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Fast Efficient Reaction Network (FERN) Solver

Prerequisites

You will need git and cmake to build FERN.

Checkout and build

From a shell, execute the following commands:

git clone https://github.com/jayjaybillings/fern
mkdir fern-build
cd fern-build
cmake ../fern -DCMAKE_BUILD_TYPE=Debug -G"Eclipse CDT4 - Unix Makefiles" -DCMAKE_ECLIPSE_VERSION=4.5
make

Build flags, such as -Wall, can be set by prepending the CXX_FLAGS variable to the cmake command as such

CXX_FLAGS='-Wall' cmake ../fern -DCMAKE_BUILD_TYPE=Debug -G"Eclipse CDT4 - Unix Makefiles" -DCMAKE_ECLIPSE_VERSION=4.5

Optimization flags should be handled by setting -DCMAKE_BUILD_TYPE=Release instead of Debug. Likewise, an optimized build with debug information can be acheived by setting -DCMAKE_BUILD_TYPE=RelWithDebugInfo.

Running FERN

You can run FERN from any directory and it only requires one of its INI files to run. So, assuming you are in the build directory and using one of the test files in the data directory, you would run

./fern-exec ../fern/data/alpha.ini

Questions

Questions can be directed to me at jayjaybillings gmail com.

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