Cannot run advect_model (new user)
lalligagger opened this issue · 2 comments
lalligagger commented
Hi, I've just started taking a look into xarray-simlab and would love to try using for some modeling I'm doing! Currently I'm not able to get all the way through the example model, after doing a pip install.
I have defined my processes/ models as in the "Creating Models" example:
@xs.process
class UniformGrid1D:
"""Create a 1-dimensional, equally spaced grid."""
spacing = xs.variable(description="uniform spacing", static=True)
length = xs.variable(description="total length", static=True)
x = xs.index(dims="x")
def initialize(self):
self.x = np.arange(0, self.length, self.spacing)
@xs.process
class ProfileU:
"""Compute the evolution of the profile of quantity `u`."""
u_vars = xs.group("u_vars")
u = xs.variable(
dims="x", intent="inout", description="quantity u", attrs={"units": "m"}
)
def run_step(self):
self._delta_u = sum((v for v in self.u_vars))
def finalize_step(self):
self.u += self._delta_u
@xs.process
class AdvectionLax:
"""Advection using finite difference (Lax method) on
a fixed grid with periodic boundary conditions.
"""
v = xs.variable(dims=[(), "x"], description="velocity")
grid_spacing = xs.foreign(UniformGrid1D, "spacing")
u = xs.foreign(ProfileU, "u")
u_advected = xs.variable(dims="x", intent="out", groups="u_vars")
@xs.runtime(args="step_delta")
def run_step(self, dt):
factor = self.v / (2 * self.grid_spacing)
u_left = np.roll(self.u, 1)
u_right = np.roll(self.u, -1)
u_1 = 0.5 * (u_right + u_left) - factor * dt * (u_right - u_left)
self.u_advected = u_1 - self.u
@xs.process
class InitUGauss:
"""Initialize `u` profile using a Gaussian pulse."""
loc = xs.variable(description="location of initial pulse", static=True)
scale = xs.variable(description="scale of initial pulse", static=True)
x = xs.foreign(UniformGrid1D, "x")
u = xs.foreign(ProfileU, "u", intent="out")
def initialize(self):
self.u = np.exp(-1 / self.scale ** 2 * (self.x - self.loc) ** 2)
advect_model = xs.Model(
{
"grid": UniformGrid1D,
"profile": ProfileU,
"init": InitUGauss,
"advect": AdvectionLax,
}
)
here is the ds_in I generated using the autogeneration and the "Setup and Run" example values:
# %create_setup advect_model --default --verbose
ds_in = xs.create_setup(
model=advect_model,
clocks={
'time': np.linspace(0., 1., 101),
'otime': [0, 0.5, 1],
},
master_clock='time',
input_vars={
# uniform spacing
'grid__spacing': 0.01,
# total length
'grid__length': 1.5,
# location of initial pulse
'init__loc': 0.3,
# scale of initial pulse
'init__scale': 0.1,
# velocity
'advect__v': 1.,
},
output_vars={
'profile__u': 'otime'
}
)
On run, I get key errors on ('advect', 'u_advected')....
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
<ipython-input-15-41c902d1e936> in <module>
2
3 with advect_model:
----> 4 out_ds2 = (ds_in.xsimlab.update_vars(input_vars=in_vars).xsimlab.run())
~/.virtualenvs/stac/lib/python3.9/site-packages/xsimlab/xr_accessor.py in run(self, model, batch_dim, check_dims, validate, store, encoding, decoding, hooks, parallel, scheduler, safe_mode)
821 )
822
--> 823 driver.run_model()
824
825 return driver.get_results()
~/.virtualenvs/stac/lib/python3.9/site-packages/xsimlab/drivers.py in run_model(self)
470
471 if self.batch_dim is None:
--> 472 _run(
473 ds_in,
474 self.model,
~/.virtualenvs/stac/lib/python3.9/site-packages/xsimlab/drivers.py in _run(dataset, model, store, hooks, validate, batch, batch_size, parallel, scheduler)
347 in_vars = _get_input_vars(ds_step, model)
348 model.update_state(in_vars, validate=validate_inputs, ignore_static=False)
--> 349 signal = model.execute("run_step", rt_context, **execute_kwargs)
350
351 if signal == RuntimeSignal.BREAK:
~/.virtualenvs/stac/lib/python3.9/site-packages/xsimlab/model.py in execute(self, stage, runtime_context, hooks, validate, parallel, scheduler)
1021 else:
1022 for p_obj in self._processes.values():
-> 1023 _, (_, signal_process) = self._execute_process(p_obj, *execute_args)
1024
1025 if signal_process == RuntimeSignal.BREAK:
~/.virtualenvs/stac/lib/python3.9/site-packages/xsimlab/model.py in _execute_process(self, p_obj, stage, runtime_context, hooks, validate, state)
840 return p_name, ({}, signal_pre)
841
--> 842 state_out, signal_out = executor.execute(
843 p_obj, stage, runtime_context, state=state
844 )
~/.virtualenvs/stac/lib/python3.9/site-packages/xsimlab/process.py in execute(self, p_obj, stage, runtime_context, state)
528 return {}, RuntimeSignal.NONE
529 else:
--> 530 signal_out = executor.execute(p_obj, runtime_context, state=state)
531
532 skeys = [p_obj.__xsimlab_state_keys__[k] for k in self.out_vars]
~/.virtualenvs/stac/lib/python3.9/site-packages/xsimlab/process.py in execute(self, p_obj, runtime_context, state)
392 args = [runtime_context[k] for k in self.args]
393
--> 394 signal = self.meth(p_obj, *args)
395
396 if signal is None:
<ipython-input-2-1a1f078aa29b> in run_step(self)
20
21 def run_step(self):
---> 22 self._delta_u = sum((v for v in self.u_vars))
23
24 def finalize_step(self):
<ipython-input-2-1a1f078aa29b> in <genexpr>(.0)
20
21 def run_step(self):
---> 22 self._delta_u = sum((v for v in self.u_vars))
23
24 def finalize_step(self):
~/.virtualenvs/stac/lib/python3.9/site-packages/xsimlab/process.py in getter_state_or_on_demand(self)
275
276 for key in state_keys:
--> 277 yield self.__xsimlab_state__[key]
278
279 for key in od_keys:
KeyError: ('advect', 'u_advected')
lalligagger commented
- attempting to run model with
ds_out = ds_in.xsimlab.run(model=advect_model)
lalligagger commented
This worked when using the advect model here: https://github.com/xarray-contrib/xarray-simlab/blob/master/doc/scripts/advection_model.py
Looking forward to using this more and maybe helping out once I get up the learning curve!