GROMACS 4.5 MANUAL PDF

If you have superuser privileges, then you will have the option of just installing to the default locations. If you have a site installation policy that prohibits this, or lack superuser privileges, or wish to maintain multiple GROMACS installations, then you will need to choose somewhere suitable to install. GROMACS is able to compile as a set of shared libraries, which greatly reduces the disk footprint of the installation, but this can be tricky on some platforms. If you encounter problems at the linking stages below, it is recommended that you configure everything for static libraries i.

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If auto-detection fails the first option should be used. This is becauise when the MPI compiler-wrapper approach is used, as nvcc can not reliably use compiler wrappers, the nvcc host compiler needs to be set manually. Although mixing compilers is not advised, this will most probably work, but if sich a setup fails, a CPU compiler supported by nvcc should be used. The file can be edited using a text editor, but after that cmake should be run again. Note that the build has to be reconfigured to commit any changes.

The respective include, lib, or bin is appended to the path. For each option a list of paths can be specified on Unix seperated with ":". These are enviroment variables and not command line arguments and are used as e. However, these flags will be appended to the predefined flags for the corresponding platform and build type such as Debug or Release.

All settings can be found in CMakeCache. Note, that in general CMake picks up whatever is available, so this option only instructs CMake to prefer static libraries when both static and shared are available. If no static version of an external library is available, even when the aforementioned option is ON, the shared library will be used.

Also note, that the resulting binaries will still be dynamically linked against system libraries. However, in order to make this work one has to make sure that every external library is available and detected as static to check this either use ccmake or look in CMakeCache.

Note that the mdrun produced by this compilation will be able to run parallel over threads on many cores as long as it is within the same box confirmation requested. The changes for using MPI are highlighted in yellow.

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