reduce computation in encore

yuxuanzhuang · May 2, 2024 · 05fd7f2 · 05fd7f2
1 parent 97cb5f7
commit 05fd7f2
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Showing 2 changed files with 13 additions and 10 deletions.
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -128,6 +128,9 @@ jobs:
     displayName: 'Check installed packages'
   - powershell: |
       cd testsuite
+      $env:OPENBLAS_NUM_THREADS=1
+      $env:GOTO_NUM_THREADS=1
+      $env:OMP_NUM_THREADS=1
       pytest MDAnalysisTests --disable-pytest-warnings -n auto --timeout=200 -rsx --cov=MDAnalysis
     displayName: 'Run MDAnalysis Test Suite'
   - script: |

diff --git a/testsuite/MDAnalysisTests/analysis/test_encore.py b/testsuite/MDAnalysisTests/analysis/test_encore.py
@@ -45,6 +45,7 @@
 def function(x):
     return x**2
 
+
 class TestEncore(object):
     @pytest.fixture(scope='class')
     def ens1_template(self):
@@ -124,10 +125,10 @@ def test_triangular_matrix(self):
                        reason="Not yet supported on Windows.")
     def test_parallel_calculation(self):
 
-        arguments = [tuple([i]) for i in np.arange(0,100)]
+        arguments = [tuple([i]) for i in np.arange(0,10)]
 
         parallel_calculation = encore.utils.ParallelCalculation(function=function,
-                                                                n_jobs=4,
+                                                                n_jobs=2,
                                                                 args=arguments)
         results = parallel_calculation.run()
 
@@ -141,12 +142,12 @@ def test_rmsd_matrix_with_superimposition(self, ens1):
         conf_dist_matrix = encore.confdistmatrix.conformational_distance_matrix(
             ens1,
             encore.confdistmatrix.set_rmsd_matrix_elements,
-            select="name CA",
+            select="name CA and resnum 1:3",
             pairwise_align=True,
             weights='mass',
             n_jobs=1)
 
-        reference = rms.RMSD(ens1, select="name CA")
+        reference = rms.RMSD(ens1, select="name CA and resnum 1:3")
         reference.run()
         err_msg = (
             "Calculated RMSD values differ from "
@@ -158,24 +159,25 @@ def test_rmsd_matrix_with_superimposition_custom_weights(self, ens1):
         conf_dist_matrix = encore.confdistmatrix.conformational_distance_matrix(
             ens1,
             encore.confdistmatrix.set_rmsd_matrix_elements,
-            select="name CA",
+            select="name CA and resnum 1:3",
             pairwise_align=True,
             weights='mass',
             n_jobs=1)
 
         conf_dist_matrix_custom = encore.confdistmatrix.conformational_distance_matrix(
             ens1,
             encore.confdistmatrix.set_rmsd_matrix_elements,
-            select="name CA",
+            select="name CA and resnum 1:3",
             pairwise_align=True,
-            weights=(ens1.select_atoms('name CA').masses, ens1.select_atoms('name CA').masses),
+            weights=(ens1.select_atoms("name CA and resnum 1:3").masses,
+                     ens1.select_atoms("name CA and resnum 1:3").masses),
             n_jobs=1)
 
         for i in range(conf_dist_matrix_custom.size):
             assert_allclose(conf_dist_matrix_custom[0, i], conf_dist_matrix[0, i], rtol=0, atol=1.5e-7)
 
     def test_rmsd_matrix_without_superimposition(self, ens1):
-        selection_string = "name CA"
+        selection_string = "name CA and resnum 1:3"
         selection = ens1.select_atoms(selection_string)
         reference_rmsd = []
         coordinates = ens1.trajectory.timeseries(selection, order='fac')
@@ -678,8 +680,6 @@ def test_cluster_repr(self):
         repr_message = "<Cluster with 1 elements, centroid=1, id=1>"
         assert_equal(repr(cluster), repr_message)
 
-
-
 class TestEncoreClusteringSklearn(object):
     """The tests in this class were duplicated from the affinity propagation
     tests in scikit-learn"""