Comments (7)
pnbabu
commented on August 18, 2024
@ewa thanks for writing in. Could you provide more information like the CMake output and the rest of the compilation logs? Could you also attach the generated code from NESTML? The generated files must be in the target directory from where the notebook is running.
from nestml.
ewa8
commented on August 18, 2024
Here are the generated files:
neuron msnff3d16d131484a588d128b3206348245:
state:
V_m mV = -65.0 mV
U_m real = 0.0
I pA = 0.0 pA # input current
dop real = 0.0
end
equations:
kernel kernel_ampa = exp(-t/tau_decay_AMPA)
kernel kernel_nmda = exp(-t/tau_decay_NMDA)
kernel kernel_gaba = exp(-t/tau_decay_GABA_A)
inline I_syn_ampa pA = convolve(kernel_ampa, spikes_ampa)
inline I_syn_nmda pA = convolve(kernel_nmda, spikes_nmda)
inline I_syn_gaba pA = convolve(kernel_gaba, spikes_gaba)
inline ampa pA = I_syn_ampa * (E_rev_AMPA - V_m)
inline nmda pA = I_syn_nmda * (E_rev_NMDA - V_m)
inline I_gaba pA = I_syn_gaba * (E_rev_GABA_A - V_m)
inline I_nmda pA = nmda * (1.0 + alpha_1*y1)
inline I_ampa pA = ampa * (1.0 - alpha_2*y2)
inline B real = 1.0/(1.0+(0.28)*exp(-0.062*V_m))
inline I_syn pA = I_ampa + B*I_nmda + I_gaba
inline v_r mV = vp * (1.0 + c_1 * y1)
inline k real = Kplus * (1.0 - alpha * y2)
V_m' = (k * (V_m - v_r) * (V_m - V_T)/mV - U_m*mV + ((I + I_e + I_syn)* GOhm))/ (C_m*(ms/pF))
U_m' = a * (b * (V_m - v_r) - U_m*mV)/(mV * ms)
end
parameters:
a real = 0.03
b real = -2.0
c mV = -50 mV
d real = 100
I_e pA = 0pA # constant external input current
V_th mV = 35mV #V peak
V_min mV = -inf * mV
Kplus real = 0.7
vp mV = -60.0 mV #resting potential
V_T mV = -40.0 mV #threshold potential
C_m pF = 100.0 pF # membrane capacitance
c_1 real = 0.0289 # K
c_2 real = 0.331 # L
y1 real = 0.3 # active D1 receptors
y2 real = 0.3 # active D2 receptors
alpha_1 real = 0.5 # synaptic dopamine
alpha_2 real = 0.5 # synaptic dopamine
alpha real = 0.032
tau_decay_AMPA ms = 2.0 ms
tau_decay_GABA_A ms = 2.0 ms
tau_decay_NMDA ms = 2.0 ms
E_rev_AMPA real = 0.0
E_rev_GABA_A real = 0.0
E_rev_NMDA real = 0.0
end
input:
spikes_ampa mV <-spike
spikes_nmda mV <-spike
spikes_gaba mV <-spike
I_stim pA <-continuous
end
output: spike
update:
integrate_odes()
# Add synaptic current
# lower bound of membrane potential
V_m = (V_m < V_min)?V_min:V_m
# threshold crossing
if V_m >= 30mV:
dop = d * (1.0 - c_2 * y1)
V_m = c
U_m += dop
emit_spike()
end
end
end
synapse neuromodulated_stdpff3d16d131484a588d128b3206348245:
state:
w real = 1.
n real = 0. # Neuromodulator concentration
c real = 0. # Eligibility trace
pre_tr real = 0.
post_tr real = 0.
end
parameters:
the_delay ms = 1 ms @nest::delay # !!! cannot have a variable called "delay"
tau_tr_pre ms = 20 ms # STDP time constant for weight changes caused by pre-before-post spike pairings.
tau_tr_post ms = 20 ms # STDP time constant for weight changes caused by post-before-pre spike pairings.
tau_c ms = 1000 ms # Time constant of eligibility trace
tau_n ms = 200 ms # Time constant of dopaminergic trace
b real = 0. # Dopaminergic baseline concentration
Wmax real = 200. # Maximal synaptic weight
Wmin real = 0. # Minimal synaptic weight
A_plus real = 1. # Multiplier applied to weight changes caused by pre-before-post spike pairings. If b (dopamine baseline concentration) is zero, then A_plus is simply the multiplier for facilitation (as in the stdp_synapse model). If b is not zero, then A_plus will be the multiplier for facilitation only if n - b is positive, where n is the instantenous dopamine concentration in the volume transmitter. If n - b is negative, A_plus will be the multiplier for depression.
A_minus real = 1.5 # Multiplier applied to weight changes caused by post-before-pre spike pairings. If b (dopamine baseline concentration) is zero, then A_minus is simply the multiplier for depression (as in the stdp_synapse model). If b is not zero, then A_minus will be the multiplier for depression only if n - b is positive, where n is the instantenous dopamine concentration in the volume transmitter. If n - b is negative, A_minus will be the multiplier for facilitation.
A_vt real = 1. # Multiplier applied to dopa spikes
end
equations:
pre_tr' = -pre_tr / tau_tr_pre
post_tr' = -post_tr / tau_tr_post
end
internals:
tau_s 1/ms = (tau_c + tau_n) / (tau_c * tau_n)
end
input:
pre_spikes nS <- spike
post_spikes nS <- spike
mod_spikes real <- spike
end
output: spike
onReceive(mod_spikes):
n += A_vt / tau_n
end
onReceive(post_spikes):
post_tr += 1.
# facilitation
c += A_plus * pre_tr
end
onReceive(pre_spikes):
pre_tr += 1.
# depression
c -= A_minus * post_tr
# deliver spike to postsynaptic partner
deliver_spike(w, the_delay)
end
# update from time t to t + resolution()
update:
# resolution() returns the timestep to be made (in units of time)
# the sequence here matters: the update step for w requires the "old" values of c and n
w -= c * ( n / tau_s * expm1( -tau_s * resolution() ) \
- b * tau_c * expm1( -resolution() / tau_c ))
w = max(0., w)
c = c * exp(-resolution() / tau_c)
n = n * exp(-resolution() / tau_n)
end
end
And here are the latest logs (let me know if you also need some of the earlier logs):
[74,msnff3d16d131484a588d128b3206348245_nestml__with_neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml, INFO, [37:13;37:13]]: Implicit casting from (compatible) type 'integer' to 'real'.
[75,GLOBAL, INFO]: Analysing/transforming synapse neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml.
[76,neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml, INFO, [1:0;74:0]]: Starts processing of the model 'neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml'
[77,neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml, DEBUG, [1:0;74:0]]: Start building symbol table!
[78,neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml, INFO, [43:9;43:16]]: Implicit casting from (compatible) type '1 / ms' to 'real'.
[79,neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml, INFO, [67:9;68:57]]: Implicit casting from (compatible) type 'ms' to 'real'.
[80,neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml, DEBUG, [1:0;74:0]]: Start building symbol table!
[81,neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml, INFO, [43:9;43:16]]: Implicit casting from (compatible) type '1 / ms' to 'real'.
[82,neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml, INFO, [67:9;68:57]]: Implicit casting from (compatible) type 'ms' to 'real'.
[83,GLOBAL, INFO]: Rendering template /Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/msnff3d16d131484a588d128b3206348245_nestml.cpp
[84,GLOBAL, INFO]: Rendering template /Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/msnff3d16d131484a588d128b3206348245_nestml.h
[85,msnff3d16d131484a588d128b3206348245_nestml, INFO, [1:0;84:0]]: Successfully generated code for the model: 'msnff3d16d131484a588d128b3206348245_nestml' in: '/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target' !
[86,GLOBAL, INFO]: Rendering template /Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/msnff3d16d131484a588d128b3206348245_nestml__with_neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml.cpp
[87,GLOBAL, INFO]: Rendering template /Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/msnff3d16d131484a588d128b3206348245_nestml__with_neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml.h
[88,msnff3d16d131484a588d128b3206348245_nestml__with_neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml, INFO, [1:0;84:0]]: Successfully generated code for the model: 'msnff3d16d131484a588d128b3206348245_nestml__with_neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml' in: '/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target' !
[89,GLOBAL, INFO]: Rendering template /Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml.h
[90,neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml, INFO, [1:0;74:0]]: Successfully generated code for the model: 'neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml' in: '/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target' !
[91,GLOBAL, INFO]: Rendering template /Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/CMakeLists.txt
[92,GLOBAL, INFO]: Rendering template /Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/nestml_ff3d16d131484a588d128b3206348245_module.h
[93,GLOBAL, INFO]: Rendering template /Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/nestml_ff3d16d131484a588d128b3206348245_module.cpp
[94,GLOBAL, INFO]: Rendering template /Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/CMakeLists.txt
[95,GLOBAL, INFO]: Rendering template /Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/nestml_ff3d16d131484a588d128b3206348245_module.h
[96,GLOBAL, INFO]: Rendering template /Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/nestml_ff3d16d131484a588d128b3206348245_module.cpp
[97,GLOBAL, INFO]: Rendering template /Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/CMakeLists.txt
[98,GLOBAL, INFO]: Rendering template /Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/nestml_ff3d16d131484a588d128b3206348245_module.h
[99,GLOBAL, INFO]: Rendering template /Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/nestml_ff3d16d131484a588d128b3206348245_module.cpp
[100,GLOBAL, INFO]: Successfully generated NEST module code in '/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target' !
-- The CXX compiler identification is AppleClang 14.0.0.14000029
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/clang++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-------------------------------------------------------
nestml_ff3d16d131484a588d128b3206348245_module Configuration Summary
-------------------------------------------------------
C++ compiler : /usr/bin/clang++
Build static libs : OFF
C++ compiler flags :
NEST compiler flags : -O2 -std=c++11 -Wall -Xclang -fopenmp -O3 -DNDEBUG
NEST include dirs : -I/opt/homebrew/Cellar/nest/3.3_1/include/nest -I/opt/homebrew/include -I/opt/homebrew/opt/readline/include -I/opt/homebrew/include
NEST libraries flags : -L/opt/homebrew/Cellar/nest/3.3_1/lib/nest -lnestutil -lnest -lsli -lnestkernel -Xclang -fopenmp /opt/homebrew/lib/libltdl.dylib /opt/homebrew/opt/readline/lib/libreadline.dylib /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/usr/lib/libncurses.tbd /opt/homebrew/lib/libgsl.dylib /opt/homebrew/lib/libgslcblas.dylib
-------------------------------------------------------
You can now build and install 'nestml_ff3d16d131484a588d128b3206348245_module' using
make
make install
The library file libnestml_ff3d16d131484a588d128b3206348245_module.so will be installed to
/opt/homebrew/Cellar/nest/3.3_1/lib/nest
The module can be loaded into NEST using
(nestml_ff3d16d131484a588d128b3206348245_module) Install (in SLI)
nest.Install(nestml_ff3d16d131484a588d128b3206348245_module) (in PyNEST)
CMake Warning (dev) in CMakeLists.txt:
No cmake_minimum_required command is present. A line of code such as
cmake_minimum_required(VERSION 3.22)
should be added at the top of the file. The version specified may be lower
if you wish to support older CMake versions for this project. For more
information run "cmake --help-policy CMP0000".
This warning is for project developers. Use -Wno-dev to suppress it.
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target
[ 25%] Building CXX object CMakeFiles/nestml_ff3d16d131484a588d128b3206348245_module_module.dir/nestml_ff3d16d131484a588d128b3206348245_module.o
In file included from /Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/nestml_ff3d16d131484a588d128b3206348245_module.cpp:47:
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/msnff3d16d131484a588d128b3206348245_nestml.h:372:17: warning: 'msnff3d16d131484a588d128b3206348245_nestml::get_C_m' hides overloaded virtual function [-Woverloaded-virtual]
inline double get_C_m() const
^
/opt/homebrew/Cellar/nest/3.3_1/include/nest/node.h:689:18: note: hidden overloaded virtual function 'nest::Node::get_C_m' declared here: different number of parameters (1 vs 0)
virtual double get_C_m( int comp );
^
In file included from /Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/nestml_ff3d16d131484a588d128b3206348245_module.cpp:49:
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/msnff3d16d131484a588d128b3206348245_nestml__with_neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml.h:425:17: warning: 'msnff3d16d131484a588d128b3206348245_nestml__with_neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml::get_C_m' hides overloaded virtual function [-Woverloaded-virtual]
inline double get_C_m() const
^
/opt/homebrew/Cellar/nest/3.3_1/include/nest/node.h:689:18: note: hidden overloaded virtual function 'nest::Node::get_C_m' declared here: different number of parameters (1 vs 0)
virtual double get_C_m( int comp );
^
In file included from /Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/nestml_ff3d16d131484a588d128b3206348245_module.cpp:49:
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/msnff3d16d131484a588d128b3206348245_nestml__with_neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml.h:234:8: warning: 'register_stdp_connection' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
void register_stdp_connection( double t_first_read, double delay );
^
/opt/homebrew/Cellar/nest/3.3_1/include/nest/node.h:457:16: note: overridden virtual function is here
virtual void register_stdp_connection( double, double );
^
In file included from /Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/nestml_ff3d16d131484a588d128b3206348245_module.cpp:52:
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml.h:593:22: warning: unused variable 'minus_dt' [-Wunused-variable]
const double minus_dt = t_lastspike_ - ( start->t_ + __dendritic_delay );
^
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml.h:616:22: warning: unused variable '_tr_t' [-Wunused-variable]
const double _tr_t = start->t_;
^
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml.h:543:18: warning: unused variable '__resolution' [-Wunused-variable]
const double __resolution = nest::Time::get_resolution().get_ms(); // do not remove, this is necessary for the resolution() function
^
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml.h:733:12: warning: unused variable 'cd' [-Wunused-variable]
double cd;
^
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml.h:889:16: warning: unused variable '__resolution' [-Wunused-variable]
const double __resolution = nest::Time::get_resolution().get_ms(); // do not remove, this is necessary for the resolution() function
^
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml.h:904:16: warning: unused variable '__resolution' [-Wunused-variable]
const double __resolution = nest::Time::get_resolution().get_ms(); // do not remove, this is necessary for the resolution() function
^
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml.h:1053:18: warning: unused variable '_tr_t' [-Wunused-variable]
const double _tr_t = start->t_;
^
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml.h:1035:10: warning: unused variable 'timestep' [-Wunused-variable]
double timestep = 0;
^
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml.h:545:10: warning: unused variable 'get_thread' [-Wunused-variable]
auto get_thread = [tid]()
^
/opt/homebrew/Cellar/nest/3.3_1/include/nest/connector_base.h:379:18: note: in instantiation of member function 'nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml<nest::TargetIdentifierPtrRport>::send' requested here
C_[ lcid ].send(
^
/opt/homebrew/Cellar/nest/3.3_1/include/nest/connector_base.h:223:12: note: in instantiation of member function 'nest::Connector<nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml<nest::TargetIdentifierPtrRport>>::send_to_all' requested here
explicit Connector( const synindex syn_id )
^
/opt/homebrew/Cellar/nest/3.3_1/include/nest/connector_model_impl.h:271:45: note: in instantiation of member function 'nest::Connector<nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml<nest::TargetIdentifierPtrRport>>::Connector' requested here
thread_local_connectors[ syn_id ] = new Connector< ConnectionT >( syn_id );
^
/opt/homebrew/Cellar/nest/3.3_1/include/nest/connector_model_impl.h:252:3: note: in instantiation of member function 'nest::GenericConnectorModel<nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml<nest::TargetIdentifierPtrRport>>::add_connection_' requested here
add_connection_( src, tgt, thread_local_connectors, syn_id, connection, actual_receptor_type );
^
/opt/homebrew/Cellar/nest/3.3_1/include/nest/connector_model.h:183:3: note: in instantiation of member function 'nest::GenericConnectorModel<nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml<nest::TargetIdentifierPtrRport>>::add_connection' requested here
GenericConnectorModel( const std::string name,
^
/opt/homebrew/Cellar/nest/3.3_1/include/nest/model_manager_impl.h:61:28: note: in instantiation of member function 'nest::GenericConnectorModel<nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml<nest::TargetIdentifierPtrRport>>::GenericConnectorModel' requested here
ConnectorModel* cf = new GenericConnectorModel< ConnectionT< TargetIdentifierPtrRport > >( name,
^
/opt/homebrew/Cellar/nest/3.3_1/include/nest/nest_impl.h:35:26: note: in instantiation of function template specialization 'nest::ModelManager::register_connection_model<nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml>' requested here
kernel().model_manager.register_connection_model< ConnectorModelT >( name, flags );
^
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/nestml_ff3d16d131484a588d128b3206348245_module.cpp:113:9: note: in instantiation of function template specialization 'nest::register_connection_model<nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml>' requested here
nest::register_connection_model< nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml >( "neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml" );
^
In file included from /Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/nestml_ff3d16d131484a588d128b3206348245_module.cpp:52:
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml.h:525:7: warning: expression result unused [-Wunused-value]
dynamic_cast<msnff3d16d131484a588d128b3206348245_nestml__with_neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml&>(t);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/opt/homebrew/Cellar/nest/3.3_1/include/nest/connector_model_impl.h:276:14: note: in instantiation of member function 'nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml<nest::TargetIdentifierPtrRport>::check_connection' requested here
connection.check_connection( src, tgt, receptor_type, get_common_properties() );
^
/opt/homebrew/Cellar/nest/3.3_1/include/nest/connector_model_impl.h:252:3: note: in instantiation of member function 'nest::GenericConnectorModel<nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml<nest::TargetIdentifierPtrRport>>::add_connection_' requested here
add_connection_( src, tgt, thread_local_connectors, syn_id, connection, actual_receptor_type );
^
/opt/homebrew/Cellar/nest/3.3_1/include/nest/connector_model.h:183:3: note: in instantiation of member function 'nest::GenericConnectorModel<nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml<nest::TargetIdentifierPtrRport>>::add_connection' requested here
GenericConnectorModel( const std::string name,
^
/opt/homebrew/Cellar/nest/3.3_1/include/nest/model_manager_impl.h:61:28: note: in instantiation of member function 'nest::GenericConnectorModel<nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml<nest::TargetIdentifierPtrRport>>::GenericConnectorModel' requested here
ConnectorModel* cf = new GenericConnectorModel< ConnectionT< TargetIdentifierPtrRport > >( name,
^
/opt/homebrew/Cellar/nest/3.3_1/include/nest/nest_impl.h:35:26: note: in instantiation of function template specialization 'nest::ModelManager::register_connection_model<nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml>' requested here
kernel().model_manager.register_connection_model< ConnectorModelT >( name, flags );
^
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/nestml_ff3d16d131484a588d128b3206348245_module.cpp:113:9: note: in instantiation of function template specialization 'nest::register_connection_model<nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml>' requested here
nest::register_connection_model< nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml >( "neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml" );
^
In file included from /Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/nestml_ff3d16d131484a588d128b3206348245_module.cpp:52:
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml.h:545:10: warning: unused variable 'get_thread' [-Wunused-variable]
auto get_thread = [tid]()
^
/opt/homebrew/Cellar/nest/3.3_1/include/nest/connector_base.h:379:18: note: in instantiation of member function 'nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml<nest::TargetIdentifierIndex>::send' requested here
C_[ lcid ].send(
^
/opt/homebrew/Cellar/nest/3.3_1/include/nest/connector_base.h:223:12: note: in instantiation of member function 'nest::Connector<nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml<nest::TargetIdentifierIndex>>::send_to_all' requested here
explicit Connector( const synindex syn_id )
^
/opt/homebrew/Cellar/nest/3.3_1/include/nest/connector_model_impl.h:271:45: note: in instantiation of member function 'nest::Connector<nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml<nest::TargetIdentifierIndex>>::Connector' requested here
thread_local_connectors[ syn_id ] = new Connector< ConnectionT >( syn_id );
^
/opt/homebrew/Cellar/nest/3.3_1/include/nest/connector_model_impl.h:252:3: note: in instantiation of member function 'nest::GenericConnectorModel<nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml<nest::TargetIdentifierIndex>>::add_connection_' requested here
add_connection_( src, tgt, thread_local_connectors, syn_id, connection, actual_receptor_type );
^
/opt/homebrew/Cellar/nest/3.3_1/include/nest/connector_model.h:183:3: note: in instantiation of member function 'nest::GenericConnectorModel<nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml<nest::TargetIdentifierIndex>>::add_connection' requested here
GenericConnectorModel( const std::string name,
^
/opt/homebrew/Cellar/nest/3.3_1/include/nest/model_manager_impl.h:74:14: note: in instantiation of member function 'nest::GenericConnectorModel<nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml<nest::TargetIdentifierIndex>>::GenericConnectorModel' requested here
cf = new GenericConnectorModel< ConnectionT< TargetIdentifierIndex > >( name + "_hpc",
^
/opt/homebrew/Cellar/nest/3.3_1/include/nest/nest_impl.h:35:26: note: in instantiation of function template specialization 'nest::ModelManager::register_connection_model<nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml>' requested here
kernel().model_manager.register_connection_model< ConnectorModelT >( name, flags );
^
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/nestml_ff3d16d131484a588d128b3206348245_module.cpp:113:9: note: in instantiation of function template specialization 'nest::register_connection_model<nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml>' requested here
nest::register_connection_model< nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml >( "neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml" );
^
In file included from /Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/nestml_ff3d16d131484a588d128b3206348245_module.cpp:52:
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml.h:525:7: warning: expression result unused [-Wunused-value]
dynamic_cast<msnff3d16d131484a588d128b3206348245_nestml__with_neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml&>(t);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/opt/homebrew/Cellar/nest/3.3_1/include/nest/connector_model_impl.h:276:14: note: in instantiation of member function 'nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml<nest::TargetIdentifierIndex>::check_connection' requested here
connection.check_connection( src, tgt, receptor_type, get_common_properties() );
^
/opt/homebrew/Cellar/nest/3.3_1/include/nest/connector_model_impl.h:252:3: note: in instantiation of member function 'nest::GenericConnectorModel<nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml<nest::TargetIdentifierIndex>>::add_connection_' requested here
add_connection_( src, tgt, thread_local_connectors, syn_id, connection, actual_receptor_type );
^
/opt/homebrew/Cellar/nest/3.3_1/include/nest/connector_model.h:183:3: note: in instantiation of member function 'nest::GenericConnectorModel<nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml<nest::TargetIdentifierIndex>>::add_connection' requested here
GenericConnectorModel( const std::string name,
^
/opt/homebrew/Cellar/nest/3.3_1/include/nest/model_manager_impl.h:74:14: note: in instantiation of member function 'nest::GenericConnectorModel<nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml<nest::TargetIdentifierIndex>>::GenericConnectorModel' requested here
cf = new GenericConnectorModel< ConnectionT< TargetIdentifierIndex > >( name + "_hpc",
^
/opt/homebrew/Cellar/nest/3.3_1/include/nest/nest_impl.h:35:26: note: in instantiation of function template specialization 'nest::ModelManager::register_connection_model<nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml>' requested here
kernel().model_manager.register_connection_model< ConnectorModelT >( name, flags );
^
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/nestml_ff3d16d131484a588d128b3206348245_module.cpp:113:9: note: in instantiation of function template specialization 'nest::register_connection_model<nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml>' requested here
nest::register_connection_model< nest::neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml >( "neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml__with_msnff3d16d131484a588d128b3206348245_nestml" );
^
15 warnings generated.
[ 50%] Building CXX object CMakeFiles/nestml_ff3d16d131484a588d128b3206348245_module_module.dir/msnff3d16d131484a588d128b3206348245_nestml.o
In file included from /Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/msnff3d16d131484a588d128b3206348245_nestml.cpp:43:
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/msnff3d16d131484a588d128b3206348245_nestml.h:372:17: warning: 'msnff3d16d131484a588d128b3206348245_nestml::get_C_m' hides overloaded virtual function [-Woverloaded-virtual]
inline double get_C_m() const
^
/opt/homebrew/Cellar/nest/3.3_1/include/nest/node.h:689:18: note: hidden overloaded virtual function 'nest::Node::get_C_m' declared here: different number of parameters (1 vs 0)
virtual double get_C_m( int comp );
^
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/msnff3d16d131484a588d128b3206348245_nestml.cpp:109:16: warning: unused variable '__resolution' [-Wunused-variable]
const double __resolution = nest::Time::get_resolution().get_ms(); // do not remove, this is necessary for the resolution() function
^
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/msnff3d16d131484a588d128b3206348245_nestml.cpp:363:16: warning: unused variable '__resolution' [-Wunused-variable]
const double __resolution = nest::Time::get_resolution().get_ms(); // do not remove, this is necessary for the resolution() function
^
3 warnings generated.
[ 75%] Building CXX object CMakeFiles/nestml_ff3d16d131484a588d128b3206348245_module_module.dir/msnff3d16d131484a588d128b3206348245_nestml__with_neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml.o
In file included from /Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/msnff3d16d131484a588d128b3206348245_nestml__with_neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml.cpp:43:
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/msnff3d16d131484a588d128b3206348245_nestml__with_neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml.h:425:17: warning: 'msnff3d16d131484a588d128b3206348245_nestml__with_neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml::get_C_m' hides overloaded virtual function [-Woverloaded-virtual]
inline double get_C_m() const
^
/opt/homebrew/Cellar/nest/3.3_1/include/nest/node.h:689:18: note: hidden overloaded virtual function 'nest::Node::get_C_m' declared here: different number of parameters (1 vs 0)
virtual double get_C_m( int comp );
^
In file included from /Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/msnff3d16d131484a588d128b3206348245_nestml__with_neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml.cpp:43:
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/msnff3d16d131484a588d128b3206348245_nestml__with_neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml.h:234:8: warning: 'register_stdp_connection' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
void register_stdp_connection( double t_first_read, double delay );
^
/opt/homebrew/Cellar/nest/3.3_1/include/nest/node.h:457:16: note: overridden virtual function is here
virtual void register_stdp_connection( double, double );
^
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/msnff3d16d131484a588d128b3206348245_nestml__with_neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml.cpp:110:16: warning: unused variable '__resolution' [-Wunused-variable]
const double __resolution = nest::Time::get_resolution().get_ms(); // do not remove, this is necessary for the resolution() function
^
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/msnff3d16d131484a588d128b3206348245_nestml__with_neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml.cpp:389:16: warning: unused variable '__resolution' [-Wunused-variable]
const double __resolution = nest::Time::get_resolution().get_ms(); // do not remove, this is necessary for the resolution() function
^
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target/msnff3d16d131484a588d128b3206348245_nestml__with_neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml.cpp:651:84: error: expression is not assignable
S_.post_tr__for_neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml += 1.0;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
4 warnings and 1 error generated.
make[2]: *** [CMakeFiles/nestml_ff3d16d131484a588d128b3206348245_module_module.dir/msnff3d16d131484a588d128b3206348245_nestml__with_neuromodulated_stdpff3d16d131484a588d128b3206348245_nestml.o] Error 1
make[1]: *** [CMakeFiles/nestml_ff3d16d131484a588d128b3206348245_module_module.dir/all] Error 2
make: *** [all] Error 2
CalledProcessError Traceback (most recent call last)
File ~/Library/Python/3.10/lib/python/site-packages/NESTML-5.1.0.post0.dev0-py3.10.egg/pynestml/codegeneration/nest_builder.py:152, in NESTBuilder.build(self)
151 try:
--> 152 subprocess.check_call(make_all_cmd, stderr=subprocess.STDOUT, shell=shell,
153 cwd=str(os.path.join(target_path)))
154 except subprocess.CalledProcessError as e:
File /opt/homebrew/Cellar/[email protected]/3.10.2/Frameworks/Python.framework/Versions/3.10/lib/python3.10/subprocess.py:369, in check_call(*popenargs, **kwargs)
368 cmd = popenargs[0]
--> 369 raise CalledProcessError(retcode, cmd)
370 return 0
CalledProcessError: Command '['make', 'all']' returned non-zero exit status 2.
During handling of the above exception, another exception occurred:
GeneratedCodeBuildException Traceback (most recent call last)
/Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/01 - General behaviour.ipynb Cell 5 in <cell line: 3>()
1 # generate and build code
2 module_name, neuron_model_name, synapse_model_name = \
----> 3 generate_code_for("nest_module/msn.nestml",
4 "nest_module/stdp.nestml",
5 post_ports=["post_spikes"],
6 mod_ports=["mod_spikes"])
...
--> 155 raise GeneratedCodeBuildException('Error occurred during \'make all\'! More detailed error messages can be found in stdout.')
157 # finally execute make install
158 try:
GeneratedCodeBuildException: Error occurred during 'make all'! More detailed error messages can be found in stdout.
from nestml.
pnbabu
commented on August 18, 2024
@ewa8 thanks for the logs. Could you also share the generated C++ files (.h and .cpp) from NESTML present in the path /Users/ewarusiecka/Documents/University/DTU/Special_course/MSN/target?
from nestml.
ewa8
commented on August 18, 2024
Archive.zip
Hi @pnbabu, here are the generated files
from nestml.
pnbabu
commented on August 18, 2024
@ewa8 apologies for the delayed response. Could you let us know how you installed NEST? We observe some extra optimization flags in the cmake logs and would like to understand where it's coming from.
NEST compiler flags : -O2 -std=c++11 -Wall -Xclang -fopenmp -O3 -DNDEBUG
from nestml.
clinssen
commented on August 18, 2024
Also from my side sorry for the delay! After merging #861, the models you provided compile OK for me (although I did not do any behavioural testing). Could I ask you to check again with the latest NESTML master version? Thanks!
from nestml.
clinssen
commented on August 18, 2024
Closing due to inactivity, please re-open if this has not been resolved yet!
from nestml.
Related Issues (20)
- Improve nomenclature for tests
- Fix scaling for delta pulses
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- Symbol resolution bug for locally defined variables
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- Sender_id information available in the update block HOT 5
- ``get_parent()`` is excruciatingly slow
- Address review comments on #879
- Improve handling of NEST synaptic delay parameter
- Issue in generate_code_for() HOT 2
- Documentation issue on hh_cond_exp_traub neuron model HOT 1
- `nest.ResetKernel()` resets installed modules HOT 3
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- NESTCodeGeneratorUtils.generate_code_for() touches source files on each call
- any chance for support of sympy 1.12.1 HOT 1
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