Dear Hedyeh,

Could you post the complete .nestml file (on the list or to me directly if you prefer) so we can try to reproduce the issue?

Much obliged!
Charl


On Wed, Aug 30, 2023, at 10:51, Hedyeh Rezaei wrote:
Dear Jochen,

Thanks a lot, a giant step forward!
I now get another error:

Variable 'g_ex' not defined!

Ode equation lhs-variable 'g_ex$' not defined in state block!

Ode equation lhs-variable 'g_in$' not defined in state block!

Ode equation lhs-variable 'g_NMDA$' not defined in state block!

...

AttributeError: 'NoneType' object has no attribute 'is_state'


While my state block contains:
state:
        r integer = 0             # counts number of tick during the refractory period
        V_m mV = E_L              # membrane potential
   
        # inputs from the inhibitory conductance
        g_in real = 0
        g_in$ real = g_I_const * (1 / tau_rise_GABA_A - 1 / tau_decay_GABA_A)

        # inputs from the excitatory conductance
        g_ex real = 0
        g_ex$ real = g_E_const * (1 / tau_rise_AMPA - 1 / tau_decay_AMPA)
       
        # inputs from the excitatory NMDA conductance
        g_NMDA real = 0
        g_NMDA$ real = g_NMDA_const * (1 / tau_rise_NMDA - 1 / tau_decay_NMDA)
     
Any suggestions?

Thanks,
Hedyeh

On Wed, Aug 30, 2023 at 9:47 AM Jochen Martin Eppler <j.eppler@fz-juelich.de> wrote:

Dear Hedyeh,

the end keyword has recently been removed from NESTML. You indicate blocks now solely by indentation as in Python.

Cheers,
Jochen!



On 30.08.23 08:42, Hedyeh Rezaei wrote:



Dear all,

 

I have installed nestml via conda and developed a code describing an LIF neuron with bi-exponential synaptic currents including NMDA, while the charge mediated by AMPA and NMDA receptors are not independent. When I try to compile the .nestml file, it gives me an error as:

 

from pynestml.frontend.pynestml_frontend import generate_nest_target

 

WARNING:root:PyGSL is not available. The stiffness test will be skipped.

WARNING:root:Error when importing: No module named 'pygsl'

 

In [2]: generate_nest_target(input_path="/home/hrezaei/neuron_model_NMDA.nestml",

   ...:                      target_path="/tmp/nestml-component",

   ...:                      logging_level="ERROR")

line 61:4 extraneous input 'end' expecting {DEDENT, 'function', 'state', 'parameters', 'internals', 'update', 'equations', 'input', 'output'}

line 63:4 extraneous input 'equations' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'}

line 64:8 extraneous input '        ' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'}

line 67:8 extraneous input 'kernel' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'}

line 70:8 extraneous input 'kernel' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'}

...

r"""Generate and build code for NEST Simulator.

Parameters

A dictionary containing additional options for the target code generator.

"""

I was wondering what the reason could be. I would appreciate it if you could help.

Thanks in advance.

 

Best,

Hedyeh


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-- 
Dr. Jochen Martin Eppler (he/him)
Simulation and Data Lab Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation
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