def test_general(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
# with mask
saved_data = pt.radgyr(traj, '@CA')
data = pt.pmap(pt.radgyr, traj, '@CA')
data = pt.tools.dict_to_ndarray(data)
aa_eq([saved_data], data)
# with a series of functions
func_list = [pt.radgyr, pt.molsurf, pt.rmsd]
ref = traj[-3]
for n_cores in [2, 3]:
for func in func_list:
if func in [
pt.rmsd,
]:
pout = pt.tools.dict_to_ndarray(
pt.pmap(
func=func, traj=traj, ref=ref, n_cores=n_cores))
serial_out = flatten(func(traj, ref=ref))
else:
pout = pt.tools.dict_to_ndarray(
pt.pmap(n_cores=n_cores, func=func, traj=traj))
serial_out = flatten(func(traj))
aa_eq(pout[0], serial_out)
# test worker
# need to test this since coverages seems not recognize partial func
data = worker_by_func(
rank=2,
n_cores=8,
func=pt.radgyr,
traj=traj,
args=(),
kwargs={'mask': '@CA'},
iter_options={})
assert data[
1] == 1, 'n_frames for rank=2 should be 1 (only 10 frames in total)'
def test_different_references(self):
traj = self.traj
func = pt.rmsd
for i in range(0, 8, 2):
ref = self.traj[i]
for n_cores in [
2,
3,
]:
pout = pt.tools.dict_to_ndarray(
pt.pmap(n_cores=n_cores, func=func, traj=traj, ref=ref))
serial_out = flatten(func(traj, ref=ref))
aa_eq(pout[0], serial_out)