Building Neulite Kernel

This page explains the build procedure for the Neulite kernel, a C program for simulation execution.

Prerequisites

The following software is required:

  • C compiler supporting C17 (gcc 7.0 or higher recommended)

  • make

Build Procedure

Step 1: Clone the neulite Repository

Note

Skip this step if you have already cloned it during the bionetlite setup.

Clone the neulite repository:

git clone https://github.com/neulite/neulite.git

Step 2: Navigate to Kernel Directory

Navigate to the default kernel (double exponential) directory:

cd neulite/kernel

Step 3: Build

Build using Makefile:

# Build
make

This generates the executable nl.

Step 4: Execution

Execute the built nl by specifying the population file generated by Bionetlite (e.g., <network_name>_population.csv ) and the synapse connection file (e.g., <src>_<trg>_connection.csv ) as arguments:

# Run Neulite kernel
./nl <network_name>_population.csv <src>_<trg>_connection.csv

For MPI parallel execution:

# MPI parallel execution
mpirun -np 4 ./nl <network_name>_population.csv <src>_<trg>_connection.csv

Verification of Build

Verify that the Neulite kernel has been built correctly:

# Verify executable exists
ls -l nl

# Confirm file is executable
file nl

Troubleshooting

Compilation Error

Problem: implicit declaration of function

Solution: Use a C17-compatible compiler

# Check gcc version
gcc --version

# gcc 7.0+ required. Update if older
sudo apt-get install gcc-9

Executable not found

Problem: ./nl: No such file or directory

Solution: Make sure you are running in the build directory

# Move to build directory
cd /path/to/neulite_kernel-X.Y.Z

# Verify file exists
ls -l nl

Next Steps

Once the Neulite kernel build is complete, proceed to the following tutorial: