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Limit threads usage in numpy during test to avoid time-out #4584

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Limit threads usage in numpy during test to avoid time-out #4584

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97df4a4
limit numpy thread
yuxuanzhuang May 1, 2024
21435cf
limit numpy thread with prefix
yuxuanzhuang May 1, 2024
12adcb1
export instead
yuxuanzhuang May 1, 2024
06f8d34
reduce computation in encore
yuxuanzhuang May 2, 2024
33ba400
limit thread in azure pipeline
yuxuanzhuang May 2, 2024
757d773
use 2 nworkers
yuxuanzhuang May 3, 2024
e3192e7
limit azure to 1 core
yuxuanzhuang May 3, 2024
747bfb8
reduce parallel test time
yuxuanzhuang May 3, 2024
e46b809
Merge remote-tracking branch 'upstream/develop' into fix_timeout
yuxuanzhuang Aug 16, 2024
754ff2c
Merge remote-tracking branch 'upstream/develop' into fix_timeout
yuxuanzhuang Sep 9, 2024
555520a
restore gh-ci
yuxuanzhuang Sep 9, 2024
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17 changes: 9 additions & 8 deletions testsuite/MDAnalysisTests/analysis/test_encore.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
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args=arguments)
results = parallel_calculation.run()

Expand All @@ -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",
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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 "
Expand All @@ -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')
Expand Down
14 changes: 7 additions & 7 deletions testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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]),
Expand Down Expand Up @@ -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)

Expand Down Expand Up @@ -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
Expand Down
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