Limit threads usage in numpy during test to avoid time-out

.github/workflows/gh-ci.yaml

@@ -108,6 +108,13 @@ jobs:
     - name: run_tests
       if: contains(matrix.name, 'asv_check') != true
       run: |
+        export OPENBLAS_NUM_THREADS=1
+        export GOTO_NUM_THREADS=1
+        export OMP_NUM_THREADS=1
+        export MKL_NUM_THREADS=1
+        # limit to 2 workers to avoid overloading the CI
+        export PYTEST_XDIST_AUTO_NUM_WORKERS=2
+
         PYTEST_FLAGS="--disable-pytest-warnings --durations=50"
         if [ ${{ matrix.codecov }} = "true" ]; then
           PYTEST_FLAGS="${PYTEST_FLAGS} --cov-config=.coveragerc --cov=MDAnalysis --cov-report=xml"

azure-pipelines.yml

@@ -128,6 +128,13 @@ jobs:
     displayName: 'Check installed packages'
   - powershell: |
       cd testsuite
+      $env:OPENBLAS_NUM_THREADS=1
+      $env:GOTO_NUM_THREADS=1
+      $env:OMP_NUM_THREADS=1
+      $env:MKL_NUM_THREADS=1
+      # limit to 2 workers to avoid overloading the CI
+      $env:PYTEST_XDIST_AUTO_NUM_WORKERS=1
+
       pytest MDAnalysisTests --disable-pytest-warnings -n auto --timeout=200 -rsx --cov=MDAnalysis
     displayName: 'Run MDAnalysis Test Suite'
   - script: |

testsuite/MDAnalysisTests/analysis/test_encore.py

@@ -125,10 +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()
 
@@ -142,12 +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 "
@@ -159,24 +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')

testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py

@@ -81,8 +81,8 @@
     ),
     (NCDF,),
     (np.arange(150).reshape(5, 10, 3).astype(np.float64),),
-    (GRO, [GRO, GRO, GRO, GRO, GRO]),
-    (PDB, [PDB, PDB, PDB, PDB, PDB]),
+    (GRO, [GRO, GRO]),
+    (PDB, [PDB, PDB]),
     (GRO, [XTC, XTC]),
     (TRC_PDB_VAC, TRC_TRAJ1_VAC),
     (TRC_PDB_VAC, [TRC_TRAJ1_VAC, TRC_TRAJ2_VAC]),
@@ -121,11 +121,11 @@ def test_multiprocess_COG(u):
     ag = u.atoms[2:5]
 
     ref = np.array([cog(u, ag, i)
-                    for i in range(3)])
+                    for i in range(2)])
 
     p = multiprocessing.Pool(2)
     res = np.array([p.apply(cog, args=(u, ag, i))
-                    for i in range(3)])
+                    for i in range(2)])
     p.close()
     assert_equal(ref, res)
 
@@ -198,9 +198,9 @@ def test_creating_multiple_universe_without_offset(temp_xtc, ncopies=3):
     ('memory', np.arange(60).reshape(2, 10, 3).astype(np.float64), dict()),
     ('TRC', TRC_TRAJ1_VAC, dict()),
     ('CHAIN', [TRC_TRAJ1_VAC, TRC_TRAJ2_VAC], dict()),
-    ('CHAIN', [GRO, GRO, GRO], dict()),
-    ('CHAIN', [PDB, PDB, PDB], dict()),
-    ('CHAIN', [XTC, XTC, XTC], dict()),
+    ('CHAIN', [GRO, GRO], dict()),
+    ('CHAIN', [PDB, PDB], dict()),
+    ('CHAIN', [XTC, XTC], dict()),
 ])
 def ref_reader(request):
     fmt_name, filename, extras = request.param