Implementation of Parallelization to analysis.gnm

package/CHANGELOG

@@ -17,7 +17,8 @@ The rules for this file:
 ??/??/?? IAlibay, HeetVekariya, marinegor, lilyminium, RMeli,
          ljwoods2, aditya292002, pstaerk, PicoCentauri, BFedder,
          tyler.je.reddy, SampurnaM, leonwehrhan, kainszs, orionarcher,
-         yuxuanzhuang, PythonFZ, laksh-krishna-sharma, orbeckst, MattTDavies
+         yuxuanzhuang, PythonFZ, laksh-krishna-sharma, orbeckst, MattTDavies,
+         talagayev
 
  * 2.8.0
 
@@ -55,6 +56,7 @@ Fixes
 Enhancements
  * Introduce parallelization API to `AnalysisBase` and to `analysis.rms.RMSD` class
    (Issue #4158, PR #4304)
+ * Enables parallelization for analysis.gnm.GNMAnalysis (Issue #4672)
  * explicitly mark `analysis.pca.PCA` as not parallelizable (Issue #4680)
  * Improve error message for `AtomGroup.unwrap()` when bonds are not present.(Issue #4436, PR #4642)
  * Add `analysis.DSSP` module for protein secondary structure assignment, based on [pydssp](https://github.com/ShintaroMinami/PyDSSP)

package/MDAnalysis/analysis/gnm.py

@@ -92,7 +92,7 @@
 
 import numpy as np
 
-from .base import AnalysisBase
+from .base import AnalysisBase, ResultsGroup
 
 
 from MDAnalysis.analysis.base import Results
@@ -245,8 +245,19 @@ class GNMAnalysis(AnalysisBase):
        Use :class:`~MDAnalysis.analysis.AnalysisBase` as parent class and
        store results as attributes ``times``, ``eigenvalues`` and
        ``eigenvectors`` of the ``results`` attribute.
+
+    .. versionchanged:: 2.8.0
+       Enabled **parallel execution** with the ``multiprocessing`` and ``dask`` 
+       backends; use the new method :meth:`get_supported_backends` to see all 
+       supported backends.
     """
 
+    _analysis_algorithm_is_parallelizable = True
+
+    @classmethod
+    def get_supported_backends(cls):
+        return ("serial", "multiprocessing", "dask")
+
     def __init__(self,
                  universe,
                  select='protein and name CA',
@@ -348,6 +359,15 @@ def _conclude(self):
         self.results.eigenvalues = np.asarray(self.results.eigenvalues)
         self.results.eigenvectors = np.asarray(self.results.eigenvectors)
 
+    def _get_aggregator(self):
+        return ResultsGroup(
+            lookup={
+                "eigenvectors": ResultsGroup.ndarray_hstack,
+                "eigenvalues": ResultsGroup.ndarray_hstack,
+                "times": ResultsGroup.ndarray_hstack,
+            }
+        )
+
 
 class closeContactGNMAnalysis(GNMAnalysis):
     r"""GNMAnalysis only using close contacts.

testsuite/MDAnalysisTests/analysis/conftest.py

@@ -8,6 +8,7 @@
 )
 from MDAnalysis.analysis.rms import RMSD, RMSF
 from MDAnalysis.lib.util import is_installed
+from MDAnalysis.analysis.gnm import GNMAnalysis
 
 
 def params_for_cls(cls, exclude: list[str] = None):
@@ -87,3 +88,8 @@ def client_RMSD(request):
 @pytest.fixture(scope='module', params=params_for_cls(RMSF))
 def client_RMSF(request):
     return request.param
+
+
+@pytest.fixture(scope='module', params=params_for_cls(GNMAnalysis))
+def client_GNMAnalysis(request):
+    return request.param

testsuite/MDAnalysisTests/analysis/test_gnm.py

@@ -38,10 +38,10 @@ def universe():
     return mda.Universe(GRO, XTC)
 
 
-def test_gnm(universe, tmpdir):
+def test_gnm(universe, tmpdir, client_GNMAnalysis):
     output = os.path.join(str(tmpdir), 'output.txt')
     gnm = mda.analysis.gnm.GNMAnalysis(universe, ReportVector=output)
-    gnm.run()
+    gnm.run(**client_GNMAnalysis)
     result = gnm.results
     assert len(result.times) == 10
     assert_almost_equal(gnm.results.times, np.arange(0, 1000, 100), decimal=4)
@@ -51,9 +51,9 @@ def test_gnm(universe, tmpdir):
        4.2058769e-15, 3.9839431e-15])
 
 
-def test_gnm_run_step(universe):
+def test_gnm_run_step(universe, client_GNMAnalysis):
     gnm = mda.analysis.gnm.GNMAnalysis(universe)
-    gnm.run(step=3)
+    gnm.run(step=3, **client_GNMAnalysis)
     result = gnm.results
     assert len(result.times) == 4
     assert_almost_equal(gnm.results.times, np.arange(0, 1200, 300), decimal=4)
@@ -88,9 +88,9 @@ def test_gnm_SVD_fail(universe):
             mda.analysis.gnm.GNMAnalysis(universe).run(stop=1)
 
 
-def test_closeContactGNMAnalysis(universe):
+def test_closeContactGNMAnalysis(universe, client_GNMAnalysis):
     gnm = mda.analysis.gnm.closeContactGNMAnalysis(universe, weights="size")
-    gnm.run(stop=2)
+    gnm.run(stop=2, **client_GNMAnalysis)
     result = gnm.results
     assert len(result.times) == 2
     assert_almost_equal(gnm.results.times, (0,  100), decimal=4)
@@ -114,9 +114,9 @@ def test_closeContactGNMAnalysis(universe):
        0.0, 0.0, -2.263157894736841, -0.24333213169614382])
 
 
-def test_closeContactGNMAnalysis_weights_None(universe):
+def test_closeContactGNMAnalysis_weights_None(universe, client_GNMAnalysis):
     gnm = mda.analysis.gnm.closeContactGNMAnalysis(universe, weights=None)
-    gnm.run(stop=2)
+    gnm.run(stop=2, **client_GNMAnalysis)
     result = gnm.results
     assert len(result.times) == 2
     assert_almost_equal(gnm.results.times, (0, 100), decimal=4)