Compiling and Installing SLUG

Dependencies

The core SLUG program requires

In addition, the following are required for some functionality, but not for the core code:

  • The cfitsio library (required for FITS capabilities)
  • An implementation of MPI (required for MPI support; for full functionality, the implementation must support the MPI 3.0 or later standard)

Compilation will be easiest if you install the required libraries such that the header files are included in your CXX_INCLUDE_PATH (for Boost) and C_INCLUDE_PATH (for GSL, cfitsio, and MPI) and the compiled object files are in your LIBRARY_PATH. Alternately, you can manually specify the locations of these files by editing the Makefiles – see below. The cfitsio library is optional, and is only required if you want the ability to write FITS output. To compile without it, use the flag FITS=DISABLE_FITS when calling make (see below). The MPI libraries are required only for MPI capability, which is not enabled by default; see Using SLUG as a Library with MPI-Enabled Codes for an explanation of these capabilities and how to enable them. Note that SLUG uses some Boost libraries that must be built separately (see the Boost documentation on how to build and install Boost libraries).

In addition to the core dependencies, slugpy, the python helper library requires:

Finally, the cloudy coupling capability requires:

This is only required performing cloudy runs, and is not required for any other part of SLUG.

Compiling

If you have Boost in your CXX_INCLUDE_PATH, GSL in your C_INCLUDE_PATH, and (if you’re using it) cfitsio in your C_INCLUDE_PATH, and the compiled libraries for each of these in your LIBRARY_PATH environment variables, and your system is running either MacOSX or Linux, you should be able to compile simply by doing:

make

from the main slug directory.

To compile in debug mode, do:

make debug

instead.

To enable MPI support, do:

make MPI=ENABLE_MPI

In addition, you may need to specify the names of your preferred MPI C++ compiler by setting the variable MACH_MPICXX in your machine-specific makefile – see Machine-Specific Makefiles. The Makefiles contain reasonable guesses, but since MPI compiler names are much less standardized than general compiler names, you may need to supply yours rather than relying on the default.

If you are compiling using GSL version 1.x or without cfitsio, you must specify these options when compiling. If you are using version 1.x of the GSL, do:

make GSLVERSION=1

To compile without FITS support, do:

make FITS=DISABLE_FITS

Note that SLUG is written in C++11, and requires some C++11 features, so it may not work with older C++ compilers. The following compiler versions are known to work: gcc >= 4.8 (4.7 works on most but not all platforms), clang/llvm >= 3.3, icc >= 14.0. Earlier versions may work as well, but no guarantees.

Machine-Specific Makefiles

You can manually specify the compiler flags to be used for you machine by creating a file named Make.mach.MACHINE_NAME in the src directory, and then doing:

make MACHINE=MACHINE_NAME

An example machine-specific file, src/Make.mach.ucsc-hyades is included in the repository. You can also override or reset any compilation flag you want by editing the file src/Make.config.override.

Note on Boost Naming and Linking Issues

The Boost libraries have a somewhat complex history of naming conventions (see this stackoverflow discussion thread). As a result, depending on your platform and where you got your Boost libraries and how you compiled them, the libraries names may or may not have names that end in -mt (indicating multithreading support). There is unfortunately no easy way to guess whether this tag will be present or not in the Boost installation on any particular system, so the slug makefiles contain defaults that are guesses based on some of the most common boost installations (e.g., the macports version of Boost has the -mt tag, so the default on Darwin is to include it). If you find that your attempted compilation fails at the linking stage with an error like:

ld: library not found for -lboost_system-mt

or:

ld: library not found for -lboost_system

but you are confident that you have boost installed and the path correctly set, you can try adding or removing the -mt flag. To do so, edit the file src/Make.config.override and add the line:

MACH_BOOST_TAG          = -mt

(to turn the -mt tag on) or:

MACH_BOOST_TAG          =

(to turn the -mt tag off). Then try compiling again.