Comments (51)
@atiye-nejad thanks for writing in. If you check the neuromodulated STDP synapse model here, the update
block contains the equations for the weight update and dopamine concentration. Here, the solution of the equation for the weight is implemented. Hope this helps.
from nestml.
thanks for your reply. I guessed that the solutions may have included in the code.
just does it consider Dirac function for DA concentration changes? I mean in the third equation I wrote before instead of DA(t).
So if I would like to edit it I have to change the solutions for my edited equations?am I right?
from nestml.
just does it consider Dirac function for DA concentration changes? I mean in the third equation I wrote before instead of DA(t).
Yes, the Dirac delta is considered in OnReceive(mod_spikes)
for the dopa concentration in the model.
So if I would like to edit it I have to change the solutions for my edited equations?am I right?
Right, you have to change the solutions for the edited equations.
from nestml.
Thanks. actually it considered 1. / tau_n added in each iteration?
If I don't want to consider added value in each iteration, I mean I need values for DA concentration in a range that below that range interrupt my network, what function do you suggest?
from nestml.
@atiye-nejad note that the OnReceive(mod_spikes)
is executed only when there is a dopamine spike and not at each iteration. But the equations in the update
block are executed at each time step.
Could you please elaborate more on your second question?
from nestml.
Thanks for your reply. I am going to model DA release in synapses without considering its plasticity effect. somehow that we have a function for DA concentration that low concentration of DA active inhibitory synapses and high concentration of DA active excitatory synapses. for low concentration DA , I consider Tonic firing and for high concentration I consider phasic firing pattern. Can you help me with equations?
from nestml.
and when I solve differential equation for w, some terms are deleted in the solution? yes?why?
from nestml.
why don't you put all equations mentioned in the paper in equation block? and why you put these equations pre_tr' = -pre_tr / tau_tr_pre post_tr' = -post_tr / tau_tr_post in Equation block?while the last equation that must solve in related to w and we need w finally? I appreciate you reply me.
from nestml.
Thanks for your reply. I am going to model DA release in synapses without considering its plasticity effect. somehow that we have a function for DA concentration that low concentration of DA active inhibitory synapses and high concentration of DA active excitatory synapses. for low concentration DA , I consider Tonic firing and for high concentration I consider phasic firing pattern. Can you help me with equations
from nestml.
@atiye-nejad We have not defined all the equations in the equations block because the ode-toolbox
which we use to return the solutions to the equations does not return an analytical solution for this particular case. Hence we decided to add them directly in the update
block.
Thanks for your reply. I am going to model DA release in synapses without considering its plasticity effect. somehow that we have a function for DA concentration that low concentration of DA active inhibitory synapses and high concentration of DA active excitatory synapses. for low concentration DA , I consider Tonic firing and for high concentration I consider phasic firing pattern. Can you help me with equations
If I understand it right, your model doesn't use any plasticity mechanism. In that case, perhaps you could model the dopamine concentration in the neuron model itself and use an if-else
condition in the update
block to determine the high and low concentrations and implement your logic based on that. It would help us to understand your problem better if you have a reference paper containing the equations.
from nestml.
how should I know which equation I have to write in equation block and which one in update block?
another issue is the solution of the equation for w. some terms are omitted from the solution of w equation. why?
yes, you are right. I don't want to see DA effect in a time. neither potentiation nor suppression. just show its effect in features like synaptic strength, presynaptic or post synaptic firing rate, any feature related to synapse, both in inhibitory way and excitatory proportional to Concentration. I haven't found a paper about it in terms of mathematical point. there are some papers from biologically aspects. it is my own idea. Do you have any suggestion for it.
Do you think I can use dAP current as DA modulator somehow it changes the post synaptic current ?
I have Window and I am using wsl2 for nest. I don't know how can I use nestml in wsl2. I saw scripts of dAP current in nestml site, but I don't know how can I make .so file for the model.
from nestml.
@atiye-nejad You could start by adding all the equations in the equations block and generate code for that.
dAP current example is one of the ways we can model dendritic action potential in NESTML. Please feel free to use it and see if it works for your use case.
If you have a working NEST on WSL, you could install NESTML with the command pip install nestml
. The generate_nest_target()
function parses the model, generates the C++ code, and creates the .so file for you. Please refer to this link and also the tutorials which use the same function to generate code for NEST.
from nestml.
hi again and thanks for your support.
I wrote this for generating .so file of third factor synapse.
but at the end it gives me permission error.
```python
import matplotlib.pyplot as plt
import nest
import numpy as np
import os
from pynestml.frontend.pynestml_frontend import generate_nest_target
NEST_SIMULATOR_INSTALL_LOCATION = nest.ll_api.sli_func("statusdict/prefix ::")
print(NEST_SIMULATOR_INSTALL_LOCATION)
#sli folder here: /usr/share/nest
#header files necessary to run the make file located here: /usr/include/nest
#location of neuron models to use as starting templates: /home/bs/.local/models/neurons
generate_nest_target(input_path="/home/atiye/.local/models/neurons/aeif_cond_alpha.nestml",
target_path="/home/atiye/dopa_dAP",
module_name="nestml_dopa_module",
logging_level="INFO",
suffix="_nestml",
codegen_opts={"nest_path": NEST_SIMULATOR_INSTALL_LOCATION}
)
PermissionError: [Errno 13] Permission denied: '/home/atiye/dopa_dAP/aeif_cond_alpha_nestml.cpp'
from nestml.
in input_path
do I have to write the neurons that I would like to apply this synapse to?
the description of the components of the generate_nest_target
isn't enough. very short.
from nestml.
@atiye-nejad If you want to use the dAP neuron, you would have to use the neuron model defined in this tutorial. For any other neuron model, you need to provide the input path of neuron model you want to use. Your example code looks correct.
You can find the detailed docs for generate_target()
function here.
Regarding the Permission denied
error, it looks like your target_path
doesn't have the write permission to create the generated .cpp
code. Could you change the permissions of the directory and try again?
from nestml.
I change the permission of library and it works and generates .cpp
files in the target path
.
but now my problem is in another place. I haven't got iaf_psc_exp_active_dendrite.nestml
in my synapse model.
from nestml.
I have wsl and I use visual studio for editing the code.
I have windows. Do you think wsl could be great for me? or I have to install virtual machine to write easier in nest and nestml?
from nestml.
I don't know how can I save this
`nestml_active_dend_model = '''
neuron iaf_psc_exp_active_dendrite:
state:
V_m mV = 0 mV # membrane potential
t_dAP ms = 0 ms # dendritic action potential timer
I_dAP pA = 0 pA # dendritic action potential current magnitude
equations:
# alpha shaped postsynaptic current kernel
kernel syn_kernel = (e / tau_syn) * t * exp(-t / tau_syn)
recordable inline I_syn pA = convolve(syn_kernel, spikes_in)
V_m' = -(V_m - E_L) / tau_m + (I_syn + I_dAP + I_e) / C_m
parameters:
C_m pF = 250 pF # capacity of the membrane
tau_m ms = 20 ms # membrane time constant
tau_syn ms = 10 ms # time constant of synaptic current
V_th mV = 25 mV # action potential threshold
V_reset mV = 0 mV # reset voltage
I_e pA = 0 pA # external current
E_L mV = 0 mV # resting potential
# dendritic action potential
I_th pA = 100 pA # current threshold for a dendritic action potential
I_dAP_peak pA = 150 pA # current clamp value for I_dAP during a dendritic action potential
T_dAP ms = 10 ms # time window over which the dendritic current clamp is active
input:
spikes_in pA <- spike
output:
spike
update:
# solve ODEs
integrate_odes()
if t_dAP > 0 ms:
t_dAP -= resolution()
if t_dAP <= 0 ms:
# end of dendritic action potential
t_dAP = 0 ms
I_dAP = 0 pA
if I_syn > I_th:
# current-threshold, emit a dendritic action potential
t_dAP = T_dAP
I_dAP = I_dAP_peak
# emit somatic action potential
if V_m > V_th:
emit_spike()
V_m = V_reset
'''` into .nestml and .so to add it in library?
can you explain the step of work one by one?
from nestml.
@atiye-nejad You can save the text starting from the neuron
keyword till the end to a file with the .nestml
extension in your directory and provide that path as input_path
in the generate_target()
function.
Please go through the dAP tutorial which also has a detailed description of what each step does. It also has a way to save the model string into a file. We also have extensive documentation of NESTML language concepts here: https://nestml.readthedocs.io/en/v5.2.0/
from nestml.
nestml_active_dend_model = '''
neuron iaf_psc_exp_active_dendrite:
state:
V_m mV = 0 mV # membrane potential
t_dAP ms = 0 ms # dendritic action potential timer
I_dAP pA = 0 pA # dendritic action potential current magnitude
end
equations:
# alpha shaped postsynaptic current kernel
kernel syn_kernel = (e / tau_syn) * t * exp(-t / tau_syn)
recordable inline I_syn pA = convolve(syn_kernel, spikes_in)
V_m' = -(V_m - E_L) / tau_m + (I_syn + I_dAP + I_e) / C_m
end
parameters:
C_m pF = 250 pF # capacity of the membrane
tau_m ms = 20 ms # membrane time constant
tau_syn ms = 10 ms # time constant of synaptic current
V_th mV = 25 mV # action potential threshold
V_reset mV = 0 mV # reset voltage
I_e pA = 0 pA # external current
E_L mV = 0 mV # resting potential
# dendritic action potential
I_th pA = 100 pA # current threshold for a dendritic action potential
I_dAP_peak pA = 150 pA # current clamp value for I_dAP during a dendritic action potential
T_dAP ms = 10 ms # time window over which the dendritic current clamp is active
end
input:
spikes_in pA <- spike
end
output: spike
update:
# solve ODEs
integrate_odes()
if t_dAP > 0 ms:
t_dAP -= resolution()
if t_dAP <= 0 ms:
# end of dendritic action potential
t_dAP = 0 ms
I_dAP = 0 pA
end
end
if I_syn > I_th:
# current-threshold, emit a dendritic action potential
t_dAP = T_dAP
I_dAP = I_dAP_peak
end
# emit somatic action potential
if V_m > V_th:
emit_spike()
V_m = V_reset
end
end
end
'''
I saved the above code as iaf_psc_exp_active_dendrite.nestml
and then run the below code:
`import matplotlib.pyplot as plt
import nest
import numpy as np
import os
from pynestml.frontend.pynestml_frontend import generate_nest_target
NEST_SIMULATOR_INSTALL_LOCATION = nest.ll_api.sli_func("statusdict/prefix ::")
with open("iaf_psc_exp_active_dendrite.nestml", "w") as nestml_model_file:
print(nestml_active_dend_model, file=nestml_model_file)
with open("iaf_psc_exp_active_dendrite.nestml", "w") as nestml_model_file:
print(nestml_active_dend_model, file=nestml_model_file)
generate_nest_target(input_path="/home/atiye/.local/models/neurons/iaf_psc_exp_active_dendrite.nestml",
target_path="/home/atiye/dopa_dAP",
module_name="nestml_active_dend_module",
suffix="_nestml",
logging_level="INFO", # try "INFO" for more debug information
codegen_opts={"nest_path": NEST_SIMULATOR_INSTALL_LOCATION}
)
nest.Install("nestml_active_dend_module")
but it gives me an errorNameError: name 'nestml_active_dend_model' is not defined`
where do I have to define this name or file?
from nestml.
can you help me in thiss step ?I don't kbow how to define 'nestml_active_dend_model' ?
from nestml.
@atiye-nejad are you running this in a jupyter notebook? If so, the script looks fine to me, although you could remove the duplicate lines
with open("iaf_psc_exp_active_dendrite.nestml", "w") as nestml_model_file:
print(nestml_active_dend_model, file=nestml_model_file)
from nestml.
I have wsl2 and I am running this code in vs with python.
but it gives me this error:
line 1:0 mismatched input 'nestml_active_dend_model' expecting {<EOF>, NEWLINE, 'neuron', 'synapse'} [5,GLOBAL, ERROR]: Error occurred during parsing: abort Traceback (most recent call last): File "/home/atiye/dopa_dAP/create_dopa_dAP.py", line 28, in <module> generate_nest_target(input_path="iaf_psc_exp_active_dendrite.nestml", File "/home/atiye/.local/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py", line 227, in generate_nest_target generate_target(input_path, target_platform="NEST", target_path=target_path, logging_level=logging_level, File "/home/atiye/.local/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py", line 197, in generate_target raise Exception("Error(s) occurred while processing the model") Exception: Error(s) occurred while processing the model
from nestml.
nestml_active_dend_model = ''' neuron iaf_psc_exp_active_dendrite: state: V_m mV = 0 mV # membrane potential t_dAP ms = 0 ms # dendritic action potential timer I_dAP pA = 0 pA # dendritic action potential current magnitude end equations: # alpha shaped postsynaptic current kernel kernel syn_kernel = (e / tau_syn) * t * exp(-t / tau_syn) recordable inline I_syn pA = convolve(syn_kernel, spikes_in) V_m' = -(V_m - E_L) / tau_m + (I_syn + I_dAP + I_e) / C_m end parameters: C_m pF = 250 pF # capacity of the membrane tau_m ms = 20 ms # membrane time constant tau_syn ms = 10 ms # time constant of synaptic current V_th mV = 25 mV # action potential threshold V_reset mV = 0 mV # reset voltage I_e pA = 0 pA # external current E_L mV = 0 mV # resting potential # dendritic action potential I_th pA = 100 pA # current threshold for a dendritic action potential I_dAP_peak pA = 150 pA # current clamp value for I_dAP during a dendritic action potential T_dAP ms = 10 ms # time window over which the dendritic current clamp is active end input: spikes_in pA <- spike end output: spike update: # solve ODEs integrate_odes() if t_dAP > 0 ms: t_dAP -= resolution() if t_dAP <= 0 ms: # end of dendritic action potential t_dAP = 0 ms I_dAP = 0 pA end end if I_syn > I_th: # current-threshold, emit a dendritic action potential t_dAP = T_dAP I_dAP = I_dAP_peak end # emit somatic action potential if V_m > V_th: emit_spike() V_m = V_reset end end end '''
Here, nestml_active_dend_model
is a string defining the model inside '''
quotes. The actual nestml model starts from the neuron
keyword without the nestml_active_dend_model = '''
. So the iaf_psc_exp_active_dendrite.nestml
file should contain:
neuron iaf_psc_exp_active_dendrite:
state:
V_m mV = 0 mV # membrane potential
t_dAP ms = 0 ms # dendritic action potential timer
I_dAP pA = 0 pA # dendritic action potential current magnitude
end
equations:
# alpha shaped postsynaptic current kernel
kernel syn_kernel = (e / tau_syn) * t * exp(-t / tau_syn)
recordable inline I_syn pA = convolve(syn_kernel, spikes_in)
V_m' = -(V_m - E_L) / tau_m + (I_syn + I_dAP + I_e) / C_m
end
parameters:
C_m pF = 250 pF # capacity of the membrane
tau_m ms = 20 ms # membrane time constant
tau_syn ms = 10 ms # time constant of synaptic current
V_th mV = 25 mV # action potential threshold
V_reset mV = 0 mV # reset voltage
I_e pA = 0 pA # external current
E_L mV = 0 mV # resting potential
# dendritic action potential
I_th pA = 100 pA # current threshold for a dendritic action potential
I_dAP_peak pA = 150 pA # current clamp value for I_dAP during a dendritic action potential
T_dAP ms = 10 ms # time window over which the dendritic current clamp is active
end
input:
spikes_in pA <- spike
end
output: spike
update:
# solve ODEs
integrate_odes()
if t_dAP > 0 ms:
t_dAP -= resolution()
if t_dAP <= 0 ms:
# end of dendritic action potential
t_dAP = 0 ms
I_dAP = 0 pA
end
end
if I_syn > I_th:
# current-threshold, emit a dendritic action potential
t_dAP = T_dAP
I_dAP = I_dAP_peak
end
# emit somatic action potential
if V_m > V_th:
emit_spike()
V_m = V_reset
end
end
end
Then you have to remove the below code from your script and provide the correct input_path
of the created iaf_psc_exp_active_dendrite.nestml
file to the generate_target()
function.
with open("iaf_psc_exp_active_dendrite.nestml", "w") as nestml_model_file:
print(nestml_active_dend_model, file=nestml_model_file)
from nestml.
I edited the first part, but again I receive some errors:
`import matplotlib.pyplot as plt
import nest
import numpy as np
import os
from pynestml.frontend.pynestml_frontend import generate_nest_target
NEST_SIMULATOR_INSTALL_LOCATION = nest.ll_api.sli_func("statusdict/prefix ::")
print(NEST_SIMULATOR_INSTALL_LOCATION)
#sli folder here: /usr/share/nest
#header files necessary to run the make file located here: /usr/include/nest
#location of neuron models to use as starting templates: /home/bs/.local/models/neurons
generate_nest_target(input_path="/home/atiye/dopa_dAP/iaf_psc_exp_active_dendrite.nestml",
target_path="/home/atiye/dopa_dAP",
module_name="nestml_active_dend_module",
suffix="_nestml",
logging_level="ERROR", # try "INFO" for more debug information
codegen_opts={"nest_path": NEST_SIMULATOR_INSTALL_LOCATION})
nest.Install("nestml_active_dend_module")`
error:
Traceback (most recent call last): File "/home/atiye/dopa_dAP/create_dopa_dAP.py", line 18, in generate_nest_target(input_path="/home/atiye/dopa_dAP/iaf_psc_exp_active_dendrite.nestml", File "/home/atiye/.local/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py", line 227, in generate_nest_target generate_target(input_path, target_platform="NEST", target_path=target_path, logging_level=logging_level, File "/home/atiye/.local/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py", line 196, in generate_target if not process() == 0: File "/home/atiye/.local/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py", line 352, in process _builder.build() File "/home/atiye/.local/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py", line 151, in build subprocess.check_call(cmake_cmd, stderr=subprocess.STDOUT, shell=shell, File "/usr/lib/python3.10/subprocess.py", line 364, in check_call retcode = call(*popenargs, **kwargs) File "/usr/lib/python3.10/subprocess.py", line 345, in call with Popen(*popenargs, **kwargs) as p: File "/usr/lib/python3.10/subprocess.py", line 969, in init self._execute_child(args, executable, preexec_fn, close_fds, File "/usr/lib/python3.10/subprocess.py", line 1845, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: [Errno 2] No such file or directory: 'cmake'
I am using vs to run python files in wsl2. is problem related to it?
How can I saveiaf_psc_exp_active_dendrite.nestml file in wsl2?
from nestml.
do we have to save the below scripts in .nestml
or will it create after generate function? how should I save it in wsl2?
If we have it, in this file, we have embedded dAP in a iaf_psc_exp
neuron. why should we use generate function again?
neuron iaf_psc_exp_active_dendrite:
state:
V_m mV = 0 mV # membrane potential
t_dAP ms = 0 ms # dendritic action potential timer
I_dAP pA = 0 pA # dendritic action potential current magnitude
end
equations:
# alpha shaped postsynaptic current kernel
kernel syn_kernel = (e / tau_syn) * t * exp(-t / tau_syn)
recordable inline I_syn pA = convolve(syn_kernel, spikes_in)
V_m' = -(V_m - E_L) / tau_m + (I_syn + I_dAP + I_e) / C_m
end
parameters:
C_m pF = 250 pF # capacity of the membrane
tau_m ms = 20 ms # membrane time constant
tau_syn ms = 10 ms # time constant of synaptic current
V_th mV = 25 mV # action potential threshold
V_reset mV = 0 mV # reset voltage
I_e pA = 0 pA # external current
E_L mV = 0 mV # resting potential
# dendritic action potential
I_th pA = 100 pA # current threshold for a dendritic action potential
I_dAP_peak pA = 150 pA # current clamp value for I_dAP during a dendritic action potential
T_dAP ms = 10 ms # time window over which the dendritic current clamp is active
end
input:
spikes_in pA <- spike
end
output: spike
update:
# solve ODEs
integrate_odes()
if t_dAP > 0 ms:
t_dAP -= resolution()
if t_dAP <= 0 ms:
# end of dendritic action potential
t_dAP = 0 ms
I_dAP = 0 pA
end
end
if I_syn > I_th:
# current-threshold, emit a dendritic action potential
t_dAP = T_dAP
I_dAP = I_dAP_peak
end
# emit somatic action potential
if V_m > V_th:
emit_spike()
V_m = V_reset
end
end
end
from nestml.
where do you write dopamine_synapse. Nestml and how do you save it? Since I am using wsl2 and use VS to run my codes, can you tell me how I can save the scripts to .nestml?
from nestml.
I think I found the problem. when I run python setup.py test
during nestml installation, I receive errors. during installation, it is written done. but for test after some seconds, give me errors.
FAILED (errors=1)
Test failed: <unittest.runner.TextTestResult run=132 errors=1 failures=0>
error: Test failed: <unittest.runner.TextTestResult run=132 errors=1 failures=0>
how can I fix it?
from nestml.
@atiye-nejad the test failure is expected as it is a negative test case that is supposed to fail.
You can just open any editor and save the .nestml
file.
From your failure log, I think the failure is because cmake
is not present.
FileNotFoundError: [Errno 2] No such file or directory: 'cmake'
Could you please install cmake
and try again?
from nestml.
I install cmake
, but again I have some errors
Traceback (most recent call last):
File "/home/atiye/dopa_dAP/create_dopa_dAP.py", line 18, in <module>
generate_nest_target(input_path="/home/atiye/nestml/models/neurons/iaf_psc_exp_active_dendrite.nestml",
File "/home/atiye/.local/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py", line 227, in generate_nest_target
generate_target(input_path, target_platform="NEST", target_path=target_path, logging_level=logging_level,
File "/home/atiye/.local/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py", line 196, in generate_target
if not process() == 0:
File "/home/atiye/.local/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py", line 352, in process
_builder.build()
File "/home/atiye/.local/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py", line 161, in build
raise GeneratedCodeBuildException('Error occurred during \'make all\'! More detailed error messages can be found in stdout.')
pynestml.exceptions.generated_code_build_exception.GeneratedCodeBuildException: Error occurred during 'make all'! More detailed error messages can be found in stdout.
from nestml.
@atiye-nejad there is a compilation error in the generated code. Could you please share the entire cmake
logs?
from nestml.
you mean CMakeOutput.log file?
`The system is: Linux - 5.10.16.3-microsoft-standard-WSL2 - x86_64
Compiling the CXX compiler identification source file "CMakeCXXCompilerId.cpp" succeeded.
Compiler: /usr/bin/g++
Build flags:
Id flags:
The output was:
0
Compilation of the CXX compiler identification source "CMakeCXXCompilerId.cpp" produced "a.out"
The CXX compiler identification is GNU, found in "/home/atiye/dopa_dAP/CMakeFiles/3.22.1/CompilerIdCXX/a.out"
Detecting CXX compiler ABI info compiled with the following output:
Change Dir: /home/atiye/dopa_dAP/CMakeFiles/CMakeTmp
Run Build Command(s):/usr/bin/gmake -f Makefile cmTC_28a76/fast && /usr/bin/gmake -f CMakeFiles/cmTC_28a76.dir/build.make CMakeFiles/cmTC_28a76.dir/build
gmake[1]: Entering directory '/home/atiye/dopa_dAP/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_28a76.dir/CMakeCXXCompilerABI.cpp.o
/usr/bin/g++ -v -o CMakeFiles/cmTC_28a76.dir/CMakeCXXCompilerABI.cpp.o -c /usr/share/cmake-3.22/Modules/CMakeCXXCompilerABI.cpp
Using built-in specs.
COLLECT_GCC=/usr/bin/g++
OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
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`
from nestml.
@atiye-nejad could you please share the logs that you see before this exception? There must be some C++ compilation errors.
I install
cmake
, but again I have some errorsTraceback (most recent call last): File "/home/atiye/dopa_dAP/create_dopa_dAP.py", line 18, in <module> generate_nest_target(input_path="/home/atiye/nestml/models/neurons/iaf_psc_exp_active_dendrite.nestml", File "/home/atiye/.local/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py", line 227, in generate_nest_target generate_target(input_path, target_platform="NEST", target_path=target_path, logging_level=logging_level, File "/home/atiye/.local/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py", line 196, in generate_target if not process() == 0: File "/home/atiye/.local/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py", line 352, in process _builder.build() File "/home/atiye/.local/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py", line 161, in build raise GeneratedCodeBuildException('Error occurred during \'make all\'! More detailed error messages can be found in stdout.') pynestml.exceptions.generated_code_build_exception.GeneratedCodeBuildException: Error occurred during 'make all'! More detailed error messages can be found in stdout.
from nestml.
- The CXX compiler identification is GNU 11.3.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
nestml_active_dend_module Configuration Summary
C++ compiler : /usr/bin/g++
Build static libs : OFF
C++ compiler flags :
NEST compiler flags : -g -O2 -ffile-prefix-map=/build/nest-8dIXHU/nest-3.4=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -std=c++11 -Wall -fopenmp -O2 -fdiagnostics-color=auto
NEST include dirs : -I/build/nest-8dIXHU/nest-3.4/debian/nest/usr/include/nest -I/usr/include -I/usr/include -I/usr/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/include
NEST libraries flags : -L/build/nest-8dIXHU/nest-3.4/debian/nest/usr/lib/nest -lnestutil -lsli -lnestkernel -fopenmp /usr/lib/x86_64-linux-gnu/libltdl.so /usr/lib/x86_64-linux-gnu/libreadline.so /usr/lib/x86_64-linux-gnu/libncurses.so /usr/lib/x86_64-linux-gnu/libgsl.so /usr/lib/x86_64-linux-gnu/libgslcblas.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
You can now build and install 'nestml_active_dend_module' using
make
make install
The library file libnestml_active_dend_module.so will be installed to
/build/nest-8dIXHU/nest-3.4/debian/nest/usr/lib/nest
The module can be loaded into NEST using
(nestml_active_dend_module) Install (in SLI)
nest.Install(nestml_active_dend_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: /home/atiye/dopa_dAP
[ 66%] Building CXX object CMakeFiles/nestml_active_dend_module_module.dir/nestml_active_dend_module.o
[ 66%] Building CXX object CMakeFiles/nestml_active_dend_module_module.dir/iaf_psc_exp_active_dendrite_nestml.o
/home/atiye/dopa_dAP/nestml_active_dend_module.cpp:26:10: fatal error: connection_manager_impl.h: No such file or directory
26 | #include "connection_manager_impl.h"
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [CMakeFiles/nestml_active_dend_module_module.dir/build.make:76: CMakeFiles/nestml_active_dend_module_module.dir/nestml_active_dend_module.o] Error 1
make[2]: *** Waiting for unfinished jobs....
/home/atiye/dopa_dAP/iaf_psc_exp_active_dendrite_nestml.cpp:29:10: fatal error: numerics.h: No such file or directory
29 | #include "numerics.h"
| ^~~~~~~~~~~~
compilation terminated.
make[2]: *** [CMakeFiles/nestml_active_dend_module_module.dir/build.make:90: CMakeFiles/nestml_active_dend_module_module.dir/iaf_psc_exp_active_dendrite_nestml.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:110: CMakeFiles/nestml_active_dend_module_module.dir/all] Error 2
make: *** [Makefile:156: all] Error 2
Traceback (most recent call last):
File "/home/atiye/.local/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py", line 158, in build
subprocess.check_call(make_all_cmd, stderr=subprocess.STDOUT, shell=shell,
File "/usr/lib/python3.10/subprocess.py", line 369, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['make', '-j8', 'all']' returned non-zero exit status 2.
During handling of the above exception, another exception occurred:
from nestml.
@atiye-nejad The error is because the connection_manager_impl.h
is missing which belongs to NEST. Could you let us know which version and how you installed NEST on your machine?
from nestml.
from the instruction in Nest site:
Ubuntu users can install NEST via the PPA repository.
Add the PPA repository for NEST and update apt:
sudo add-apt-repository ppa:nest-simulator/nest
sudo apt-get update
Install NEST:
sudo apt-get install nest
from nestml.
@atiye-nejad I suspect NESTML is unable to find the NEST installed. Could you please do an import nest
in a python terminal and execute nest.ll_api.sli_func("statusdict/prefix ::")
and share the output?
from nestml.
output:
cd /home/atiye/dopa_dAP ; /usr/bin/env /bin/python3 /home/atiye/.vscode-server/extensions/ms-python.python-2023.8.0/pythonFiles/lib/python/debugpy/adapter/../../debugpy/launcher 50313 -- /home/atiye/dopa_dAP/test2.py
-- N E S T --
Copyright (C) 2004 The NEST Initiative
Version: 3.4
Built: May 4 2023 12:02:19
This program is provided AS IS and comes with
NO WARRANTY. See the file LICENSE for details.
Problems or suggestions?
Visit https://www.nest-simulator.org
Type 'nest.help()' to find out more about NEST.
from nestml.
it seems it works. How can I fix the problem with errors?
from nestml.
Hi, I face this problem. do you know how can I fix it?
`[ 50%] Building CXX object CMakeFiles/nestml_dopa_module_module.dir/nestml_dopa_module.o
[ 75%] Building CXX object CMakeFiles/nestml_dopa_module_module.dir/aeif_cond_alpha_nestml__with_dopamine_synapse_nestml.o
[ 50%] Building CXX object CMakeFiles/nestml_dopa_module_module.dir/aeif_cond_alpha_nestml.o
/home/atiye/test1/dopamine-synapse-component/nestml_dopa_module.cpp:26:10: fatal error: connection_manager_impl.h: No such file or directory
26 | #include "connection_manager_impl.h"
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [CMakeFiles/nestml_dopa_module_module.dir/build.make:76: CMakeFiles/nestml_dopa_module_module.dir/nestml_dopa_module.o] Error 1
make[2]: *** Waiting for unfinished jobs....
/home/atiye/test1/dopamine-synapse-component/aeif_cond_alpha_nestml__with_dopamine_synapse_nestml.cpp:29:10: fatal error: numerics.h: No such file or directory
29 | #include "numerics.h"
| ^~~~~~~~~~~~
compilation terminated.
/home/atiye/test1/dopamine-synapse-component/aeif_cond_alpha_nestml.cpp:29:10: fatal error: numerics.h: No such file or directory
29 | #include "numerics.h"
| ^~~~~~~~~~~~
compilation terminated.
make[2]: *** [CMakeFiles/nestml_dopa_module_module.dir/build.make:104: CMakeFiles/nestml_dopa_module_module.dir/aeif_cond_alpha_nestml__with_dopamine_synapse_nestml.o] Error 1
make[2]: *** [CMakeFiles/nestml_dopa_module_module.dir/build.make:90: CMakeFiles/nestml_dopa_module_module.dir/aeif_cond_alpha_nestml.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:110: CMakeFiles/nestml_dopa_module_module.dir/all] Error 2
make: *** [Makefile:156: all] Error 2
Traceback (most recent call last):
File "/home/atiye/.local/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py", line 176, in build
subprocess.check_call(make_all_cmd, stderr=stderr, stdout=stdout, shell=shell,
File "/usr/lib/python3.10/subprocess.py", line 369, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['make', '-j8', 'all']' returned non-zero exit status 2.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/atiye/test1/test_dopa.py", line 14, in
generate_nest_target(input_path=["/home/atiye/nestml/models/neurons/aeif_cond_alpha.nestml",
File "/home/atiye/.local/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py", line 229, in generate_nest_target
generate_target(input_path, target_platform="NEST", target_path=target_path, logging_level=logging_level,
File "/home/atiye/.local/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py", line 198, in generate_target
if not process() == 0:
File "/home/atiye/.local/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py", line 351, in process
_builder.build()
File "/home/atiye/.local/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py", line 183, in build
raise GeneratedCodeBuildException(stages_exception[current_stage])
pynestml.exceptions.generated_code_build_exception.GeneratedCodeBuildException: Error occurred during 'make all'! More detailed error messages can be found in stderr.`
from nestml.
@atiye-nejad there seems to be an issue with the Ubuntu package for the nest-simulator. Can you install NEST through conda? The instructions can be found here.
@steffengraber could you please look at what could be wrong with the Ubuntu package?
from nestml.
@pnbabu thanks, finally installation in conda solved all my problems. Thanks.
from nestml.
of Course I faced this things and I don't know if it matters:
but finally I have .so
file
`/home/atine/dAP-neuron/nestml-active-dend-target/iaf_psc_exp_active_dendritenestml.cpp: In constructor 'iaf_psc_exp_active_dendritenestml::iaf_psc_exp_active_dendritenestml()':
/home/atine/dAP-neuron/nestml-active-dend-target/iaf_psc_exp_active_dendritenestml.cpp:109:16: warning: unused variable '__resolution' [-Wunused-variable]
109 | const double __resolution = nest::Time::get_resolution().get_ms(); // do not remove, this is necessary for the resolution() function
| ^~~~~~~~~~~~
/home/atine/dAP-neuron/nestml-active-dend-target/iaf_psc_exp_active_dendritenestml.cpp: In member function 'virtual void iaf_psc_exp_active_dendritenestml::update(const nest::Time&, long int, long int)':
/home/atine/dAP-neuron/nestml-active-dend-target/iaf_psc_exp_active_dendritenestml.cpp:299:24: warning: comparison of integer expressions of different signedness: 'long int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare]
299 | for (long i = 0; i < NUM_SPIKE_RECEPTORS; ++i)
| ~~^~~~~~~~~~~~~~~~~~~~~
/home/atine/dAP-neuron/nestml-active-dend-target/iaf_psc_exp_active_dendritenestml.cpp:298:10: warning: variable 'get_t' set but not used [-Wunused-but-set-variable]
298 | auto get_t = origin, lag{ return nest::Time( nest::Time::step( origin.get_steps() + lag + 1) ).get_ms(); };
| ^~~~~
[100%] Linking CXX shared module nestml_active_dend_module.so
[100%] Built target nestml_active_dend_module_module
[100%] Built target nestml_active_dend_module_module
Install the project...
-- Install configuration: ""
-- Installing: /home/atine/miniconda3/envs/wnestml/lib/nest/nestml_active_dend_module.so
Jun 12 16:13:19 Install [Info]:
loaded module nestml_active_dend_module`
from nestml.
@atiye-nejad you can safely ignore the warnings. This shouldn't affect the results of your model.
from nestml.
@pnbabu thanks, finally installation in conda solved all my problems. Thanks.
@atiye-nejad Thanks for reporting the problem and great that conda could help you. There seems to be a problem with the paths in the Debian package.
from nestml.
Hi Pooja, I am trying to install nestml through conda, but at the last step I get the error of
ModuleNotFoundError: No module named 'pynestml'.
what should I do?
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@atiye-nejad we do not have a conda package for NESTML. It can be either installed through pip
or from the source code.
from nestml.
I am following steps here:
[https://nestml.readthedocs.io/en/latest/installation.html#installing-the-latest-release-from-pypi]
but after running my code for defining new synapses I get the error
ModuleNotFoundError: No module named 'pynestml'
from nestml.
@atiye-nejad pip install
should install NESTML. Could you please check if it is installed correctly by running the following commands on the terminal?
python3
import pynestml
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@atiye-nejad can we close this issue if it is resolved at your end?
from nestml.
Closing due to inactivity. Please feel free to re-open if there is still an issue. Cheers!
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