# DimensionMismatchError in run time mode but not in standalone mode **URL:** \ **Category:** Support\ **Tags:** units\ **Created:** [22 February 2021 17:16 UTC](https://brian.discourse.group/t/dimensionmismatcherror-in-run-time-mode-but-not-in-standalone-mode/311 "2021-02-22T17:16:39Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![DavidKing2020](https://avatars.discourse-cdn.com/v4/letter/d/e0b2c6/32.png) [@DavidKing2020](https://brian.discourse.group/u/DavidKing2020)\ **Post date:** [22 February 2021 17:16 UTC](https://brian.discourse.group/t/dimensionmismatcherror-in-run-time-mode-but-not-in-standalone-mode/311/1 "2021-02-22T17:16:39Z")
I encountered a DimensionMismatchError and any help is appreciated. The following is the example: The first code save the synapse in a file: ``` from brian2 import * import numpy as np eqs = ''' dv/dt = (I-v)/tau : 1 I : 1 tau : second ''' G = NeuronGroup(2, eqs, threshold='v>1', reset='v = 0', method='exact') G.I = [2, 0] G.tau = [10, 100]*ms # Comment these two lines out to see what happens without Synapses S = Synapses(G, G, on_pre='v_post += 0.2') S.connect(i=0, j=1) S.delay = 10*ms np.savez('test', i=S.i[:], j=S.j[:], delay=S.delay[:]) ``` The second code load the saved the synapse and build the connection: ``` from brian2 import * import numpy as np #set_device('cpp_standalone', build_on_run=False) eqs = ''' dv/dt = (I-v)/tau : 1 I : 1 tau : second ''' G = NeuronGroup(2, eqs, threshold='v>1', reset='v = 0', method='exact') G.I = [2, 0] G.tau = [10, 100]*ms # Comment these two lines out to see what happens without Synapses S = Synapses(G, G, on_pre='v_post += 0.2') trained_S = np.load('test.npz') S.connect(i=trained_S['i'], j=trained_S['j']) S.delay[:] = trained_S['delay'] M = StateMonitor(G, 'v', record=True) run(100*ms) #device.build(directory='test', compile=True, run=True, debug=False) ``` The running of the 2nd code is fine in standalone mode, but in runtime mode, I’ve got the following error. ``` --------------------------------------------------------------------------- DimensionMismatchError Traceback (most recent call last) in 18 trained_S = np.load('test.npz') 19 S.connect(i=trained_S['i'], j=trained_S['j']) ---> 20 S.delay[:] = trained_S['delay'] 21 22 M = StateMonitor(G, 'v', record=True) ~/anaconda3/lib/python3.8/site-packages/brian2/core/variables.py in __setitem__ (self, item, value) 912 913 def __setitem__ (self, item, value): --> 914 self.set_item(item, value, level=1) 915 916 @device_override('variableview_set_with_expression') ~/anaconda3/lib/python3.8/site-packages/brian2/core/variables.py in set_item(self, item, value, level, namespace) 896 if item == 'True': 897 # We do not want to go through code generation for runtime --> 898 self.set_with_index_array(slice(None), value, 899 check_units=check_units) 900 else: ~/anaconda3/lib/python3.8/site-packages/brian2/core/base.py in device_override_decorated_function(*args, **kwds) 276 return getattr(curdev, name)(*args, **kwds) 277 else: --> 278 return func(*args, **kwds) 279 280 device_override_decorated_function. __doc__ = func. __doc__ ~/anaconda3/lib/python3.8/site-packages/brian2/core/variables.py in set_with_index_array(self, item, value, check_units) 1164 variable = self.variable 1165 if check_units: -> 1166 fail_for_dimension_mismatch(variable.dim, value, 1167 'Incorrect unit for setting variable %s' % self.name) 1168 if variable.scalar: ~/anaconda3/lib/python3.8/site-packages/brian2/units/fundamentalunits.py in fail_for_dimension_mismatch(obj1, obj2, error_message, **error_quantities) 185 raise DimensionMismatchError(error_message, dim1) 186 else: --> 187 raise DimensionMismatchError(error_message, dim1, dim2) 188 else: 189 return dim1, dim2 DimensionMismatchError: Incorrect unit for setting variable delay (units are s and 1). ``` To avoid this error, I need to manually as the unit as follows: ``` S.delay[:] = trained_S['delay']*second ``` ---
**Author:** ![mstimberg](https://yyz2.discourse-cdn.com/free1/user_avatar/brian.discourse.group/mstimberg/32/11_2.png) [@mstimberg](https://brian.discourse.group/u/mstimberg)\ **Post date:** [22 February 2021 17:39 UTC](https://brian.discourse.group/t/dimensionmismatcherror-in-run-time-mode-but-not-in-standalone-mode/311/2 "2021-02-22T17:39:07Z")
Hi. I’m surprised it works in standalone mode, this should actually be considered a bug 🙂 `np.savez` does not know anything about Brian quantities, so it just stores a standard numpy array without units to disk. When you load it, you therefore get an array without units which you cannot assign to the delay variable which expects a value in seconds. Multiplying the value with seconds is one solution, another would be to use `Quantity(trained_S['delay'], dim=second.dim, copy=False)`. Admittedly this is a bit complicated, but it has the advantage that it can give you a “view” on an existing array without copying it in memory. This can be useful for very large arrays – not sure that this is very relevant here, though. Finally, the simplest option would be to ask Brian to directly use a `delay` variable without units by appending an underscore, i.e. use ```auto S.delay_[:] = trained_S['delay'] ``` You could also use `S.delay_[:]` in the `np.savez` call, but it will throw away the unit information in either case. ---
**Author:** ![DavidKing2020](https://avatars.discourse-cdn.com/v4/letter/d/e0b2c6/32.png) [@DavidKing2020](https://brian.discourse.group/u/DavidKing2020)\ **Post date:** [22 February 2021 17:42 UTC](https://brian.discourse.group/t/dimensionmismatcherror-in-run-time-mode-but-not-in-standalone-mode/311/3 "2021-02-22T17:42:00Z")
Thanks Marcel. Does that mean the code running in standalone mode could have the results wrong? ---
**Author:** ![mstimberg](https://yyz2.discourse-cdn.com/free1/user_avatar/brian.discourse.group/mstimberg/32/11_2.png) [@mstimberg](https://brian.discourse.group/u/mstimberg)\ **Post date:** [22 February 2021 17:49 UTC](https://brian.discourse.group/t/dimensionmismatcherror-in-run-time-mode-but-not-in-standalone-mode/311/4 "2021-02-22T17:49:52Z")
> [@DavidKing2020](#): > > Thanks Marcel. Does that mean the code running in standalone mode could have the results wrong? No, if you didn’t convert the units manually in any way, then everything will work correctly (since this is the way things are represented internally anyway). The reason why I think it should be a bug is that when assigning values to a variable, we check whether the unit of the values match, and this should happen without regard to runtime or standalone mode. In your use case you could have stored the values in a different scale (e.g. by doing `np.savez(...delay=S.delay[:]/ms)`) and then `S.delay[:] = trained_S['delay']` would have interpreted these values in seconds without raising an error which should not happen. Of course by using `delay_` etc. you can still make the main mistake, but at least you’d be explicit about the fact that you are not using Brian’s unit checking mechanism.