53 lines
1.5 KiB
Markdown
53 lines
1.5 KiB
Markdown
# Pygmx
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A Cython wrapper for the shared library of GROMACS 5.1.
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## Installation
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Pygmx requires some python packages and an installation of GROMACS 5.1.
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### Python requirements
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* Cython
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* NumPy
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### Gromacs installation
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#### Using a module
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If gromacs is installed as a module in your system, run
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module load gromacs/5.1
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and skip to the section *Installing pygmx*.
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#### Manual setup
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The shared library of GROMACS 5.1and the corresponding c++ header files need to be present on the system.
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If the shared library is installed globally, the environment variable `LD_LIBRARY_PATH` must be set.
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The installation process will look for the header files by replacing any `lib` folder
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in `LD_LIBRARY_PATH` with `include`.
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If no header files are present, simply pull the submodule `gromacs` in this repository.
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To build the shared library, follow the [official installation instructions](http://manual.gromacs.org/documentation/5.1.2/install-guide/index.html),
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starting with step 4 (creating a build directory).
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### Installing pygmx
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When the requirements are met, the installation should be easy.
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Navigate to the top folder of the repository and run the command
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python setup.py install
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This builds the cython modules and installs them into the local python distribution.
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### Deploy on intranet
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For any installed version of mdevaluate modules do:
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version=dev # or maybe: version=$(python ../mdevaluate/setup.py --version)
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module load gromacs/5.1
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module load mdevaluate/$version
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python setup.py install --prefix=/autohome/niels/modules/mdevaluate-$version
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