JURASSIC Dependencies

This file lists the software dependencies required to build and run JURASSIC. Versions correspond to the packages provided by Ubuntu 24.04 LTS (Noble Numbat), which is the reference platform used for development and testing.

Mandatory Dependencies

Dependency	Version	Description
Git	2.43.0	Clone the repository and derive version info
GNU Make	4.3	Build system
GCC	13.3.0	C compiler
GNU Scientific Library	2.7.1	Numerical routines
netCDF-C	4.9.2	File I/O (netCDF)
HDF5	1.14.4	netCDF-4 file support

Optional Dependencies

Dependency	Version	Description
gnuplot	6.0	Used by example scripts
Cppcheck	2.13	Static code analysis
gprofng	2.42	Performance profiling tool
gcov	13.2.0	Coverage testing tool
lcov	2.0	Code coverage visualization tool
Doxygen	1.9.8	Automatic source code documentation
MkDocs	1.5.3	Build documentation locally

Notes

• Using bundled libraries: JURASSIC includes a libs/ directory that can build GSL, HDF5, and netCDF if system libraries are not available or if a self-contained build is preferred.

• Bundled build toolchain: libs/build.sh builds HDF5 with the C++ interface disabled (--disable-cxx). A GNU C compiler is required, but a C++ compiler is not required for the bundled-library build.

• netCDF version: JURASSIC uses netCDF-4/HDF5 files in several workflows, so both netCDF-C and HDF5 are required. Compression backends such as zlib are normally provided by the installed netCDF/HDF5 stack. Using external filter-based compression (e.g. zstd) requires a matching HDF5 plugin package and possibly setting HDF5_PLUGIN_PATH.

• Static linking: Fully static builds require static versions of all libraries used by the installed netCDF/HDF5 stack and usually do not support HDF5 filter plugins. Dynamic linking is recommended for most users.

Installing dependencies

Ubuntu 24.04 LTS

Use the following commands to install the dependencies on Ubuntu 24.04 LTS.

sudo apt update
sudo apt install \
  git make gcc \
  libgsl-dev \
  libnetcdf-dev libhdf5-dev

Optional tools:

sudo apt install \
  binutils cppcheck lcov \
  doxygen mkdocs \
  gnuplot

Fedora

Use the following commands to install the dependencies on Fedora.

sudo dnf install \
  git make gcc \
  gsl-devel \
  netcdf-devel hdf5-devel

Optional tools:

sudo dnf install \
  binutils cppcheck lcov \
  doxygen mkdocs \
  gnuplot