Implementation of Parallelization to MDAnalysis.analysis.contacts

package/CHANGELOG

@@ -25,10 +25,12 @@ Fixes
    the function to prevent shared state. (Issue #4655)
 
 Enhancements
+ * Enables parallelization for analysis.contacts.Contacts (Issue #4660)
  * Enable parallelization for analysis.nucleicacids.NucPairDist (Issue #4670)
  * Add check and warning for empty (all zero) coordinates in RDKit converter (PR #4824)
  * Added `precision` for XYZWriter (Issue #4775, PR #4771)
 
+
 Changes
 
 Deprecations

package/MDAnalysis/analysis/contacts.py

@@ -223,7 +223,7 @@ def is_any_closer(r, r0, dist=2.5):
 from MDAnalysis.lib.util import openany
 from MDAnalysis.analysis.distances import distance_array
 from MDAnalysis.core.groups import AtomGroup, UpdatingAtomGroup
-from .base import AnalysisBase
+from .base import AnalysisBase, ResultsGroup
 
 logger = logging.getLogger("MDAnalysis.analysis.contacts")
 
@@ -376,8 +376,22 @@ class Contacts(AnalysisBase):
        :class:`MDAnalysis.analysis.base.Results` instance.
     .. versionchanged:: 2.2.0
        :class:`Contacts` accepts both AtomGroup and string for `select`
+    .. versionchanged:: 2.9.0
+       Introduced :meth:`get_supported_backends` allowing
+       for parallel execution on :mod:`multiprocessing`
+       and :mod:`dask` backends.
     """
 
+    _analysis_algorithm_is_parallelizable = True
+
+    @classmethod
+    def get_supported_backends(cls):
+        return (
+            "serial",
+            "multiprocessing",
+            "dask",
+        )
+
     def __init__(self, u, select, refgroup, method="hard_cut", radius=4.5,
                  pbc=True, kwargs=None, **basekwargs):
         """
@@ -444,11 +458,8 @@ def __init__(self, u, select, refgroup, method="hard_cut", radius=4.5,
         self.r0 = []
         self.initial_contacts = []
 
-        #get dimension of box if pbc set to True
-        if self.pbc:
-            self._get_box = lambda ts: ts.dimensions
-        else:
-            self._get_box = lambda ts: None
+        # get dimensions via partial for parallelization compatibility
+        self._get_box = functools.partial(self._get_box_func, pbc=self.pbc)
 
         if isinstance(refgroup[0], AtomGroup):
             refA, refB = refgroup
@@ -464,7 +475,6 @@ def __init__(self, u, select, refgroup, method="hard_cut", radius=4.5,
 
         self.n_initial_contacts = self.initial_contacts[0].sum()
 
-
     @staticmethod
     def _get_atomgroup(u, sel):
         select_error_message = ("selection must be either string or a "
@@ -480,6 +490,28 @@ def _get_atomgroup(u, sel):
         else:
             raise TypeError(select_error_message)
 
+    @staticmethod
+    def _get_box_func(ts, pbc):
+        """Retrieve the dimensions of the simulation box based on PBC.
+
+        Parameters
+        ----------
+        ts : Timestep
+            The current timestep of the simulation, which contains the
+            box dimensions.
+        pbc : bool
+            A flag indicating whether periodic boundary conditions (PBC)
+            are enabled. If `True`, the box dimensions are returned,
+            else returns `None`.
+
+        Returns
+        -------
+        box_dimensions : ndarray or None
+            The dimensions of the simulation box as a NumPy array if PBC
+            is True, else returns `None`.
+        """
+        return ts.dimensions if pbc else None
+
     def _prepare(self):
         self.results.timeseries = np.empty((self.n_frames, len(self.r0)+1))
 
@@ -506,6 +538,8 @@ def timeseries(self):
         warnings.warn(wmsg, DeprecationWarning)
         return self.results.timeseries
 
+    def _get_aggregator(self):
+        return ResultsGroup(lookup={'timeseries': ResultsGroup.ndarray_vstack})
 
 def _new_selections(u_orig, selections, frame):
     """create stand alone AGs from selections at frame"""

testsuite/MDAnalysisTests/analysis/conftest.py

@@ -15,6 +15,7 @@
     HydrogenBondAnalysis,
 )
 from MDAnalysis.analysis.nucleicacids import NucPairDist
+from MDAnalysis.analysis.contacts import Contacts
 from MDAnalysis.lib.util import is_installed
 
 
@@ -149,3 +150,10 @@ def client_HydrogenBondAnalysis(request):
 @pytest.fixture(scope="module", params=params_for_cls(NucPairDist))
 def client_NucPairDist(request):
     return request.param
+
+
+# MDAnalysis.analysis.contacts
+
+@pytest.fixture(scope="module", params=params_for_cls(Contacts))
+def client_Contacts(request):
+    return request.param

testsuite/MDAnalysisTests/analysis/test_contacts.py

@@ -171,8 +171,8 @@ def universe():
         return mda.Universe(PSF, DCD)
 
     def _run_Contacts(
-        self, universe,
-        start=None, stop=None, step=None, **kwargs
+        self, universe, client_Contacts, start=None,
+        stop=None, step=None, **kwargs
     ):
         acidic = universe.select_atoms(self.sel_acidic)
         basic = universe.select_atoms(self.sel_basic)
@@ -181,7 +181,8 @@ def _run_Contacts(
             select=(self.sel_acidic, self.sel_basic),
             refgroup=(acidic, basic),
             radius=6.0,
-            **kwargs).run(start=start, stop=stop, step=step)
+            **kwargs
+        ).run(**client_Contacts, start=start, stop=stop, step=step)
 
     @pytest.mark.parametrize("seltxt", [sel_acidic, sel_basic])
     def test_select_valid_types(self, universe, seltxt):
@@ -195,7 +196,7 @@ def test_select_valid_types(self, universe, seltxt):
 
         assert ag_from_string == ag_from_ag
 
-    def test_contacts_selections(self, universe):
+    def test_contacts_selections(self, universe, client_Contacts):
         """Test if Contacts can take both string and AtomGroup as selections.
         """
         aga = universe.select_atoms(self.sel_acidic)
@@ -210,8 +211,8 @@ def test_contacts_selections(self, universe):
             refgroup=(aga, agb)
         )
 
-        cag.run()
-        csel.run()
+        cag.run(**client_Contacts)
+        csel.run(**client_Contacts)
 
         assert cag.grA == csel.grA
         assert cag.grB == csel.grB
@@ -228,26 +229,31 @@ def test_select_wrong_types(self, universe, ag):
         ) as te:
             contacts.Contacts._get_atomgroup(universe, ag)
 
-    def test_startframe(self, universe):
+    def test_startframe(self, universe, client_Contacts):
         """test_startframe: TestContactAnalysis1: start frame set to 0 (resolution of
         Issue #624)
 
         """
-        CA1 = self._run_Contacts(universe)
+        CA1 = self._run_Contacts(universe, client_Contacts=client_Contacts)
         assert len(CA1.results.timeseries) == universe.trajectory.n_frames
 
-    def test_end_zero(self, universe):
+    def test_end_zero(self, universe, client_Contacts):
         """test_end_zero: TestContactAnalysis1: stop frame 0 is not ignored"""
-        CA1 = self._run_Contacts(universe, stop=0)
+        CA1 = self._run_Contacts(
+            universe, client_Contacts=client_Contacts, stop=0
+        )
         assert len(CA1.results.timeseries) == 0
 
-    def test_slicing(self, universe):
+    def test_slicing(self, universe, client_Contacts):
         start, stop, step = 10, 30, 5
-        CA1 = self._run_Contacts(universe, start=start, stop=stop, step=step)
+        CA1 = self._run_Contacts(
+            universe, client_Contacts=client_Contacts,
+            start=start, stop=stop, step=step
+        )
         frames = np.arange(universe.trajectory.n_frames)[start:stop:step]
         assert len(CA1.results.timeseries) == len(frames)
 
-    def test_villin_folded(self):
+    def test_villin_folded(self, client_Contacts):
         # one folded, one unfolded
         f = mda.Universe(contacts_villin_folded)
         u = mda.Universe(contacts_villin_unfolded)
@@ -259,12 +265,12 @@ def test_villin_folded(self):
                               select=(sel, sel),
                               refgroup=(grF, grF),
                               method="soft_cut")
-        q.run()
+        q.run(**client_Contacts)
 
         results = soft_cut(f, u, sel, sel)
         assert_allclose(q.results.timeseries[:, 1], results[:, 1], rtol=0, atol=1.5e-7)
 
-    def test_villin_unfolded(self):
+    def test_villin_unfolded(self, client_Contacts):
         # both folded
         f = mda.Universe(contacts_villin_folded)
         u = mda.Universe(contacts_villin_folded)
@@ -276,13 +282,13 @@ def test_villin_unfolded(self):
                               select=(sel, sel),
                               refgroup=(grF, grF),
                               method="soft_cut")
-        q.run()
+        q.run(**client_Contacts)
 
         results = soft_cut(f, u, sel, sel)
         assert_allclose(q.results.timeseries[:, 1], results[:, 1], rtol=0, atol=1.5e-7)
 
-    def test_hard_cut_method(self, universe):
-        ca = self._run_Contacts(universe)
+    def test_hard_cut_method(self, universe, client_Contacts):
+        ca = self._run_Contacts(universe, client_Contacts=client_Contacts)
         expected = [1., 0.58252427, 0.52427184, 0.55339806, 0.54368932,
                     0.54368932, 0.51456311, 0.46601942, 0.48543689, 0.52427184,
                     0.46601942, 0.58252427, 0.51456311, 0.48543689, 0.48543689,
@@ -306,7 +312,7 @@ def test_hard_cut_method(self, universe):
         assert len(ca.results.timeseries) == len(expected)
         assert_allclose(ca.results.timeseries[:, 1], expected, rtol=0, atol=1.5e-7)
 
-    def test_radius_cut_method(self, universe):
+    def test_radius_cut_method(self, universe, client_Contacts):
         acidic = universe.select_atoms(self.sel_acidic)
         basic = universe.select_atoms(self.sel_basic)
         r = contacts.distance_array(acidic.positions, basic.positions)
@@ -316,15 +322,20 @@ def test_radius_cut_method(self, universe):
             r = contacts.distance_array(acidic.positions, basic.positions)
             expected.append(contacts.radius_cut_q(r[initial_contacts], None, radius=6.0))
 
-        ca = self._run_Contacts(universe, method='radius_cut')
+        ca = self._run_Contacts(
+            universe, client_Contacts=client_Contacts, method="radius_cut"
+        )
         assert_array_equal(ca.results.timeseries[:, 1], expected)
 
     @staticmethod
     def _is_any_closer(r, r0, dist=2.5):
         return np.any(r < dist)
 
-    def test_own_method(self, universe):
-        ca = self._run_Contacts(universe, method=self._is_any_closer)
+    def test_own_method(self, universe, client_Contacts):
+        ca = self._run_Contacts(
+            universe, client_Contacts=client_Contacts,
+            method=self._is_any_closer
+        )
 
         bound_expected = [1., 1., 0., 1., 1., 0., 0., 1., 0., 1., 1., 0., 0.,
                           1., 0., 0., 0., 0., 1., 1., 0., 0., 0., 1., 0., 1.,
@@ -340,21 +351,28 @@ def test_own_method(self, universe):
     def _weird_own_method(r, r0):
         return 'aaa'
 
-    def test_own_method_no_array_cast(self, universe):
+    def test_own_method_no_array_cast(self, universe, client_Contacts):
         with pytest.raises(ValueError):
-            self._run_Contacts(universe, method=self._weird_own_method, stop=2)
-
-    def test_non_callable_method(self, universe):
+            self._run_Contacts(
+                universe,
+                client_Contacts=client_Contacts,
+                method=self._weird_own_method,
+                stop=2,
+            )
+
+    def test_non_callable_method(self, universe, client_Contacts):
         with pytest.raises(ValueError):
-            self._run_Contacts(universe, method=2, stop=2)
+            self._run_Contacts(
+                universe, client_Contacts=client_Contacts, method=2, stop=2
+            )
 
     @pytest.mark.parametrize("pbc,expected", [
     (True, [1., 0.43138152, 0.3989021, 0.43824337, 0.41948765,
             0.42223239, 0.41354071, 0.43641354, 0.41216834, 0.38334858]),
     (False, [1., 0.42327791, 0.39192399, 0.40950119, 0.40902613,
              0.42470309, 0.41140143, 0.42897862, 0.41472684, 0.38574822])
     ])
-    def test_distance_box(self, pbc, expected):
+    def test_distance_box(self, pbc, expected, client_Contacts):
         u = mda.Universe(TPR, XTC)
         sel_basic = "(resname ARG LYS)"
         sel_acidic = "(resname ASP GLU)"
@@ -363,13 +381,15 @@ def test_distance_box(self, pbc, expected):
 
         r = contacts.Contacts(u, select=(sel_acidic, sel_basic),
                         refgroup=(acidic, basic), radius=6.0, pbc=pbc)
-        r.run()
+        r.run(**client_Contacts)
         assert_allclose(r.results.timeseries[:, 1], expected,rtol=0, atol=1.5e-7)
 
-    def test_warn_deprecated_attr(self, universe):
+    def test_warn_deprecated_attr(self, universe, client_Contacts):
         """Test for warning message emitted on using deprecated `timeseries`
         attribute"""
-        CA1 = self._run_Contacts(universe, stop=1)
+        CA1 = self._run_Contacts(
+            universe, client_Contacts=client_Contacts, stop=1
+        )
         wmsg = "The `timeseries` attribute was deprecated in MDAnalysis"
         with pytest.warns(DeprecationWarning, match=wmsg):
             assert_equal(CA1.timeseries, CA1.results.timeseries)
@@ -385,10 +405,11 @@ def test_n_initial_contacts(self, datafiles, expected):
         r = contacts.Contacts(u, select=select, refgroup=refgroup)
         assert_equal(r.n_initial_contacts, expected)
 
-def test_q1q2():
+
+def test_q1q2(client_Contacts):
     u = mda.Universe(PSF, DCD)
     q1q2 = contacts.q1q2(u, 'name CA', radius=8)
-    q1q2.run()
+    q1q2.run(**client_Contacts)
 
     q1_expected = [1., 0.98092643, 0.97366031, 0.97275204, 0.97002725,
                    0.97275204, 0.96276113, 0.96730245, 0.9582198, 0.96185286,