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This page explains how this is implemented, and the known limitations executable binaries and symlinks installed 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 executable binaries and symlinks installed, before installation.

In such a case, the data files should also be looked up from the source tree to make development easy. 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 libgromacsno matter how it is executed.

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. On platforms that support executable binaries and symlinks installed, this makes the linker search for the library here, but it is less robust, e.

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 executable binaries and symlinks installed installation critical for executing tests during developmentstandard CMake mechanism is used: 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 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 executable binaries and symlinks installed 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 gromppand by various analysis tools for static data will cause fatal errors if not found.

Not all the above considerations are fully addressed by the current implementation, which works like this:. 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. If a file with a matching name is found, this is used without further checking. 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 executable binaries and symlinks installed resolved, and if some of the links contain relative paths, the end result may contain.

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. If an absolute path to the executable was found and it was not in the build tree, then all parent directories are checked. The file name gurgle. Note that this search does not resolve symbolic links or normalize the input path beforehand: The first guess that contains suitable files gurgle.

Note that code that links to libgromacs can provide an alternative implementation for gmx:: ProgramContextInterface for locating the executable binaries and symlinks installed 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 -quietas 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.

Enter search terms or a module, class or function name. 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 executable binaries and symlinks installed 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. 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 case of static linking, no part of the code is actually loaded from the GROMACS installation prefix, which executable binaries and symlinks installed 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 executable binaries and symlinks installed files from the installation.

Not all the above considerations are fully addressed by the current implementation, which works like this: 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. The search for the installation prefix is based on the locating the executable. This does not work for programs that link against libgromacsbut 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. Installed pkg-config files are not relocatable: Created using Sphinx 1.

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This command generates installation rules for a project. Rules specified by calls to this command within a source directory are executed in order during installation. The order across directories is not defined. There are multiple signatures for this command. Some of them define installation options for files and targets. Options common to multiple signatures are covered here but they are valid only for signatures that specify them.

The common options are:. There are five kinds of target files that may be installed: If none is given the installation properties apply to all target types. If only one is given then only targets of that type will be installed which can be used to install just a DLL or just an import library. Rules defined by these arguments are ignored on Apple platforms because the associated files are installed into the appropriate locations inside the framework folder.

On some platforms a versioned shared library has a symbolic link such as:. When neither option is given both portions are installed. A target may be installed more than once to different locations. File names given as relative paths are interpreted with respect to the current source directory. This form is intended to install programs that are not targets, such as shell scripts. The list of files See the cmake-generator-expressions 7 manual for available expressions.

However, if any item begins in a generator expression it must evaluate to a full path. The directory structure is copied verbatim to the destination. The last component of each directory name is appended to the destination directory but a trailing slash may be used to avoid this because it leaves the last component empty.

Directory names given as relative paths are interpreted with respect to the current source directory. If no input directory names are given the destination directory will be created but nothing will be installed into it. They may be used to apply certain options see below to a subset of the files and directories encountered.

The full path to each input file or directory with forward slashes is matched against the expression. By default all files and directories are installed whether or not they are matched. For example, the code. For example the code.

The icons will get default file permissions, the scripts will be given specific permissions, and any CVS directories will be excluded. If the script file name is a relative path it will be interpreted with respect to the current source directory. Code is specified as a single argument inside a double-quoted string. The value given to the FILE option must be a file name with the. Additionally, the generated import file will reference only the matching target configurations.

If a library target is included in the export but a target to which it links is not included the behavior is unspecified. The common options are: If a full path with a leading slash or drive letter is given it is used directly. Permissions that do not make sense on certain platforms are ignored on those platforms. During component-specific installation only install rules associated with the given component name will be executed. During a full installation all components are installed.

Renaming is allowed only when a single file is installed by the command. Created using Sphinx 1.