Hi, I am going to use stdp synapse model to create another synapse model, But I wonder

<a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/us

neuromodulated_stdp.nestml equations ,about nest/nestml

Comments (51)

pnbabu commented on August 17, 2024

@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.

atiye-nejad commented on August 17, 2024

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.

pnbabu commented on August 17, 2024

@atiye-nejad

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.

atiye-nejad commented on August 17, 2024

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.

pnbabu commented on August 17, 2024

@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.

atiye-nejad commented on August 17, 2024

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 commented on August 17, 2024

and when I solve differential equation for w, some terms are deleted in the solution? yes?why?

from nestml.

atiye-nejad commented on August 17, 2024

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.

atiye-nejad commented on August 17, 2024

from nestml.

pnbabu commented on August 17, 2024

@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.

atiye-nejad commented on August 17, 2024

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.

pnbabu commented on August 17, 2024

@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.

atiye-nejad commented on August 17, 2024

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.

atiye-nejad commented on August 17, 2024

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.

pnbabu commented on August 17, 2024

@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.

atiye-nejad commented on August 17, 2024

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.

atiye-nejad commented on August 17, 2024

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.

atiye-nejad commented on August 17, 2024

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.

pnbabu commented on August 17, 2024

@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.

atiye-nejad commented on August 17, 2024

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.

atiye-nejad commented on August 17, 2024

can you help me in thiss step ?I don't kbow how to define 'nestml_active_dend_model' ?

from nestml.

pnbabu commented on August 17, 2024

@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.

atiye-nejad commented on August 17, 2024

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.

pnbabu commented on August 17, 2024

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.

atiye-nejad commented on August 17, 2024

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.

atiye-nejad commented on August 17, 2024

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.

atiye-nejad commented on August 17, 2024

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.

atiye-nejad commented on August 17, 2024

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.

pnbabu commented on August 17, 2024

@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.

atiye-nejad commented on August 17, 2024

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.

pnbabu commented on August 17, 2024

@atiye-nejad there is a compilation error in the generated code. Could you please share the entire cmake logs?

from nestml.

atiye-nejad commented on August 17, 2024

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
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 11.3.0-1ubuntu122.04.1' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-11-aYxV0E/gcc-11-11.3.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-11-aYxV0E/gcc-11-11.3.0/debian/tmp-gcn/usr --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 11.3.0 (Ubuntu 11.3.0-1ubuntu122.04.1)
COLLECT_GCC_OPTIONS='-v' '-o' 'CMakeFiles/cmTC_28a76.dir/CMakeCXXCompilerABI.cpp.o' '-c' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'CMakeFiles/cmTC_28a76.dir/'
/usr/lib/gcc/x86_64-linux-gnu/11/cc1plus -quiet -v -imultiarch x86_64-linux-gnu -D_GNU_SOURCE /usr/share/cmake-3.22/Modules/CMakeCXXCompilerABI.cpp -quiet -dumpdir CMakeFiles/cmTC_28a76.dir/ -dumpbase CMakeCXXCompilerABI.cpp.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -version -fasynchronous-unwind-tables -fstack-protector-strong -Wformat -Wformat-security -fstack-clash-protection -fcf-protection -o /tmp/ccWL8SXg.s
GNU C++17 (Ubuntu 11.3.0-1ubuntu1~22.04.1) version 11.3.0 (x86_64-linux-gnu)
compiled by GNU C version 11.3.0, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.1, isl version isl-0.24-GMP

GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/11"
ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/11/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/11/../../../../x86_64-linux-gnu/include"
#include "..." search starts here:
#include <...> search starts here:
/usr/include/c++/11
/usr/include/x86_64-linux-gnu/c++/11
/usr/include/c++/11/backward
/usr/lib/gcc/x86_64-linux-gnu/11/include
/usr/local/include
/usr/include/x86_64-linux-gnu
/usr/include
End of search list.
GNU C++17 (Ubuntu 11.3.0-1ubuntu1~22.04.1) version 11.3.0 (x86_64-linux-gnu)
compiled by GNU C version 11.3.0, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.1, isl version isl-0.24-GMP

GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: 2b9b53ff7f3a6952e2fe60119c16be53
COLLECT_GCC_OPTIONS='-v' '-o' 'CMakeFiles/cmTC_28a76.dir/CMakeCXXCompilerABI.cpp.o' '-c' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'CMakeFiles/cmTC_28a76.dir/'
as -v --64 -o CMakeFiles/cmTC_28a76.dir/CMakeCXXCompilerABI.cpp.o /tmp/ccWL8SXg.s
GNU assembler version 2.38 (x86_64-linux-gnu) using BFD version (GNU Binutils for Ubuntu) 2.38
COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-v' '-o' 'CMakeFiles/cmTC_28a76.dir/CMakeCXXCompilerABI.cpp.o' '-c' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'CMakeFiles/cmTC_28a76.dir/CMakeCXXCompilerABI.cpp.'
Linking CXX executable cmTC_28a76
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_28a76.dir/link.txt --verbose=1
/usr/bin/g++ -v -rdynamic CMakeFiles/cmTC_28a76.dir/CMakeCXXCompilerABI.cpp.o -o cmTC_28a76
Using built-in specs.
COLLECT_GCC=/usr/bin/g++
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/11/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 11.3.0-1ubuntu122.04.1' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-11-aYxV0E/gcc-11-11.3.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-11-aYxV0E/gcc-11-11.3.0/debian/tmp-gcn/usr --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 11.3.0 (Ubuntu 11.3.0-1ubuntu122.04.1)
COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-v' '-rdynamic' '-o' 'cmTC_28a76' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'cmTC_28a76.'
/usr/lib/gcc/x86_64-linux-gnu/11/collect2 -plugin /usr/lib/gcc/x86_64-linux-gnu/11/liblto_plugin.so -plugin-opt=/usr/lib/gcc/x86_64-linux-gnu/11/lto-wrapper -plugin-opt=-fresolution=/tmp/ccjVxvaF.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --build-id --eh-frame-hdr -m elf_x86_64 --hash-style=gnu --as-needed -export-dynamic -dynamic-linker /lib64/ld-linux-x86-64.so.2 -pie -z now -z relro -o cmTC_28a76 /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/Scrt1.o /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/11/crtbeginS.o -L/usr/lib/gcc/x86_64-linux-gnu/11 -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/11/../../.. CMakeFiles/cmTC_28a76.dir/CMakeCXXCompilerABI.cpp.o -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-linux-gnu/11/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crtn.o
COLLECT_GCC_OPTIONS='-v' '-rdynamic' '-o' 'cmTC_28a76' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'cmTC_28a76.'
gmake[1]: Leaving directory '/home/atiye/dopa_dAP/CMakeFiles/CMakeTmp'

Parsed CXX implicit include dir info from above output: rv=done
found start of include info
found start of implicit include info
add: [/usr/include/c++/11]
add: [/usr/include/x86_64-linux-gnu/c++/11]
add: [/usr/include/c++/11/backward]
add: [/usr/lib/gcc/x86_64-linux-gnu/11/include]
add: [/usr/local/include]
add: [/usr/include/x86_64-linux-gnu]
add: [/usr/include]
end of search list found
collapse include dir [/usr/include/c++/11] ==> [/usr/include/c++/11]
collapse include dir [/usr/include/x86_64-linux-gnu/c++/11] ==> [/usr/include/x86_64-linux-gnu/c++/11]
collapse include dir [/usr/include/c++/11/backward] ==> [/usr/include/c++/11/backward]
collapse include dir [/usr/lib/gcc/x86_64-linux-gnu/11/include] ==> [/usr/lib/gcc/x86_64-linux-gnu/11/include]
collapse include dir [/usr/local/include] ==> [/usr/local/include]
collapse include dir [/usr/include/x86_64-linux-gnu] ==> [/usr/include/x86_64-linux-gnu]
collapse include dir [/usr/include] ==> [/usr/include]
implicit include dirs: [/usr/include/c++/11;/usr/include/x86_64-linux-gnu/c++/11;/usr/include/c++/11/backward;/usr/lib/gcc/x86_64-linux-gnu/11/include;/usr/local/include;/usr/include/x86_64-linux-gnu;/usr/include]

Parsed CXX implicit link information from above output:
link line regex: [^( |.[/])(ld|CMAKE_LINK_STARTFILE-NOTFOUND|([^/]+-)?ld|collect2)[^/\]*( |$)]
ignore line: [Change Dir: /home/atiye/dopa_dAP/CMakeFiles/CMakeTmp]
ignore line: []
ignore line: [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]
ignore line: [gmake[1]: Entering directory '/home/atiye/dopa_dAP/CMakeFiles/CMakeTmp']
ignore line: [Building CXX object CMakeFiles/cmTC_28a76.dir/CMakeCXXCompilerABI.cpp.o]
ignore line: [/usr/bin/g++ -v -o CMakeFiles/cmTC_28a76.dir/CMakeCXXCompilerABI.cpp.o -c /usr/share/cmake-3.22/Modules/CMakeCXXCompilerABI.cpp]
ignore line: [Using built-in specs.]
ignore line: [COLLECT_GCC=/usr/bin/g++]
ignore line: [OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa]
ignore line: [OFFLOAD_TARGET_DEFAULT=1]
ignore line: [Target: x86_64-linux-gnu]
ignore line: [Configured with: ../src/configure -v --with-pkgversion='Ubuntu 11.3.0-1ubuntu122.04.1' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c ada c++ go brig d fortran objc obj-c++ m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32 m64 mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-11-aYxV0E/gcc-11-11.3.0/debian/tmp-nvptx/usr amdgcn-amdhsa=/build/gcc-11-aYxV0E/gcc-11-11.3.0/debian/tmp-gcn/usr --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2]
ignore line: [Thread model: posix]
ignore line: [Supported LTO compression algorithms: zlib zstd]
ignore line: [gcc version 11.3.0 (Ubuntu 11.3.0-1ubuntu122.04.1) ]
ignore line: [COLLECT_GCC_OPTIONS='-v' '-o' 'CMakeFiles/cmTC_28a76.dir/CMakeCXXCompilerABI.cpp.o' '-c' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'CMakeFiles/cmTC_28a76.dir/']
ignore line: [ /usr/lib/gcc/x86_64-linux-gnu/11/cc1plus -quiet -v -imultiarch x86_64-linux-gnu -D_GNU_SOURCE /usr/share/cmake-3.22/Modules/CMakeCXXCompilerABI.cpp -quiet -dumpdir CMakeFiles/cmTC_28a76.dir/ -dumpbase CMakeCXXCompilerABI.cpp.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -version -fasynchronous-unwind-tables -fstack-protector-strong -Wformat -Wformat-security -fstack-clash-protection -fcf-protection -o /tmp/ccWL8SXg.s]
ignore line: [GNU C++17 (Ubuntu 11.3.0-1ubuntu122.04.1) version 11.3.0 (x86_64-linux-gnu)]
ignore line: [ compiled by GNU C version 11.3.0 GMP version 6.2.1 MPFR version 4.1.0 MPC version 1.2.1 isl version isl-0.24-GMP]
ignore line: []
ignore line: [GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072]
ignore line: [ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/11"]
ignore line: [ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"]
ignore line: [ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/11/include-fixed"]
ignore line: [ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/11/../../../../x86_64-linux-gnu/include"]
ignore line: [#include "..." search starts here:]
ignore line: [#include <...> search starts here:]
ignore line: [ /usr/include/c++/11]
ignore line: [ /usr/include/x86_64-linux-gnu/c++/11]
ignore line: [ /usr/include/c++/11/backward]
ignore line: [ /usr/lib/gcc/x86_64-linux-gnu/11/include]
ignore line: [ /usr/local/include]
ignore line: [ /usr/include/x86_64-linux-gnu]
ignore line: [ /usr/include]
ignore line: [End of search list.]
ignore line: [GNU C++17 (Ubuntu 11.3.0-1ubuntu122.04.1) version 11.3.0 (x86_64-linux-gnu)]
ignore line: [ compiled by GNU C version 11.3.0 GMP version 6.2.1 MPFR version 4.1.0 MPC version 1.2.1 isl version isl-0.24-GMP]
ignore line: []
ignore line: [GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072]
ignore line: [Compiler executable checksum: 2b9b53ff7f3a6952e2fe60119c16be53]
ignore line: [COLLECT_GCC_OPTIONS='-v' '-o' 'CMakeFiles/cmTC_28a76.dir/CMakeCXXCompilerABI.cpp.o' '-c' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'CMakeFiles/cmTC_28a76.dir/']
ignore line: [ as -v --64 -o CMakeFiles/cmTC_28a76.dir/CMakeCXXCompilerABI.cpp.o /tmp/ccWL8SXg.s]
ignore line: [GNU assembler version 2.38 (x86_64-linux-gnu) using BFD version (GNU Binutils for Ubuntu) 2.38]
ignore line: [COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/]
ignore line: [LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../:/lib/:/usr/lib/]
ignore line: [COLLECT_GCC_OPTIONS='-v' '-o' 'CMakeFiles/cmTC_28a76.dir/CMakeCXXCompilerABI.cpp.o' '-c' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'CMakeFiles/cmTC_28a76.dir/CMakeCXXCompilerABI.cpp.']
ignore line: [Linking CXX executable cmTC_28a76]
ignore line: [/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_28a76.dir/link.txt --verbose=1]
ignore line: [/usr/bin/g++ -v -rdynamic CMakeFiles/cmTC_28a76.dir/CMakeCXXCompilerABI.cpp.o -o cmTC_28a76 ]
ignore line: [Using built-in specs.]
ignore line: [COLLECT_GCC=/usr/bin/g++]
ignore line: [COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/11/lto-wrapper]
ignore line: [OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa]
ignore line: [OFFLOAD_TARGET_DEFAULT=1]
ignore line: [Target: x86_64-linux-gnu]
ignore line: [Configured with: ../src/configure -v --with-pkgversion='Ubuntu 11.3.0-1ubuntu122.04.1' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c ada c++ go brig d fortran objc obj-c++ m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32 m64 mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-11-aYxV0E/gcc-11-11.3.0/debian/tmp-nvptx/usr amdgcn-amdhsa=/build/gcc-11-aYxV0E/gcc-11-11.3.0/debian/tmp-gcn/usr --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2]
ignore line: [Thread model: posix]
ignore line: [Supported LTO compression algorithms: zlib zstd]
ignore line: [gcc version 11.3.0 (Ubuntu 11.3.0-1ubuntu122.04.1) ]
ignore line: [COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/]
ignore line: [LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../:/lib/:/usr/lib/]
ignore line: [COLLECT_GCC_OPTIONS='-v' '-rdynamic' '-o' 'cmTC_28a76' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'cmTC_28a76.']
link line: [ /usr/lib/gcc/x86_64-linux-gnu/11/collect2 -plugin /usr/lib/gcc/x86_64-linux-gnu/11/liblto_plugin.so -plugin-opt=/usr/lib/gcc/x86_64-linux-gnu/11/lto-wrapper -plugin-opt=-fresolution=/tmp/ccjVxvaF.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --build-id --eh-frame-hdr -m elf_x86_64 --hash-style=gnu --as-needed -export-dynamic -dynamic-linker /lib64/ld-linux-x86-64.so.2 -pie -z now -z relro -o cmTC_28a76 /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/Scrt1.o /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/11/crtbeginS.o -L/usr/lib/gcc/x86_64-linux-gnu/11 -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/11/../../.. CMakeFiles/cmTC_28a76.dir/CMakeCXXCompilerABI.cpp.o -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-linux-gnu/11/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crtn.o]
arg [/usr/lib/gcc/x86_64-linux-gnu/11/collect2] ==> ignore
arg [-plugin] ==> ignore
arg [/usr/lib/gcc/x86_64-linux-gnu/11/liblto_plugin.so] ==> ignore
arg [-plugin-opt=/usr/lib/gcc/x86_64-linux-gnu/11/lto-wrapper] ==> ignore
arg [-plugin-opt=-fresolution=/tmp/ccjVxvaF.res] ==> ignore
arg [-plugin-opt=-pass-through=-lgcc_s] ==> ignore
arg [-plugin-opt=-pass-through=-lgcc] ==> ignore
arg [-plugin-opt=-pass-through=-lc] ==> ignore
arg [-plugin-opt=-pass-through=-lgcc_s] ==> ignore
arg [-plugin-opt=-pass-through=-lgcc] ==> ignore
arg [--build-id] ==> ignore
arg [--eh-frame-hdr] ==> ignore
arg [-m] ==> ignore
arg [elf_x86_64] ==> ignore
arg [--hash-style=gnu] ==> ignore
arg [--as-needed] ==> ignore
arg [-export-dynamic] ==> ignore
arg [-dynamic-linker] ==> ignore
arg [/lib64/ld-linux-x86-64.so.2] ==> ignore
arg [-pie] ==> ignore
arg [-znow] ==> ignore
arg [-zrelro] ==> ignore
arg [-o] ==> ignore
arg [cmTC_28a76] ==> ignore
arg [/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/Scrt1.o] ==> obj [/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/Scrt1.o]
arg [/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crti.o] ==> obj [/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crti.o]
arg [/usr/lib/gcc/x86_64-linux-gnu/11/crtbeginS.o] ==> obj [/usr/lib/gcc/x86_64-linux-gnu/11/crtbeginS.o]
arg [-L/usr/lib/gcc/x86_64-linux-gnu/11] ==> dir [/usr/lib/gcc/x86_64-linux-gnu/11]
arg [-L/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu] ==> dir [/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu]
arg [-L/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib] ==> dir [/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib]
arg [-L/lib/x86_64-linux-gnu] ==> dir [/lib/x86_64-linux-gnu]
arg [-L/lib/../lib] ==> dir [/lib/../lib]
arg [-L/usr/lib/x86_64-linux-gnu] ==> dir [/usr/lib/x86_64-linux-gnu]
arg [-L/usr/lib/../lib] ==> dir [/usr/lib/../lib]
arg [-L/usr/lib/gcc/x86_64-linux-gnu/11/../../..] ==> dir [/usr/lib/gcc/x86_64-linux-gnu/11/../../..]
arg [CMakeFiles/cmTC_28a76.dir/CMakeCXXCompilerABI.cpp.o] ==> ignore
arg [-lstdc++] ==> lib [stdc++]
arg [-lm] ==> lib [m]
arg [-lgcc_s] ==> lib [gcc_s]
arg [-lgcc] ==> lib [gcc]
arg [-lc] ==> lib [c]
arg [-lgcc_s] ==> lib [gcc_s]
arg [-lgcc] ==> lib [gcc]
arg [/usr/lib/gcc/x86_64-linux-gnu/11/crtendS.o] ==> obj [/usr/lib/gcc/x86_64-linux-gnu/11/crtendS.o]
arg [/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crtn.o] ==> obj [/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crtn.o]
collapse obj [/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/Scrt1.o] ==> [/usr/lib/x86_64-linux-gnu/Scrt1.o]
collapse obj [/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crti.o] ==> [/usr/lib/x86_64-linux-gnu/crti.o]
collapse obj [/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crtn.o] ==> [/usr/lib/x86_64-linux-gnu/crtn.o]
collapse library dir [/usr/lib/gcc/x86_64-linux-gnu/11] ==> [/usr/lib/gcc/x86_64-linux-gnu/11]
collapse library dir [/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu] ==> [/usr/lib/x86_64-linux-gnu]
collapse library dir [/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib] ==> [/usr/lib]
collapse library dir [/lib/x86_64-linux-gnu] ==> [/lib/x86_64-linux-gnu]
collapse library dir [/lib/../lib] ==> [/lib]
collapse library dir [/usr/lib/x86_64-linux-gnu] ==> [/usr/lib/x86_64-linux-gnu]
collapse library dir [/usr/lib/../lib] ==> [/usr/lib]
collapse library dir [/usr/lib/gcc/x86_64-linux-gnu/11/../../..] ==> [/usr/lib]
implicit libs: [stdc++;m;gcc_s;gcc;c;gcc_s;gcc]
implicit objs: [/usr/lib/x86_64-linux-gnu/Scrt1.o;/usr/lib/x86_64-linux-gnu/crti.o;/usr/lib/gcc/x86_64-linux-gnu/11/crtbeginS.o;/usr/lib/gcc/x86_64-linux-gnu/11/crtendS.o;/usr/lib/x86_64-linux-gnu/crtn.o]
implicit dirs: [/usr/lib/gcc/x86_64-linux-gnu/11;/usr/lib/x86_64-linux-gnu;/usr/lib;/lib/x86_64-linux-gnu;/lib]
implicit fwks: []

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_2dc94/fast && /usr/bin/gmake -f CMakeFiles/cmTC_2dc94.dir/build.make CMakeFiles/cmTC_2dc94.dir/build
gmake[1]: Entering directory '/home/atiye/dopa_dAP/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_2dc94.dir/CMakeCXXCompilerABI.cpp.o
/usr/bin/g++ -v -o CMakeFiles/cmTC_2dc94.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
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 11.3.0-1ubuntu122.04.1' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-11-aYxV0E/gcc-11-11.3.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-11-aYxV0E/gcc-11-11.3.0/debian/tmp-gcn/usr --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 11.3.0 (Ubuntu 11.3.0-1ubuntu122.04.1)
COLLECT_GCC_OPTIONS='-v' '-o' 'CMakeFiles/cmTC_2dc94.dir/CMakeCXXCompilerABI.cpp.o' '-c' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'CMakeFiles/cmTC_2dc94.dir/'
/usr/lib/gcc/x86_64-linux-gnu/11/cc1plus -quiet -v -imultiarch x86_64-linux-gnu -D_GNU_SOURCE /usr/share/cmake-3.22/Modules/CMakeCXXCompilerABI.cpp -quiet -dumpdir CMakeFiles/cmTC_2dc94.dir/ -dumpbase CMakeCXXCompilerABI.cpp.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -version -fasynchronous-unwind-tables -fstack-protector-strong -Wformat -Wformat-security -fstack-clash-protection -fcf-protection -o /tmp/ccsCwpC9.s
GNU C++17 (Ubuntu 11.3.0-1ubuntu1~22.04.1) version 11.3.0 (x86_64-linux-gnu)
compiled by GNU C version 11.3.0, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.1, isl version isl-0.24-GMP

GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: 2b9b53ff7f3a6952e2fe60119c16be53
COLLECT_GCC_OPTIONS='-v' '-o' 'CMakeFiles/cmTC_2dc94.dir/CMakeCXXCompilerABI.cpp.o' '-c' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'CMakeFiles/cmTC_2dc94.dir/'
as -v --64 -o CMakeFiles/cmTC_2dc94.dir/CMakeCXXCompilerABI.cpp.o /tmp/ccsCwpC9.s
GNU assembler version 2.38 (x86_64-linux-gnu) using BFD version (GNU Binutils for Ubuntu) 2.38
COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-v' '-o' 'CMakeFiles/cmTC_2dc94.dir/CMakeCXXCompilerABI.cpp.o' '-c' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'CMakeFiles/cmTC_2dc94.dir/CMakeCXXCompilerABI.cpp.'
Linking CXX executable cmTC_2dc94
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_2dc94.dir/link.txt --verbose=1
/usr/bin/g++ -v -rdynamic CMakeFiles/cmTC_2dc94.dir/CMakeCXXCompilerABI.cpp.o -o cmTC_2dc94
Using built-in specs.
COLLECT_GCC=/usr/bin/g++
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/11/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 11.3.0-1ubuntu122.04.1' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-11-aYxV0E/gcc-11-11.3.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-11-aYxV0E/gcc-11-11.3.0/debian/tmp-gcn/usr --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 11.3.0 (Ubuntu 11.3.0-1ubuntu122.04.1)
COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-v' '-rdynamic' '-o' 'cmTC_2dc94' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'cmTC_2dc94.'
/usr/lib/gcc/x86_64-linux-gnu/11/collect2 -plugin /usr/lib/gcc/x86_64-linux-gnu/11/liblto_plugin.so -plugin-opt=/usr/lib/gcc/x86_64-linux-gnu/11/lto-wrapper -plugin-opt=-fresolution=/tmp/cc4pBngk.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --build-id --eh-frame-hdr -m elf_x86_64 --hash-style=gnu --as-needed -export-dynamic -dynamic-linker /lib64/ld-linux-x86-64.so.2 -pie -z now -z relro -o cmTC_2dc94 /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/Scrt1.o /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/11/crtbeginS.o -L/usr/lib/gcc/x86_64-linux-gnu/11 -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/11/../../.. CMakeFiles/cmTC_2dc94.dir/CMakeCXXCompilerABI.cpp.o -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-linux-gnu/11/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crtn.o
COLLECT_GCC_OPTIONS='-v' '-rdynamic' '-o' 'cmTC_2dc94' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'cmTC_2dc94.'
gmake[1]: Leaving directory '/home/atiye/dopa_dAP/CMakeFiles/CMakeTmp'

Parsed CXX implicit link information from above output:
link line regex: [^( |.[/])(ld|CMAKE_LINK_STARTFILE-NOTFOUND|([^/]+-)?ld|collect2)[^/\]*( |$)]
ignore line: [Change Dir: /home/atiye/dopa_dAP/CMakeFiles/CMakeTmp]
ignore line: []
ignore line: [Run Build Command(s):/usr/bin/gmake -f Makefile cmTC_2dc94/fast && /usr/bin/gmake -f CMakeFiles/cmTC_2dc94.dir/build.make CMakeFiles/cmTC_2dc94.dir/build]
ignore line: [gmake[1]: Entering directory '/home/atiye/dopa_dAP/CMakeFiles/CMakeTmp']
ignore line: [Building CXX object CMakeFiles/cmTC_2dc94.dir/CMakeCXXCompilerABI.cpp.o]
ignore line: [/usr/bin/g++ -v -o CMakeFiles/cmTC_2dc94.dir/CMakeCXXCompilerABI.cpp.o -c /usr/share/cmake-3.22/Modules/CMakeCXXCompilerABI.cpp]
ignore line: [Using built-in specs.]
ignore line: [COLLECT_GCC=/usr/bin/g++]
ignore line: [OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa]
ignore line: [OFFLOAD_TARGET_DEFAULT=1]
ignore line: [Target: x86_64-linux-gnu]
ignore line: [Configured with: ../src/configure -v --with-pkgversion='Ubuntu 11.3.0-1ubuntu122.04.1' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c ada c++ go brig d fortran objc obj-c++ m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32 m64 mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-11-aYxV0E/gcc-11-11.3.0/debian/tmp-nvptx/usr amdgcn-amdhsa=/build/gcc-11-aYxV0E/gcc-11-11.3.0/debian/tmp-gcn/usr --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2]
ignore line: [Thread model: posix]
ignore line: [Supported LTO compression algorithms: zlib zstd]
ignore line: [gcc version 11.3.0 (Ubuntu 11.3.0-1ubuntu122.04.1) ]
ignore line: [COLLECT_GCC_OPTIONS='-v' '-o' 'CMakeFiles/cmTC_2dc94.dir/CMakeCXXCompilerABI.cpp.o' '-c' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'CMakeFiles/cmTC_2dc94.dir/']
ignore line: [ /usr/lib/gcc/x86_64-linux-gnu/11/cc1plus -quiet -v -imultiarch x86_64-linux-gnu -D_GNU_SOURCE /usr/share/cmake-3.22/Modules/CMakeCXXCompilerABI.cpp -quiet -dumpdir CMakeFiles/cmTC_2dc94.dir/ -dumpbase CMakeCXXCompilerABI.cpp.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -version -fasynchronous-unwind-tables -fstack-protector-strong -Wformat -Wformat-security -fstack-clash-protection -fcf-protection -o /tmp/ccsCwpC9.s]
ignore line: [GNU C++17 (Ubuntu 11.3.0-1ubuntu122.04.1) version 11.3.0 (x86_64-linux-gnu)]
ignore line: [ compiled by GNU C version 11.3.0 GMP version 6.2.1 MPFR version 4.1.0 MPC version 1.2.1 isl version isl-0.24-GMP]
ignore line: []
ignore line: [GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072]
ignore line: [ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/11"]
ignore line: [ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"]
ignore line: [ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/11/include-fixed"]
ignore line: [ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/11/../../../../x86_64-linux-gnu/include"]
ignore line: [#include "..." search starts here:]
ignore line: [#include <...> search starts here:]
ignore line: [ /usr/include/c++/11]
ignore line: [ /usr/include/x86_64-linux-gnu/c++/11]
ignore line: [ /usr/include/c++/11/backward]
ignore line: [ /usr/lib/gcc/x86_64-linux-gnu/11/include]
ignore line: [ /usr/local/include]
ignore line: [ /usr/include/x86_64-linux-gnu]
ignore line: [ /usr/include]
ignore line: [End of search list.]
ignore line: [GNU C++17 (Ubuntu 11.3.0-1ubuntu122.04.1) version 11.3.0 (x86_64-linux-gnu)]
ignore line: [ compiled by GNU C version 11.3.0 GMP version 6.2.1 MPFR version 4.1.0 MPC version 1.2.1 isl version isl-0.24-GMP]
ignore line: []
ignore line: [GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072]
ignore line: [Compiler executable checksum: 2b9b53ff7f3a6952e2fe60119c16be53]
ignore line: [COLLECT_GCC_OPTIONS='-v' '-o' 'CMakeFiles/cmTC_2dc94.dir/CMakeCXXCompilerABI.cpp.o' '-c' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'CMakeFiles/cmTC_2dc94.dir/']
ignore line: [ as -v --64 -o CMakeFiles/cmTC_2dc94.dir/CMakeCXXCompilerABI.cpp.o /tmp/ccsCwpC9.s]
ignore line: [GNU assembler version 2.38 (x86_64-linux-gnu) using BFD version (GNU Binutils for Ubuntu) 2.38]
ignore line: [COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/]
ignore line: [LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../:/lib/:/usr/lib/]
ignore line: [COLLECT_GCC_OPTIONS='-v' '-o' 'CMakeFiles/cmTC_2dc94.dir/CMakeCXXCompilerABI.cpp.o' '-c' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'CMakeFiles/cmTC_2dc94.dir/CMakeCXXCompilerABI.cpp.']
ignore line: [Linking CXX executable cmTC_2dc94]
ignore line: [/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_2dc94.dir/link.txt --verbose=1]
ignore line: [/usr/bin/g++ -v -rdynamic CMakeFiles/cmTC_2dc94.dir/CMakeCXXCompilerABI.cpp.o -o cmTC_2dc94 ]
ignore line: [Using built-in specs.]
ignore line: [COLLECT_GCC=/usr/bin/g++]
ignore line: [COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/11/lto-wrapper]
ignore line: [OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa]
ignore line: [OFFLOAD_TARGET_DEFAULT=1]
ignore line: [Target: x86_64-linux-gnu]
ignore line: [Configured with: ../src/configure -v --with-pkgversion='Ubuntu 11.3.0-1ubuntu122.04.1' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c ada c++ go brig d fortran objc obj-c++ m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32 m64 mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-11-aYxV0E/gcc-11-11.3.0/debian/tmp-nvptx/usr amdgcn-amdhsa=/build/gcc-11-aYxV0E/gcc-11-11.3.0/debian/tmp-gcn/usr --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2]
ignore line: [Thread model: posix]
ignore line: [Supported LTO compression algorithms: zlib zstd]
ignore line: [gcc version 11.3.0 (Ubuntu 11.3.0-1ubuntu122.04.1) ]
ignore line: [COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/]
ignore line: [LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../:/lib/:/usr/lib/]
ignore line: [COLLECT_GCC_OPTIONS='-v' '-rdynamic' '-o' 'cmTC_2dc94' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'cmTC_2dc94.']
link line: [ /usr/lib/gcc/x86_64-linux-gnu/11/collect2 -plugin /usr/lib/gcc/x86_64-linux-gnu/11/liblto_plugin.so -plugin-opt=/usr/lib/gcc/x86_64-linux-gnu/11/lto-wrapper -plugin-opt=-fresolution=/tmp/cc4pBngk.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --build-id --eh-frame-hdr -m elf_x86_64 --hash-style=gnu --as-needed -export-dynamic -dynamic-linker /lib64/ld-linux-x86-64.so.2 -pie -z now -z relro -o cmTC_2dc94 /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/Scrt1.o /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/11/crtbeginS.o -L/usr/lib/gcc/x86_64-linux-gnu/11 -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/11/../../.. CMakeFiles/cmTC_2dc94.dir/CMakeCXXCompilerABI.cpp.o -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-linux-gnu/11/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crtn.o]
arg [/usr/lib/gcc/x86_64-linux-gnu/11/collect2] ==> ignore
arg [-plugin] ==> ignore
arg [/usr/lib/gcc/x86_64-linux-gnu/11/liblto_plugin.so] ==> ignore
arg [-plugin-opt=/usr/lib/gcc/x86_64-linux-gnu/11/lto-wrapper] ==> ignore
arg [-plugin-opt=-fresolution=/tmp/cc4pBngk.res] ==> ignore
arg [-plugin-opt=-pass-through=-lgcc_s] ==> ignore
arg [-plugin-opt=-pass-through=-lgcc] ==> ignore
arg [-plugin-opt=-pass-through=-lc] ==> ignore
arg [-plugin-opt=-pass-through=-lgcc_s] ==> ignore
arg [-plugin-opt=-pass-through=-lgcc] ==> ignore
arg [--build-id] ==> ignore
arg [--eh-frame-hdr] ==> ignore
arg [-m] ==> ignore
arg [elf_x86_64] ==> ignore
arg [--hash-style=gnu] ==> ignore
arg [--as-needed] ==> ignore
arg [-export-dynamic] ==> ignore
arg [-dynamic-linker] ==> ignore
arg [/lib64/ld-linux-x86-64.so.2] ==> ignore
arg [-pie] ==> ignore
arg [-znow] ==> ignore
arg [-zrelro] ==> ignore
arg [-o] ==> ignore
arg [cmTC_2dc94] ==> ignore
arg [/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/Scrt1.o] ==> obj [/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/Scrt1.o]
arg [/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crti.o] ==> obj [/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crti.o]
arg [/usr/lib/gcc/x86_64-linux-gnu/11/crtbeginS.o] ==> obj [/usr/lib/gcc/x86_64-linux-gnu/11/crtbeginS.o]
arg [-L/usr/lib/gcc/x86_64-linux-gnu/11] ==> dir [/usr/lib/gcc/x86_64-linux-gnu/11]
arg [-L/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu] ==> dir [/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu]
arg [-L/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib] ==> dir [/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib]
arg [-L/lib/x86_64-linux-gnu] ==> dir [/lib/x86_64-linux-gnu]
arg [-L/lib/../lib] ==> dir [/lib/../lib]
arg [-L/usr/lib/x86_64-linux-gnu] ==> dir [/usr/lib/x86_64-linux-gnu]
arg [-L/usr/lib/../lib] ==> dir [/usr/lib/../lib]
arg [-L/usr/lib/gcc/x86_64-linux-gnu/11/../../..] ==> dir [/usr/lib/gcc/x86_64-linux-gnu/11/../../..]
arg [CMakeFiles/cmTC_2dc94.dir/CMakeCXXCompilerABI.cpp.o] ==> ignore
arg [-lstdc++] ==> lib [stdc++]
arg [-lm] ==> lib [m]
arg [-lgcc_s] ==> lib [gcc_s]
arg [-lgcc] ==> lib [gcc]
arg [-lc] ==> lib [c]
arg [-lgcc_s] ==> lib [gcc_s]
arg [-lgcc] ==> lib [gcc]
arg [/usr/lib/gcc/x86_64-linux-gnu/11/crtendS.o] ==> obj [/usr/lib/gcc/x86_64-linux-gnu/11/crtendS.o]
arg [/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crtn.o] ==> obj [/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crtn.o]
collapse obj [/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/Scrt1.o] ==> [/usr/lib/x86_64-linux-gnu/Scrt1.o]
collapse obj [/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crti.o] ==> [/usr/lib/x86_64-linux-gnu/crti.o]
collapse obj [/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/crtn.o] ==> [/usr/lib/x86_64-linux-gnu/crtn.o]
collapse library dir [/usr/lib/gcc/x86_64-linux-gnu/11] ==> [/usr/lib/gcc/x86_64-linux-gnu/11]
collapse library dir [/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu] ==> [/usr/lib/x86_64-linux-gnu]
collapse library dir [/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib] ==> [/usr/lib]
collapse library dir [/lib/x86_64-linux-gnu] ==> [/lib/x86_64-linux-gnu]
collapse library dir [/lib/../lib] ==> [/lib]
collapse library dir [/usr/lib/x86_64-linux-gnu] ==> [/usr/lib/x86_64-linux-gnu]
collapse library dir [/usr/lib/../lib] ==> [/usr/lib]
collapse library dir [/usr/lib/gcc/x86_64-linux-gnu/11/../../..] ==> [/usr/lib]
implicit libs: [stdc++;m;gcc_s;gcc;c;gcc_s;gcc]
implicit objs: [/usr/lib/x86_64-linux-gnu/Scrt1.o;/usr/lib/x86_64-linux-gnu/crti.o;/usr/lib/gcc/x86_64-linux-gnu/11/crtbeginS.o;/usr/lib/gcc/x86_64-linux-gnu/11/crtendS.o;/usr/lib/x86_64-linux-gnu/crtn.o]
implicit dirs: [/usr/lib/gcc/x86_64-linux-gnu/11;/usr/lib/x86_64-linux-gnu;/usr/lib;/lib/x86_64-linux-gnu;/lib]
implicit fwks: []

from nestml.

pnbabu commented on August 17, 2024

@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 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 commented on August 17, 2024

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.

pnbabu commented on August 17, 2024

@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.

atiye-nejad commented on August 17, 2024

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.

pnbabu commented on August 17, 2024

@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.

atiye-nejad commented on August 17, 2024

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 --

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.

atiye-nejad commented on August 17, 2024

it seems it works. How can I fix the problem with errors?

from nestml.

atiye-nejad commented on August 17, 2024

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.

pnbabu commented on August 17, 2024

@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.

atiye-nejad commented on August 17, 2024

@pnbabu thanks, finally installation in conda solved all my problems. Thanks.

from nestml.

atiye-nejad commented on August 17, 2024

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.

pnbabu commented on August 17, 2024

@atiye-nejad you can safely ignore the warnings. This shouldn't affect the results of your model.

from nestml.

steffengraber commented on August 17, 2024

@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.

atiye-nejad commented on August 17, 2024

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?

from nestml.

pnbabu commented on August 17, 2024

@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.

atiye-nejad commented on August 17, 2024

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.

pnbabu commented on August 17, 2024

@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

from nestml.

pnbabu commented on August 17, 2024

@atiye-nejad can we close this issue if it is resolved at your end?

from nestml.

clinssen commented on August 17, 2024

Closing due to inactivity. Please feel free to re-open if there is still an issue. Cheers!

from nestml.

neuromodulated_stdp.nestml equations about nestml HOT 51 CLOSED

Comments (51)

nestml_active_dend_module Configuration Summary

Related Issues (20)

Recommend Projects

React

Vue.js

Typescript

TensorFlow

Django

Laravel

D3

Recommend Topics

javascript

web

server

Machine learning

Visualization

Game

Recommend Org

Facebook

Microsoft

Google

Alibaba

D3

Tencent