Errors with Conda installation of brian2 on a mac with M1 processor

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Description of problem

I have attempted to install brian to on a mac with M1 processor using the anaconda environment.
Although the installation appears to have been completed when running the brian2.test() I am getting numerous errors

Minimal code to reproduce problem

conda create -n brian2env python=3.8
source activate brian2env
conda install -c conda-forge brian2
conda config --add channels conda-forge
conda install brian2
conda install matplotlib pytest ipython notebook
conda install -c brian-team brian2tools

What you have already tried

I found the docker solution in this group but I am not very familiar with dockers and would like to try and make it work with conda environments if possible before trying the docker approach

Full traceback of error (if relevant)

The error output is too long to paste here (can send in a file if necessary) but here a part of the summary

short test summary info

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_neurongroup.py::test_linked_var_in_reset - brian2.core.base.BrianObjectException: Error encountered with object named…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_neurongroup.py::test_linked_var_in_reset_size_1 - brian2.core.base.BrianObjectException: Error encountered with objec…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_neurongroup.py::test_threshold_reset - brian2.core.base.BrianObjectException: Error encountered with object named "ne…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_neurongroup.py::test_custom_events_schedule - brian2.core.base.BrianObjectException: Error encountered with object na…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_neurongroup.py::test_state_variable_set_strings - brian2.core.base.BrianObjectException: Error encountered with objec…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_neurongroup.py::test_sim_with_scalar_variable - brian2.core.base.BrianObjectException: Error encountered with object …

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_neurongroup.py::test_sim_with_scalar_subexpression - brian2.core.base.BrianObjectException: Error encountered with ob…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_neurongroup.py::test_constant_variable_subexpression - brian2.core.base.BrianObjectException: Error encountered with …

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_neurongroup.py::test_random_vector_values - brian2.core.base.BrianObjectException: Error encountered with object name…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_neurongroup.py::test_random_values_fixed_and_random - brian2.core.base.BrianObjectException: Error encountered with o…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_neurongroup.py::test_run_regularly_scheduling - brian2.core.base.BrianObjectException: Error encountered with object …

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_neurongroup.py::test_run_regularly_scheduling_2 - brian2.core.base.BrianObjectException: Error encountered with objec…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_neurongroup.py::test_run_regularly_dt - brian2.core.base.BrianObjectException: Error encountered with object named "n…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_neurongroup.py::test_run_regularly_shared - brian2.core.base.BrianObjectException: Error encountered with object name…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_neurongroup.py::test_semantics_floor_division - brian2.core.base.BrianObjectException: Error encountered with object …

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_neurongroup.py::test_semantics_floating_point_division - brian2.core.base.BrianObjectException: Error encountered wit…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_neurongroup.py::test_semantics_mod - brian2.core.base.BrianObjectException: Error encountered with object named "neur…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_poissongroup.py::test_single_rates - brian2.core.base.BrianObjectException: Error encountered with object named "pois…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_poissongroup.py::test_rate_arrays - brian2.core.base.BrianObjectException: Error encountered with object named "poiss…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_poissongroup.py::test_time_dependent_rate - brian2.core.base.BrianObjectException: Error encountered with object name…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_poissongroup.py::test_propagation - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ failed w…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_poissongroup.py::test_poissongroup_subgroup - distutils.errors.CompileError: command 'x86_64-apple-darwin13.4.0-clang…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_poissoninput.py::test_poissoninput - brian2.core.base.BrianObjectException: Error encountered with object named "pois…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_poissoninput.py::test_poissoninput_refractory - brian2.core.base.BrianObjectException: Error encountered with object …

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_refractory.py::test_refractoriness_basic - brian2.core.base.BrianObjectException: Error encountered with object named…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_refractory.py::test_refractoriness_variables[5*ms] - brian2.core.base.BrianObjectException: Error encountered with ob…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_refractory.py::test_refractoriness_variables[(t-lastspike + 1e-3dt) < 5ms] - brian2.core.base.BrianObjectException:…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_refractory.py::test_refractoriness_variables[time_since_spike + 1e-3dt < 5ms] - brian2.core.base.BrianObjectExcepti…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_refractory.py::test_refractoriness_variables[ref_subexpression] - brian2.core.base.BrianObjectException: Error encoun…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_refractory.py::test_refractoriness_variables[(t-lastspike + 1e-3*dt) < ref] - brian2.core.base.BrianObjectException: …

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_refractory.py::test_refractoriness_variables[ref] - brian2.core.base.BrianObjectException: Error encountered with obj…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_refractory.py::test_refractoriness_variables[ref_no_unit*ms] - brian2.core.base.BrianObjectException: Error encounter…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_refractory.py::test_refractoriness_threshold_basic - brian2.core.base.BrianObjectException: Error encountered with ob…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_refractory.py::test_refractoriness_repeated - brian2.core.base.BrianObjectException: Error encountered with object na…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_refractory.py::test_refractoriness_repeated_legacy - brian2.core.base.BrianObjectException: Error encountered with ob…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_refractory.py::test_refractoriness_threshold[ref_time0] - brian2.core.base.BrianObjectException: Error encountered wi…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_refractory.py::test_refractoriness_threshold[10*ms] - brian2.core.base.BrianObjectException: Error encountered with o…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_refractory.py::test_refractoriness_threshold[timestep(t-lastspike, dt) < timestep(10*ms, dt)] - brian2.core.base.Bria…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_refractory.py::test_refractoriness_threshold[timestep(t-lastspike, dt) < timestep(ref, dt)] - brian2.core.base.BrianO…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_refractory.py::test_refractoriness_threshold[ref] - brian2.core.base.BrianObjectException: Error encountered with obj…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_refractory.py::test_refractoriness_threshold[ref_no_unit*ms] - brian2.core.base.BrianObjectException: Error encounter…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_refractory.py::test_conditional_write_behaviour - distutils.errors.CompileError: command 'x86_64-apple-darwin13.4.0-c…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_refractory.py::test_conditional_write_automatic_and_manual - distutils.errors.CompileError: command 'x86_64-apple-dar…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_spatialneuron.py::test_finitecable - brian2.core.base.BrianObjectException: Error encountered with object named "spat…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_spatialneuron.py::test_rallpack1 - brian2.core.base.BrianObjectException: Error encountered with object named "statem…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_spatialneuron.py::test_rallpack2 - brian2.core.base.BrianObjectException: Error encountered with object named "statem…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_spatialneuron.py::test_rall - brian2.core.base.BrianObjectException: Error encountered with object named "spatialneur…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_spatialneuron.py::test_basic_diffusion - brian2.core.base.BrianObjectException: Error encountered with object named "…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_spatialneuron.py::test_spatialneuron_capacitive_currents - brian2.core.base.BrianObjectException: Error encountered w…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_spikegenerator.py::test_spikegenerator_connected - distutils.errors.CompileError: command 'x86_64-apple-darwin13.4.0-…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_spikegenerator.py::test_spikegenerator_basic - brian2.core.base.BrianObjectException: Error encountered with object n…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_spikegenerator.py::test_spikegenerator_basic_sorted - brian2.core.base.BrianObjectException: Error encountered with o…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_spikegenerator.py::test_spikegenerator_basic_sorted_with_sorted - brian2.core.base.BrianObjectException: Error encoun…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_spikegenerator.py::test_spikegenerator_period - brian2.core.base.BrianObjectException: Error encountered with object …

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_spikegenerator.py::test_spikegenerator_period_repeat - brian2.core.base.BrianObjectException: Error encountered with …

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_spikegenerator.py::test_spikegenerator_change_spikes - brian2.core.base.BrianObjectException: Error encountered with …

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_spikegenerator.py::test_spikegenerator_change_period - brian2.core.base.BrianObjectException: Error encountered with …

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_spikegenerator.py::test_spikegenerator_rounding - brian2.core.base.BrianObjectException: Error encountered with objec…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_spikegenerator.py::test_spikegenerator_multiple_runs - brian2.core.base.BrianObjectException: Error encountered with …

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_spikegenerator.py::test_spikegenerator_restore - brian2.core.base.BrianObjectException: Error encountered with object…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_stateupdaters.py::test_multiple_noise_variables_extended - brian2.core.base.BrianObjectException: Error encountered w…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_stateupdaters.py::test_multiple_noise_variables_deterministic_noise - brian2.core.base.BrianObjectException: Error en…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_stateupdaters.py::test_pure_noise_deterministic - brian2.core.base.BrianObjectException: Error encountered with objec…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_stateupdaters.py::test_subexpressions_basic - brian2.core.base.BrianObjectException: Error encountered with object na…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_stateupdaters.py::test_subexpressions - brian2.core.base.BrianObjectException: Error encountered with object named "s…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_stateupdaters.py::test_refractory - brian2.core.base.BrianObjectException: Error encountered with object named "neuro…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_stateupdaters.py::test_refractory_stochastic - brian2.core.base.BrianObjectException: Error encountered with object n…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_subgroup.py::test_state_monitor - brian2.core.base.BrianObjectException: Error encountered with object named "statemo…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_subgroup.py::test_synapse_creation - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ failed …

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_subgroup.py::test_synapse_creation_state_vars - distutils.errors.CompileError: command 'x86_64-apple-darwin13.4.0-cla…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_subgroup.py::test_synapse_creation_generator - distutils.errors.CompileError: command 'x86_64-apple-darwin13.4.0-clan…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_subgroup.py::test_synapse_creation_generator_multiple_synapses - distutils.errors.CompileError: command 'x86_64-apple…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_subgroup.py::test_synapse_creation_generator_complex_ranges - distutils.errors.CompileError: command 'x86_64-apple-da…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_subgroup.py::test_synapse_creation_generator_random - distutils.errors.CompileError: command 'x86_64-apple-darwin13.4…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_subgroup.py::test_synapse_access - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ failed wi…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_subgroup.py::test_synapses_access_subgroups - distutils.errors.CompileError: command 'x86_64-apple-darwin13.4.0-clang…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_subgroup.py::test_subgroup_summed_variable - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_subgroup.py::test_subexpression_references - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_subgroup.py::test_subexpression_no_references - distutils.errors.CompileError: command 'x86_64-apple-darwin13.4.0-cla…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_subgroup.py::test_synaptic_propagation - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ fai…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_subgroup.py::test_synaptic_propagation_2 - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ f…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_subgroup.py::test_run_regularly - brian2.core.base.BrianObjectException: Error encountered with object named "neurong…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_subgroup.py::test_spike_monitor - brian2.core.base.BrianObjectException: Error encountered with object named "neurong…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_subgroup.py::test_no_reference_2 - brian2.core.base.BrianObjectException: Error encountered with object named "statem…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_subgroup.py::test_no_reference_3 - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ failed wi…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_subgroup.py::test_no_reference_4 - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ failed wi…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_incoming_outgoing - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ failed…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_connection_arrays - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ failed…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_connection_string_deterministic_full - distutils.errors.CompileError: command 'x86_64-apple-darwin1…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_connection_string_deterministic_full_no_self - distutils.errors.CompileError: command 'x86_64-apple…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_connection_string_deterministic_full_one_to_one - distutils.errors.CompileError: command 'x86_64-ap…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_connection_string_deterministic_full_custom - distutils.errors.CompileError: command 'x86_64-apple-…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_connection_string_deterministic_multiple_and - distutils.errors.CompileError: command 'x86_64-apple…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_connection_random_with_condition - distutils.errors.CompileError: command 'x86_64-apple-darwin13.4…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_connection_random_with_indices - distutils.errors.CompileError: command 'x86_64-apple-darwin13.4.0-…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_connection_random_without_condition - distutils.errors.CompileError: command 'x86_64-apple-darwin13…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_connection_multiple_synapses - distutils.errors.CompileError: command 'x86_64-apple-darwin13.4.0-cl…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_state_variable_assignment - distutils.errors.CompileError: command 'x86_64-apple-darwin13.4.0-clang…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_state_variable_indexing - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ …

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_indices - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ failed with exit…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_subexpression_references - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_constant_variable_subexpression_in_synapses - distutils.errors.CompileError: command 'x86_64-apple-…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_nested_subexpression_references - distutils.errors.CompileError: command 'x86_64-apple-darwin13.4.0…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_delay_specification - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ fail…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_delays_pathways - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ failed w…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_delays_pathways_subgroups - distutils.errors.CompileError: command 'x86_64-apple-darwin13.4.0-clang…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_pre_post_simple - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ failed w…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_transmission_simple - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ fail…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_transmission_custom_event - distutils.errors.CompileError: command 'x86_64-apple-darwin13.4.0-clang…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_transmission - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ failed with…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_transmission_all_to_one_heterogeneous_delays - distutils.errors.CompileError: command 'x86_64-apple…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_transmission_one_to_all_heterogeneous_delays - distutils.errors.CompileError: command 'x86_64-apple…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_transmission_scalar_delay - distutils.errors.CompileError: command 'x86_64-apple-darwin13.4.0-clang…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_transmission_scalar_delay_different_clocks - distutils.errors.CompileError: command 'x86_64-apple-d…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_transmission_boolean_variable - distutils.errors.CompileError: command 'x86_64-apple-darwin13.4.0-c…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_equations_with_clocks - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ fa…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_changed_dt_spikes_in_queue - distutils.errors.CompileError: command 'x86_64-apple-darwin13.4.0-clan…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_summed_variable - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ failed w…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_summed_variable_pre_and_post - distutils.errors.CompileError: command 'x86_64-apple-darwin13.4.0-cl…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_summed_variable_differing_group_size - distutils.errors.CompileError: command 'x86_64-apple-darwin1…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_summed_variables_subgroups - distutils.errors.CompileError: command 'x86_64-apple-darwin13.4.0-clan…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_scalar_parameter_access - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ …

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_scalar_subexpression - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ fai…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_sim_with_scalar_variable - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_sim_with_scalar_subexpression - distutils.errors.CompileError: command 'x86_64-apple-darwin13.4.0-c…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_sim_with_constant_subexpression - distutils.errors.CompileError: command 'x86_64-apple-darwin13.4.0…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_external_variables - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ faile…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_event_driven - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ failed with…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_vectorisation - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ failed wit…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_vectorisation_STDP_like - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ …

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_synaptic_equations - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ faile…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_synapse_with_run_regularly - distutils.errors.CompileError: command 'x86_64-apple-darwin13.4.0-clan…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_synapses_to_synapses - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ fai…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_synapses_to_synapses_statevar_access - distutils.errors.CompileError: command 'x86_64-apple-darwin1…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_synapses_to_synapses_different_sizes - distutils.errors.CompileError: command 'x86_64-apple-darwin1…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_synapses_to_synapses_summed_variable - distutils.errors.CompileError: command 'x86_64-apple-darwin1…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_synapse_generator_out_of_range - distutils.errors.CompileError: command 'x86_64-apple-darwin13.4.0-…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_synapse_generator_deterministic - distutils.errors.CompileError: command 'x86_64-apple-darwin13.4.0…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_synapse_generator_random - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_synapse_generator_random_with_condition - distutils.errors.CompileError: command 'x86_64-apple-darw…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_synapses_refractory - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’ fail…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_synapses.py::test_synapses_refractory_rand - distutils.errors.CompileError: command ‘x86_64-apple-darwin13.4.0-clang’…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_thresholder.py::test_simple_threshold - brian2.core.base.BrianObjectException: Error encountered with object named "n…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_thresholder.py::test_scalar_threshold - brian2.core.base.BrianObjectException: Error encountered with object named "n…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_timedarray.py::test_timedarray_semantics - brian2.core.base.BrianObjectException: Error encountered with object named…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_timedarray.py::test_timedarray_no_units - brian2.core.base.BrianObjectException: Error encountered with object named …

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_timedarray.py::test_timedarray_with_units - brian2.core.base.BrianObjectException: Error encountered with object name…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_timedarray.py::test_timedarray_2d - brian2.core.base.BrianObjectException: Error encountered with object named "state…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_timedarray.py::test_timedarray_no_upsampling - brian2.core.base.BrianObjectException: Error encountered with object n…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_timedarray.py::test_long_timedarray - brian2.core.base.BrianObjectException: Error encountered with object named "sta…

FAILED opt/anaconda3/envs/brian2env/lib/python3.8/site-packages/brian2/tests/test_timedarray.py::test_timedarray_repeated_use - brian2.core.base.BrianObjectException: Error encountered with object na…

225 failed , 23 passed, 8 skipped, 410 deselected, 405 warnings in 357.07s (0:05:57)

ERROR: 2/4 test suite(s) did not complete successfully (see above).

Out[ 4 ]: False

2

Hello!
That’s suspiciously similar to the number of errors I’m getting on my intel processor mac. I think there’s something going on with Brian and cython (and maybe some other things) on mac.

The good news is if you set:
prefs.codegen.target = 'numpy'
[more info here]
you should be able to run most Brian code! (i haven’t run into any issues outside the test suite so far)
The bad news is this will likely be slower than if Brian had access to Cython.

My guess is your problems overlap with those discussed [here] in which case it might be good to continue the discussion there
-Adam

1 Like
3

Just in addition to @adam comment, we tasted brian2 on M1, but inside a docker container. You can find the docker file for this image in Oleksii Leonov’s git repository . It seems docker is the best way to go until Linux will natively run on M1.

I am not sure whether it helps, but you have an option to work around the problem at least.

1 Like
4

Thank you for this, indeed prefs.codegen.target = 'numpy' allows me indeed to run most brian code but not all despite the brian2.test code failings tons of tests.

Many thanks, Margarita.

1 Like
5

Thank you, will keep this in mind as a back up plan.

Many thanks, Margarita

6

Hi @mzachariou, as @adam suggested, this may well be a general OS X/clang issue, could you please try the steps in my last comment in Problem with Cython - #3 by adam ? Since you installed Brian with conda, you’d need to uninstall it with conda remove --force brian2 first (or test things in a separate environment).
Best,
Marcel

7

@mzachariou as an update, we now seem to have a solution which enables cython and brian to work together on mac inside a conda environment! I think it’s only been tested on macs with an intel processor, but if you get the chance to try the steps in the other thread and let us know whether it works, that would be great!

[instructions to follow]

[discussion in “Problem with Cython”]

1 Like
8

Many thanks Marcel and Adam,

I tried out the proposed solution and it worked like a charm for the cython test.

I also tried to run the brian2.test() command and the only major error appears to be the following:
Running doctests

==================================== ERRORS ====================================

____________________ ERROR collecting sphinxext/briandoc.py ____________________

…/…/…/lib/python3.8/site-packages/brian2/sphinxext/briandoc.py :22: in

from docutils import statemachine

E ModuleNotFoundError: No module named 'docutils’

___________________ ERROR collecting sphinxext/docscrape.py ____________________

…/…/…/lib/python3.8/site-packages/brian2/sphinxext/docscrape.py :13: in

from sphinx.pycode import ModuleAnalyzer

E ModuleNotFoundError: No module named 'sphinx’

________________ ERROR collecting sphinxext/docscrape_sphinx.py ________________

…/…/…/lib/python3.8/site-packages/brian2/sphinxext/docscrape_sphinx.py :3: in

import sphinx

E ModuleNotFoundError: No module named 'sphinx’

=========================== short test summary info ============================

ERROR …/…/…/lib/python3.8/site-packages/brian2/sphinxext/briandoc.py - Mod…

ERROR …/…/…/lib/python3.8/site-packages/brian2/sphinxext/docscrape.py - Mo…

ERROR …/…/…/lib/python3.8/site-packages/brian2/sphinxext/docscrape_sphinx.py

!!! Interrupted: 3 errors during collection !!!

3 errors in 0.32s

9

Wonderful! I’m excited to hear those steps work on M1 macs also!

I think sphinx and docutils are optional packages that might not get installed with a default brain2 install. My guess is they’re not critical for running simulations since they’re associated with documenting the codebase.

You could try simply

conda install -c conda-forge sphinx
conda install -c conda-forge docutils

and then try the tests again. Although the “right” way to get these packages is probably through brian2tools or some other optional install step that Marcel might be able to point us too

1 Like
10

Just to confirm what @adam said: this is a bit of a bug in our test suite, since it tries to test our documentation infrastructure by default (which would only be relevant if you wanted to regenerate the documentation that you can find on brian2.readthedocs.org on your own machine). This infrastructure is built on sphinx which itself depends on docutils. So in summary: don’t worry about these errors, these tests should not run by default since the package they test is not at all relevant for running simulations.

2 Likes
11

Great, thank you both for all the help!

1 Like
12

This workaround solved the issue on my Intel machine but on my M1 one I’m still getting a ton of failed Python tests.
I think this could be because I installed Brian via pip, as I’m not able to do so via conda install -c conda-forge brian2 or mamba install -c conda-forge brian2 (I tried both MiniForge and MambaForge):

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  • brian2

Current channels:

To search for alternate channels that may provide the conda package you’re
looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

13

Hi @Tioz90. Did you install the latest development version of Brian with something like pip install --upgrade --pre -i https://test.pypi.org/simple/ Brian2 or is this for the latest “official” release?
When you say “workaround”, do you refer to setting the “CC” and “CXX” environment variables?
Finally, could you please paste the output of the test run? Since a lot of errors will most likely be the same, you can run (from within Python):

>>> import brian2
>>> brian2.test(additional_args=['-x'])

This will make the test suite stop after the first failed test instead of running them all.

14

to add to this, you should be able to try setting the environment variables regardless of conda by simply executing <...>/activate.d/env_vars.sh in the instructions manually. It might be helpful to see what the errors are both before and after doing this.

(and then <...>/deactivate/d/env_vars.sh after testing)

15

No, this is the latest stable release (brian2 2.4.2).

The workaround was the one posted by @Adam , which previously solved my Cython issues on my Intel MacBook.

Here is the output without the workaround: Last login: Tue Nov 16 12:23:37 on ttys001(base) thomastiotto@mac-mini ~ % con - Pastebin.com

And with the workaround: #!/bin/sh#!/bin/shLast login: Tue Nov 16 12:10:59 on ttys000(base) thomast - Pastebin.com

Edit: I tried with the latest dev version and it seems to work! Unlike with the stable release, pip was able to compile the wheel and then I got no errors when running:

import brian2
brian2.test('cython', test_codegen_independent=False, additional_args=['-x'])

Edit 2: I tried the dev version without the workaround and everything still seems to work. :grinning_face_with_smiling_eyes:

2 Likes
16

Ah, great, then we should be all set. The next release (i.e. what is currently the dev version) is long overdue, but I plan to finally get around to publishing it the end of this week.

1 Like