Sundials Installation Guide

This README provides a step-by-step guide to install Sundials from source and set up the scikits.odes Python package with Sundials support.

Prerequisites

Ensure the following tools and libraries are installed on your system:

• build-essential
• cmake
• git
• python3 and pip
• numpy and scipy (Python packages)

Steps to Install Sundials

1. Clone the Sundials Repository

   git clone https://github.com/LLNL/sundials.git /home/ian/sundials/source

2. Create a Build Directory

   mkdir -p /home/ian/sundials/build
   cd /home/ian/sundials/build

3. Configure the Build with CMake

   cmake -DCMAKE_INSTALL_PREFIX=/home/ian/sundials/install -DBUILD_SHARED_LIBS=ON -DEXAMPLES_ENABLE=OFF ../source

4. Build and Install Sundials

   make -j$(nproc)
   make install

   The compiled libraries and headers will be installed in /home/ian/sundials/install.

Steps to Install scikits.odes

1. Set Environment Variables Ensure the Sundials library paths are accessible:

   export CFLAGS='-I/home/ian/sundials/install/include'
   export LDFLAGS='-L/home/ian/sundials/install/lib'

2. Install scikits.odes Use pip to install the package:

   pip install scikits.odes

   This will install scikits.odes with Sundials support.

Environment Setup

Before building or running any examples, set up your environment with these variables:

# Add Sundials libraries to the system's library path
export LD_LIBRARY_PATH=/home/ian/sundials/install/lib:$LD_LIBRARY_PATH

# Set up compilation flags for building with Sundials
export CFLAGS="-I/home/ian/sundials/install/include"
export CXXFLAGS="-I/home/ian/sundials/install/include"
export LDFLAGS="-L/home/ian/sundials/install/lib"

# For pkg-config (if needed)
export PKG_CONFIG_PATH=/home/ian/sundials/install/lib/pkgconfig:$PKG_CONFIG_PATH

# For CMake to find Sundials
export CMAKE_PREFIX_PATH=/home/ian/sundials/install:$CMAKE_PREFIX_PATH

Add these environment variables to your ~/.bashrc or ~/.profile to make them permanent:

echo 'export LD_LIBRARY_PATH=/home/ian/sundials/install/lib:$LD_LIBRARY_PATH' >> ~/.bashrc
echo 'export CFLAGS="-I/home/ian/sundials/install/include"' >> ~/.bashrc
echo 'export CXXFLAGS="-I/home/ian/sundials/install/include"' >> ~/.bashrc
echo 'export LDFLAGS="-L/home/ian/sundials/install/lib"' >> ~/.bashrc
echo 'export PKG_CONFIG_PATH=/home/ian/sundials/install/lib/pkgconfig:$PKG_CONFIG_PATH' >> ~/.bashrc
echo 'export CMAKE_PREFIX_PATH=/home/ian/sundials/install:$CMAKE_PREFIX_PATH' >> ~/.bashrc

Remember to source your ~/.bashrc after adding these lines:

source ~/.bashrc

Building and Running C++ Examples

Prerequisites for C++ Examples

Make sure you have:

• A C++ compiler (g++ or clang++)
• CMake
• SUNDIALS libraries properly installed (follow the installation steps above)

Compiling the C++ Files

1. Build simple_test.cpp

   g++ -o simple_test simple_test.cpp \
       -I/home/ian/sundials/install/include \
       -L/home/ian/sundials/install/lib \
       -lsundials_cvode -lsundials_nvecserial \
       -lsundials_sunmatrixdense -lsundials_sunlinsoldense \
       -lsundials_sunnonlinsol

2. Build benchmark_ode_solver.cpp (if present)

   g++ -o benchmark_ode_solver benchmark_ode_solver.cpp \
       -I/home/ian/sundials/install/include \
       -L/home/ian/sundials/install/lib \
       -lsundials_cvode -lsundials_nvecserial \
       -lsundials_sunmatrixdense -lsundials_sunlinsoldense \
       -lsundials_sunnonlinsol

Running the Examples

1. Run simple_test

   ./simple_test

   This will run ODE solver tests with:
   • A simple system (dy/dt = -y)
   • Robertson's stiff system
   • Different step counts (100, 1000, 10000)
   • Both analytical and finite difference Jacobians

The program will output:

• SUNDIALS version
• Solution values at regular intervals
• Detailed timing statistics for each run
• Average performance metrics across multiple runs

Troubleshooting

If you encounter library loading errors, ensure the SUNDIALS libraries are in your system's library path:

export LD_LIBRARY_PATH=/home/ian/sundials/install/lib:$LD_LIBRARY_PATH

Verification

To verify the installation, you can run a simple Python script using scikits.odes to solve an ODE. If you encounter any issues, ensure the environment variables are correctly set and the Sundials library is properly installed.

Notes

• The Sundials library is installed in /home/ian/sundials/install.
• Example programs and outputs are available in the install/examples directory.
• If you need to rebuild Sundials, clean the build directory and repeat the steps.

For further assistance, refer to the Sundials documentation or contact support.