Support parallelization of conf filter #268
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Signed-off-by: zjgemi <liuxin_zijian@163.com>
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📝 Walkthrough📝 WalkthroughWalkthroughThe changes involve modifications to several classes across multiple files, primarily focusing on enhancing the configuration filtering process. The Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant TrajRenderLammps
participant ConfFilters
participant ConfFilter
participant DistanceConfFilter
User->>TrajRenderLammps: request get_confs
TrajRenderLammps->>ConfFilters: call check(ms)
ConfFilters->>ConfFilter: call batched_check(frames)
ConfFilter-->>ConfFilters: return validity list
ConfFilters-->>TrajRenderLammps: return valid configurations
TrajRenderLammps-->>User: return configurations
sequenceDiagram
participant User
participant DistanceConfFilter
User->>DistanceConfFilter: request batched_check(frames)
DistanceConfFilter->>ProcessPoolExecutor: execute checks
ProcessPoolExecutor-->>DistanceConfFilter: return results
DistanceConfFilter-->>User: return valid frames
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Actionable comments posted: 7
🧹 Outside diff range and nitpick comments (6)
dpgen2/exploration/render/traj_render_lammps.py (1)
133-133: Approve the simplification with suggestions for improvementThe change simplifies the filtering process and aligns with the PR objective of supporting parallelization. It likely improves performance by leveraging batch processing in
ConfFilters.However, consider the following suggestions:
- Add error handling to ensure
conf_filters.check(ms)returns the expectedMultiSystemsobject.- Update the method's docstring to reflect the new behavior and requirements of
conf_filters.Consider applying this diff to improve error handling and documentation:
def get_confs( self, trajs: Union[List[Path], List[HDF5Dataset]], id_selected: List[List[int]], type_map: Optional[List[str]] = None, conf_filters: Optional["ConfFilters"] = None, optional_outputs: Optional[List[Path]] = None, ) -> dpdata.MultiSystems: + """ + Get configurations from trajectories and apply filters. + + :param conf_filters: Must implement a `check` method that accepts and returns a MultiSystems object. + """ # ... (existing code) if conf_filters is not None: - ms = conf_filters.check(ms) + filtered_ms = conf_filters.check(ms) + if not isinstance(filtered_ms, dpdata.MultiSystems): + raise TypeError("conf_filters.check() must return a MultiSystems object") + ms = filtered_ms return msdpgen2/exploration/selector/conf_filter.py (1)
55-55: Use list comprehension for clarityConsider using a list comprehension instead of
list(map(...))for better readability:- return list(map(self.check, frames)) + return [self.check(frame) for frame in frames]tests/exploration/test_conf_filter.py (1)
53-56: Enhance code readability by commenting on coordinate modifications.The direct manipulation of
faked_sys["coords"]modifies specific frames and coordinates, but the intent is not immediately clear. Adding comments to explain the purpose of these assignments will improve code clarity for future maintainers.dpgen2/exploration/selector/distance_conf_filter.py (3)
214-217: Improve clarity ofdoc_max_workersdocumentationTo enhance understanding, consider rephrasing the documentation string for
max_workers.Apply this diff to update the documentation:
doc_max_workers = ( - "The maximum number of processes used to filter configurations, None represents as many as the processors of the machine, and 1 for serial" + "The maximum number of processes used to filter configurations. None uses all available processors, and 1 forces serial execution." )
300-303: Enhance documentation formax_workersinBoxSkewnessConfFilter.argsConsider updating the documentation string for better clarity.
Apply this diff:
doc_max_workers = ( - "The maximum number of processes used to filter configurations, None represents as many as the processors of the machine, and 1 for serial" + "The maximum number of processes used to filter configurations. None uses all available processors, and 1 forces serial execution." )
378-381: Refine thedoc_max_workerstext inBoxLengthFilter.argsUpdating the documentation string can provide clearer guidance to users.
Apply this diff:
doc_max_workers = ( - "The maximum number of processes used to filter configurations, None represents as many as the processors of the machine, and 1 for serial" + "The maximum number of processes used to filter configurations. None uses all available processors, and 1 forces serial execution." )
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (4)
- dpgen2/exploration/render/traj_render_lammps.py (1 hunks)
- dpgen2/exploration/selector/conf_filter.py (3 hunks)
- dpgen2/exploration/selector/distance_conf_filter.py (10 hunks)
- tests/exploration/test_conf_filter.py (1 hunks)
🧰 Additional context used
🔇 Additional comments (8)
tests/exploration/test_conf_filter.py (2)
100-104: Confirm that filtering with no matching frames behaves correctly.The test checks that no frames are selected when none meet the filter criteria. Ensure that
sel_ms.get_nframes()correctly returns0, and that the system handles empty results without errors.
58-61: Verify the correctness of filter chaining and result extraction.Ensure that chaining the
.add()method works as intended withConfFilters, and thatfilters.check(ms)[0]accurately retrieves the filtered system. Verify that the filtering logic applies all filters in sequence and produces the expected results.You can run the following script to confirm the filter chaining behavior:
✅ Verification successful
Filter chaining and result extraction verified to function correctly.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that ConfFilters correctly chains filters and returns expected results. # Test: Search for the implementation details of ConfFilters. rg 'class ConfFilters' -A 15 # Test: Check usages of the .add() and .check() methods to confirm chaining. rg 'filters.add' -A 2Length of output: 2176
Script:
#!/bin/bash # Description: Extract the full implementation of the `check` method in the ConfFilters class. ast-grep --pattern $'class ConfFilters { $$$ check($_, $_) { $$$ } $$$ }'Length of output: 86
Script:
#!/bin/bash # Description: Use ripgrep to locate the `check` method within the `ConfFilters` class and retrieve its implementation. # Search for the `ConfFilters` class and extract the class definition context rg 'class ConfFilters' -A 50 # Specifically search for the `def check` method within the `ConfFilters` class and extract its implementation rg -C 5 'def check' dpgen2/exploration/selector/conf_filter.pyLength of output: 2930
dpgen2/exploration/selector/distance_conf_filter.py (6)
2-4: Approved: ImportingProcessPoolExecutorfor parallel processingThe addition of
ProcessPoolExecutoris appropriate for enabling parallel execution in thebatched_checkmethods.
194-203: Verify thatdpdata.Systeminstances are serializable for multiprocessingSince
ProcessPoolExecutorleverages multiprocessing, confirm thatdpdata.Systemobjects inframesare picklable. If they contain unpicklable attributes, this could result in runtime errors when executingexecutor.map.
246-247: Approved: Addedmax_workersparameter toBoxSkewnessConfFilterIncluding
max_workersenhances the filter by enabling parallel processing in thebatched_checkmethod.
280-289: Verify multiprocessing compatibility inbatched_checkofBoxSkewnessConfFilterEnsure that the frames passed to
ProcessPoolExecutorare compatible with multiprocessing. Serialization issues withdpdata.Systeminstances could cause errors during parallel execution.
324-325: Approved: Introducedmax_workerstoBoxLengthFilterfor parallelismThe addition of
max_workersallows for parallel processing, improving the performance of thebatched_checkmethod.
358-367: Confirm serialization of frames inBoxLengthFilter.batched_checkVerify that the objects in
framesare serializable to prevent issues when usingProcessPoolExecutor.
| selected_idx = sum( | ||
| [[(i, j) for j in range(s.get_nframes())] for i, s in enumerate(ms)], [] | ||
| ) |
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🛠️ Refactor suggestion
Optimize list flattening for performance
Using sum(..., []) to flatten a list of lists can be inefficient. Consider using itertools.chain.from_iterable for better performance, especially with large datasets:
import itertools
selected_idx = list(itertools.chain.from_iterable(
[(i, j) for j in range(s.get_nframes())] for i, s in enumerate(ms)
))| @@ -27,110 +27,78 @@ def check( | |||
| self, | |||
| frame: dpdata.System, | |||
| ) -> bool: | |||
| return True | |||
| return frame["coords"][0][0][0] > 0.0 | |||
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Add error handling to prevent potential index errors in FooFilter.check.
The current implementation assumes that frame["coords"][0][0][0] exists, which could lead to an IndexError if the coordinate data doesn't have the expected dimensions. Consider adding validation to ensure the coordinate array is properly structured before accessing it.
| class BarFilter(ConfFilter): | ||
| def check( | ||
| self, | ||
| frame: dpdata.System, | ||
| ) -> bool: | ||
| return frame["coords"][0][0][1] > 0.0 | ||
|
|
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Add error handling to prevent potential index errors in BarFilter.check.
Similar to FooFilter, this method assumes that frame["coords"][0][0][1] exists. To avoid potential IndexError exceptions, ensure that the coordinate data is validated for the expected dimensions before accessing it.
| class BazFilter(ConfFilter): | ||
| def check( | ||
| self, | ||
| frame: dpdata.System, | ||
| ) -> bool: | ||
| return frame["coords"][0][0][2] > 0.0 |
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Add error handling to prevent potential index errors in BazFilter.check.
This method also assumes that frame["coords"][0][0][2] exists. Adding checks to validate the coordinate data's dimensions can prevent runtime errors due to unexpected data structures.
| faked_sys["coords"][1][0] = 1.0 | ||
| faked_sys["coords"][3][0] = 3.0 |
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🛠️ Refactor suggestion
Consider refactoring repetitive test setup code for consistency.
The setup code for faked_sys, ms, and filters is repeated across multiple test methods. Refactoring this code into a helper method can improve maintainability and reduce duplication.
Also applies to: 71-74
| faked_sys["coords"][0][0] = 0.5 | ||
| faked_sys["coords"][1][0] = 1.0 | ||
| faked_sys["coords"][2][0] = 2.0 | ||
| faked_sys["coords"][3][0] = 3.0 |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Refactor repeated code to enhance maintainability.
Similar to previous tests, the repeated setup of systems and filters can be consolidated into a shared method or fixture. This will make the tests cleaner and easier to manage.
Also applies to: 87-90
| def __init__(self, max_workers=None, custom_safe_dist=None, safe_dist_ratio=1.0): | ||
| self.max_workers = max_workers |
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Ensure default value of max_workers aligns with expected behavior
Using max_workers=None allows ProcessPoolExecutor to utilize all available CPUs, which may lead to resource contention on systems with many cores. Consider setting a sensible default or providing guidance to users on choosing an appropriate value based on their environment.
| selected_idx = sum( | ||
| [[(i, j) for j in range(s.get_nframes())] for i, s in enumerate(ms)], [] | ||
| ) |
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It is not clear for me why we need a sum here. You may also consider the suggestion by rabbitAI
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #268 +/- ##
==========================================
- Coverage 83.65% 83.62% -0.04%
==========================================
Files 104 104
Lines 6028 6057 +29
==========================================
+ Hits 5043 5065 +22
- Misses 985 992 +7 ☔ View full report in Codecov by Sentry. |
Signed-off-by: zjgemi <liuxin_zijian@163.com>
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
dpgen2/exploration/selector/conf_filter.py (2)
38-55: LGTM: Newbatched_checkmethodThe new
batched_checkmethod is a great addition for enabling batch processing of configurations. The implementation is concise and efficient.Consider using a list comprehension instead of
mapfor slightly better readability:def batched_check(self, frames: List[dpdata.System]) -> List[bool]: return [self.check(frame) for frame in frames]This change is optional and doesn't affect performance significantly.
75-89: LGTM with suggestions: Improvedcheckmethod implementationThe new implementation correctly handles multiple systems and frames, efficiently using the
batched_checkmethod of each filter. However, there are a few suggestions for improvement:
Consider using more descriptive variable names, e.g.,
system_indexinstead ofiandframe_indexinstead ofj.The nested loops for creating
selected_idxcan be replaced with a list comprehension for better readability and potentially better performance:selected_idx = [(i, j) for i, s in enumerate(ms) for j in range(s.get_nframes())]
- Consider using
enumeratein the final loop for better readability:for i, system_indices in enumerate(selected_idx_list): if system_indices: ms2.append(ms[i].sub_system(system_indices))These changes will improve code readability without affecting functionality.
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- dpgen2/exploration/selector/conf_filter.py (3 hunks)
🧰 Additional context used
🔇 Additional comments (2)
dpgen2/exploration/selector/conf_filter.py (2)
9-11: LGTM: Import change for type hintingThe addition of
Listimport fromtypingis appropriate for the new type hints in thebatched_checkmethod.
73-74: Verify impact of signature changeThe change in the
checkmethod signature fromdpdata.Systemtodpdata.MultiSystemsfor both input and output is appropriate for the new batched processing approach.Please ensure that all calls to this method throughout the codebase have been updated to accommodate this change. Run the following script to verify:
Summary by CodeRabbit
Release Notes
New Features
BarFilter,BazFilter) with specific checks for frame coordinates.Bug Fixes
Tests