Relocatable binaries#

GROMACS (mostly) implements the concept of relocatable binaries, i.e., that after initial installation to CMAKE_INSTALL_PREFIX (or binary packaging with CPack), the whole installation tree can be moved to a different folder and GROMACS continues to work without further changes to the installation tree. This page explains how this is implemented, and the known limitations in the implementation. This information is mainly of interest to developers who need to understand this or change the code, but it can also be useful for people installing or packaging GROMACS.

A related feature that needs to be considered in all the code related to this is that the executables should work directly when executed from the build tree, before installation. In such a case, the data files should also be looked up from the source tree to make development easy.

Finding shared libraries#

If GROMACS is built with dynamic linking, the first part of making the binaries relocatable is to make it possible for the executable to find libgromacs, no matter how it is executed. On platforms that support a relative RPATH, this is used to make the GROMACS executables find the libgromacs from the same installation prefix. This makes the executables fully relocatable when it comes to linking, as long as the relative folder structure between the executables and the library is kept the same.

If the RPATH mechanism does not work, GMXRC also adds the absolute path to the libgromacs installed with it to LD_LIBRARY_PATH. On platforms that support this, this makes the linker search for the library here, but it is less robust, e.g., when mixing calls to different versions of GROMACS. Note that GMXRC is currently not relocatable, but hardcodes the absolute path.

On native Windows, DLLs are not fully supported; it is currently only possible to compile a DLL with MinGW, not with Visual Studio or with Intel compilers. In this case, the DLLs are placed in the bin/ directory instead of lib/ (automatically by CMake, based on the generic binary type assignment in CMakeLists.txt). Windows automatically searches DLLs from the executable directory, so the correct DLL should always be found.

For external libraries, standard CMake linking mechanisms are used and RPATH for the external dependencies is included in the executable; on Windows, dynamic linking may require extra effort to make the loader locate the correct external libraries.

To support executing the built binaries from the build tree without installation (critical for executing tests during development), standard CMake mechanism is used: when the binaries are built, the RPATH is set to the build tree, and during installation, the RPATH in the binaries is rewritten by CMake to the final (relative) value. As an extra optimization, if the installation tree has the same relative folder structure as the build tree, the final relative RPATH is used already during the initial build.

The RPATH settings are in the root CMakeLists.txt. It is possible to disable the use of RPATH during installation with standard CMake variables, such as setting CMAKE_SKIP_INSTALL_RPATH=ON.

Finding data files#

The other, GROMACS-specific part, of making the binaries relocatable is to make them able to find data files from the installation tree. Such data files are used for multiple purposes, including showing the quotes at the end of program execution. If the quote database is not found, the quotes are simply not printed, but other files (mostly used by system preparation tools like gmx pdb2gmx and gmx grompp, and by various analysis tools for static data) will cause fatal errors if not found.

There are several considerations here:

  • For relocation to work, finding the data files cannot rely on any hard-coded absolute path, but it must find out the location of the executing code by inspecting the system. As a fallback, environment variables or such set by GMXRC or similar could be used (but currently are not).

  • When running executables from the build tree, it is desirable that they will automatically use the data files from the matching source tree to facilitate easy testing. The data files are not copied into the build tree, and the user is free to choose any relative locations for the source and build trees. Also, the data files are not in the same relative path in the source tree and in the installation tree (the source tree has share/top/, the installation tree share/gromacs/top/; the latter is customizable during CMake configuration).

  • In addition to GROMACS executables, programs that link against libgromacs need to be able to find the data files if they call certain functions in the library. In this case, the executable may not be in the same directory where GROMACS is. In case of static linking, no part of the code is actually loaded from the GROMACS installation prefix, which makes it impossible to find the data files without external information.

  • The user can always use the GMXLIB environment variable to provide alternative locations for the data files, but ideally this should never be necessary for using the data files from the installation.

Not all the above considerations are fully addressed by the current implementation, which works like this:

  1. It finds the path to the current executable based on argv[0]. If the value contains a directory, this is interpreted as absolute or as relative to the current working directory. If there is no directory, then a file by that name is searched from the directories listed in PATH. On Windows, the current directory is also searched before PATH. If a file with a matching name is found, this is used without further checking.

  2. If the executable is found and is a symbolic link, the symbolic links are traversed until a real file is found. Note that links in the directory name are not resolved, and if some of the links contain relative paths, the end result may contain .. components and such.

  3. If an absolute path to the executable was found, the code checks whether the executable is located in the build output directory (using stat() or similar to account for possible symbolic links in the directory components). If it is, then the hard-coded source tree location is returned.

  4. If an absolute path to the executable was found and it was not in the build tree, then all parent directories are checked. If a parent directory contains share/gromacs/top/gurgle.dat, this directory is returned as the installation prefix. The file name gurgle.dat and the location are considered unique enough to ensure that the correct directory has been found. The installation directory for read-only architecture-independent data files can be customized during CMake configuration by setting CMAKE_INSTALL_DATADIR, and the subdirectory under this that hosts the GROMACS-specific data is set by GMX_INSTALL_DATASUBDIR.

    Note that this search does not resolve symbolic links or normalize the input path beforehand: if there are .. components and symbolic links in the path, the search may proceed to unexpected directories, but this should not be an issue as the correct installation prefix should be found before encountering such symbolic links (as long as the bin/ directory is not a symbolic link).

  5. If the data files have not been found yet, try a few hard-coded guesses (like the original installation CMAKE_INSTALL_PREFIX and /usr/local/). The first guess that contains suitable files (gurgle.dat) is returned.

  6. If still nothing is found, return CMAKE_INSTALL_PREFIX and let the subsequent data file opening fail.

The above logic to find the installation prefix is in src/gromacs/commandline/cmdlineprogramcontext.cpp. Note that code that links to libgromacs can provide an alternative implementation for gmx::IProgramContext for locating the data files, and is then fully responsible of the above considerations.

Information about the used data directories is printed into the console output (unless run with -quiet), as well as to (some) error messages when locating data files, to help diagnosing issues.

There is no mechanism to disable this probing search or affect the process during compilation time, except for the CMake variables mentioned above.

Known issues#

  • GMXRC is not relocatable: it hardcodes the absolute installation path in one assignment within the script, which no longer works after relocation. Contributions to get rid of this on all the shells the GMXRC currently supports are welcome.

  • There is no version checking in the search for the data files; in case of issues with the search, it may happen that the installation prefix from some other installation of GROMACS is returned instead, and only cryptic errors about missing or invalid files may reveal this.

  • If the searching for the installation prefix is not successful, hard-coded absolute guesses are used, and one of those returned. These guesses include the absolute path in CMAKE_INSTALL_PREFIX used during compilation of libgromacs, which will be incorrect after relocation.

  • The search for the installation prefix is based on the locating the executable. This does not work for programs that link against libgromacs, but are not installed in the same prefix. For such cases, the hard-coded guesses will be used, so the search will not find the correct data files after relocation. The calling code can, however, programmatically provide the GROMACS installation prefix, but ideally this would work without offloading work to the calling code.

  • One option to (partially) solve the two above issues would be to use the GMXDATA environment variable set by GMXRC as the fallback (currently this environment variable is set, but very rarely used).

  • Installed pkg-config files are not relocatable: they hardcode the absolute installation path.