Linux, Python, C ++, Brain2 and errors.

Piotr Bujakowski

Piotr Bujakowski

Piotr Bujakowski

Associate
Joined
18 Aug 2020
Posts
26
Location
London
Hi.

I try to make and run first time AI Neural Network on my computer.
Knowledge Python is basic.

I'm using Linux Ubuntu.

I install whole in system using apt.
When show communicate about pip, then I'm doing that.
[Is a lot of problems with right file names and compatibility.]

I try to configure to direction in home catalogue [advice from Gemini].
Port 65432 is unblocked in firewall.

Helpful is Gemini, but can't solve problems what I have now.

Please help me with that.

Python engine:

import brian2
import socket
import numpy as np

from brian2 import Neuron, Eq


# Define neuron equations
eqs = '''
dv/dt = (I - gl*(v-Vl) - gNa*(m**3)*h*(v-VNa) - gK*(n**4)*(v-VK)) / Cm
dm/dt = alpha_m(v)*(1-m) - beta_m(v)*m
dh/dt = alpha_h(v)*(1-h) - beta_h(v)*h
dn/dt = alpha_n(v)*(1-n) - beta_n(v)*n
'''

# Define parameters and functions for the equations (replace with actual definitions)
Vl = -65*mV # Leak reversal potential
VNa = 50*mV # Sodium reversal potential
VK = -70*mV # Potassium reversal potential
Cm = 1*uF/cm2 # Membrane capacitance
gl = 0.3e-3*siemens/cm2 # Leak conductance
gNa = 120e-3*siemens/cm2 # Sodium conductance
gK = 36e-3*siemens/cm2 # Potassium conductance

# Define neuron object using custom equations
neurons = Neuron(eqs=eqs, methods={'alpha_m': alpha_m, 'beta_m': beta_m, 'alpha_h': alpha_h, 'beta_h': beta_h, 'alpha_n': alpha_n, 'beta_n': beta_n}) # Include all required methods


# Standard variables
num_neurons = 1000
duration = 1000 # Simulation duration in milliseconds

# **(Replace with your implementation)**
# Hodgkin-Huxley neuron model with STDP learning (replace with your specific neuron and synapse definitions)
# ... (Include your specific code for defining synapses and learning rules)


# Data variables
average_firing_rates = []
average_synaptic_weights = []

# Recording functions
def record_firing_rates():
global average_firing_rates
average_firing_rates.append(np.mean(spike_monitor.count / (duration * 1000))) # Convert to Hz

def record_synaptic_weights():
global average_synaptic_weights
weights = synapses.weight # Assuming you have a 'synapses' object with weight attribute
average_synaptic_weights.append(np.mean(weights))

# Network monitors
spike_monitor = brian2.SpikeMonitor(source=neurons)
brian2.NetworkOperation(record_firing_rates, dt=10*brian2.ms) # Record every 10 ms
brian2.NetworkOperation(record_synaptic_weights, dt=100*brian2.ms) # Record every 100 ms

# Network socket setup (replace with your IP address and port)
HOST = '127.0.0.1' # Standard loopback interface address (localhost)
PORT = 65432 # Port to listen on (non-privileged ports are > 1023)
s = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
s.bind((HOST, PORT))

# Run the simulation
brian2.run(duration * brian2.ms)

# Send data to C++ program (replace with IPC if on the same machine)
data = {'firing_rates': average_firing_rates, 'synaptic_weights': average_synaptic_weights}
data_str = str(data) # Convert data to string for sending
s.sendall(data_str.encode())

# Close the socket
s.close()
Click to expand...

I have too second code in C++:

#include <iostream>
#include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
#include <string.h>
#include <sys/types.h>
#include <sys/socket.h>
#include <netinet/in.h>
#include <arpa/inet.h>
#include <sstream>
#include <jsoncpp/json.h> // Include JSON library for parsing

int main() {
// Standard variables
int port = 65432; // Port used by Brian 2 simulation
std::string host = "localhost"; // Replace with IP address of Brian 2 (if not localhost)

// Socket setup
int sockfd;
struct sockaddr_in servaddr;

sockfd = socket(AF_INET, SOCK_STREAM, 0);
if (sockfd == -1) {
perror("socket creation failed");
exit(EXIT_FAILURE);
}

memset(&servaddr, 0, sizeof(servaddr));

servaddr.sin_family = AF_INET;
servaddr.sin_port = htons(port);
servaddr.sin_addr.s_addr = inet_addr(host.c_str());

if (connect(sockfd, (struct sockaddr*)&servaddr, sizeof(servaddr)) != 0) {
perror("connection failed");
exit(EXIT_FAILURE);
}

// Data receiving and processing loop
while (1) {
char buffer[1024]; // Adjust buffer size based on data volume
int n = recv(sockfd, buffer, sizeof(buffer), 0);
if (n == 0) {
printf("Connection closed by server\n");
break;
} else if (n == -1) {
perror("recv failed");
exit(EXIT_FAILURE);
}

// Parse received data (assuming JSON format)
std::string data_str(buffer, n);
Json::Reader reader;
Json::Value data;
if (!reader.parse(data_str, data)) {
Click to expand...

Error:

Python 3.12.3 (main, Apr 10 2024, 05:33:47) [GCC 13.2.0] on linux
Type "help", "copyright", "credits" or "license()" for more information.

= RESTART: /home/peter/python/ai_neural_brain_2/engine_brain_2.py =
ERROR Brian 2 encountered an unexpected error. If you think this is a bug in Brian 2, please report this issue either to the discourse forum at <http://brian.discourse.group/>, or to the issue tracker at <https://github.com/brian-team/brian2/issues>. Please include this file with debug information in your report: /tmp/brian_debug_vkzoele7.log Additionally, you can also include a copy of the script that was run, available at: /tmp/brian_script_fgiuug_k.py Thanks! [brian2]
Traceback (most recent call last):
File "/usr/lib/python3.12/idlelib/run.py", line 580, in runcode
exec(code, self.locals)
File "/home/peter/python/ai_neural_brain_2/engine_brain_2.py", line 5, in <module>
from brian2 import Neuron, Eq
ImportError: cannot import name 'Neuron' from 'brian2' (/usr/lib/python3/dist-packages/brian2/__init__.py)
Click to expand...
 
Last edited:
Throrik said:
One of your errors is that you’re failing to call Neuron, Eq. Do they exist within Brian2? Checking the documentation you can try replacing it with:

Python: 
from brian2 import *

Which will import everything, and you can see if that’s the issue.
Click to expand...

ERROR Brian 2 encountered an unexpected error. If you think this is a bug in Brian 2, please report this issue either to the discourse forum at <http://brian.discourse.group/>, or to the issue tracker at <https://github.com/brian-team/brian2/issues>. Please include this file with debug information in your report: /tmp/brian_debug_qs10hpz8.log Additionally, you can also include a copy of the script that was run, available at: /tmp/brian_script_lhty_uks.py Thanks! [brian2]
Traceback (most recent call last):
File "/usr/lib/python3.12/idlelib/run.py", line 580, in runcode
exec(code, self.locals)
File "/home/peter/python/ai_neural_brain_2/engine_brain_2.py", line 27, in <module>
neurons = Neuron(eqs=eqs, methods={'alpha_m': alpha_m, 'beta_m': beta_m, 'alpha_h': alpha_h, 'beta_h': beta_h, 'alpha_n': alpha_n, 'beta_n': beta_n}) # Include all required methods
^^^^^^
NameError: name 'Neuron' is not defined
Click to expand...
sudo apt install python3-brian
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
python3-brian is already the newest version (2.5.4-4build1).
0 upgraded, 0 newly installed, 0 to remove and 31 not upgraded.


sudo apt-get reinstall python3-brian
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
0 upgraded, 0 newly installed, 1 reinstalled, 0 to remove and 31 not upgraded.
Need to get 0 B/622 kB of archives.
After this operation, 0 B of additional disk space will be used.
(Reading database ... 336660 files and directories currently installed.)
Preparing to unpack .../python3-brian_2.5.4-4build1_all.deb ...
Unpacking python3-brian (2.5.4-4build1) over (2.5.4-4build1) ...
Setting up python3-brian (2.5.4-4build1) ...


python -m pip install matplotlib pytest ipython notebook
Command 'python' not found, did you mean:
command 'python3' from deb python3
command 'python' from deb python-is-python3


python3 -m pip install matplotlib pytest ipython notebook
error: externally-managed-environment

× This environment is externally managed
╰─> To install Python packages system-wide, try apt install
python3-xyz, where xyz is the package you are trying to
install.

If you wish to install a non-Debian-packaged Python package,
create a virtual environment using python3 -m venv path/to/venv.
Then use path/to/venv/bin/python and path/to/venv/bin/pip. Make
sure you have python3-full installed.

If you wish to install a non-Debian packaged Python application,
it may be easiest to use pipx install xyz, which will manage a
virtual environment for you. Make sure you have pipx installed.

See /usr/share/doc/python3.12/README.venv for more information.

note: If you believe this is a mistake, please contact your Python installation or OS distribution provider. You can override this, at the risk of breaking your Python installation or OS, by passing --break-system-packages.
hint: See PEP 668 for the detailed specification.


python -m pip install brian2tools
Command 'python' not found, did you mean:
command 'python3' from deb python3
command 'python' from deb python-is-python3


python3 -m pip install brian2tools
error: externally-managed-environment

× This environment is externally managed
╰─> To install Python packages system-wide, try apt install
python3-xyz, where xyz is the package you are trying to
install.

If you wish to install a non-Debian-packaged Python package,
create a virtual environment using python3 -m venv path/to/venv.
Then use path/to/venv/bin/python and path/to/venv/bin/pip. Make
sure you have python3-full installed.

If you wish to install a non-Debian packaged Python application,
it may be easiest to use pipx install xyz, which will manage a
virtual environment for you. Make sure you have pipx installed.

See /usr/share/doc/python3.12/README.venv for more information.

note: If you believe this is a mistake, please contact your Python installation or OS distribution provider. You can override this, at the risk of breaking your Python installation or OS, by passing --break-system-packages.
hint: See PEP 668 for the detailed specification.
Click to expand...
 
Last edited:
I have fun with that.
1 time I almost blow up CPU.

Python: 
import brian2 as b2
import matplotlib.pyplot as plt
from IPython.display import Image, display
import multiprocessing

# Set the number of threads to the number of CPU cores
b2.prefs.devices.cpp_standalone.openmp_threads = multiprocessing.cpu_count()

# Neuron parameters
Cm = 1000 * b2.ufarad  # membrane capacitance
gl = 500 * b2.nsiemens  # leak conductance
El = -65 * b2.mV  # leak reversal potential
V_th = -50 * b2.mV  # spike threshold
V_reset = -65 * b2.mV  # reset potential after spike

# Synapse parameters
tau_syn = 1000 * b2.ms  # synaptic time constant
E_syn = 0 * b2.mV  # synaptic reversal potential
w_syn = 0.1 * b2.nS  # synaptic weight

# Neuron model equations
eqs = '''
dv/dt = (gl * (El - v) + I + Isyn) / Cm : volt
I : amp  # input current
Isyn : amp  # synaptic current
'''

# Create a group of neurons
num_neurons = 1000000 #human 100 000 000 000
neuron = b2.NeuronGroup(num_neurons, eqs, threshold='v > V_th', reset='v = V_reset', method='exact')
neuron.v = El  # initial condition

# Create synapses
synapses = b2.Synapses(neuron, neuron,
                       model='''w : siemens
                                Isyn_post = w * (v_pre - v_post) : amp (summed)''',
                       on_pre='Isyn_post += w * (E_syn - v_post)')
# connect each neuron to 10% of the other neurons
synapses.connect(condition='i != j', p=1000)
synapses.w = w_syn

# Create a constant input current
input_current = 200 * b2.pamp  # amplitude of the input current
neuron.I = input_current

# Record the membrane potential
monitor = b2.StateMonitor(neuron, 'v', record=True)

# Run the simulation for 100 ms
duration = 1000 * b2.ms
b2.run(duration)

# Plot the membrane potential over time for the first neuron
plt.figure(figsize=(100, 10))
plt.plot(monitor.t / b2.ms, monitor.v[0] / b2.mV)
plt.xlabel('Time (ms)')
plt.ylabel('Membrane potential (mV)')
plt.title('Membrane potential of the first neuron over time')
plt.grid(True)
plt.show()

# Optionally, you can also plot the membrane potentials of other neurons
plt.figure(figsize=(100, 10))
for i in range(100):  # plot the first 5 neurons for better visualization
    plt.plot(monitor.t / b2.ms, monitor.v[i] / b2.mV, label=f'Neuron {i}')
plt.xlabel('Time (ms)')
plt.ylabel('Membrane potential (mV)')
plt.title('Membrane potentials of multiple neurons over time')
plt.legend()
plt.grid(True)
plt.show()

# Display the uploaded diagrams
display(Image)
 
At that, a moment works.
How make that to stage when I can talk with that?

Edit:

I install that:

sudo apt-get installpython3-charset-normalizer python3-pyaudio espeak-ng-espeak python3-espeak python3-pykml python3-charset-normalizer qt6-speech-speechd-plugin qt6-speech-flite-plugin qtspeech5-flite-plugin python3-guess-language python3-nltk python3-virtualenv python3-venv python3-charset-normalizer python3-virtualenv
Click to expand...

pipx install SpeechRecognition python3-charset-normalizer pyttsx3
Click to expand...

pip always have problems ...

The next stage will be virtualization of the person.
 
Last edited:
I try to use Vosk, but all time is:

Python 3.12.3 (main, Apr 10 2024, 05:33:47) [GCC 13.2.0] on linux
Type "help", "copyright", "credits" or "license()" for more information.

= RESTART: /home/peter/python/ai_neural_brain_2/engine_brain_2_11_neurons_group_and_synapses_talking.py
ERROR Brian 2 encountered an unexpected error. If you think this is a bug in Brian 2, please report this issue either to the discourse forum at <http://brian.discourse.group/>, or to the issue tracker at <https://github.com/brian-team/brian2/issues>. Please include this file with debug information in your report: /tmp/brian_debug_vmaxybiq.log Additionally, you can also include a copy of the script that was run, available at: /tmp/brian_script_pehr7l4x.py Thanks! [brian2]
Traceback (most recent call last):
File "/usr/lib/python3.12/idlelib/run.py", line 580, in runcode
exec(code, self.locals)
File "/home/peter/python/ai_neural_brain_2/engine_brain_2_11_neurons_group_and_synapses_talking.py", line 6, in <module>
import vosk
ModuleNotFoundError: No module named 'vosk'
Click to expand...

I make that:

peter@peter-ThinkPad-P51:~$ source /home/peter/venv/bin/activate
(venv) peter@peter-ThinkPad-P51:~$ source /home/peter/venv/bin/activate
(venv) peter@peter-ThinkPad-P51:~$ python3 -c "import vosk; print('Vosk successfully imported!')"
bash: !': event not found
(venv) peter@peter-ThinkPad-P51:~$ echo $(python3 -c "import vosk; print('Vosk successfully imported!')")
bash: !': event not found
bash: !': event not found
bash: !': event not found
(venv) peter@peter-ThinkPad-P51:~$ echo $(python3 -c "import vosk; print('Vosk successfully imported!')")
bash: !': event not found
(venv) peter@peter-ThinkPad-P51:~$ python3 -c "import vosk; print('Vosk successfully imported!')
bash: !': event not found
(venv) peter@peter-ThinkPad-P51:~$ echo $(python3 -c 'import vosk; print("Vosk successfully imported!")')
Vosk successfully imported!
(venv) peter@peter-ThinkPad-P51:~$
Click to expand...

And:

sudo chmod 775 -R /home/peter/venv/*
sudo chmod 775 -R /home/peter/venv/
sudo chmod +x -R /home/peter/venv/
sudo chmod +x -R /home/peter/venv/*
sudo chown peter -R /home/peter/venv/*
sudo chown peter -R /home/peter/venv/
Click to expand...

Nothing change.

Someone can help me with that?

Thanks.
 
I try to use Vosk, but all time is:

Code: 
Python 3.12.3 (main, Apr 10 2024, 05:33:47) [GCC 13.2.0] on linux
Type "help", "copyright", "credits" or "license()" for more information.

= RESTART: /home/peter/python/ai_neural_brain_2/engine_brain_2_11_neurons_group_and_synapses_talking.py
ERROR      Brian 2 encountered an unexpected error. If you think this is a bug in Brian 2, please report this issue either to the discourse forum at <http://brian.discourse.group/>, or to the issue tracker at <https://github.com/brian-team/brian2/issues>. Please include this file with debug information in your report: /tmp/brian_debug_vmaxybiq.log  Additionally, you can also include a copy of the script that was run, available at: /tmp/brian_script_pehr7l4x.py Thanks! [brian2]
Traceback (most recent call last):
  File "/usr/lib/python3.12/idlelib/run.py", line 580, in runcode
    exec(code, self.locals)
  File "/home/peter/python/ai_neural_brain_2/engine_brain_2_11_neurons_group_and_synapses_talking.py", line 6, in <module>
    import vosk
ModuleNotFoundError: No module named 'vosk'

I make that:

Code: 
peter@peter-ThinkPad-P51:~$ source /home/peter/venv/bin/activate
(venv) peter@peter-ThinkPad-P51:~$ source /home/peter/venv/bin/activate
(venv) peter@peter-ThinkPad-P51:~$ python3 -c "import vosk; print('Vosk successfully imported!')"
bash: !': event not found
(venv) peter@peter-ThinkPad-P51:~$ echo $(python3 -c "import vosk; print('Vosk successfully imported!')")
bash: !': event not found
bash: !': event not found
bash: !': event not found
(venv) peter@peter-ThinkPad-P51:~$ echo $(python3 -c "import vosk; print('Vosk successfully imported!')")
bash: !': event not found
(venv) peter@peter-ThinkPad-P51:~$ python3 -c "import vosk; print('Vosk successfully imported!')
bash: !': event not found
(venv) peter@peter-ThinkPad-P51:~$ echo $(python3 -c 'import vosk; print("Vosk successfully imported!")')
Vosk successfully imported!
(venv) peter@peter-ThinkPad-P51:~$

And:

Code: 
sudo chmod 775 -R /home/peter/venv/*
sudo chmod 775 -R /home/peter/venv/
sudo chmod +x -R /home/peter/venv/
sudo chmod +x -R /home/peter/venv/*
sudo chown peter -R /home/peter/venv/*
sudo chown peter -R /home/peter/venv/

Code: 
set -H
echo "print('Hello, World!')" | python3
bash: !': event not found
set +H
echo "print('Hello, World!')" | python3
Hello, World!

Nothing change.

Someone can help me with that?

Thanks.
 
Last edited:
I have 2 catalogs:
- myenvy
- venv

I make back.

I copied both to self without replace and with replace.

Nothing change.

Is that same.

Code: 
I make that again.
sudo chmod 775 -R /home/peter/venv/*
sudo chmod 775 -R /home/peter/venv/
sudo chmod +x -R /home/peter/venv/
sudo chmod +x -R /home/peter/venv/*
sudo chown peter -R /home/peter/venv/*
sudo chown peter -R /home/peter/venv/

sudo chmod 775 -R /home/peter/myenv/*
sudo chmod 775 -R /home/peter/myenv/
sudo chmod +x -R /home/peter/myenv/
sudo chmod +x -R /home/peter/myenv/*
sudo chown peter -R /home/peter/myenv/*
sudo chown peter -R /home/peter/myenv/
Code: 
echo 'We are single quoted here!'
We are single quoted here!

echo "We are double quoted here!"
We are double quoted here!
 
Last edited:
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