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
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
NEST Users mailing list --users@nest-simulator.org To unsubscribe send an email tousers-leave@nest-simulator.org
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
NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
-- Dr. Jochen Martin Eppler (he/him) Simulation and Data Lab Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation
Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens, Prof. Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior
NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
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
NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
-- Dr. Jochen Martin Eppler (he/him) Simulation and Data Lab Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation
Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens, Prof. Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior
NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
Dear Charl,
I sent my .nestml file to your email address. I would be grateful if you could help. Looking forward to hearing from you.
Best regards, Hedyeh
On Wed, Aug 30, 2023 at 10:53 AM Charl Linssen nest-users@turingbirds.com wrote:
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
NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
-- Dr. Jochen Martin Eppler (he/him) Simulation and Data Lab Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation
Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens, Prof. Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior
NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
-
Charl Linssen -
Hedyeh Rezaei -
Jochen Martin Eppler