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Installation

This section describes how to build and install JURASSIC on a Linux system or high-performance computing (HPC) environment. JURASSIC is designed for batch-style execution and is typically compiled from source.

System requirements

JURASSIC is primarily developed and tested on Linux systems. The following requirements apply:

  • 64-bit Linux operating system
  • C compiler with OpenMP support
  • GNU Scientific Library (GSL)
  • netCDF-C library
  • MPI library (optional, retrieval only)
  • GNU Make or a compatible build system

MPI is required only if MPI-enabled retrieval executables are built. All other components can be built and run without MPI.

Required software

The following software components are required to build JURASSIC:

  • C compiler
    Required for auxiliary components and libraries (e.g. gcc, icc).

  • GNU Make
    Required to build the bundled libraries and the JURASSIC executables.

  • GNU Scientific Library (GSL)
    Required for numerical kernels and linear algebra support.

  • netCDF-C library
    Required for netCDF input/output support used throughout the toolchain.

  • MPI library (optional, retrieval only)
    For example:

  • OpenMPI

  • MPICH
  • Intel MPI

MPI is used exclusively by the retrieval code to distribute independent retrieval tasks across processes. No other JURASSIC executables use MPI internally.

  • GNU Plot (optional)
    Used by example projects to generate diagnostic plots.

  • Optional Fortran compiler
    A Fortran compiler is not required for the default repository build. It may be useful on HPC systems or when integrating external tooling that depends on Fortran-enabled libraries.

Obtaining the source code

The JURASSIC source code is hosted on GitHub. Clone the repository using:

git clone https://github.com/slcs-jsc/jurassic.git
cd jurassic

Alternatively, you may download a source archive from the GitHub repository.

Configuring the build

JURASSIC uses a Makefile-based build system in src/Makefile. Prior to compilation, you may need to edit that file or set make variables to match your local compiler and MPI setup.

Typical configuration options include:

  • Selection of the C compiler and any optional external toolchains
  • Compiler optimization and debugging flags
  • Enabling or disabling MPI support (retrieval only)
  • Enabling OpenMP parallelization

On HPC systems, it is recommended to load the appropriate compiler and MPI modules before configuring the build.

Building JURASSIC

Build bundled dependencies

For the default repository build, first compile the bundled third-party libraries:

cd libs
bash build.sh

This populates libs/build/, which is the default include/library location used by src/Makefile.

Default build (no MPI)

To build JURASSIC without MPI support:

cd src
make

This builds all executables in serial/OpenMP mode. MPI is not required for this configuration.

Building with MPI-enabled retrieval

To enable MPI support for the retrieval executable, build with:

cd src
make MPI=1

This will:

  • compile the full tool suite with the MPI compiler wrapper,
  • automatically select mpicc (unless CC is set explicitly),
  • define the MPI preprocessor macro used by the retrieval source code.

MPI-specific runtime behavior is implemented only in the retrieval executable. The other binaries are still rebuilt under the selected MPI toolchain when MPI=1 is used.

Clean rebuild

To perform a clean rebuild:

cd src
make clean
make

Verifying the installation

After compilation, verify the installation by running the test suite or the example projects described in the Quickstart.

cd src
make check

A successful test run or example simulation indicates that JURASSIC has been built correctly and that all required dependencies are working as expected.

Installation on HPC systems

On shared HPC systems, JURASSIC is typically installed in a user workspace rather than system-wide. Recommended practices include:

  • Building JURASSIC with the same compiler and MPI library used for production retrieval runs
  • Enabling MPI only when running MPI-enabled retrievals
  • Using environment modules to manage compiler and MPI versions
  • Testing retrieval scalability with a small number of MPI ranks before large-scale production runs

Further details on MPI execution and performance considerations are provided in the HPC workflows documentation.

Troubleshooting

Common issues during installation include:

  • Missing or incompatible compiler versions
  • Using an MPI-enabled build without mpicc or an MPI runtime
  • Mismatches between compile-time and runtime MPI environments
  • Incorrect OpenMP settings

If you encounter problems, consult the build output carefully and verify that your compiler and MPI environment are correctly configured. Additional help may be available through the project maintainers.

Next steps

Once JURASSIC is installed, proceed to the Quickstart to run your first simulation, or consult the User Manual for detailed information on configuration and usage.