
     xp = array_api_compat.array_namespace(coord_ext, atype_ext, nlist)
     out_descriptor = []
     out_gr = []
     out_g2 = None
     out_h2 = None
     out_sw = None
+    try:
         if self.sel_no_mixed_types is not None:
             nl_distinguish_types = nlist_distinguish_types(
                 nlist,
                 atype_ext,
                 self.sel_no_mixed_types,
             )
         else:
             nl_distinguish_types = None
         for descrpt, nci in zip(self.descrpt_list, self.nlist_cut_idx):
             if self.mixed_types() == descrpt.mixed_types():
                 nl = xp.take(nlist, nci, axis=2)
             else:
                 assert nl_distinguish_types is not None
                 nl = nl_distinguish_types[:, :, nci]
             odescriptor, gr, g2, h2, sw = descrpt(coord_ext, atype_ext, nl, mapping)
             out_descriptor.append(odescriptor)
             if gr is not None:
                 out_gr.append(gr)
         out_descriptor = xp.concat(out_descriptor, axis=-1)
         out_gr = xp.concat(out_gr, axis=-2) if out_gr else None
+    except Exception as e:
+        raise RuntimeError(f"Array operation failed with backend {xp.__name__}: {str(e)}")
     return out_descriptor, out_gr, out_g2, out_h2, out_sw
📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 159361d and 4a71f2b.

📒 Files selected for processing (11)
  • deepmd/dpmodel/descriptor/hybrid.py (6 hunks)
  • deepmd/jax/descriptor/init.py (2 hunks)
  • deepmd/jax/descriptor/hybrid.py (1 hunks)
  • doc/model/train-hybrid.md (1 hunks)
  • source/tests/array_api_strict/descriptor/init.py (1 hunks)
  • source/tests/array_api_strict/descriptor/base_descriptor.py (1 hunks)
  • source/tests/array_api_strict/descriptor/dpa1.py (2 hunks)
  • source/tests/array_api_strict/descriptor/hybrid.py (1 hunks)
  • source/tests/array_api_strict/descriptor/se_e2_a.py (1 hunks)
  • source/tests/array_api_strict/descriptor/se_e2_r.py (1 hunks)
  • source/tests/consistent/descriptor/test_hybrid.py (4 hunks)
✅ Files skipped from review due to trivial changes (2)
  • source/tests/array_api_strict/descriptor/init.py
  • source/tests/array_api_strict/descriptor/base_descriptor.py
🔇 Additional comments (22)
deepmd/jax/descriptor/__init__.py (1)

5-7: LGTM! Clean and consistent changes.

The import statement and __all__ list update follow the established patterns in the codebase, maintaining consistency with other descriptor implementations.

Also applies to: 19-19

source/tests/array_api_strict/descriptor/hybrid.py (3)

1-14: LGTM! Well-organized imports with proper licensing.

The file structure follows best practices with:

  • Clear license header
  • Properly organized imports
  • Appropriate type hints

16-17: LGTM! Proper class registration and inheritance.

The class is correctly registered as a descriptor plugin and extends the appropriate base class.


18-24: 🛠️ Refactor suggestion

Verify error handling for array conversion and deserialization.

While the implementation is functionally correct, it might benefit from explicit error handling:

  1. Array conversion might fail for invalid inputs in nlist_cut_idx
  2. Serialization/deserialization might fail for incompatible descriptors in descrpt_list

Consider adding error handling:

 def __setattr__(self, name: str, value: Any) -> None:
     if name in {"nlist_cut_idx"}:
-        value = [to_array_api_strict_array(vv) for vv in value]
+        try:
+            value = [to_array_api_strict_array(vv) for vv in value]
+        except (TypeError, ValueError) as e:
+            raise ValueError(f"Failed to convert nlist_cut_idx: {e}")
     elif name in {"descrpt_list"}:
-        value = [BaseDescriptor.deserialize(vv.serialize()) for vv in value]
+        try:
+            value = [BaseDescriptor.deserialize(vv.serialize()) for vv in value]
+        except Exception as e:
+            raise ValueError(f"Failed to process descrpt_list: {e}")
 
     return super().__setattr__(name, value)

Let's verify the usage patterns:

deepmd/jax/descriptor/hybrid.py (3)

1-15: LGTM! Clean and well-organized imports.

The imports are properly organized, with clear grouping and specific imports rather than wildcards. The license header is correctly included.


17-19: LGTM! Proper class registration and decoration.

The class is correctly registered with BaseDescriptor and properly decorated as a flax module.


20-26: Verify consistent attribute handling across JAX descriptors.

Let's ensure this attribute handling pattern is consistent with other JAX descriptors in the codebase.

✅ Verification successful

Let me gather more specific information about the attribute handling in the other JAX descriptors.


Attribute handling in hybrid.py is unique and correct for its use case

The verification shows that nlist_cut_idx and descrpt_list attributes are unique to the hybrid descriptor and not present in other JAX descriptors. Each descriptor implements __setattr__ specifically for its own attributes:

  • se_e2_r.py and se_e2_a.py handle dstd, davg, embeddings, and env_mat
  • dpa1.py handles various attributes related to attention layers and networks
  • hybrid.py correctly handles its unique attributes nlist_cut_idx and descrpt_list

The implementation in hybrid.py follows the same pattern as other descriptors - converting values to appropriate types using serialization/deserialization or array conversion, which is consistent with the codebase's approach.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for similar attribute handling patterns in other JAX descriptors

# Look for other JAX descriptor implementations
echo "Searching for other JAX descriptors..."
rg -l "BaseDescriptor.register" "deepmd/jax/descriptor/"

# Check for similar __setattr__ patterns
echo "Checking for similar attribute handling patterns..."
ast-grep --pattern 'class $_ {
  $$$
  __setattr__($_, $_, $_) {
    $$$
  }
  $$$
}'

Length of output: 470


Script:

#!/bin/bash
# Check implementation details of __setattr__ in other JAX descriptors
echo "Checking se_e2_r.py..."
rg "__setattr__" "deepmd/jax/descriptor/se_e2_r.py" -A 10

echo -e "\nChecking se_e2_a.py..."
rg "__setattr__" "deepmd/jax/descriptor/se_e2_a.py" -A 10

echo -e "\nChecking dpa1.py..."
rg "__setattr__" "deepmd/jax/descriptor/dpa1.py" -A 10

# Also check for usage of nlist_cut_idx and descrpt_list
echo -e "\nChecking usage of nlist_cut_idx and descrpt_list..."
rg "nlist_cut_idx|descrpt_list" "deepmd/jax/descriptor/"

Length of output: 3690

source/tests/array_api_strict/descriptor/se_e2_r.py (3)

17-19: LGTM: Clean import statement

The import is well-structured and appropriately scoped.


Line range hint 24-37: LGTM: Well-structured attribute handling

The implementation provides clear, type-specific handling for each attribute type with appropriate conversions and validations.


22-23: Verify descriptor registration uniqueness

The class is registered under two different names. While this is valid, we should verify there are no conflicts with existing registrations.

✅ Verification successful

Let me gather more information to understand the implementation details of these registrations.


Multiple framework-specific implementations found - no conflicts

The dual registration of "se_e2_r" and "se_r" is intentionally replicated across different framework implementations (TensorFlow, PyTorch, JAX) and each implementation is properly scoped within its respective framework's namespace through different base classes:

  • TensorFlow: @Descriptor.register()
  • PyTorch/JAX/Tests: @BaseDescriptor.register()
  • DPModel: @BaseDescriptor.register()

The registrations in the test file follow the same pattern as the framework implementations, and there are no conflicting registrations within the same namespace.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for any existing uses of these descriptor names
# to ensure we're not overwriting existing functionality

# Search for any other registrations of these descriptors
echo "Checking for existing registrations of se_e2_r and se_r..."
rg -l "register\([\"']se_e2_r[\"']\)" --type py
rg -l "register\([\"']se_r[\"']\)" --type py

Length of output: 597


Script:

#!/bin/bash
# Check the actual implementation of these registrations to understand potential conflicts
echo "Checking se_e2_r implementations..."
rg -A 5 "register\([\"']se_e2_r[\"']\)" --type py

echo -e "\nChecking se_r implementations..."
rg -A 5 "register\([\"']se_r[\"']\)" --type py

Length of output: 4554

source/tests/array_api_strict/descriptor/se_e2_a.py (2)

17-23: LGTM! Clean import organization and clear class registration.

The dual registration with both "se_e2_a" and "se_a" identifiers provides good flexibility for users while maintaining backward compatibility.


Line range hint 24-36: Verify array API compatibility across the codebase.

Let's ensure consistent usage of array API strict arrays in related files.

✅ Verification successful

Based on the search results, I can now generate the final response:

Array API strict array conversion is consistently implemented across the codebase.

The implementation in DescrptSeA follows the established pattern used throughout the codebase:

  • The to_array_api_strict_array function is used consistently in related descriptor files (se_e2_r.py, se_e2_a.py, hybrid.py, dpa1.py)
  • The array conversion is properly handled for the specific attributes (dstd, davg)
  • The implementation aligns with other array API strict implementations in the utils and fitting modules
🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for consistent array API usage in related descriptor files
# Expected: All array conversions should use to_array_api_strict_array

# Search for array conversion patterns in descriptor-related files
rg -l "to_array_api_strict_array" --type python

Length of output: 78


Script:

#!/bin/bash
# Search for array conversion patterns in all files
rg -l "to_array_api_strict_array"

# Also search for the specific class and its usage
rg -l "DescrptSeA"

# Look for array API related imports and usage
rg "array_api" -A 2

Length of output: 44835

doc/model/train-hybrid.md (1)

1-1: Verify JAX backend implementation completeness.

The documentation has been updated to include JAX support. Let's verify that all necessary JAX implementation components are in place.

Also applies to: 4-4

✅ Verification successful

Let me gather more specific information about the JAX implementation.


Let me check one more aspect to verify the actual JAX implementation:


JAX hybrid descriptor implementation is verified and complete

The documentation update is accurate as the JAX backend implementation for hybrid descriptors is properly in place with:

  • Implementation file at deepmd/jax/descriptor/hybrid.py
  • Proper class registration and imports in deepmd/jax/descriptor/__init__.py
  • Test coverage in source/tests/consistent/descriptor/test_hybrid.py
  • Inheritance from base implementation (DescrptHybridDP) with JAX-specific array handling
🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify JAX implementation components

# Test 1: Check for JAX descriptor implementation
echo "Checking for JAX descriptor implementation..."
ast-grep --pattern 'class DescrptHybrid'

# Test 2: Check for hybrid descriptor registration
echo "Checking for hybrid descriptor registration..."
rg -l "register_descriptor.*hybrid"

# Test 3: Check for JAX-specific tests
echo "Checking for JAX-specific tests..."
fd test_hybrid.py

Length of output: 433


Script:

#!/bin/bash
# Check for JAX-specific hybrid descriptor implementation
echo "Checking JAX hybrid descriptor implementation..."
rg -A 5 "class.*Hybrid.*JAX|class.*JAX.*Hybrid"

# Check for hybrid descriptor registration in JAX
echo "Checking JAX hybrid descriptor registration..."
rg -A 5 "register.*hybrid.*jax|jax.*hybrid"

# Check test coverage for JAX hybrid
echo "Checking JAX hybrid tests..."
rg -A 5 "test.*hybrid.*jax|jax.*hybrid" source/tests/consistent/descriptor/test_hybrid.py

# Check for JAX-specific configuration or examples
echo "Checking for JAX hybrid examples..."
rg "jax.*hybrid|hybrid.*jax" doc/model/train-hybrid.md

Length of output: 2334


Script:

#!/bin/bash
# Check the actual JAX hybrid descriptor implementation
echo "Checking JAX hybrid descriptor implementation file..."
rg -A 10 "class DescrptHybrid" deepmd/jax/descriptor/hybrid.py

# Check if the implementation file exists
echo "Verifying file existence..."
fd hybrid.py deepmd/jax/descriptor/

Length of output: 692

source/tests/array_api_strict/descriptor/dpa1.py (2)

30-32: LGTM: Clean import addition

The BaseDescriptor import is properly organized and necessary for the registration decorators.


78-79: Verify unique registration identifiers

The registration looks good, but let's verify that these identifiers aren't used elsewhere in the codebase.

✅ Verification successful

Multiple framework-specific implementations found - registration pattern is correct

The registrations are intentionally duplicated across different framework implementations:

  • PyTorch implementation in deepmd/pt/model/descriptor/dpa1.py
  • JAX implementation in deepmd/jax/descriptor/dpa1.py
  • Native implementation in deepmd/dpmodel/descriptor/dpa1.py
  • Array API test implementation in source/tests/array_api_strict/descriptor/dpa1.py

Each implementation is framework-specific and uses the same identifiers to provide consistent API across different backends. This is a common pattern in ML frameworks supporting multiple backends.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for any other uses of these identifiers in descriptor registrations
# Expect: Only one registration for each identifier

# Search for other registrations using these identifiers
echo "Checking for 'dpa1' registrations:"
rg -l "@BaseDescriptor\.register\(['\"]dpa1['\"]\)"

echo "Checking for 'se_atten' registrations:"
rg -l "@BaseDescriptor\.register\(['\"]se_atten['\"]\)"

Length of output: 593


Script:

#!/bin/bash
# Let's check the content of these files to understand if they are different implementations or duplicates
echo "Content of source/tests/array_api_strict/descriptor/dpa1.py:"
rg -A 2 "@BaseDescriptor\.register\(['\"]dpa1['\"]\)" source/tests/array_api_strict/descriptor/dpa1.py

echo -e "\nContent of deepmd/pt/model/descriptor/dpa1.py:"
rg -A 2 "@BaseDescriptor\.register\(['\"]dpa1['\"]\)" deepmd/pt/model/descriptor/dpa1.py

echo -e "\nContent of deepmd/dpmodel/descriptor/dpa1.py:"
rg -A 2 "@BaseDescriptor\.register\(['\"]dpa1['\"]\)" deepmd/dpmodel/descriptor/dpa1.py

echo -e "\nContent of deepmd/jax/descriptor/dpa1.py:"
rg -A 2 "@BaseDescriptor\.register\(['\"]dpa1['\"]\)" deepmd/jax/descriptor/dpa1.py

Length of output: 1309

source/tests/consistent/descriptor/test_hybrid.py (4)

15-16: LGTM! Import changes are consistent with existing patterns.

The new imports for JAX and Array API Strict installation flags follow the established pattern.


33-42: LGTM! Backend class definitions follow established patterns.

The conditional imports for JAX and Array API Strict backends are well-structured and consistent with existing implementations.


83-84: LGTM! Class properties are properly defined.

The new backend class properties maintain consistency with existing backend definitions.


87-89: LGTM! Skip flags are properly implemented.

The skip flags for JAX and Array API Strict backends are correctly defined and follow the established pattern for conditional test execution.

deepmd/dpmodel/descriptor/hybrid.py (3)

9-9: LGTM: Good addition of array_api_compat.

The addition of array_api_compat import enables backend-agnostic array operations, which is essential for supporting multiple array libraries like NumPy and JAX.


70-70: LGTM: Good refactoring of variable scope.

Converting nlist_cut_idx to a local variable during initialization is a good practice as it:

  1. Keeps intermediate computation results local
  2. Makes the code more maintainable by clearly separating temporary computation from instance state

Also applies to: 96-97


247-247: LGTM with a performance consideration.

The changes to use array_api_compat operations (xp.take and xp.concat) make the code backend-agnostic, which is great for flexibility. However, xp.take might have different performance characteristics compared to direct indexing depending on the backend.

Let's verify the performance impact:

Also applies to: 264-264, 274-275

deepmd/jax/descriptor/hybrid.py Show resolved Hide resolved
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codecov bot commented Oct 30, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 84.37%. Comparing base (159361d) to head (4a71f2b).
Report is 7 commits behind head on devel.

Additional details and impacted files
@@           Coverage Diff           @@
##            devel    #4275   +/-   ##
=======================================
  Coverage   84.37%   84.37%           
=======================================
  Files         551      552    +1     
  Lines       51585    51602   +17     
  Branches     3052     3052           
=======================================
+ Hits        43524    43540   +16     
- Misses       7100     7102    +2     
+ Partials      961      960    -1     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@njzjz njzjz requested a review from wanghan-iapcm October 30, 2024 20:06
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